|
| Status |
Public on May 01, 2024 |
| Title |
IRI_4，kidney,H4K12la |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
treatment: IRI
|
| 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 |
SAMN41114563 |
| SRA |
SRX24400302 |
