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Sample GSM5723701 Query DataSets for GSM5723701
Status Public on Sep 21, 2023
Title WT-P-2
Sample type SRA
 
Source name Pachytene
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: WT
tissue: Spermatocyte
developmental stage: Pachytene
Extracted molecule polyA RNA
Extraction protocol Leptotene/zygotene and pachytene spermatogenic cells were collected with Fluorescence activated Cell Sorting (FACS) with purity verification.
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level was further normalized with the ERCC spike-in.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
 
Submission date Dec 08, 2021
Last update date Sep 21, 2023
Contact name Heng-yu Fan
E-mail(s) Fanhengyu_lab@163.com, 21907079@zju.edu.cn
Organization name Life Sciences Institute
Lab Fan heng-yu
Street address Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL21273
Series (1)
GSE190430 Genome-wide Map of R-loop Reveals its interplays with Transcription and Genome Integrity during Germ Cell Meiosis
Relations
BioSample SAMN23773700
SRA SRX13351366

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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