|
| Status |
Public on Sep 28, 2021 |
| Title |
ST88 cell, BRD4 ChIP, sh Ctr, number 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NF1-derived MPNST
cell line: ST88-14
chip antibody: Anti-BRD4 Antibody Rabbit polyclonal, Bethyl, Cat# A301-985A50
treatment: sh Ctr
|
| Treatment protocol |
Chromatin immunoprecipitation was performed essentially as described (Fontanals-Cirera et al., 2017). In brief, ST88-14 cells were infected with shControl or shHuR#1 lentivirus, selected with puromycin for 2 days, replated and then 2 days later cross-linked with 1% formaldehyde for 10 min at RT and reaction quenched with 125 mM glycine for 5 min. The isolated nuclei were resuspended in nuclei lysis buffer and sonicated using a Bioruptor Sonicator (Diagenode). The samples were immunoprecipitated with the appropriate antibodies overnight at 4 ºC. Protein G beads (Thermo Fisher Scientific) were added and incubated for 1 h, and the immunoprecipitates were washed twice, each with low-salt, high-salt and LiCl buffer. The eluted DNA was reverse-crosslinked and purified using PCR purification kit (Qiagen).
|
| Growth protocol |
Human MPNST cell line were maintained in Dulbecco’s modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (Thermo Fisher Scientific) and 1% (v/v) antibiotic/antimycotic (Thermo Fisher Scientific) under standard conditions of 37 ºC and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PCR purification kit (Qiagen).
Sequencing libraries were prepared following TruSeq® ChIP Sample Preparation Guide with the corresponding kit (Illumina Inc.). ChIPseq libraries were single-read sequenced for 51 nucleotides in a HiSeq2500 (Illumina Inc.)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C_BRD4_x_peaks.broadPeak
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
The sequencing data were mapped to the hg38 genome assembly via Bowtie.
Biological replicates merged and peak calling was performed using Model-based analysis of ChIP-seq (MACS) 2 (Zhang et al., 2008) to identify regions of ChIP-Seq enrichment over background (input) with an enrichment threshold of adjusted p-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Peaks called from merged biological replicates by MACS2 are submitted as tab separated text files with ".broadPeak" extension.
|
| |
|
| Submission date |
Oct 01, 2018 |
| Last update date |
Sep 28, 2021 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
|
| Organization name |
CIC bioGUNE
|
| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
|
| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE120686 |
The Role of the RNA-binding protein HuR in MPNST growth and metastasis [ChIP-seq] |
| GSE120687 |
The Role of the RNA-binding protein HuR in MPNST growth and metastasis |
|
| Relations |
| BioSample |
SAMN10148293 |
| SRA |
SRX4779788 |
