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Sample GSM5607500 Query DataSets for GSM5607500
Status Public on Oct 04, 2021
Title circSry KO 1
Sample type SRA
 
Source name Primary spermatocyte
Organism Mus musculus
Characteristics cell type: spermatocyte
strain: C57BL/6
development stage: adult 8 weeks
genotype: circSry KO
Extracted molecule total RNA
Extraction protocol Primary spermatocytes were collected using flow cytometry via Hoechst staining of single cell suspension of testes and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 1μg
Data processing Clean data of RNA sequencing reads were aligned to mouse reference sequence GRCm39 using STAR (2.7.0f)
. Read counts and TPM (Transcripts Per Kilobase Million) were counted using RSEM (1.3.2).
Differential expression genes (DEG) (FDR < 0.05, log2 (fold change) (log2 FC) ≥ 1 or ≤ −1) were calculated by edgeR (3.28.1) package. The DEG genes were carried out Gene Ontology Pathway analysis and Kyoto Encyclopedia of Genes and Genomes analysis by clusterProfiler (3.14.3) and org.Hs.eg.db (3.10.0) packages.
Heatmap (1.0.12) was used for the heatmap visualization; colors represent the Z-score derived from the log2 transformed FPKM data. Principal Component Analysis (PCA) was performed by R packages, including tidyr(1.1.2), dplyr (1.0.2) and ggplot2 (3.3.2).
Genome_build: mm9
 
Submission date Oct 01, 2021
Last update date Oct 04, 2021
Contact name Yanze Song
E-mail(s) wwwsyzcf@sina.com
Phone 18513119850
Organization name Chinese Academy of Sciences,Institute of Zoology
Street address 1 Beichen West Road
City Beijing
State/province Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL17021
Series (1)
GSE185184 CircSry regulates spermatogenesis by enhancing γH2AX expression via sponging miR138-5p
Relations
BioSample SAMN21975765
SRA SRX12439827

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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