|
| Status |
Public on Jul 01, 2022 |
| Title |
Granta519-ESR2 input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Mantle cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mantle cell lymphoma
cell line: Granta-519
chip antibody: none
treatment: All Cells were treated with 100 nM diarylpropionitrile(DPN) dissolved in DMSO for 2h before ChIP experiment.
genotype/variation: ESR2 over-expression
|
| Treatment protocol |
All Cells were treated with 100 nM diarylpropionitrile(DPN) dissolved in DMSO for 2h before ChIP experiment.
|
| Growth protocol |
Stable Granta-519 cell lines with or without transduced full-length ESR2 expression (Granta519-ESR2 or Granta519-mock) were cultured in phenol red free RPMI 1640 with 10% charcoal stripped FBS, 100 IU penicillin/mL and 100ug/mL streptomycin in 5% CO2 at 37 °C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and nuclear chormatin fractions were separated and sonicated, followed by immunoprecipitated with ESR2 anitboides (PPZ0506, R&D systems). Magnetic beads were used to pull down the immunoprecipitated DNA and separated by elution buffer containing proteinase K. Then ChIP DNA was purified with QIAquick PCR Purification kit (Qiagen).
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
ESR2 over expression
|
| Data processing |
After using FastQC v0.11.9 to check the QC of ChIPseq fastq.gz files, trim_galore v0.6.6 was used to remove adapters and low quality reads. ChIP-Seq reads were mapped to the human reference genome assembly hg38(GRCh38) using bowtie2 v2.3.4.3. Sequencing tags were read and imported using HOMER v4.11 followed by calling peaks with default settings and normalized to the input. Only peaks with FDR < 0.001 and fold enrichment over input tag count >4 (default settings) were kept. De novo motif analysis was performed by HOMER within +/- 100 bp from the peak center.
Genome_build: hg38(GRCh38)
Supplementary_files_format_and_content: bigwig was created using HOMER makeBigWig.pl.
|
| |
|
| Submission date |
Dec 09, 2021 |
| Last update date |
Jul 01, 2022 |
| Contact name |
Dan Huang |
| E-mail(s) |
hdan0777@gmail.com
|
| Organization name |
Karolinska Institutet
|
| Department |
Biosciences and Nutrition
|
| Street address |
Neo, Department of Biosciences and Nutrition, Huddinge, Stockholm.
|
| City |
Stockholm |
| ZIP/Postal code |
14183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE190599 |
Genome-wide maps of ESR2 chromatin state in Mantle cell lymphoma cells |
|
| Relations |
| BioSample |
SAMN23829232 |
| SRA |
SRX13367420 |
