Search results for the GEO ID: GSE33789  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM835796 | GPL570 |
|
ESC UNDIFF LINE BG02 PASSAGE 50
|
ESC UNDIFF LINE BG02 PASSAGE 50
|
class: ESC
condition: UNDIFF
cell line: BG02
passage: 50
gender: MALE
|
ESC UNDIFF LINE BG02 PASSAGE 50
|
| Sample_geo_accession | GSM835796
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835796/suppl/GSM835796_SAMPLE_2.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835797 | GPL570 |
|
ESC UNDIFF LINE BG02 PASSAGE 54
|
ESC UNDIFF LINE BG02 PASSAGE 54
|
class: ESC
condition: UNDIFF
cell line: BG02
passage: 54
gender: MALE
|
ESC UNDIFF LINE BG02 PASSAGE 54
|
| Sample_geo_accession | GSM835797
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835797/suppl/GSM835797_SAMPLE_7.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835798 | GPL570 |
|
ESC UNDIFF LINE ES02 PASSAGE 45
|
ESC UNDIFF LINE ES02 PASSAGE 45
|
class: ESC
condition: UNDIFF
cell line: ES02
passage: 45
gender: FEMALE
|
ESC UNDIFF LINE ES02 PASSAGE 45
|
| Sample_geo_accession | GSM835798
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835798/suppl/GSM835798_SAMPLE_9.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835799 | GPL570 |
|
ESC UNDIFF LINE ES02 PASSAGE 49
|
ESC UNDIFF LINE ES02 PASSAGE 49
|
class: ESC
condition: UNDIFF
cell line: ES02
passage: 49
gender: FEMALE
|
ESC UNDIFF LINE ES02 PASSAGE 49
|
| Sample_geo_accession | GSM835799
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835799/suppl/GSM835799_SAMPLE_4.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835800 | GPL570 |
|
ESC UNDIFF LINE TE03 PASSAGE 66
|
ESC UNDIFF LINE TE03 PASSAGE 66
|
class: ESC
condition: UNDIFF
cell line: TE03
passage: 66
gender: FEMALE
|
ESC UNDIFF LINE TE03 PASSAGE 66
|
| Sample_geo_accession | GSM835800
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835800/suppl/GSM835800_SAMPLE_10.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835801 | GPL570 |
|
ESC UNDIFF LINE TE03 PASSAGE 70
|
ESC UNDIFF LINE TE03 PASSAGE 70
|
class: ESC
condition: UNDIFF
cell line: TE03
passage: 70
gender: FEMALE
|
ESC UNDIFF LINE TE03 PASSAGE 70
|
| Sample_geo_accession | GSM835801
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835801/suppl/GSM835801_SAMPLE_6.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835802 | GPL570 |
|
ESC UNDIFF LINE UC01 PASSAGE 56
|
ESC UNDIFF LINE UC01 PASSAGE 56
|
class: ESC
condition: UNDIFF
cell line: UC01
passage: 56
gender: FEMALE
|
ESC UNDIFF LINE UC01 PASSAGE 56
|
| Sample_geo_accession | GSM835802
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835802/suppl/GSM835802_SAMPLE_1.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835803 | GPL570 |
|
ESC UNDIFF LINE UC01 PASSAGE 60
|
ESC UNDIFF LINE UC01 PASSAGE 60
|
class: ESC
condition: UNDIFF
cell line: UC01
passage: 60
gender: FEMALE
|
ESC UNDIFF LINE UC01 PASSAGE 60
|
| Sample_geo_accession | GSM835803
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835803/suppl/GSM835803_SAMPLE_3.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835804 | GPL570 |
|
ESC UNDIFF LINE WA01 PASSAGE 52
|
ESC UNDIFF LINE WA01 PASSAGE 52
|
class: ESC
condition: UNDIFF
cell line: WA01
passage: 52
gender: MALE
|
ESC UNDIFF LINE WA01 PASSAGE 52
|
| Sample_geo_accession | GSM835804
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835804/suppl/GSM835804_SAMPLE_11.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835805 | GPL570 |
|
ESC UNDIFF LINE WA01 PASSAGE 56
|
ESC UNDIFF LINE WA01 PASSAGE 56
|
class: ESC
condition: UNDIFF
cell line: WA01
passage: 56
gender: MALE
|
ESC UNDIFF LINE WA01 PASSAGE 56
|
| Sample_geo_accession | GSM835805
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835805/suppl/GSM835805_SAMPLE_8.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835806 | GPL570 |
|
UniRef Processing Control 1
|
UniRef Processing Control
|
class: UniRef
condition: N/A
cell line: N/A
passage: N/A
gender: N/A
|
UniRef Processing Control
|
| Sample_geo_accession | GSM835806
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835806/suppl/GSM835806_SAMPLE_5.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
GSM835807 | GPL570 |
|
UniRef Processing Control 2
|
UniRef Processing Control
|
class: UniRef
condition: N/A
cell line: N/A
passage: N/A
gender: N/A
|
UniRef Processing Control
|
| Sample_geo_accession | GSM835807
| | Sample_status | Public on Oct 31 2012
| | Sample_submission_date | Nov 17 2011
| | Sample_last_update_date | Mar 13 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133_Plus2 GeneChip (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).
| | Sample_hyb_protocol | Labeled cRNA were hybridized to Affymetrix Human U133_Plus2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.
| | Sample_scan_protocol | Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate gene probe measurements for each hybridized cRNA.
| | Sample_data_processing | The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe measurements generated for each hybridized cRNA and generate 54,675 MAS5 normalized gene fragment expression values for each hybridized cRNA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kory,R,Johnson
| | Sample_contact_email | johnsonko@ninds.nih.gov
| | Sample_contact_phone | 301-402-1956
| | Sample_contact_laboratory | Bioinformatics Section
| | Sample_contact_department | DIR IT & Bioinformatics
| | Sample_contact_institute | NINDS/NIH
| | Sample_contact_address | 10/5S223, 9000 Rockville Pike
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM835nnn/GSM835807/suppl/GSM835807_SAMPLE_12.CEL.gz
| | Sample_series_id | GSE33789
| | Sample_series_id | GSE34200
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
