Result

Search results for the GEO ID: GSE37109

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GSM ID

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Title

Source name

Description

Characteristics

GSM910916

GPL1261

ESC

mouse embryonic stem cells

cell type: mouse embryonic stem cells genotype: MOF +/+ strain: C57BL/6 passage: 15 to 18

Gene expression data from embryonic stem cells

Sample_geo_accession	GSM910916
Sample_status	Public on Apr 12 2012
Sample_submission_date	Apr 09 2012
Sample_last_update_date	Apr 12 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Before the microarray experiments, ES cells were seeded in plates without feeder cells for two passages to remove MEF cells.
Sample_growth_protocol_ch1	ES cells were derived from day 3.5dpc mice and were maintained on MEF feed cells in the presence of LIF, typically in 60mm plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs were extracted from ESCs by Trizol (Invitrogen) and further purified by RNA purification kit (Qiagen). The quality of RNA were tested by Nanodrop
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray is processed using Ambion Premier Kit
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy mouse430_2 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Array Chips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	The data were analyzed with the affy package of bioconductor implemented in the R statistical environment. pakage R version 2.10.0 (2009-10-26), i386-pc-mingw32
Sample_data_processing	Expression values for each gene is calculated using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. These data can be converted to the natural scale by exponentiating (e.g., convert by using 2x, where x is the expression value).
Sample_data_processing	Rafael A. Irizarry, Bridget Hobbs, Francois Collin, et al. Exploration, normal-ization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64, 2003.
Sample_platform_id	GPL1261
Sample_contact_name	Yali,,Dou
Sample_contact_laboratory	Dou
Sample_contact_department	Department of Pathology, Department of Biological Chemistry
Sample_contact_institute	University of Michigan
Sample_contact_address	Rm 5215A, MS I, 1301 Catherine Rd,
Sample_contact_city	Ann Arbor
Sample_contact_state	MI
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM910nnn/GSM910916/suppl/GSM910916_MOF_WT.CEL.gz
Sample_series_id	GSE37109
Sample_data_row_count	45101

GSM910917

GPL1261

Mof null ESC

mouse embryonic stem cells

cell type: mouse embryonic stem cells genotype: MOF-/- strain: C57BL/6 passage: 15 to 18

Gene expression data from embryonic stem cells

Sample_geo_accession	GSM910917
Sample_status	Public on Apr 12 2012
Sample_submission_date	Apr 09 2012
Sample_last_update_date	Apr 12 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Before the microarray experiments, ES cells were seeded in plates without feeder cells for two passages to remove MEF cells.
Sample_growth_protocol_ch1	ES cells were derived from day 3.5dpc mice and were maintained on MEF feed cells in the presence of LIF, typically in 60mm plates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNAs were extracted from ESCs by Trizol (Invitrogen) and further purified by RNA purification kit (Qiagen). The quality of RNA were tested by Nanodrop
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray is processed using Ambion Premier Kit
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy mouse430_2 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Array Chips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	The data were analyzed with the affy package of bioconductor implemented in the R statistical environment. pakage R version 2.10.0 (2009-10-26), i386-pc-mingw32
Sample_data_processing	Expression values for each gene is calculated using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. These data can be converted to the natural scale by exponentiating (e.g., convert by using 2x, where x is the expression value).
Sample_data_processing	Rafael A. Irizarry, Bridget Hobbs, Francois Collin, et al. Exploration, normal-ization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4:249-64, 2003.
Sample_platform_id	GPL1261
Sample_contact_name	Yali,,Dou
Sample_contact_laboratory	Dou
Sample_contact_department	Department of Pathology, Department of Biological Chemistry
Sample_contact_institute	University of Michigan
Sample_contact_address	Rm 5215A, MS I, 1301 Catherine Rd,
Sample_contact_city	Ann Arbor
Sample_contact_state	MI
Sample_contact_zip/postal_code	48109
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM910nnn/GSM910917/suppl/GSM910917_MOF_KO.CEL.gz
Sample_series_id	GSE37109
Sample_data_row_count	45101

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