|
| Status |
Public on Jan 09, 2014 |
| Title |
MEF_H3K36me3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: conditional Jmjd2c knockout MEFs
treatment: -
chip antibody: H3K36me3
strain: C57BL/6
|
| Treatment protocol |
MEFs were grown in the absence or presence of 500 nM OHT for 72h prior to harvesting.
|
| Growth protocol |
Early passage MEFs were cultured in D-MEM (GIBCO) supplemented with 10% FBS (Hyclone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed using formaldehyde crosslinked chromatin sonicated to an average size of 200-600 bp and the indicated antibodies.
5-10 ng of DNA was processed using NEBNext and Illumina ChIP seq kits according to the manufacturer's instructions. In brief, DNA was adaptor-ligated, subjected to gel size selection, amplified and analyzed by Solexa/Illumina high-throughput sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pool of four sequencing runs (read lengths 42 and 96)
|
| Data processing |
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the mouse genome using the the BOWTIE tool (version 0.12.7) with default parameters except: “-S -m 1” OR “-S -m 1 –solexa1.3-quals”
BedGraph files were generated by extending each aligned read to 250 bp in the 3' direction & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph: BedGraph files were generated by extending each aligned read in the 3' direction to 250 bp & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
|
| |
|
| Submission date |
Jan 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Marianne Terndrup Pedersen |
| E-mail(s) |
marianne.pedersen@bric.ku.dk
|
| Organization name |
BRIC
|
| Department |
University of Copenhagen
|
| Lab |
Kim B. Jensen
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE28332 |
The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites |
| GSE53939 |
The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (ChIP-seq MEFs) |
|
| Relations |
| BioSample |
SAMN02580325 |
| SRA |
SRX424023 |
