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Sample GSM2631953 Query DataSets for GSM2631953
Status Public on May 19, 2017
Title Zmym3 KO c-KIT+ pre-meiotic cellsreplicate 2
Sample type SRA
 
Source name testes
Organism Mus musculus
Characteristics strain: CBA/C57
gender: male
development stage: 2-month-old
genotype: knockout type
Treatment protocol Zmym3 WT and KO SSC were cultured on laminin-coated dishes. c-KIT+ cells were induced from both WT and KO SSCs by 100 nM RA 36 h after RA treatment. For collecting the spermatocytes, the testes were firstly digested into single cells. The cells were firstly FACS sorted to collect tetraploid cells which were further sorted into two populations based on their forward scatter (FSC) and side scatter (SSC) features. The population of larger sizes consisted mainly of pachytene spermatocytes of about 80% purity based on the co-immunostaining of SYCP3 and rH2AX were collected.
Extracted molecule total RNA
Extraction protocol Total RNA from mouse testis cells and mSSCs was extracted using Trizol. The RNA libraries were constructed by Illumina library preparation protocols. High-throughput sequencing was performed on HiSeq4000/HiSeq X 10.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs.
 
Submission date May 18, 2017
Last update date May 15, 2019
Contact name Chunsheng Han
E-mail(s) hancs@ioz.ac.cn
Phone 86-10-64807105
Organization name Chinese Academy of Sciences
Department Institute of Zoology
Lab State Key Laboratory of Reproductive Biology
Street address 1-5 Beichen West Road, Chaoyang District
City Beijing
State/province Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL21103
Series (1)
GSE99076 Gene knockout of Zmym3 in mice arrests spermatogenesis at meiotic metaphase with defects in spindle assembly checkpoint
Relations
BioSample SAMN07141711
SRA SRX2834262

Supplementary file Size Download File type/resource
GSM2631953_KOSSC-RA-2-fpkm.xlsx 564.9 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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