|
| Status |
Public on Jun 01, 2020 |
| Title |
RKO parental H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RKO ATCC CRL-2577
cell type: parental
chip antibody: Anti-Histone H3K4me1
chip antibody source: Abcam ab8895
|
| Growth protocol |
The parental and KMT2C knock-in cell lines were cultured in McCoy’s 5 A medium (Gibco, /Life Technologies, cat. no 26600-080) with 10% heat inactivated FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% paraformaldehyde for 8 minutes. Chromatin was analyzed by ChIP-sequencing the Diagenode iDeal ChIP-seq kit for histones according to the manufacturer’s instructions. Chromatin extracts from one million cells were sonicated to yield 100 to 500 bp fragments using a Bioruptor Pico sonication device (Diagenode) on high power for two rounds of 6 cycles with 30 s on 30 s off at 4 °C. ChIP-seq was performed using 1 microgram of H3K4me1 antibody (ab8895, Abcam) per ChIP. Cross-links were reversed (4 h at 65 °C) and DNA was purified using the Qiagen MinElute PCR purification kit. Samples were quantified using Qubit (HS dsDNA) and 10 ng of DNA was used for library preparation.
Libraries were prepared for sequencing using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® and sequenced on a HiSeq 2500 System (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Raw data for anti-histone H3K4me1 and input provided
|
| Data processing |
ChIP-seq data were aligned using Bowtie 2 (default parameters). BAM files were uploaded into Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Peak calling was performed with MACS peak builder in Seqmonk.
FANTOM5 enhancers were identified by bidirectional transcription using the capped analysis of gene expression technique and obtained from the FANTOM data resource online (http://enhancer.binf.ku.dk/presets/). H3K4me1 signal was quantified by calculating the log2 of the reads per million for each sample relative to input (ChIP/Input).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Data given are the H3K4me1 ChIP-seq peaks identified with MACS using Seqmonk given in BED file format for GRC37/hg19. Supplementary file contains ChIP/Input scores at human enhancers from the FANTOM 5 project for each sample.
|
| |
|
| Submission date |
May 24, 2019 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Chatarina Larsson |
| Organization name |
Uppsala University
|
| Department |
Immunology, Genetics and Pathology
|
| Street address |
Rudbeck Laboratory
|
| City |
Uppsala |
| ZIP/Postal code |
SE-751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE131755 |
Restoration of KMT2C in human colorectal cancer cell lines HCT116 and RKO reinforces genome wide H3K4me1 profiles |
|
| Relations |
| BioSample |
SAMN11849699 |
| SRA |
SRX5893313 |
