|
| Status |
Public on Sep 27, 2018 |
| Title |
NT2D1_CT_KMT2D_-RA_abgent |
| Sample type |
SRA |
| |
|
| Source name |
NT2D1_CT_KMT2D_-RA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NT2/D1
cell type: embryonal carcinoma cell line
cell status: pluripotent
genotype/variation: CRISPR/Cas9 control NT2/D1 cells
chip antibody: rabbit (AP6183a, abgent)
|
| Treatment protocol |
1 µM all trans retinoic acid (ATRA) for 3 days; 16 µM MS049 (PRMT6 inhibitor) 3 days; PRMT6 rescue with Doxy treatment 6 days
|
| Growth protocol |
NT2/D1 and U2OS 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 |
88_E9m_ChIP66_130218_CGATGT
|
| 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
|
| |
|
| Submission date |
Jul 17, 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 |
| GSE117200 |
Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN09668441 |
| SRA |
SRX4397527 |
