Search results for the GEO ID: GSE12390  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM310838 | GPL570 |
|
BJ hIPS #5p9 sample 1
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
| Sample_geo_accession | GSM310838
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310838/suppl/GSM310838.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310838/suppl/GSM310838.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310838/suppl/GSM310838_Human-5p9-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310839 | GPL570 |
|
BJ hIPS #5p9 sample 2
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #5 passage 9, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310839
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310839/suppl/GSM310839.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310839/suppl/GSM310839.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310839/suppl/GSM310839_Human-5p9-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310844 | GPL570 |
|
BJ hIPS #5p9 sample 3
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #5 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #5 passage 9, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310844
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310844/suppl/GSM310844.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310844/suppl/GSM310844.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310844/suppl/GSM310844_Human-5p9-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310845 | GPL570 |
|
BJ hIPS #6p9 sample 1
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #6 passage 9, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310845
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310845/suppl/GSM310845.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310845/suppl/GSM310845.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310845/suppl/GSM310845_Human-6p9-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310846 | GPL570 |
|
BJ hIPS #6p9 sample 2
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #6 passage 9, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310846
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310846/suppl/GSM310846.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310846/suppl/GSM310846.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310846/suppl/GSM310846_Human-6p9-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310847 | GPL570 |
|
BJ hIPS #6p9 sample 3
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
human induced pluripotent stem cells, #6 passage nr 9 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #6 passage 9, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310847
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310847/suppl/GSM310847.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310847/suppl/GSM310847.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310847/suppl/GSM310847_Human-6p9-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310848 | GPL570 |
|
BJ hIPS #8p10 sample 1
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #8 passage 10, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310848
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310848/suppl/GSM310848.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310848/suppl/GSM310848.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310848/suppl/GSM310848_Human-8p10-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310849 | GPL570 |
|
BJ hIPS #8p10 sample 2
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #8 passage 10, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310849
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310849/suppl/GSM310849.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310849/suppl/GSM310849.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310849/suppl/GSM310849_Human-8p10-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310850 | GPL570 |
|
BJ hIPS #8p10 sample 3
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
human induced pluripotent stem cells, #8 passage nr 10 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #8 passage 10, using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310850
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310850/suppl/GSM310850.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310850/suppl/GSM310850.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310850/suppl/GSM310850_Human-8p10-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310851 | GPL570 |
|
BJ hIPS #12p5 sample 1
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #12 passage 5 using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310851
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310851/suppl/GSM310851.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310851/suppl/GSM310851.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310851/suppl/GSM310851_Human-12p5-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310852 | GPL570 |
|
BJ hIPS #12p5 sample 2
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #12 passage 5 using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310852
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310852/suppl/GSM310852.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310852/suppl/GSM310852.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310852/suppl/GSM310852_Human-12p5-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310853 | GPL570 |
|
BJ hIPS #12p5 sample 3
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
human induced pluripotent stem cells, #12 passage nr 5 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells, #12 passage 5 using a confluent plate. Donor line human BJ
|
| Sample_geo_accession | GSM310853
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310853/suppl/GSM310853.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310853/suppl/GSM310853.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310853/suppl/GSM310853_Human-12p5-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310854 | GPL570 |
|
BJ sample 1
|
human BJ (Donor line)
|
human BJ (Donor line)
|
Gene expression data from human BJ (Donor line) using a confluent plate.
|
| Sample_geo_accession | GSM310854
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310854/suppl/GSM310854.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310854/suppl/GSM310854.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310854/suppl/GSM310854_Human-BJ_Exp-2-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310855 | GPL570 |
|
BJ sample 2
|
human BJ (Donor line)
|
human BJ (Donor line)
|
Gene expression data from human BJ (Donor line) using a confluent plate.
|
| Sample_geo_accession | GSM310855
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310855/suppl/GSM310855.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310855/suppl/GSM310855.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310855/suppl/GSM310855_Human-BJ_Exp-2-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310856 | GPL570 |
|
BJ sample 3
|
human BJ (Donor line)
|
human BJ (Donor line)
|
Gene expression data from human BJ (Donor line) using a confluent plate.
|
| Sample_geo_accession | GSM310856
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310856/suppl/GSM310856.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310856/suppl/GSM310856.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310856/suppl/GSM310856_Human-BJ_Exp-2-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310857 | GPL570 |
|
BJ hIPS #12p6 afp 4 #12 p 7 sample 1
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells (secondary), #12 p 6, 4 passages as differentiated cells, reinduction and generation of secondary human induced pluripotent stem cells # 12 passage nr 7 confluent plate Donor BJ
|
| Sample_geo_accession | GSM310857
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310857/suppl/GSM310857.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310857/suppl/GSM310857.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310857/suppl/GSM310857_Human-12p6_Afp4_12p7-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310858 | GPL570 |
|
BJ hIPS #12p6 afp 4 #12 p 7 sample 2
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells (secondary), #12 p 6, 4 passages as differentiated cells, reinduction and generation of secondary human induced pluripotent stem cells # 12 passage nr 7 confluent plate Donor BJ
|
| Sample_geo_accession | GSM310858
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310858/suppl/GSM310858.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310858/suppl/GSM310858.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310858/suppl/GSM310858_Human-12p6_Afp4_12p7-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310859 | GPL570 |
|
BJ hIPS #12p6 afp 4 #12 p 7 sample 3
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
human induced pluripotent stem cells (secondary), #12 passage nr 7 confluent plate Donor BJ
|
Gene expression data from human induced pluripotent stem cells (secondary), #12 p 6, 4 passages as differentiated cells, reinduction and generation of secondary human induced pluripotent stem cells # 12 passage nr 7 confluent plate Donor BJ
|
| Sample_geo_accession | GSM310859
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310859/suppl/GSM310859.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310859/suppl/GSM310859.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310859/suppl/GSM310859_Human-12p6_Afp4_12p7-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310860 | GPL570 |
|
HUES 8 p 30 sample 1
|
human embryonic stem cells HUES 8 p 30
|
human embryonic stem cells HUES 8 p 30
|
Gene expression data from human embryonic stem cell line HUES 8 p 30, taken from a confluent plate.
|
| Sample_geo_accession | GSM310860
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310860/suppl/GSM310860.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310860/suppl/GSM310860.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310860/suppl/GSM310860_Hues8p30-rep.1_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310861 | GPL570 |
|
HUES 8 p 30 sample 2
|
human embryonic stem cells HUES 8 p 30
|
human embryonic stem cells HUES 8 p 30
|
Gene expression data from human embryonic stem cell line HUES 8 p 30, taken from a confluent plate.
|
| Sample_geo_accession | GSM310861
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310861/suppl/GSM310861.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310861/suppl/GSM310861.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310861/suppl/GSM310861_Hues8p30-rep.2_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
|
GSM310862 | GPL570 |
|
HUES 8 p 30 sample 3
|
human embryonic stem cells HUES 8 p 30
|
human embryonic stem cells HUES 8 p 30
|
Gene expression data from human embryonic stem cell line HUES 8 p 30, taken from a confluent plate.
|
| Sample_geo_accession | GSM310862
| | Sample_status | Public on Sep 12 2008
| | Sample_submission_date | Aug 07 2008
| | Sample_last_update_date | Sep 12 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNeasy with on column DNA digest was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA were tested for integrity and concentration using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA). Based on RNA Integrity Numbers (RIN), of 9.8 or higher, and ribosomal ratios samples were chosen to proceed with RNA amplification starting with 1.0 µg total RNA. Labeled cRNA targets were generated from total RNA samples using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Applied Biosystems / Ambion, Austin, TX.) according to the corresponding instruction manual. Aliquots of labeled cRNA were assessed using the RNA 6000 Nano Assay and RNA LabChips on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).
| | Sample_hyb_protocol | Biotinylated and fragmented cRNA targets (15 μg) were hybridized to Human Genome U133 Plus 2.0 arrays using the GeneChip Fluidics Station 450 according to the manufacturer’s standard protocol.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G and the image data on each individual microarray chip was scaled to 150 target intensity, using the GeneChip Command Console Software (AGCC software v.1.0) (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. The further processed data are linked to the Sample below.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Tim,,Ahfeldt
| | Sample_contact_email | ahfeldt@gmail.com
| | Sample_contact_phone | 6178380289
| | Sample_contact_laboratory | Chad Cowan
| | Sample_contact_department | Massachusetts General Hospital
| | Sample_contact_institute | Center for Regenerative Medicine
| | Sample_contact_address | 185 Cambridge Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310862/suppl/GSM310862.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310862/suppl/GSM310862.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310862/suppl/GSM310862_Hues8p30-rep.3_further_processed.txt.gz
| | Sample_series_id | GSE12390
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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