|
| Status |
Public on Sep 21, 2023 |
| Title |
WT-P-1 |
| Sample type |
SRA |
| |
|
| Source name |
Pachytene
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: WT
tissue: Spermatocyte
developmental stage: Pachytene
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Leptotene/zygotene and pachytene spermatogenic cells were collected with Fluorescence activated Cell Sorting (FACS) with purity verification.
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level was further normalized with the ERCC spike-in.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
|
| |
|
| Submission date |
Dec 08, 2021 |
| Last update date |
Sep 21, 2023 |
| Contact name |
Heng-yu Fan |
| E-mail(s) |
Fanhengyu_lab@163.com, 21907079@zju.edu.cn
|
| Organization name |
Life Sciences Institute
|
| Lab |
Fan heng-yu
|
| Street address |
Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE190430 |
Genome-wide Map of R-loop Reveals its interplays with Transcription and Genome Integrity during Germ Cell Meiosis |
|
| Relations |
| BioSample |
SAMN23773699 |
| SRA |
SRX13351365 |
