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Sample GSM1142602 Query DataSets for GSM1142602
Status Public on Jul 31, 2013
Title RNA in the female somatic cells at 15.5 dpc
Sample type SRA
Source name fetal female somatic gonadal cells at 15.5 dpc
Organism Mus musculus
Characteristics strain/background: CF1 x TgOG2
cell type: gonadal somatic cells
gender: female
age: 15.5 dpc
Treatment protocol N/A
Growth protocol in vivo
Extracted molecule total RNA
Extraction protocol GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryo and fetus gonads using a MoFlo or Aria II flow cytometer. Total RNA was extracted using RNA Bee (Tel Test Inc.). Contaminating DNA was removed with the DNA-free Kit (Ambion). The amount of RNA was monitored using a Nanodrop spectrophotometer followed by a quality check using the Bioanalyzer. All RNA samples had a RIN>9.0. 2µg total RNA samples were depleted for rRNA using the RiboZero Kit (Epicenter, Illumina).
RNA-seq libraries were prepared and paired-end sequencing was performed using the IntegenX RNA kit (Illumina) with read length/coverage of 2x100.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description D_FSC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the female somatic cells at 15.5 dpc.
Strand-specific RNA-Seq.
Data processing Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
Read counts for each RefSeq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts for each RefSeq gene.
Supplementary_files_format_and_content: Two bedGraph files (forward and reverse strand separately) for each sample.
Submission date May 15, 2013
Last update date May 15, 2019
Contact name Xiwei Wu
Organization name City of Hope National Medical Center
Department Molecular and Cellular Biology
Street address 1500 E. Duarte Rd.
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platform ID GPL13112
Series (2)
GSE46953 Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (RNA-Seq)
GSE46954 Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation
BioSample SAMN02144600
SRA SRX278426

Supplementary file Size Download File type/resource
GSM1142602_D-FSC_forward.bedGraph.gz 7.8 Mb (ftp)(http) BEDGRAPH
GSM1142602_D-FSC_reverse.bedGraph.gz 7.9 Mb (ftp)(http) BEDGRAPH
GSM1142602_D_counts.txt.gz 374.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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