Search results for the GEO ID: GSE11428  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM288293 | GPL570 |
|
LNCaP siControl, biological replicate 1
|
LNCaP cells, siRNA control treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288293
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288293/suppl/GSM288293.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288294 | GPL570 |
|
LNCaP siControl, biological replicate 2
|
LNCaP cells, siRNA control treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288294
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288294/suppl/GSM288294.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288295 | GPL570 |
|
LNCaP siControl, biological replicate 3
|
LNCaP cells, siRNA control treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288295
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288295/suppl/GSM288295.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288296 | GPL570 |
|
abl siControl, biological replicate 1
|
abl cellls, siRNA control treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288296
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288296/suppl/GSM288296.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288297 | GPL570 |
|
abl siControl, biological replicate 2
|
abl cellls, siRNA control treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288297
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288297/suppl/GSM288297.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288298 | GPL570 |
|
abl siControl, biological replicate 3
|
abl cellls, siRNA control treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288298
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288298/suppl/GSM288298.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288299 | GPL570 |
|
LNCaP siAR, biological replicate 1
|
LNCaP cells, siRNA against AR treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288299
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288299/suppl/GSM288299.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288300 | GPL570 |
|
LNCaP siAR, biological replicate 2
|
LNCaP cells, siRNA against AR treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288300
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288300/suppl/GSM288300.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288301 | GPL570 |
|
LNCaP siAR, biological replicate 3
|
LNCaP cells, siRNA against AR treated
|
androgen-dependent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288301
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288301/suppl/GSM288301.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288302 | GPL570 |
|
abl siAR, biological replicate 1
|
abl cells, siRNA against AR treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288302
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288302/suppl/GSM288302.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288303 | GPL570 |
|
abl siAR, biological replicate 2
|
abl cells, siRNA against AR treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288303
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288303/suppl/GSM288303.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288304 | GPL570 |
|
abl siAR, biological replicate 3
|
abl cells, siRNA against AR treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288304
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288304/suppl/GSM288304.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288305 | GPL570 |
|
abl vehicle, biological replicate 1
|
abl cells, ethanol treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288305
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288305/suppl/GSM288305.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288306 | GPL570 |
|
abl vehicle, biological replicate 2
|
abl cells, ethanol treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288306
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288306/suppl/GSM288306.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288307 | GPL570 |
|
abl vehicle, biological replicate 3
|
abl cells, ethanol treated
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288307
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288307/suppl/GSM288307.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288308 | GPL570 |
|
abl DHT 4hr, biological replicate 1
|
abl cells, DHT treated for 4hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288308
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288308/suppl/GSM288308.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288309 | GPL570 |
|
abl DHT 4hr, biological replicate 2
|
abl cells, DHT treated for 4hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288309
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288309/suppl/GSM288309.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288310 | GPL570 |
|
abl DHT 4hr, biological replicate 3
|
abl cells, DHT treated for 4hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288310
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288310/suppl/GSM288310.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288311 | GPL570 |
|
abl DHT 16hr, biological replicate 1
|
abl cellls, DHT treated for 16 hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288311
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288311/suppl/GSM288311.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288312 | GPL570 |
|
abl DHT 16hr, biological replicate 2
|
abl cellls, DHT treated for 16 hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288312
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288312/suppl/GSM288312.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
GSM288313 | GPL570 |
|
abl DHT 16hr, biological replicate 3
|
abl cellls, DHT treated for 16 hrs
|
androgen-independent prostate cancer cell line
|
gene expression data from prostate cancer cell lines
|
| Sample_geo_accession | GSM288313
| | Sample_status | Public on Jul 25 2009
| | Sample_submission_date | May 13 2008
| | Sample_last_update_date | May 01 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | LNCaP and abl cells were tranfected with siAR or siControl. Abl cells were treated with DHT (100nM) for 4 hr and 16 hr.
| | Sample_growth_protocol_ch1 | The growth medium for LNCaP and abl cells is phenol-red free RPMI 1640 medium containing 5% charcoal/dextran-stripped fetal bovine serum (FBS). abl cells starved in the above medium for 3 days and then treated with or without 100 nM DHT for 4 h and 16 h. LNCaP and abl cells were plated one day before siRNA transfection and RNA was extracted 72 hr after transfection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy kit (Qiagen) was used to purify total RNAs.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).
| | Sample_hyb_protocol | After fragmentation of the sample (cRNA), add hybridization mix: 150 ul 2X MES Hybridization Buffer 3 ul 10 mg/mL Herring Sperm DNA, sheared 3 ul 3 nM Control Oligo B2 (5'-Bio-GTCAAGATGCTACCGTTCA-3') 3 ul 50 mg/mL Acetylated BSA 15 ul 20X Eukaryotic Hybridization Controls Adjust volume with DEPC H2O to 300 ul total volume (if fragmentation volume is 50 ul, need 76 ul water) -Heat frozen targets at 95 °C, 5 min (omit this step if samples are not frozen) -Cool targets at 45 °C, 5 min -Spin targets at max, 5 min -Add 200 ul targets to each properly labeled chip -Incubate chips at 45 °C, 60 RPM, 16-18 h -Return the remaining volume of unused target to -20 °C -The next day, remove target & fill chips with non-stringent buffer (A) with no bubbles. -Wrap chips in foil and store at 4 °C until you start fluidics. Allow chips to equilibrate to room temperature before start fluidics and scanning -run fluidics protocol EukGE-WS2v4_450 using Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | scan on Affymetrix GeneChip Scanner (GCS) 3000
| | Sample_data_processing | creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036
| | Sample_platform_id | GPL570
| | Sample_contact_name | Arjun,Kumar,Manrai
| | Sample_contact_email | manrai@post.harvard.edu
| | Sample_contact_laboratory | X. Shirley Liu
| | Sample_contact_department | Department of Biostatistics and Computational Biology
| | Sample_contact_institute | Dana Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street, Mail Stop LW225
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM288nnn/GSM288313/suppl/GSM288313.CEL.gz
| | Sample_series_id | GSE11428
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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