 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 02, 2023 |
| Title |
α-KG-1 |
| Sample type |
SRA |
| |
|
| Source name |
neonatal primary cardiomyocytes-H3K27me3
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
cell type: neonatal primary cardiomyocytes
strain: Sprague Dawley
treatment: alpha KG
chip-antibody: H3K27me3
|
| Treatment protocol |
The cardiomyocytes were treated with α-KG (5mM) or control (PBS) for 24 hours.
|
| Growth protocol |
Neonata primary rat cardiomyocytes were routinely cultured on precoated plates in DMEM medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Cells were fixed with formaldehyde and DNA was crosslinked to proteins;Cells were lysed, chromatin was separated, and chromatin was randomly cleaved by ultrasound or enzyme treatment.Then the specific recognition reaction of antigen and antibody is used to precipitate the DNA fragment bound to the target protein.DNA fragments were released and extracted by cross-linking.Library construction (including terminal repair, addition of A, addition of connector, length screening, PCR amplification) and high-throughput sequencing.For chip-SEq, there is usually enough broken chromatin left to be used directly for subsequent DNA extraction as a control, called Input.Mock immunoprecipitation can also be simulated using homotype antibodies, pre-immunization sera, or antibodies of the same species origin. The resulting DNA can be extracted as a control, known as Mock.Usually, before building the library, if some target sequences are known, the effect of ChIP can be verified by qPCR, etc.After the library was constructed, quality inspection was carried out. After passing the quality inspection, subsequent machine sequencing was carried out.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The resulting raw image data file is recognized by CASAVA base.
Since chip-Seq interrupt fragments are usually small, and the percentage of unique sequences in the total number of sequences is the focus of attention,BWA (Burrows Wheeler Aligner) can be used to more accurately compare reads to reference genomes (Li, H. and R. Durbin, 2009).
The main purpose of data filtering is to remove low quality data and ensure the quality of clean data.We cut off the sequencing joints and low-quality fragments of the sequencing data in the way of trim. If the length of the remaining reads after trimming is long enough, they can still be used for the subsequent analysis, so as to efficiently utilize the sequencing data. The subsequent analysis is based on clean data.
MACS2 software (Yong Zhang,Tao Liu et al., 2008) (threshold qvalue<=0.05) was used to complete peak calling, and statistics were conducted on the number, width and distribution of peaks to screen out peak related genes, etc.
Assembly: rn6
Supplementary files format and content: peak text files
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Jul 02, 2023 |
| Contact name |
Yu Shi |
| E-mail(s) |
[email protected]
|
| Phone |
15692776868
|
| Organization name |
Military Medical University
|
| Department |
Cardiology
|
| Lab |
cardiovascular disease institute
|
| Street address |
10 Changjiang Branch Road
|
| City |
Chongqing |
| State/province |
Chongqing |
| ZIP/Postal code |
400042 |
| Country |
China |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE202240 |
H3K27me3 ChIP-sequencing of control and α-KG treated neonatal primary cardiomyocytes |
|
| Relations |
| BioSample |
SAMN27573726 |
| SRA |
SRX14849482 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6106907_a_kg_1.bw |
176.1 Mb |
(ftp)(http) |
BW |
| GSM6106907_a_kg_1_genes_with_peak.txt.gz |
375.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
