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Sample GSM2080811 Query DataSets for GSM2080811
Status Public on Jul 20, 2017
Title small_RNA_seq: leptotene/zygotene, biological replicate 2, technical replicate 1
Sample type SRA
Source name male germ cells
Organism Mus musculus
Characteristics strain: C57BL6/J
isolation: FACS with Hoechst-33342 staining
Stage: leptotene/zygotene
age: postnatal 3-4wks
Treatment protocol Total RNA was isolated by acid phenol extraction using Isogene (Nippon Gene) from FACS-purified spermatogonia and spermatocytes (L/Z)
Extracted molecule total RNA
Extraction protocol standard procedure involving phenol/chloroform extraction, and isopropanol precipitation
The libraries were prepared using TruSeq Small RNA Sample Prep kit (Illumina)
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Description SE50bp
Data processing The same libraries were sequenced twice (technical replicates 1 and 2)
The sequencing methods for technical replicate 1 ; sequenced by HiSeq2500 (Rapid mode for 50-bp single-end sequencing, yielding 4-8 million reads per sample)
The sequencing methods for technical replicate 2 ; sequenced by HiSeq1500 (High-output mode for 100-bp single-end sequencing, yielding 4-8 million reads per sample)
The adaptor sequence was trimed by cutadapt, and read numbers for each insert sequence were counted
The sequences were mapped to the consensus sequences of mouse retrotransposons using Seqmap allowing 2-bp missmatches.
Genome_build: repeatmaskerlibraries-20130422
Supplementary_files_format_and_content: tab-divided text files for sequence read numbers and comma-divided text files for rpm values for each retrotransposon.
Submission date Mar 04, 2016
Last update date May 15, 2019
Contact name Kota Inoue
Phone +8192-642-6760
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Division of Epigenomics and Development
Street address 3-1-1 Maidashi, Higashiku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL17021
Series (2)
GSE70890 Small RNA sequencing analysis for male germ cells during spermatogenesis
GSE70891 The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells
BioSample SAMN04532044
SRA SRX1613269

Supplementary file Size Download File type/resource
GSM2080811_small_RNA_LZ_Pld6KO_rep2.1.txt.gz 4.8 Mb (ftp)(http) TXT
GSM2080811_summary_small_RNA_LZ_Pld6KO_rep2.1.csv.gz 5.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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