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Sample GSM5360578 Query DataSets for GSM5360578
Status Public on Jan 17, 2022
Title TCFL5-ChIP-seq
Sample type SRA
 
Source name testes
Organism Mus musculus
Characteristics strain: C57BL/6
age: post natal day 21
genotype: Tcfl5+/+
tissue: testis
chip antibody: TCFL5(Abcam, Ab188075)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated testicular lysate and protein-DNA complexes were isolated with antibody.
The DNA is combined with End Repair Mix, and incubate at 20℃ for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37℃ for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20℃ for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected (about 100-300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity as well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (QPCR). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit. The sequencing will be performed with the BGISEQ-500 sequencing system, featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB) technology for superior data quality (BGI-Shenzhen, China).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model BGISEQ-500
 
Data processing Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke.
Cleaned reads were mapped to the reference genome of Mouse GRCm38/mm10 using SOAPaligner/SOAP2 (version: 2.2.5)
MACS2 (version: 2.1.2) were used to call peaks (open chromatin regions).
The different enrichment peaks from different samples was plotted by MAnorm(v1.1).
Also the gene element annotation of peak or different enrichment peak from different samples was carry out by bedtools intersect mode with overlap 50%
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: soap files were generated by SOAPaligner/SOAP2 (version: 2.2.5), representing cleaned reads mapped to the reference genome of GRCm38/mm10
 
Submission date Jun 06, 2021
Last update date Jan 17, 2022
Contact name Weiya Xu
E-mail(s) weiyaxu@njmu.edu.cn
Organization name Nanjing Medical University
Department State Key Laboratory of Reproductive Medicine
Lab XinWu
Street address No. 818, Tianyuan East Road
City Nanjing
State/province Jiangsu
ZIP/Postal code 211100
Country China
 
Platform ID GPL23479
Series (2)
GSE176239 Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice [ChIP-seq]
GSE176240 Transcription factor-like 5 is a potential DNA/RNA binding protein essential for maintaining male fertility in mice.
Relations
BioSample SAMN19588445
SRA SRX11079069

Supplementary file Size Download File type/resource
GSM5360578_TCFL5-ChIP-seq.bw 358.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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