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Sample GSM1821383 Query DataSets for GSM1821383
Status Public on Jul 20, 2017
Title small_RNA_seq: leptotene/zygotene, biological replicate 2
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, spermatocytes (L/Z and P/D) and round spermatids
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 1500
Description SE50bp
Data processing The sequencing methods ; sequenced by HiSeq1500 (rapid mode for 50-bp single-end sequencing, yielding 14–40 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 Jul 14, 2015
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 GPL18480
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 SAMN03857949
SRA SRX1096752

Supplementary file Size Download File type/resource
GSM1821383_smallRNA_LZ_rep2.txt.gz 34.3 Mb (ftp)(http) TXT
GSM1821383_summary_small_RNA_LZ_WT_rep2.csv.gz 7.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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