Search results for the GEO ID: GSE15715 |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM393453 | GPL1261 |
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Bmi1 wildtype MEF
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Bmi1 wildtype mouse embryonic fibroblast cells
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strain: C57BL/6
gender: Male
reference: Jacobs, J.J. et al. Nat.Genetics. 2000
antibody: anti-uH2A(E6C5)
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Expression study was performed in conjunction with genome-wide localization of ubiquitylated H2A.
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Sample_geo_accession | GSM393453
| Sample_status | Public on Apr 30 2009
| Sample_submission_date | Apr 16 2009
| Sample_last_update_date | Apr 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | None
| Sample_growth_protocol_ch1 | TBX2 immortalized cells were cultured in DMEM supplemented with 10% FBS. Cells were split 1:5 every three days using 0.01% Trypsin-EDTA for the duration of culturing.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Qiagen RNeasy Kit by manufacturers protocol for extraction from animal cells.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 7 ug of total RNA was used to synthesize cDNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).
| Sample_hyb_protocol | 10 ug of cRNA was used for hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640. The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.
| Sample_scan_protocol | the arrays were scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.
| Sample_data_processing | MAS5 algorithm was used for data generation.
| Sample_platform_id | GPL1261
| Sample_contact_name | Eric,M.,Kallin
| Sample_contact_email | eric.kallin@crg.es
| Sample_contact_laboratory | Thomas Graf
| Sample_contact_department | Differentiation and Cancer
| Sample_contact_institute | Center for Genomic Regulation
| Sample_contact_address | C/ Dr. Aiguader, 88
| Sample_contact_city | Barcelona
| Sample_contact_state | Barcelona
| Sample_contact_zip/postal_code | 08003
| Sample_contact_country | Spain
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393453/suppl/GSM393453.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393453/suppl/GSM393453.CHP.gz
| Sample_series_id | GSE15715
| Sample_series_id | GSE15909
| Sample_data_row_count | 45101
| |
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GSM393454 | GPL1261 |
|
Bmi1 knockout MEF
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Bmi1 knockout mouse embryonic fibroblast cells
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strain: C57BL/6
gender: Male
reference: Jacobs, J.J. et al. Nat.Genetics. 2000
antibody: anti-uH2A(E6C5)
|
Expression study was performed in conjunction with genome-wide localization of ubiquitylated H2A.
|
Sample_geo_accession | GSM393454
| Sample_status | Public on Apr 30 2009
| Sample_submission_date | Apr 16 2009
| Sample_last_update_date | Apr 30 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | None
| Sample_growth_protocol_ch1 | TBX2 immortalized cells were cultured in DMEM supplemented with 10% FBS. Cells were split 1:5 every three days using 0.01% Trypsin-EDTA for the duration of culturing.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Qiagen RNeasy Kit by manufacturers protocol for extraction from animal cells.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 7 ug of total RNA was used to synthesize cDNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction. Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization. 15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 ug/ul fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).
| Sample_hyb_protocol | 10 ug of cRNA was used for hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640. The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400.
| Sample_scan_protocol | the arrays were scanned with the Hewlett Packard GeneArray Scanner. Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.
| Sample_data_processing | MAS5 algorithm was used for data generation.
| Sample_platform_id | GPL1261
| Sample_contact_name | Eric,M.,Kallin
| Sample_contact_email | eric.kallin@crg.es
| Sample_contact_laboratory | Thomas Graf
| Sample_contact_department | Differentiation and Cancer
| Sample_contact_institute | Center for Genomic Regulation
| Sample_contact_address | C/ Dr. Aiguader, 88
| Sample_contact_city | Barcelona
| Sample_contact_state | Barcelona
| Sample_contact_zip/postal_code | 08003
| Sample_contact_country | Spain
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393454/suppl/GSM393454.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM393nnn/GSM393454/suppl/GSM393454.CHP.gz
| Sample_series_id | GSE15715
| Sample_series_id | GSE15909
| Sample_data_row_count | 45101
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