|
| Status |
Public on Sep 27, 2018 |
| Title |
NT2D1_KO_H3K27me3_-RA |
| Sample type |
SRA |
| |
|
| Source name |
embryonal carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: pluripotent
cell line: NT2/D1
chip antibody: rabbit (Millipore, 07-449)
|
| Treatment protocol |
1 µM all trans retinoic acid (ATRA) for 3 days
|
| Growth protocol |
NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonified and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies.
Libraries were prepared according to the manufacturer’s protocol (Diagenode, MicroPlex Library Preparation Kit)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells and PRMT6 re-expression with doxy
|
| Data processing |
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2
Aligned files (bam) were filtered for duplicated aligned reads
MACS 1.4 was used to perform the peak calling
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function with binsize=50, peak files incorporate the number of peaks after filtering for given sample; bigwig files were normalized with CPM (Count Per Million)
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Uta Maria Bauer |
| E-mail(s) |
bauer@imt.uni-marburg.de
|
| Organization name |
Philipps University Marburg
|
| Department |
Institute of Molecular Biology and Tumor Research
|
| Lab |
AG Bauer
|
| Street address |
Hans-Meerwein-Str. 2
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (2) |
| GSE107612 |
Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes |
| GSE117341 |
Repressive mark H3K27me3 in PRMT6 KO NT2/D1 cells |
|
| Relations |
| BioSample |
SAMN09690393 |
| SRA |
SRX4405557 |
