Search results for the GEO ID: GSE6629  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM153779 | GPL570 |
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HEK293 Transcriptome maps (duplicate 1)
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HEK293 cells
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Fetus derived cell line from female human embryonic kidney.
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Data accompanying the paper: Domain-Wide Regulation of Gene Expression in the Human Genome, Gierman HJ et al. (submitted).
HEK293 cells were grown under standard conditions and harvested at 70% confluency. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate transcriptome maps.
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| Sample_geo_accession | GSM153779
| | Sample_status | Public on Sep 01 2007
| | Sample_submission_date | Jan 03 2007
| | Sample_last_update_date | Aug 08 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| | Sample_treatment_protocol_ch1 | n.a.
| | Sample_growth_protocol_ch1 | HEK293 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.
| | Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 algorithm (target signal | 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM153nnn/GSM153779/suppl/GSM153779.CEL.gz
| | Sample_series_id | GSE6629
| | Sample_data_row_count | 54675
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GSM153780 | GPL570 |
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HEK293 Transcriptome maps (duplicate 2)
|
HEK293 cells
|
Fetus derived cell line from female human embryonic kidney.
|
Data accompanying the paper: Domain-Wide Regulation of Gene Expression in the Human Genome, Gierman HJ et al. (submitted).
HEK293 cells were grown under standard conditions and harvested at 70% confluency. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate transcriptome maps.
|
| Sample_geo_accession | GSM153780
| | Sample_status | Public on Sep 01 2007
| | Sample_submission_date | Jan 03 2007
| | Sample_last_update_date | Aug 08 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Academic Medical Centre, Amsterdam, The Netherlands.
| | Sample_treatment_protocol_ch1 | n.a.
| | Sample_growth_protocol_ch1 | HEK293 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 μg of total RNA was used for cRNA synthesis and fragmented. Labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.
| | Sample_data_processing = Expression data (.cel files) were normalized with the MAS5 algorithm (target signal | 100) using GCOS software (Affymetrix). Data from the duplicate arraying experiments were averaged and further analyzed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM153nnn/GSM153780/suppl/GSM153780.CEL.gz
| | Sample_series_id | GSE6629
| | Sample_data_row_count | 54675
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