|
| Status |
Public on Jun 14, 2019 |
| Title |
E12.5_wildtype_biorep3 |
| Sample type |
SRA |
| |
|
| Source name |
Male Germ Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: N/A
rip antibody: N/A
strain: 129
background: 129T2/SvEmsJ
allele: Dnd1(+/+);Oct4-GFP(+/+)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
testes were collected from genotyped fetuses at E12.5, E13.5 and E14.5, testes were disassociated, male germ cells were purified using FACS for GFP, total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
RNA libraries were prepared for sequencing according to the Smart-seq2 protocol (Picelli et al., 2014) using the Nextera XT DNA Sample Prep Kit (illumina #15032352)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Dnd1Ter_RNAseq.xlsx
|
| Data processing |
Illumina Hi-seq 2500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment to mm9 using Bowtie 2 (version 2.2.4) with default settings
Assembly with Cufflinks pipeline (version 2.2.0) (Top-Hat, Cufflinks, Cuffmerge) with default settings
Gene levels quantified using Cuffquant (version 2.2.0)
Differential expression analysis using Cuffdiff (version 2.2.0)
mm9
Output of tab-delimited text files with RPKM and differential expression values for each Sample
|
| |
|
| Submission date |
Jun 13, 2019 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Victor A Ruthig |
| E-mail(s) |
Victor.Ruthig@CUAnschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pediatrics, Section of Developmental Biology
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE132719 |
The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming |
|
| Relations |
| BioSample |
SAMN12055414 |
| SRA |
SRX6068267 |
