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Search results for the GEO ID: GSE48830

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GSM1185378

GPL570

01-HDFs-p5

Primary adult human skin cells

cell type: Primary adult human skin cells

Gene expression data from cell lines

Sample_geo_accession	GSM1185378
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185378/suppl/GSM1185378_01-HDFs-p5.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185379

GPL570

02-HDFs-p5

Primary adult human skin cells

cell type: Primary adult human skin cells

Gene expression data from cell lines

Sample_geo_accession	GSM1185379
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185379/suppl/GSM1185379_02-HDFs-p5.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185380

GPL570

03-hIPSC-preEx-p32

Human induced pluripotent stem cells - pre-Excision

cell type: Human induced pluripotent stem cells - pre-Excision

Gene expression data from cell lines

Sample_geo_accession	GSM1185380
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185380/suppl/GSM1185380_03-hIPSC-preEx-p32.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185381

GPL570

04-hIPSC-preEx-p32

Human induced pluripotent stem cells - pre-Excision

cell type: Human induced pluripotent stem cells - pre-Excision

Gene expression data from cell lines

Sample_geo_accession	GSM1185381
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185381/suppl/GSM1185381_04-hIPSC-preEx-p32.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185382

GPL570

05-hIPSC-postEx-p28

Human induced pluripotent stem cells - post-Excision

cell type: Human induced pluripotent stem cells - post-Excision

Gene expression data from cell lines

Sample_geo_accession	GSM1185382
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185382/suppl/GSM1185382_05-hIPSC-postEx-p28.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185383

GPL570

06-hIPSC-postEx-p28

Human induced pluripotent stem cells - post-Excision

cell type: Human induced pluripotent stem cells - post-Excision

Gene expression data from cell lines

Sample_geo_accession	GSM1185383
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185383/suppl/GSM1185383_06-hIPSC-postEx-p28.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185384

GPL570

07-hESCs-H9-p29

Human embryonic stem cells (H9)

cell type: Human embryonic stem cells (H9) cell line: H9

Gene expression data from cell lines

Sample_geo_accession	GSM1185384
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185384/suppl/GSM1185384_07-hESCs-H9-p29.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

GSM1185385

GPL570

08-hESCs-H9-p29

Human embryonic stem cells (H9)

cell type: Human embryonic stem cells (H9) cell line: H9

Gene expression data from cell lines

Sample_geo_accession	GSM1185385
Sample_status	Public on Jul 13 2013
Sample_submission_date	Jul 12 2013
Sample_last_update_date	Jul 13 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Up to 30 million HDFs per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed thrice with PBS. For the pluripotent stem cells, the total cells were manually collected from 6 wells of a 6-well plate at 50-80% confluence, washed with ESC media and then used for analysis.
Sample_growth_protocol_ch1	All human biopsy-derived cells and fibroblast lines were cultured in complete DMEM/F-12 media consisting of Dulbecco’s modified Eagle’s medium nutrient mixture/F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS), 1x minimum essential medium non-essential amino acids, 1x Glutamax, and 100 IU/mL penicillin-streptomycin (all from Invitrogen/Gibco, Grand Island, NY, USA) and maintained at 37°C in a 5% CO2 incubator. Culture media were changed every two days. Cells were allowed to expand to 80% to 90% confluency before passaging with 0.05% trypsin-ethylenediaminetetraacetic acid (EDTA) (Invitrogen) and replating at a 1:3 ratio. A large bank of early-passage HUF1 cells was cryopreserved in culture media supplemented with 10% dimethyl sulphoxide (DMSO) (Sigma-Aldrich, St. Louis, MO, USA). All research adhered to National Academy of Sciences guidelines. Human embryonic stem cells (H9), adult pre-excision line (termed C-8, or pre-excised iPSC) and adult post-excision line (termed 2.3, or post-excised iPSC), derived as explained below, were all initially maintained on 0.2% gelatin-coated 6-well plates covered with 35,000 cells per cm2 of irradiated mouse embryonic fibroblasts (MEFs) (GlobalStem, Rockville, MD, USA) with standard embryonic stem cell media consisting of DMEM/F-12 supplemented with 20% Knockout Serum Replacement, 1x Glutamax, 1x non-essential amino acids, 100 IU/mL penicillin-streptomycin (all from Invitrogen), 1x β-mercaptoethanol (Millipore, Billerica, MA, USA), and 10 ng/mL recombinant human basic fibroblast growth factor (bFGF) (Globalstem). All cells were transitioned into a feeder-free system and subsequently maintained on reduced growth factor Matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 10 ng/mL bFGF (Globalstem) and 1x Primocin (InvivoGen, San Diego, CA, USA). Media were changed daily. Cells were passaged every 4 to 5 days, depending on colony density and size. Differentiation was removed daily from colonies by using pulled glass pipettes. To passage the pluripotent stem cells, an 18-gauge needle was used to cross-hatch colonies in a grid format, with subsequent gentle agitation to remove the pieces with a P200 pipette. Usually, 4 to 8 colonies were passaged onto freshly coated Matrigel plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from two biological replicates of each cell population using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions. This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA
Sample_hyb_protocol	Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.
Sample_platform_id	GPL570
Sample_contact_name	James,A,Byrne
Sample_contact_department	Department of Molecular and Medical Pharmacology
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	610 Charles E. Young Drive East
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1185nnn/GSM1185385/suppl/GSM1185385_08-hESCs-H9-p29.CEL.gz
Sample_series_id	GSE48830
Sample_data_row_count	54675

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