Search results for the GEO ID: GSE14711  |
(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 |
GSM366942 | GPL570 |
|
PDB fibroblasts
|
PDB fibroblasts
|
Human fibroblasts
|
Fibroblasts cultured in fibroblast medium
|
| Sample_geo_accession | GSM366942
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 03 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_growth_protocol_ch1 | Fibroblasts were cultured in fibroblast medium [DMEM supplemented with 15% FBS (Hyclone), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen) and penicillin/streptomycin (Invitrogen)].
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM366nnn/GSM366942/suppl/GSM366942.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367061 | GPL570 |
|
hES BG01
|
Human embryonic stem cells
|
Human ES cell line BG01
|
Human embryonic stem cells cultured with a mouse embryonic fibroblast feeder layer; NIH Code: BG01
|
| Sample_geo_accession | GSM367061
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | BresaGen, Inc., Athens, GA
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367061/suppl/GSM367061.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367062 | GPL570 |
|
hES H9
|
Human embryonic stem cells
|
Human ES cell line H9
|
Human embryonic stem cells cultured with a fibroblast feeder layer; NIH Code: WA09
|
| Sample_geo_accession | GSM367062
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Wisconsin Alumni Research Foundation, Madison, WI
| | Sample_growth_protocol_ch1 | Human embryonic stem cells H9 were maintained on MMC-inactivated MEFs or on MMC-inactivated human fibroblasts (D551; American Type Culture Collection, Manassas, VA) according to the manufacturer’s protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367062/suppl/GSM367062.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367219 | GPL570 |
|
iPS PDB 1lox-17Puro-5
|
Factor-free human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient. Lentiviral vectors were excised after integration using Cre-recombinase.
|
| Sample_geo_accession | GSM367219
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4). Lentiviral vectors were then excised after integration using Cre-recombinase.
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367219/suppl/GSM367219.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367240 | GPL570 |
|
iPS PDB 1lox-17Puro-10
|
Factor-free human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient. Lentiviral vectors were excised after integration using Cre-recombinase.
|
| Sample_geo_accession | GSM367240
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4). Lentiviral vectors were then excised after integration using Cre-recombinase.
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367240/suppl/GSM367240.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367241 | GPL570 |
|
iPS PDB 1lox-21Puro-20
|
Factor-free human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient. Lentiviral vectors were excised after integration using Cre-recombinase.
|
| Sample_geo_accession | GSM367241
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4). Lentiviral vectors were then excised after integration using Cre-recombinase.
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367241/suppl/GSM367241.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367242 | GPL570 |
|
iPS PDB 1lox-21Puro-26
|
Factor-free human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Factor-free human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient. Lentiviral vectors were excised after integration using Cre-recombinase.
|
| Sample_geo_accession | GSM367242
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4). Lentiviral vectors were then excised after integration using Cre-recombinase.
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367242/suppl/GSM367242.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367243 | GPL570 |
|
iPS PDB 2lox-5
|
Virus-carrying human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient
|
| Sample_geo_accession | GSM367243
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367243/suppl/GSM367243.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367244 | GPL570 |
|
iPS PDB 2lox-22
|
Virus-carrying human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient
|
| Sample_geo_accession | GSM367244
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367244/suppl/GSM367244.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367245 | GPL570 |
|
iPS PDB 2lox-21
|
Virus-carrying human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient
|
| Sample_geo_accession | GSM367245
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367245/suppl/GSM367245.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | Sample_data_row_count | 54675
| | |
|
GSM367258 | GPL570 |
|
iPS PDB 2lox-17
|
Virus-carrying human induced pluripotent stem cells (hIPSC)
|
parental cell line: AG20442
|
Human induced pluripotent stem cells derived from dermal fibroblasts from a male Parkinson's disease patient
|
| Sample_geo_accession | GSM367258
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Feb 04 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Coriell Cell Repository
| | Sample_treatment_protocol_ch1 | Dermal fibroblasts from a patient with idiopathic Parkinson's disease were reprogrammed with lentiviruses transducing 3 reprogramming factors (OCT4, SOX2, KLF4).
| | Sample_growth_protocol_ch1 | Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM ß-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 2 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analog during cRNA amplification.
| | Sample_hyb_protocol | Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according to the Affymetrix hybridization manual. Arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
| | Sample_scan_protocol | Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using the GeneChip Operating Software v1.4.
| | Sample_data_processing | Arrays were processed using the MAS5 algorithm and absent/present calls for each probeset were determined using the standard Affymetrix algorithm, both as implemented in Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Frank,,Soldner
| | Sample_contact_email | soldner@wi.mit.edu
| | Sample_contact_phone | 617-258-5000
| | Sample_contact_laboratory | Jaenisch
| | Sample_contact_institute | Whitehead Institute for Biomedical Research
| | Sample_contact_address | 9 Cambridge Center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM367nnn/GSM367258/suppl/GSM367258.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE14711
| | 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: |
|
|
|
