|
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
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|
|
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
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|
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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 |