|
| Status |
Public on Sep 11, 2022 |
| Title |
Empty_CHIP |
| Sample type |
SRA |
| |
|
| Source name |
TC28a2 cells transfected with an empty vector
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: TC28a2 cells
antibody: Rabbit anti-HA tag antibody (clone C29F4, Cell Signaling Technology)
transfection: empty vector
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with anti-HA tag antibody.
Libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer’s instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Sample 1(01idEMPTYHACHIP_S1_R1_001.fastq.gz)
|
| Data processing |
The nf-core/chipseq pipeline (version 1.2.2; Ewels et al.,2020) written in the Nextflow domain specific language was used to perform the primary analysis of the samples.
The ChIP-seq reads were aligned to the UCSC GRCh38 reference genome using the BWA aligner (Li and Durbin, 2009) .
Mapped reads were further converted to normalized bigWig files scaled to 1 million mapped reads using BEDTools for presentation as genome browser tracks (Quinlan et al, 2010).
The peak calling was performed using MACS2 in narrowPeak mode.
Genome_build: GRCh38
|
| |
|
| Submission date |
Jan 27, 2022 |
| Last update date |
Sep 11, 2022 |
| Contact name |
Padma Natarajan |
| E-mail(s) |
ccbb@scripps.edu
|
| Organization name |
The Scripps Research Institute
|
| Department |
CCBB
|
| Street address |
10550 N.Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE183955 |
Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis [ChIP-seq] |
| GSE183956 |
Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis |
|
| Relations |
| BioSample |
SAMN25337623 |
| SRA |
SRX13952611 |
