|
| Status |
Public on Mar 14, 2013 |
| Title |
Ring1-delta-Rnf2+_E11.5_male_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primordial germ cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Ring1-delta;Rnf2+
developmental stage: E11.5
gender: male
cell type: primordial germ cells
genetic background: 129/Sv and C57BL6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 500 PGCs per embryo using RNeasy Micro Kit (QIAGEN). The RNA amplification and cDNA generation were performed using NuGEN Ovation RNA-seq System V2 (Part No. 7102)
sequencing libraries were prepared using Truseq DNA Sample Preparation Kit (low-throughput protocol) (Part# 15005180 Rev. C)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling was carried out with Illuina RTA software (version 1.13.48) and TruSeq libraries were de-multiplexed with the script configureBclToFastq.pl and CASAVA_v1.8.0
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the Refseq transcripts (downloaded Aug 13, 2012) were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Reads mapping to several locations were fractionated and distributed equally among all mapping sites.
Genome_build: mm9 and Refseq Transcripts downloaded on Aug 13, 2012
Supplementary_files_format_and_content: tabular file with read counts per transcript for all Refseq transcripts
|
| |
|
| Submission date |
Dec 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Roloff |
| E-mail(s) |
[email protected]
|
| Organization name |
FMI
|
| Department |
Functional Genomics
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE42852 |
PRC1 coordinates timing of sexual differentiation of female primordial germ cells (RNA-Seq) |
|
| Relations |
| SRA |
SRX209534 |
| BioSample |
SAMN01830801 |
