|
| Status |
Public on Sep 27, 2018 |
| Title |
IgG_KO-2_-RA |
| Sample type |
SRA |
| |
|
| Source name |
embryonal carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NT2/D1
cell type: pluripotent embryonal carcinoma cell line
genotype/variation: CRISPR/Cas9-mediated deletion of PRMT6
atra: -
chip antibody: IgG rabbit (I5006, Sigma)
|
| 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 sonicated 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.
|
| 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 (GRCh37)
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function.
Supplementary_files_format_and_content: *peaks.txt.: Tab-delimited text; Peak files incorporate the number of peaks after filtering for given sample.
|
| |
|
| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE107609 |
Genomic occurrence analysis of PRMT6-dependent H3R2me2a |
| GSE107612 |
Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes |
|
| Relations |
| BioSample |
SAMN08120265 |
| SRA |
SRX3437599 |
