|
| Status |
Public on Mar 03, 2023 |
| Title |
In_266_1 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J neonatal primary cardiomyocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neonatal primary cardiomyocytes
strain: C57BL/6J
chip antibody: none (input)
|
| Treatment protocol |
The cells were subjected to hypoxia/ischemia at 37 °C under 5% CO2 and 1% O2 for 12 h.
|
| Growth protocol |
Neonatal CMs were isolated by enzymatic disassociation from 1-day-old neonatal mouse hearts; the crude method of collagenase type II enzymatic digestion was applied to isolate the cells. The final cell suspension including CMs was separated by allowing the cell suspension to sediment in an uncoated culture dish at 37 °C for 1 h. Preplating was performed to help fibroblasts adhere to the culture dish and separate them from the CMs, which remained floating in the suspension. To inhibit fibroblast proliferation, 0.1 mM bromodeoxyuridine was added. The cells were then used for experiments as stated. After separation, the cells were incubated at 37 °C under 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and CD38-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mm10 reference genome using BWA(0.7.10)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 version 2.1.1 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS
|
| |
|
| Submission date |
Mar 03, 2020 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Xingyue Zhang |
| E-mail(s) |
zhangxingyue806@sina.com
|
| Organization name |
Southwest Hospitial
|
| Street address |
30,GaotanyanStreet,Shapingba
|
| City |
ChongQing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE146275 |
CD38 causes autophagic flux inhibition and cardiac dysfunction through a transcriptional inhibition pathway under hypoxia/ischemia conditions |
|
| Relations |
| BioSample |
SAMN14266955 |
| SRA |
SRX7831025 |
