Search results for the GEO ID: GSE17513  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM436530 | GPL1261 |
|
Red+/Green+ progenitor, experiment A
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436530
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436530/suppl/GSM436530_KC2007090701.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436531 | GPL1261 |
|
Red+/Green- progenitor, experiment A
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436531
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436531/suppl/GSM436531_KC2007090702.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436532 | GPL1261 |
|
Red-/Green+ progenitor, experiment A
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436532
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436532/suppl/GSM436532_KC2007090703.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436533 | GPL1261 |
|
Red-/Green- progenitor, experiment A
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436533
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436533/suppl/GSM436533_KC2007090704.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436534 | GPL1261 |
|
Red+/Green+ progenitor, experiment B
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436534
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436534/suppl/GSM436534_KC2007090705.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436535 | GPL1261 |
|
Red+/Green- progenitor, experiment B
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436535
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436535/suppl/GSM436535_KC2007090706.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436536 | GPL1261 |
|
Red-/Green+ progenitor, experiment B
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436536
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436536/suppl/GSM436536_KC2007090707.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436537 | GPL1261 |
|
Red-/Green- progenitor, experiment B
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436537
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436537/suppl/GSM436537_KC2007090708.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436538 | GPL1261 |
|
Red+/Green+ progenitor, experiment C
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436538
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436538/suppl/GSM436538_KC2007090709.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436539 | GPL1261 |
|
Red+/Green- progenitor, experiment C
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed positive, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436539
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436539/suppl/GSM436539_KC2007090710.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436540 | GPL1261 |
|
Red-/Green+ progenitor, experiment C
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP positive
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436540
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436540/suppl/GSM436540_KC2007090711.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
|
GSM436541 | GPL1261 |
|
Red-/Green- progenitor, experiment C
|
Color sorted embryonic stem cell progenitors
|
developmental stage: dissociated day 6 embryoid bodies
transgenic reporter: second heart field specific reporter dsRed negative, cardiac specific enhancer eGFP negative
|
Gene expression data from embryonic stem cell derived cardiac progenitors
|
| Sample_geo_accession | GSM436541
| | Sample_status | Public on Sep 01 2009
| | Sample_submission_date | Aug 05 2009
| | Sample_last_update_date | Aug 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Single cell suspension were generated from day 6 Ebs and the cells were FACS purified into 4 populations as follows: Red+/Green+ (R+G+), Red+/Green- (R+G-), Red-/Green+ (R-G+), Red+/Green- (R-G-),
| | Sample_growth_protocol_ch1 | Embryonic stem cells were grown according to standard protocols and differentiated in vitro by hanging droplet formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA 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 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430_2] Affymetrix Mouse Genome 430 2.0 Arrayy. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | MAS 5 processed data, all subsequent data analysis was performed with the GenePattern software suite from the Broad Institure. The PreprocessDataSet was used to identify probes with a minchange of 3.5, mindelta of 20, threshold of 2, ceiling of 20000, and max sigma binning of 1. This resulted in the preprocessed data set. Heirarchical clustering was then performed using the GenePattern Heirarchical clustering algorithm with a Pearson correlation and Pairwise complete linkage. The clustered data was used to generate a heat map with the HeatMapImage module.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ibrahim,J,Domian
| | Sample_contact_email | idomian@partners.org
| | Sample_contact_laboratory | Domian
| | Sample_contact_department | Division of Cardiology
| | Sample_contact_institute | Massachusetts General Hospital
| | 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/GSM436nnn/GSM436541/suppl/GSM436541_KC2007090712.CEL.gz
| | Sample_series_id | GSE17513
| | Sample_data_row_count | 45101
| | |
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