Result

Search results for the GEO ID: GSE30192

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM747404

GPL1261

C2C12 untreated day3 rep1

RNA from untreated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: untreated

gene expression from untreated C2C12 myoblasts (day 3)

Sample_geo_accession	GSM747404
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747404/suppl/GSM747404_026955_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

GSM747405

GPL1261

C2C12 untreated day3 rep2

RNA from untreated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: untreated

gene expression from untreated C2C12 myoblasts (day 3)

Sample_geo_accession	GSM747405
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747405/suppl/GSM747405_026956_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

GSM747406

GPL1261

C2C12 untreated day3 rep3

RNA from untreated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: untreated

gene expression from untreated C2C12 myoblasts (day 3)

Sample_geo_accession	GSM747406
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747406/suppl/GSM747406_026957_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

GSM747407

GPL1261

C2C12 5AC treated day3 rep1

RNA from 5AC treated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: 10 uM 5-azacytidine

gene expression from 5AC treated C2C12 myotblasts (day 3)

Sample_geo_accession	GSM747407
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747407/suppl/GSM747407_026958_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

GSM747408

GPL1261

C2C12 5AC treated day3 rep2

RNA from 5AC treated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: 10 uM 5-azacytidine

gene expression from 5AC treated C2C12 myotblasts (day 3)

Sample_geo_accession	GSM747408
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747408/suppl/GSM747408_026959_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

GSM747409

GPL1261

C2C12 5AC treated day3 rep3

RNA from 5AC treated, subconfluent C2C12 myoblasts, day 3

cell line: C2C12 treatment: 10 uM 5-azacytidine

gene expression from 5AC treated C2C12 myotblasts (day 3)

Sample_geo_accession	GSM747409
Sample_status	Public on Jan 01 2012
Sample_submission_date	Jun 24 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
Sample_growth_protocol_ch1	C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
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 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_scan_protocol	GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
Sample_data_processing	Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
Sample_platform_id	GPL1261
Sample_contact_name	Marlinda,,Hupkes
Sample_contact_email	m.hupkes@science.ru.nl
Sample_contact_phone	+31(0)243652519
Sample_contact_department	Cell and Applied Biology
Sample_contact_institute	Radboud University Nijmegen
Sample_contact_address	Heyendaalseweg 135
Sample_contact_city	Nijmegen
Sample_contact_zip/postal_code	6525 AJ
Sample_contact_country	Netherlands
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM747nnn/GSM747409/suppl/GSM747409_026960_Mouse430_2.CEL.gz
Sample_series_id	GSE30192
Sample_data_row_count	45101

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