Result

Search results for the GEO ID: GSE48790

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GSM ID

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Title

Source name

Description

Characteristics

GSM570858

GPL1261

HPRTKO, biological rep1

HPRT KO ES cells

cell type: Embrionic stem cell line genotype: HPRT -/-

Sample_geo_accession	GSM570858
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570858/suppl/GSM570858_AB22_A.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570858/suppl/GSM570858_AB22_A.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM570859

GPL1261

HPRTKO, biological rep2

HPRT KO ES cells

cell type: Embrionic stem cell line genotype: HPRT -/-

Sample_geo_accession	GSM570859
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570859/suppl/GSM570859_AB22_B.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570859/suppl/GSM570859_AB22_B.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM570860

GPL1261

GTF2iTrap line, biological rep 1

gentrap derived AB2.2 ES cell

cell type: Embrionic stem cell line genotype: HPRT -/-: GTF2I +/-

Sample_geo_accession	GSM570860
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570860/suppl/GSM570860_XSO353._A.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570860/suppl/GSM570860_XSO353._A.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM570861

GPL1261

GTF2iTrap line, biological rep 2

gentrap derived AB2.2 ES cell

cell type: Embrionic stem cell line genotype: HPRT -/-: GTF2I +/-

Sample_geo_accession	GSM570861
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570861/suppl/GSM570861_XSO353._B.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570861/suppl/GSM570861_XSO353._B.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM570862

GPL1261

Wild-type, biological rep1

Wild-type ES cells

cell type: Embrionic stem cell line genotype: wild-type

Sample_geo_accession	GSM570862
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570862/suppl/GSM570862_R1_A.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570862/suppl/GSM570862_R1_A.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM570863

GPL1261

Wild-type, biological rep2

Wild-type ES cells

cell type: Embrionic stem cell line genotype: wild-type

Sample_geo_accession	GSM570863
Sample_status	Public on Jul 12 2013
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570863/suppl/GSM570863_R1_B.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570863/suppl/GSM570863_R1_B.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM1012186

GPL1261

Gtf2i Mutant line, biological rep 1

gene-targeted derived R1 cell line

tissue: Embrionic stem cell line genotype/variation: Δexon2/+

G6.A.CEL

Sample_geo_accession	GSM1012186
Sample_status	Public on Jul 12 2013
Sample_submission_date	Oct 01 2012
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/ul were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1012nnn/GSM1012186/suppl/GSM1012186_G6_A.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1012nnn/GSM1012186/suppl/GSM1012186_G6_A.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

GSM1012187

GPL1261

Gtf2i Mutant line, biological rep 2

gene-targeted derived R1 cell line

tissue: Embrionic stem cell line genotype/variation: Δexon2/+

G6.B.CEL

Sample_geo_accession	GSM1012187
Sample_status	Public on Jul 12 2013
Sample_submission_date	Oct 01 2012
Sample_last_update_date	Jul 12 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.
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	Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/ul were used to perform a Affymetric mouse 430_2 expression array
Sample_scan_protocol	The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).
Sample_data_processing	Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values
Sample_platform_id	GPL1261
Sample_contact_name	Victoria,,Campuzano
Sample_contact_email	victoria.campuzano@upf.edu
Sample_contact_laboratory	Genetic
Sample_contact_department	CEXS
Sample_contact_institute	Universitat Pompeu Fabra
Sample_contact_address	Dr Aiguader, 88
Sample_contact_city	Barcelona
Sample_contact_zip/postal_code	08003
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1012nnn/GSM1012187/suppl/GSM1012187_G6_B.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1012nnn/GSM1012187/suppl/GSM1012187_G6_B.mas5.CHP.gz
Sample_series_id	GSE48790
Sample_data_row_count	45101

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