Result

Search results for the GEO ID: GSE40444

(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

GSM994321

GPL570

hESC-H9-p29-1

H9 embryonic stem cells, untreated

cell line: H9 cell type: human embryonic stem cells treatment: none

hESC-H9-p29-1 Untreated human embryonic stem cells (H9). Cells are derived from a blastocyst.

Sample_geo_accession	GSM994321
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994321/suppl/GSM994321_hESC-H9-p29-1.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994322

GPL570

hESC-H9-p29-2

H9 embryonic stem cells, untreated

cell line: H9 cell type: human embryonic stem cells treatment: none

hESC-H9-p29-2 Untreated human embryonic stem cells (H9). Cells are derived from a blastocyst.

Sample_geo_accession	GSM994322
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994322/suppl/GSM994322_hESC-H9-p29-2.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994323

GPL570

HUF1-p4-plus-SynRNA-1

HUF1 skin fibroblasts, OCT4 synthetic mRNA

cell line: HUF1 cell type: skin fibroblasts treatment: OCT4 synthetic mRNA

HUF1-p4-plus-SynRNA-1 Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA. Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994323
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994323/suppl/GSM994323_HUF1-p4-plus-SynRNA-1.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994324

GPL570

HUF1-p4-plus-SynRNA-2

HUF1 skin fibroblasts, OCT4 synthetic mRNA

cell line: HUF1 cell type: skin fibroblasts treatment: OCT4 synthetic mRNA

HUF1-p4-plus-SynRNA-2 Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA. Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994324
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994324/suppl/GSM994324_HUF1-p4-plus-SynRNA-2.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994325

GPL570

HUF1-p4-plus-SynRNA-plus-BAY11-1

HUF1 skin fibroblasts, OCT4 synthetic mRNA and BAY11

cell line: HUF1 cell type: skin fibroblasts treatment: OCT4 synthetic mRNA and BAY11

HUF1-p4-plus-SynRNA-plus-BAY11-1 Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA and BAY11. Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994325
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994325/suppl/GSM994325_HUF1-p4-plus-SynRNA-plus-BAY11-1.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994326

GPL570

HUF1-p4-plus-SynRNA-plus-BAY11-2

HUF1 skin fibroblasts, OCT4 synthetic mRNA and BAY11

cell line: HUF1 cell type: skin fibroblasts treatment: OCT4 synthetic mRNA and BAY11

HUF1-p4-plus-SynRNA-plus-BAY11-2 Human skin fibroblasts (HUF1) treated with OCT4 synthetic mRNA and BAY11. Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994326
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994326/suppl/GSM994326_HUF1-p4-plus-SynRNA-plus-BAY11-2.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994327

GPL570

HUF1-p5-1

HUF1 skin fibroblasts, untreated

cell line: HUF1 cell type: skin fibroblasts treatment: none

HUF1-p5-1 Untreated human skin fibroblasts (HUF1). Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994327
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994327/suppl/GSM994327_HUF1-p5-1.CEL.gz
Sample_series_id	GSE40444
Sample_data_row_count	54675

GSM994328

GPL570

HUF1-p5-2

HUF1 skin fibroblasts, untreated

cell line: HUF1 cell type: skin fibroblasts treatment: none

HUF1-p5-2 Untreated human skin fibroblasts (HUF1). Cells are derived from a skin biopsy.

Sample_geo_accession	GSM994328
Sample_status	Public on Aug 29 2012
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Aug 29 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Synthetic mRNA Transfection: All work was done in strict RNase-free conditions. Synthetic mRNA was thawed on ice and then quickly diluted before degradation. Synthetic mRNA was diluted using Opti-MEM basal media (Invitrogen) with 100ng/µL synthetic mRNA diluted 5x and RNAiMAX (Invitrogen), with 5µL of RNAiMAX per microgram of RNA (1.2µg total synthetic mRNA and thus 6µL RNAiMAX), was diluted 10x. The synthetic mRNA was diluted into 48µL of Opti-MEM and 6µL of RNAiMAX was diluted into 54µL of Opti-MEM for the 10x dilution. Each dilution was separate, and the tube was flicked 5-6 times to mix. The two dilutions were then pooled, mixed again by 6 tube flicks, and then incubated at room temperature for 15 minutes. This mixture was then added directly into fibroblast culture media, without antibiotics as required by protocol. The cells were left to incubate with the synthetic mRNA for 4 hours, after which the media was d with fresh BAY11 or BX795 along with B18R all in standard fibroblast media.
Sample_treatment_protocol_ch1
Sample_treatment_protocol_ch1	25,000 passage 5 HUF cells were plated across four wells in a 24-well plate in standard DMEM/FBS media without antibiotics. 12 hours later, the cells were incubated with 1µM BAY11 + 200ng/mL B18R over two wells whereas the other two wells received just B18R at 200ng/mL final concentration. The final volume was 500µL in each well. After 24 hours incubation, the cells were then transfected with the modified synthetic mRNA as detailed above. This was done everyday for 3 days, and after the last incubation period of 24 hours, the cells were harvested for mRNA using Roche's High Pure RNA Isolation Kit according to the manufacturer's instructions. hESCs and control fibroblasts were harvested in the same manner.
Sample_growth_protocol_ch1	In vitro Culture of Human Embryonic Stem Cells-H9: H9 embryonic stem cells (hESC) (UCLA Broad Stem Cell Research Center-Stem Cell Core) were cultured in standard ESC conditions as published [26]. Briefly, hESC medium consisting of DMEM/F12 supplemented with 20% Knockout Serum ment (KSR), 1x Glutamax, 1x non-essential amino acids, 100 IU/mL Penicillin-Streptomycin (all from Invitrogen), 1x beta-mercaptoethanol (Millipore, Billerica, MA), and 10ng/mL recombinant human basic fibroblast growth factor (bFGF, Globalstem, Rockville, MD).
Sample_growth_protocol_ch1
Sample_growth_protocol_ch1	In vitro Culture of Primary Human Skin Cells: The human skin-derived (HUF1) primary cell line used in this study was obtained from a 4mm adult skin punch biopsy and cultured as described [26]. Briefly, all human biopsy-derived cells were cultured in complete DMEM/F12 media consisting of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS), 1x MEM 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 was changed every two days. Cells were allowed to expand to 80-90% confluency before passaging with 0.05% trypsin-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.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was purified from each replicate using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	100ng of total RNA was amplified using NuGEN Ovation RNA Amplification System V2. Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single-strand cDNA.
Sample_hyb_protocol	Following fragmentation, 3.75ug of single-strand cDNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 640 using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). 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. Data from control HUF cells was used as a baseline control to compare the replicates of HUF cells with or without BAY11 and hESCs.
Sample_platform_id	GPL570
Sample_contact_name	James,Anthony,Byrne
Sample_contact_email	byrnej@ohsu.edu
Sample_contact_phone	5036905335
Sample_contact_laboratory	Wolf lab
Sample_contact_department	Reproductive Sciences
Sample_contact_institute	ONPRC
Sample_contact_address	505 NW 185th Ave
Sample_contact_city	Beaverton
Sample_contact_state	OR
Sample_contact_zip/postal_code	97006
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM994nnn/GSM994328/suppl/GSM994328_HUF1-p5-2.CEL.gz
Sample_series_id	GSE40444
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:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes