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Sample GSM1051316 Query DataSets for GSM1051316
Status Public on Mar 14, 2013
Title Ring1-delta-Rnf2+_E11.5_male_rep1
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 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
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)
SRA SRX209533
BioSample SAMN01830800

Supplementary file Size Download File type/resource
GSM1051316_AP_PGCs_11_01.bed.gz 269.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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