|
Status |
Public on Sep 13, 2016 |
Title |
E10.5 Control 57-5 |
Sample type |
SRA |
|
|
Source name |
E10.5W 57-5
|
Organism |
Mus musculus |
Characteristics |
developmental stage: E10.5 cell type: primordial germ cells genotype: wild type gender: male
|
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 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 |
E10.5 male WT rep1 RPKM_table_E10_5.txt
|
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
|
|
|
Submission date |
May 11, 2016 |
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 |
SAMN04978458 |
SRA |
SRX1756377 |