Search results for the GEO ID: GSE35200  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM863392 | GPL3921 |
|
HL60-shControl-rep1
|
HL-60 cell line infected with scrambled control shRNA
|
cell line: HL-60
shRNA construct: Scrambled Control
|
HL-60 cell line infected with scrambled control shRNA, biological rep1
Sample name: HL60_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A01_596706.CEL
|
| Sample_geo_accession | GSM863392
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863392/suppl/GSM863392.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863393 | GPL3921 |
|
HL60-shControl-rep2
|
HL-60 cell line infected with scrambled control shRNA
|
cell line: HL-60
shRNA construct: Scrambled Control
|
HL-60 cell line infected with scrambled control shRNA, biological rep2
Sample name: HL60_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A02_596668.CEL
|
| Sample_geo_accession | GSM863393
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863393/suppl/GSM863393.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863394 | GPL3921 |
|
HL60-shControl-rep3
|
HL-60 cell line infected with scrambled control shRNA
|
cell line: HL-60
shRNA construct: Scrambled Control
|
HL-60 cell line infected with scrambled control shRNA, biological rep3
Sample name: HL60_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A07_596570.CEL
|
| Sample_geo_accession | GSM863394
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863394/suppl/GSM863394.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863395 | GPL3921 |
|
HL60-shGSK3B-Construct1-rep1
|
HL-60 cell line infected with GSK3B Construct 1 shRNA
|
cell line: HL-60
shRNA construct: GSK3B Construct 1
|
HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: HL60_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A03_596652.CEL
|
| Sample_geo_accession | GSM863395
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863395/suppl/GSM863395.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863396 | GPL3921 |
|
HL60-shGSK3B-Construct1-rep2
|
HL-60 cell line infected with GSK3B Construct 1 shRNA
|
cell line: HL-60
shRNA construct: GSK3B Construct 1
|
HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: HL60_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A08_596694.CEL
|
| Sample_geo_accession | GSM863396
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863396/suppl/GSM863396.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863397 | GPL3921 |
|
HL60-shGSK3B-Construct2-rep1
|
HL-60 cell line infected with GSK3B Construct 2 shRNA
|
cell line: HL-60
shRNA construct: GSK3B Construct 2
|
HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: HL60_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A04_596674.CEL
|
| Sample_geo_accession | GSM863397
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863397/suppl/GSM863397.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863398 | GPL3921 |
|
HL60-shGSK3B-Construct2-rep2
|
HL-60 cell line infected with GSK3B Construct 2 shRNA
|
cell line: HL-60
shRNA construct: GSK3B Construct 2
|
HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: HL60_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A09_596622.CEL
|
| Sample_geo_accession | GSM863398
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863398/suppl/GSM863398.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863399 | GPL3921 |
|
HL60-shGSK3A-Construct5-rep1
|
HL-60 cell line infected with GSK3A Construct 5 shRNA
|
cell line: HL-60
shRNA construct: GSK3A Construct 5
|
HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: HL60_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A05_596562.CEL
|
| Sample_geo_accession | GSM863399
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863399/suppl/GSM863399.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863400 | GPL3921 |
|
HL60-shGSK3A-Construct5-rep2
|
HL-60 cell line infected with GSK3A Construct 5 shRNA
|
cell line: HL-60
shRNA construct: GSK3A Construct 5
|
HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: HL60_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A10_596670.CEL
|
| Sample_geo_accession | GSM863400
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863400/suppl/GSM863400.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863401 | GPL3921 |
|
HL60-shGSK3A-Construct6-rep1
|
HL-60 cell line infected with GSK3A Construct 6 shRNA
|
cell line: HL-60
shRNA construct: GSK3A Construct 6
|
HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: HL60_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A06_596738.CEL
|
| Sample_geo_accession | GSM863401
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863401/suppl/GSM863401.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863402 | GPL3921 |
|
HL60-shGSK3A-Construct6-rep2
|
HL-60 cell line infected with GSK3A Construct 6 shRNA
|
cell line: HL-60
shRNA construct: GSK3A Construct 6
|
HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: HL60_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A11_596684.CEL
|
| Sample_geo_accession | GSM863402
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863402/suppl/GSM863402.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863403 | GPL3921 |
|
THP1-shControl-rep1
|
THP-1 cell line infected with scrambled control shRNA
|
cell line: THP-1
shRNA construct: Scrambled Control
|
THP-1 cell line infected with scrambled control shRNA, biological rep1
Sample name: THP1_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B01_596662.CEL
|
| Sample_geo_accession | GSM863403
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863403/suppl/GSM863403.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863404 | GPL3921 |
|
THP1-shControl-rep2
|
THP-1 cell line infected with scrambled control shRNA
|
cell line: THP-1
shRNA construct: Scrambled Control
|
THP-1 cell line infected with scrambled control shRNA, biological rep2
Sample name: THP1_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B02_596660.CEL
|
| Sample_geo_accession | GSM863404
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863404/suppl/GSM863404.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863405 | GPL3921 |
|
THP1-shControl-rep3
|
THP-1 cell line infected with scrambled control shRNA
|
cell line: THP-1
shRNA construct: Scrambled Control
|
THP-1 cell line infected with scrambled control shRNA, biological rep3
Sample name: THP1_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B07_596722.CEL
|
| Sample_geo_accession | GSM863405
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863405/suppl/GSM863405.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863406 | GPL3921 |
|
THP1-shGSK3B-Construct1-rep1
|
THP-1 cell line infected with GSK3B Construct 1 shRNA
|
cell line: THP-1
shRNA construct: GSK3B Construct 1
|
THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: THP1_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B03_596576.CEL
|
| Sample_geo_accession | GSM863406
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863406/suppl/GSM863406.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863407 | GPL3921 |
|
THP1-shGSK3B-Construct1-rep2
|
THP-1 cell line infected with GSK3B Construct 1 shRNA
|
cell line: THP-1
shRNA construct: GSK3B Construct 1
|
THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: THP1_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B08_596590.CEL
|
| Sample_geo_accession | GSM863407
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863407/suppl/GSM863407.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863408 | GPL3921 |
|
THP1-shGSK3B-Construct2-rep1
|
THP-1 cell line infected with GSK3B Construct 2 shRNA
|
cell line: THP-1
shRNA construct: GSK3B Construct 2
|
THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: THP1_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B04_596688.CEL
|
| Sample_geo_accession | GSM863408
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863408/suppl/GSM863408.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863409 | GPL3921 |
|
THP1-shGSK3B-Construct2-rep2
|
THP-1 cell line infected with GSK3B Construct 2 shRNA
|
cell line: THP-1
shRNA construct: GSK3B Construct 2
|
THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: THP1_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B09_596702.CEL
|
| Sample_geo_accession | GSM863409
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863409/suppl/GSM863409.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863410 | GPL3921 |
|
THP1-shGSK3A-Construct5-rep1
|
THP-1 cell line infected with GSK3A Construct 5 shRNA
|
cell line: THP-1
shRNA construct: GSK3A Construct 5
|
THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: THP1_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B05_596730.CEL
|
| Sample_geo_accession | GSM863410
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863410/suppl/GSM863410.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863411 | GPL3921 |
|
THP1-shGSK3A-Construct5-rep2
|
THP-1 cell line infected with GSK3A Construct 5 shRNA
|
cell line: THP-1
shRNA construct: GSK3A Construct 5
|
THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: THP1_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B10_596686.CEL
|
| Sample_geo_accession | GSM863411
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863411/suppl/GSM863411.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863412 | GPL3921 |
|
THP1-shGSK3A-Construct6-rep1
|
THP-1 cell line infected with GSK3A Construct 6 shRNA
|
cell line: THP-1
shRNA construct: GSK3A Construct 6
|
THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: THP1_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B06_596642.CEL
|
| Sample_geo_accession | GSM863412
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863412/suppl/GSM863412.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863413 | GPL3921 |
|
THP1-shGSK3A-Construct6-rep2
|
THP-1 cell line infected with GSK3A Construct 6 shRNA
|
cell line: THP-1
shRNA construct: GSK3A Construct 6
|
THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: THP1_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B11_596554.CEL
|
| Sample_geo_accession | GSM863413
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863413/suppl/GSM863413.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863414 | GPL3921 |
|
MOLM14-shControl-rep1
|
MOLM-14 cell line infected with scrambled control shRNA
|
cell line: MOLM-14
shRNA construct: Scrambled Control
|
MOLM-14 cell line infected with scrambled control shRNA, biological rep1
Sample name: MOLM14_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C01_596616.CEL
|
| Sample_geo_accession | GSM863414
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863414/suppl/GSM863414.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863415 | GPL3921 |
|
MOLM14-shControl-rep2
|
MOLM-14 cell line infected with scrambled control shRNA
|
cell line: MOLM-14
shRNA construct: Scrambled Control
|
MOLM-14 cell line infected with scrambled control shRNA, biological rep2
Sample name: MOLM14_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C02_596656.CEL
|
| Sample_geo_accession | GSM863415
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863415/suppl/GSM863415.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863416 | GPL3921 |
|
MOLM14-shControl-rep3
|
MOLM-14 cell line infected with scrambled control shRNA
|
cell line: MOLM-14
shRNA construct: Scrambled Control
|
MOLM-14 cell line infected with scrambled control shRNA, biological rep3
Sample name: MOLM14_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C07_596588.CEL
|
| Sample_geo_accession | GSM863416
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863416/suppl/GSM863416.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863417 | GPL3921 |
|
MOLM14-shGSK3B-Construct1-rep1
|
MOLM-14 cell line infected with GSK3B Construct 1 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3B Construct 1
|
MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: MOLM14_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C03_596594.CEL
|
| Sample_geo_accession | GSM863417
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863417/suppl/GSM863417.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863418 | GPL3921 |
|
MOLM14-shGSK3B-Construct1-rep2
|
MOLM-14 cell line infected with GSK3B Construct 1 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3B Construct 1
|
MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: MOLM14_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C08_596612.CEL
|
| Sample_geo_accession | GSM863418
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863418/suppl/GSM863418.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863419 | GPL3921 |
|
MOLM14-shGSK3B-Construct2-rep1
|
MOLM-14 cell line infected with GSK3B Construct 2 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3B Construct 2
|
MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: MOLM14_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C04_596732.CEL
|
| Sample_geo_accession | GSM863419
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863419/suppl/GSM863419.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863420 | GPL3921 |
|
MOLM14-shGSK3B-Construct2-rep2
|
MOLM-14 cell line infected with GSK3B Construct 2 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3B Construct 2
|
MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: MOLM14_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C09_596558.CEL
|
| Sample_geo_accession | GSM863420
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863420/suppl/GSM863420.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863421 | GPL3921 |
|
MOLM14-shGSK3A-Construct5-rep1
|
MOLM-14 cell line infected with GSK3A Construct 5 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3A Construct 5
|
MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: MOLM14_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C05_596604.CEL
|
| Sample_geo_accession | GSM863421
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863421/suppl/GSM863421.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863422 | GPL3921 |
|
MOLM14-shGSK3A-Construct5-rep2
|
MOLM-14 cell line infected with GSK3A Construct 5 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3A Construct 5
|
MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: MOLM14_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C10_596704.CEL
|
| Sample_geo_accession | GSM863422
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863422/suppl/GSM863422.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863423 | GPL3921 |
|
MOLM14-shGSK3A-Construct6-rep1
|
MOLM-14 cell line infected with GSK3A Construct 6 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3A Construct 6
|
MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: MOLM14_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C06_596630.CEL
|
| Sample_geo_accession | GSM863423
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863423/suppl/GSM863423.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863424 | GPL3921 |
|
MOLM14-shGSK3A-Construct6-rep2
|
MOLM-14 cell line infected with GSK3A Construct 6 shRNA
|
cell line: MOLM-14
shRNA construct: GSK3A Construct 6
|
MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: MOLM14_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C11_596726.CEL
|
| Sample_geo_accession | GSM863424
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863424/suppl/GSM863424.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863425 | GPL3921 |
|
U937-shControl-rep1
|
U937 cell line infected with scrambled control shRNA
|
cell line: U937
shRNA construct: Scrambled Control
|
U937 cell line infected with scrambled control shRNA, biological rep1
Sample name: U937_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D01_596638.CEL
|
| Sample_geo_accession | GSM863425
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863425/suppl/GSM863425.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863426 | GPL3921 |
|
U937-shControl-rep2
|
U937 cell line infected with scrambled control shRNA
|
cell line: U937
shRNA construct: Scrambled Control
|
U937 cell line infected with scrambled control shRNA, biological rep2
Sample name: U937_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D02_596628.CEL
|
| Sample_geo_accession | GSM863426
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863426/suppl/GSM863426.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863427 | GPL3921 |
|
U937-shControl-rep3
|
U937 cell line infected with scrambled control shRNA
|
cell line: U937
shRNA construct: Scrambled Control
|
U937 cell line infected with scrambled control shRNA, biological rep3
Sample name: U937_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D07_596720.CEL
|
| Sample_geo_accession | GSM863427
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863427/suppl/GSM863427.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863428 | GPL3921 |
|
U937-shGSK3B-Construct1-rep1
|
U937 cell line infected with GSK3B Construct 1 shRNA
|
cell line: U937
shRNA construct: GSK3B Construct 1
|
U937 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: U937_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D03_596708.CEL
|
| Sample_geo_accession | GSM863428
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863428/suppl/GSM863428.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863429 | GPL3921 |
|
U937-shGSK3B-Construct1-rep2
|
U937 cell line infected with GSK3B Construct 1 shRNA
|
cell line: U937
shRNA construct: GSK3B Construct 1
|
U937 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: U937_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D08_596716.CEL
|
| Sample_geo_accession | GSM863429
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863429/suppl/GSM863429.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863430 | GPL3921 |
|
U937-shGSK3B-Construct2-rep1
|
U937 cell line infected with GSK3B Construct 2 shRNA
|
cell line: U937
shRNA construct: GSK3B Construct 2
|
U937 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: U937_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D04_596654.CEL
|
| Sample_geo_accession | GSM863430
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863430/suppl/GSM863430.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863431 | GPL3921 |
|
U937-shGSK3B-Construct2-rep2
|
U937 cell line infected with GSK3B Construct 2 shRNA
|
cell line: U937
shRNA construct: GSK3B Construct 2
|
U937 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: U937_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D09_596680.CEL
|
| Sample_geo_accession | GSM863431
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863431/suppl/GSM863431.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863432 | GPL3921 |
|
U937-shGSK3A-Construct5-rep1
|
U937 cell line infected with GSK3A Construct 5 shRNA
|
cell line: U937
shRNA construct: GSK3A Construct 5
|
U937 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: U937_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D05_596632.CEL
|
| Sample_geo_accession | GSM863432
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863432/suppl/GSM863432.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863433 | GPL3921 |
|
U937-shGSK3A-Construct5-rep2
|
U937 cell line infected with GSK3A Construct 5 shRNA
|
cell line: U937
shRNA construct: GSK3A Construct 5
|
U937 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: U937_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D10_596608.CEL
|
| Sample_geo_accession | GSM863433
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863433/suppl/GSM863433.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863434 | GPL3921 |
|
U937-shGSK3A-Construct6-rep1
|
U937 cell line infected with GSK3A Construct 6 shRNA
|
cell line: U937
shRNA construct: GSK3A Construct 6
|
U937 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: U937_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D06_596676.CEL
|
| Sample_geo_accession | GSM863434
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863434/suppl/GSM863434.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
|
GSM863435 | GPL3921 |
|
U937-shGSK3A-Construct6-rep2
|
U937 cell line infected with GSK3A Construct 6 shRNA
|
cell line: U937
shRNA construct: GSK3A Construct 6
|
U937 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: U937_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D11_596666.CEL
|
| Sample_geo_accession | GSM863435
| | Sample_status | Public on Feb 27 2012
| | Sample_submission_date | Jan 18 2012
| | Sample_last_update_date | Feb 27 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.
| | Sample_growth_protocol_ch1 | All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
| | Sample_data_processing | The ABS_CALL values were generated in R with the MAS5 algorithm.
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM863nnn/GSM863435/suppl/GSM863435.CEL.gz
| | Sample_series_id | GSE35200
| | Sample_data_row_count | 22277
| | |
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