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Sample GSM8243000 Query DataSets for GSM8243000
Status Public on May 01, 2024
Title Sham_1,kidney,H4K12la
Sample type SRA
 
Source name kidney
Organism Mus musculus
Characteristics tissue: kidney
treatment: Sham
Extracted molecule genomic DNA
Extraction protocol CUT &Tag assay was conducted with Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (TD901, Vazyme) according to the manufacturer’s instructions.
The DNA fragment samples were isolated and amplified for library construction based on the manufacturer’s instructions (TD202, Vazyme ).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Index of the reference genome was built using Bowtie2 and clean reads were aligned to the reference genome. All peak calling was performed with MACS2 using ‘macs2 -q 0.05 --call-summits --nomodel--shift -100 --extsize 200 --keep-dup all’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering. The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene.
Peak Annotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Bigwig data of each sample
Library strategy: CUT&Tag
 
Submission date Apr 30, 2024
Last update date May 01, 2024
Contact name yating wang
E-mail(s) wangyt73@mail.sysu.edu.cn
Phone 15920488562
Organization name The First Affiliated Hospital, Sun Yat-sen University
Department Department of Nephrology
Lab NHC Key Laboratory of Clinical Nephrology (Sun Yat-sen University) and Guangdong Provincial Key Laboratory of Nephrology
Street address 58th Zhongshan Road II The First Affiliated Hospital ,Sun Yat-Sen University
City Guangzhou
State/province Guangdong
ZIP/Postal code 510080
Country China
 
Platform ID GPL24247
Series (1)
GSE266243 PFKFB3 drives renal fibrosis through promoting histone lactylation-mediated NF-𝜅B activation [CUT&Tag]
Relations
BioSample SAMN41114558
SRA SRX24400297

Supplementary file Size Download File type/resource
GSM8243000_Sham_1_bigwig.bw 73.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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