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Sample GSM3561109 Query DataSets for GSM3561109
Status Public on Jan 14, 2019
Title H6_3 [RNA]
Sample type SRA
 
Source name Mouse testicular peritubular myoid (PTM) cells
Organism Mus musculus
Characteristics treatment: heat 6hr after
cell type: Mouse testicular peritubular myoid (PTM) cells
passage: Primary
strain: C57BL/6J
Treatment protocol Cell culture dishes of peritubular myoid cells were placed in 42℃ sterile water bath for 30 min and then put back in cell culture incubator. Cells were collected 1 hour and 6 hours after heat treatment.
Growth protocol The isolated PTM cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the NC, H1, and H6 PTM cells using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: Including RPKM values for each sample
 
Submission date Jan 13, 2019
Last update date Jan 24, 2019
Contact name Su-Ren Chen
E-mail(s) chensuren@ioz.ac.cn
Organization name Institute of Zoology, Chinese Academy of Sciences
Department State Key Laboratory of Stem Cell and Reproductive Biology
Street address 1Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL23479
Series (2)
GSE125010 Effect of heat stress on mouse testicular peritubular myoid cells [RNA-seq]
GSE125635 Effect of heat stress on mouse testicular peritubular myoid cells
Relations
BioSample SAMN10736300
SRA SRX5245309

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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