|
| Status |
Public on Jun 01, 2024 |
| Title |
Lin_2_Chip_Seq_for_Nynrin |
| Sample type |
SRA |
| |
|
| Source name |
Lineage-negative cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: 3xFlag-Nynrin-Tg mice
age: 8 weeks old
cell line: Lineage-negative cells
chip antibody: Flag
|
| Growth protocol |
PBS+1%FBS, cells were incubated on ice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lineage-negative cells of BM from 3×Flag-Nynrin-Tg mice were fixed with 1% formaldehyde for 10min.Then cells were demobilized and lysed.
ChIP-seq libraries were prepared using TruePrepTM DNA Library Prep Kit V2 from Vazyme. 10ng of DNA was used as starting material for input and IP samples.Libraries were amplified using 16 cycles on thermocycler.Post amplification libraries were size selected at 100-500bp in length using Agencourt AMPure XP beads from Beckman Coulter.Libraries were validated using Agilent High Sensitivity DNA kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Using Cutadapt to remove splice sequences from Raw data,the Trimmomatic program to remove low-quality sequences
Using FastQC program for quality control analysis of Clean data, Bowtie2 program for comparing Clean data t tothe reference genome
Calculating the capture efficiency, ChIP coverage and average sequencing depth
Using MACS2 for Peak-calling analysis on the genome, IDR program for peak screening with high confidence between samples
Using the ChIPseeker package for comments on Peaks, MEME program for Motif analysis, MAnorm program for Peaks
Assembly: mm10
|
| |
|
| Submission date |
Nov 26, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
CHENGFANG ZHOU |
| E-mail(s) |
chengfangzhou47@gmail.com
|
| Phone |
(86)13368348471
|
| Organization name |
Army Medical University
|
| Department |
Department of Hematology, Southwest Hospital
|
| Street address |
No. 30, Gaotanyan Street.
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE248635 |
Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening (ChIP_Seq) |
| GSE248639 |
Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening. |
|
| Relations |
| BioSample |
SAMN38440414 |
| SRA |
SRX22643566 |
