Search results for the GEO ID: GSE6890  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM157866 | GPL570 |
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K562 Transcriptome map
|
K562 cells
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lymphoblastoid cells
|
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).
|
| Sample_geo_accession | GSM157866
| | Sample_status | Public on Apr 23 2007
| | Sample_submission_date | Jan 24 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC, ATCC number CCL-243
| | Sample_treatment_protocol_ch1 | n.a.
| | Sample_growth_protocol_ch1 | K562 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 | 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 | Roel,,van Driel
| | Sample_contact_email | van.driel@science.uva.nl
| | Sample_contact_phone | +31205257270
| | Sample_contact_laboratory | Swammerdam Institute for Life Sciences
| | Sample_contact_department | BioCentrum
| | Sample_contact_institute | University of Amsterdam
| | Sample_contact_address | Kruislaan 318
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1098 SM
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM157nnn/GSM157866/suppl/GSM157866.CEL.gz
| | Sample_series_id | GSE6890
| | Sample_data_row_count | 54675
| | |
|
GSM157867 | GPL570 |
|
SH-EP Transcriptome map
|
SH-EP2 cells
|
human neuroblastoma cells
|
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).
|
| Sample_geo_accession | GSM157867
| | Sample_status | Public on Apr 23 2007
| | Sample_submission_date | Jan 24 2007
| | Sample_last_update_date | Apr 23 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 | SH-EP 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 | 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 | Roel,,van Driel
| | Sample_contact_email | van.driel@science.uva.nl
| | Sample_contact_phone | +31205257270
| | Sample_contact_laboratory | Swammerdam Institute for Life Sciences
| | Sample_contact_department | BioCentrum
| | Sample_contact_institute | University of Amsterdam
| | Sample_contact_address | Kruislaan 318
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1098 SM
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM157nnn/GSM157867/suppl/GSM157867.CEL.gz
| | Sample_series_id | GSE6890
| | Sample_data_row_count | 54675
| | |
|
GSM157868 | GPL570 |
|
HeLa Transcriptome maps
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HeLa cells
|
cervix carcinoma cells
|
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).
|
| Sample_geo_accession | GSM157868
| | Sample_status | Public on Apr 23 2007
| | Sample_submission_date | Jan 24 2007
| | Sample_last_update_date | Apr 23 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC, ATCC number CCL-2
| | Sample_treatment_protocol_ch1 | n.a.
| | Sample_growth_protocol_ch1 | HeLa 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 | 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 | Roel,,van Driel
| | Sample_contact_email | van.driel@science.uva.nl
| | Sample_contact_phone | +31205257270
| | Sample_contact_laboratory | Swammerdam Institute for Life Sciences
| | Sample_contact_department | BioCentrum
| | Sample_contact_institute | University of Amsterdam
| | Sample_contact_address | Kruislaan 318
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1098 SM
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM157nnn/GSM157868/suppl/GSM157868.cel.gz
| | Sample_series_id | GSE6890
| | Sample_data_row_count | 54675
| | |
|
GSM157869 | GPL570 |
|
04-147 Transcriptome map
|
04-147 cells
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Human primary fibroblasts derived from female skin
|
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).
|
| Sample_geo_accession | GSM157869
| | Sample_status | Public on Apr 23 2007
| | Sample_submission_date | Jan 24 2007
| | Sample_last_update_date | Apr 23 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 | 04-147 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 | 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 | Roel,,van Driel
| | Sample_contact_email | van.driel@science.uva.nl
| | Sample_contact_phone | +31205257270
| | Sample_contact_laboratory | Swammerdam Institute for Life Sciences
| | Sample_contact_department | BioCentrum
| | Sample_contact_institute | University of Amsterdam
| | Sample_contact_address | Kruislaan 318
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1098 SM
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM157nnn/GSM157869/suppl/GSM157869.CEL.gz
| | Sample_series_id | GSE6890
| | Sample_data_row_count | 54675
| | |
|
GSM157870 | GPL570 |
|
HCT116 Transcriptome map
|
HCT116 cells
|
human colon carcinoma cells
|
Data accompanying the paper: "The 3D structure of human interphase
chromosomes is related to the transcriptome map. Goetze et al.,
(submitted).
|
| Sample_geo_accession | GSM157870
| | Sample_status | Public on Apr 23 2007
| | Sample_submission_date | Jan 24 2007
| | Sample_last_update_date | Aug 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC, ATCC number CCL-247
| | Sample_treatment_protocol_ch1 | n.a.
| | Sample_growth_protocol_ch1 | H116 cells were cultured in McCoy’s 5 medium (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 | 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 | Roel,,van Driel
| | Sample_contact_email | van.driel@science.uva.nl
| | Sample_contact_phone | +31205257270
| | Sample_contact_laboratory | Swammerdam Institute for Life Sciences
| | Sample_contact_department | BioCentrum
| | Sample_contact_institute | University of Amsterdam
| | Sample_contact_address | Kruislaan 318
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1098 SM
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM157nnn/GSM157870/suppl/GSM157870.CEL.gz
| | Sample_series_id | GSE6890
| | Sample_data_row_count | 54675
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