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Sample GSM1938059 Query DataSets for GSM1938059
Status Public on Sep 13, 2016
Title E13.5 Female Control rep1
Sample type SRA
 
Source name WT10_5
Organism Mus musculus
Characteristics developmental stage: E13.5
cell type: primordial germ cells
genotype: wild type
gender: female
Growth protocol Embryos were obtained from crosses between Oct4-IRES-Gfp (OG) (Lengner et al., 2007); Dnmt12lox (Jackson-Grusby et al., 2001) homozygous females and Blimp1-Cre (BC) males. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established (0.5 dpc).
Extracted molecule polyA RNA
Extraction protocol GFP positive PGCs at E13.5 were sorted and collected in a 1.5ml microcentrifuge tube containing 350ul of RLT buffer. RNA was extracted using the RNeasy Micro Kit (Qiagen).
The RNA was subsequently amplified through the use of the Ovation RNA-Seq System V2 kit (Nugen), and bar codes were added using the Encore Rapid Library Systems kit (Nugen).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description female WT rep1
female_gene_exp.diff
Data processing RNA-seq alignment using Tophat 2.1.0 with default parameters
Calculate RPKM and by using cuffdiff (cufflinks-2.2.1) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: output from cuffdiff, RPKM values for WT and MT, p-value for DEG
 
Submission date Nov 12, 2015
Last update date May 15, 2019
Contact name Pao-Yang Chen
Organization name Academia Sinica
Department Institute of Plant and Microbial Biology
Lab Pao-Yang Chen
Street address 128 Sec. 2, Academia Rd, Nankang,
City Taipei
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL17021
Series (1)
GSE74938 RNA-seq profiling of mouse PGC (Mus musculus)
Relations
BioSample SAMN04262036
SRA SRX1427743

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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