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Sample GSM3307587 Query DataSets for GSM3307587
Status Public on Oct 21, 2019
Title Control-6
Sample type SRA
 
Source name testis
Organism Mus musculus
Characteristics strain: B6D2F1 inbred
tissue: testis
age: post natal day 7
genotype: Pramef12+/-
Growth protocol B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P2 or P7 aged control and knockout mice.
Extracted molecule polyA RNA
Extraction protocol Testes were isolated, total RNA was isolated using RNeasy Mini Kit and mRNA was purified by Dynabeads mRNA Purification Kit.
First strand cDNA was synthesized with SuperScript III Reverse Transcriptase. For second strand cDNA synthesis, the 100 μl reaction system included: 20 μl of first strand cDNA synthesis mix, 10 μl of 10x second strand buffer (500 mM Tris-HCl, pH 7.5; 50 mM MgCl2; 10 mM DTT), 3 μl of dNTP mix (10 mM), 1 μl of RNase H (2U/μl), 5 μl of DNA Pol I (10U/μl) and 61 μl water. The mixtures were incubated for 2 h at 16°C. The libraries were constructed with Nextera DNA Sample Preparation Kit (Illumina) per the manufacturer’s protocol. Generally, double-strand cDNA was fragmented, subjected to adapter ligation and amplified.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina HiSeq 2500 sequencing, 50bp reads.
Adapter removal with cutadapt v1.16
Alignment to Mus musculus genome with hisat v2.1.0
Assignment of reads to gene features with Subread featureCounts v1.6.1
Signal detection via differential expression analysis between triplicate groups with DESeq2 1.18.1
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads assigned to gene features, as computed by Subread featureCounts v1.6.1
 
Submission date Jul 26, 2018
Last update date Oct 23, 2019
Contact name Cameron Palmer
E-mail(s) palmercd@nih.gov
Organization name National Institutes of Health
Department National Institute of Diabetes and Digestive and Kidney Diseases
Lab Laboratory of Cellular and Developmental Biology
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL17021
Series (2)
GSE117706 ‘Sertoli cell-only’ phenotype and single-cell RNA-seq define PRAMEF12 as a germline-specific factor for male stem cell maintenance and differentiation [RNA-Seq]
GSE117708 ‘Sertoli cell-only’ phenotype and single-cell RNA-seq define PRAMEF12 as a germline-specific factor for male stem cell maintenance and differentiation
Relations
BioSample SAMN09724206
SRA SRX4472969

Supplementary file Size Download File type/resource
GSM3307587_control_P7_3.cutadapt.bam.featurecounts.s0.tsv.gz 3.4 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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