Search results for the GEO ID: GSE31122  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM770676 | GPL570 |
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BT12 cells, not treated (DMSO only)
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BT12 cells, not treated (DMSO only)
|
cell line: BT12
cell type: atypical teratoid/rhabdoid tumor cells
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Atypical Teratoid / Rhabdoid Tumor cell line
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| Sample_geo_accession | GSM770676
| | Sample_status | Public on Nov 14 2011
| | Sample_submission_date | Aug 02 2011
| | Sample_last_update_date | Nov 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and subsequently treated for 24hr with IC25 concentrations of SNDX-275 (Sigma), or equivalent doses of DMSO (control).
| | Sample_growth_protocol_ch1 | Cells were grown in RPMI-1640 supplemented with 10% FBS at 37C with 5% CO2
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770676/suppl/GSM770676_ATRT_BT12_DMSO.CEL.gz
| | Sample_series_id | GSE31122
| | Sample_data_row_count | 54675
| | |
|
GSM770677 | GPL570 |
|
BT12 cells, treated with IC25 of SNDX275
|
BT12 cells, treated with IC25 of SNDX275
|
cell line: BT12
cell type: atypical teratoid/rhabdoid tumor cells
|
Atypical Teratoid / Rhabdoid Tumor cell line
|
| Sample_geo_accession | GSM770677
| | Sample_status | Public on Nov 14 2011
| | Sample_submission_date | Aug 02 2011
| | Sample_last_update_date | Nov 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and subsequently treated for 24hr with IC25 concentrations of SNDX-275 (Sigma), or equivalent doses of DMSO (control).
| | Sample_growth_protocol_ch1 | Cells were grown in RPMI-1640 supplemented with 10% FBS at 37C with 5% CO2
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770677/suppl/GSM770677_ATRT_BT12_SNDX275.CEL.gz
| | Sample_series_id | GSE31122
| | Sample_data_row_count | 54675
| | |
|
GSM770678 | GPL570 |
|
BT16 cells, not treated (DMSO only)
|
BT16 cells, not treated (DMSO only)
|
cell line: BT16
cell type: atypical teratoid/rhabdoid tumor cells
|
Atypical Teratoid / Rhabdoid Tumor cell line
|
| Sample_geo_accession | GSM770678
| | Sample_status | Public on Nov 14 2011
| | Sample_submission_date | Aug 02 2011
| | Sample_last_update_date | Nov 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and subsequently treated for 24hr with IC25 concentrations of SNDX-275 (Sigma), or equivalent doses of DMSO (control).
| | Sample_growth_protocol_ch1 | Cells were grown in RPMI-1640 supplemented with 10% FBS at 37C with 5% CO2
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770678/suppl/GSM770678_ATRT_BT16_DMSO.CEL.gz
| | Sample_series_id | GSE31122
| | Sample_data_row_count | 54675
| | |
|
GSM770679 | GPL570 |
|
BT16 cells, treated with IC25 of SNDX275
|
BT16 cells, treated with IC25 of SNDX275
|
cell line: BT16
cell type: atypical teratoid/rhabdoid tumor cells
|
Atypical Teratoid / Rhabdoid Tumor cell line
|
| Sample_geo_accession | GSM770679
| | Sample_status | Public on Nov 14 2011
| | Sample_submission_date | Aug 02 2011
| | Sample_last_update_date | Nov 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were plated and subsequently treated for 24hr with IC25 concentrations of SNDX-275 (Sigma), or equivalent doses of DMSO (control).
| | Sample_growth_protocol_ch1 | Cells were grown in RPMI-1640 supplemented with 10% FBS at 37C with 5% CO2
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from each sample using an RNeasy kit (Qiagen) according to the manufacturer’s directions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer. For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.
| | Sample_hyb_protocol | For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).
| | Sample_scan_protocol | All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).
| | Sample_data_processing | Data were background corrected and normalized using the gcRMA algorithm, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Diane,K,Birks
| | Sample_contact_email | Diane.Birks@ucdenver.edu
| | Sample_contact_phone | 303-724-4024
| | Sample_contact_department | Neurosurgery
| | Sample_contact_institute | University of Colorado, Denver - Anschutz Medical Campus
| | Sample_contact_address | 12800 E 19th Ave
| | Sample_contact_city | Aurora
| | Sample_contact_state | CO
| | Sample_contact_zip/postal_code | 80122
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770679/suppl/GSM770679_ATRT_BT16_SNDX275.CEL.gz
| | Sample_series_id | GSE31122
| | Sample_data_row_count | 54675
| | |
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