Result

Search results for the GEO ID: GSE40421

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GSM ID

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Title

Source name

Description

Characteristics

GSM993772

GPL1355

Fibroblast, biological rep1

Rat embryonic fibroblasts

strain: Sprague-Dawley cell type: embryonic fibroblasts

Sample_geo_accession	GSM993772
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993772/suppl/GSM993772_Marius_Wernig_1F_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993773

GPL1355

Fibroblast, biological rep2

Rat embryonic fibroblasts

strain: Sprague-Dawley cell type: embryonic fibroblasts

Sample_geo_accession	GSM993773
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993773/suppl/GSM993773_Marius_Wernig_2F_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993774

GPL1355

OPC, day zero

Primary OPC from neonatal brain

strain: Sprague-Dawley tissue: neonatal brain cell type: primary oligodendrocyte precursor cells (OPCs)

Sample_geo_accession	GSM993774
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993774/suppl/GSM993774_Marius_Wernig_3O_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993775

GPL1355

iOPC, biological rep1

iOPCs three weeks after infection

strain: Sprague-Dawley cell type: induced oligodendrocyte precursor cells (iOPCs)

Sample_geo_accession	GSM993775
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993775/suppl/GSM993775_Marius_Wernig_4iO_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993776

GPL1355

iOPC, biological rep2

iOPCs three weeks after infection

strain: Sprague-Dawley cell type: induced oligodendrocyte precursor cells (iOPCs)

Sample_geo_accession	GSM993776
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993776/suppl/GSM993776_Marius_Wernig_5iO_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993777

GPL1355

OL, day three, biological rep1

OPC three days after differentiation

strain: Sprague-Dawley cell type: oligodendroglia (OL)

Sample_geo_accession	GSM993777
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993777/suppl/GSM993777_Marius_Wernig_6D3_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993778

GPL1355

OL, day three, biological rep2

OPC three days after differentiation

strain: Sprague-Dawley cell type: oligodendroglia (OL)

Sample_geo_accession	GSM993778
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993778/suppl/GSM993778_Marius_Wernig_7D3_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993779

GPL1355

OL, day six, biological rep1

OPC six days after differentiation

strain: Sprague-Dawley cell type: oligodendroglia (OL)

Sample_geo_accession	GSM993779
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993779/suppl/GSM993779_Marius_Wernig_8D6_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

GSM993780

GPL1355

OL, day six, biological rep2

OPC six days after differentiation

strain: Sprague-Dawley cell type: oligodendroglia (OL)

Sample_geo_accession	GSM993780
Sample_status	Public on Apr 07 2013
Sample_submission_date	Aug 28 2012
Sample_last_update_date	Apr 07 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_growth_protocol_ch1	Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.
Sample_platform_id	GPL1355
Sample_contact_name	Samuele,,Marro
Sample_contact_email	samuele.marro@gmail.com
Sample_contact_laboratory	Marius Wernig
Sample_contact_institute	Stanford University
Sample_contact_address	256 Campus Drive
Sample_contact_city	Stanford
Sample_contact_state	California
Sample_contact_zip/postal_code	94305
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM993nnn/GSM993780/suppl/GSM993780_Marius_Wernig_9D6_Rat230_2.CEL.gz
Sample_series_id	GSE40421
Sample_data_row_count	31099

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