|
| Status |
Public on Nov 12, 2020 |
| Title |
p65-TNF-12d+withdraw-10d+TNF12h |
| Sample type |
SRA |
| |
|
| Source name |
p65-TNF-12d+withdraw-10d+TNF12h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK 293 transfected with reporter construct
cell type: somatic cell
treatment: TNF-α treatment 12 days, then withdraw to recover 10 days, and add TNF-α 12 hours
developmental stage: embryos
library strategy: ChIP
antibody: sc-372, Santa Cruz
|
| Treatment protocol |
The final concentration of TNF is 50 ng/mL.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
ChIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). P65 antibody (Cat# sc-372) was purchased from Santa Cruz.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
embryonic kidney
|
| Data processing |
RNA-seq basecalls performed by BGI, Shenzhen
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension of average fragments size.
Supplementary_files_format_and_content: RPKM values were calculated by Cuffdiff and stored as tab separated texts.
|
| |
|
| Submission date |
Jun 09, 2020 |
| Last update date |
Nov 14, 2020 |
| Contact name |
Zhuqiang Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Biophysics, CAS
|
| Street address |
15 Datun Road, Chaoyang District.
|
| City |
Beijing |
| State/province |
--- |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE152146 |
TNF induced inflammatory transcription dynamics and epigenetic changes |
|
| Relations |
| BioSample |
SAMN15192105 |
| SRA |
SRX8512551 |
