|
| Status |
Public on Jan 31, 2021 |
| Title |
ES-KO |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Stem cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype: LSH Knock out
cell type: Stem cell
ip: hydroxymethylcytosine (5hmC)
|
| Growth protocol |
MEF (DMEM, 10%FBS, penicillin/streptomicin), ES (DMEM, 15%FBS, NEAA, 2mM L-Glu, penicillin/streptomicin, LIF, 100nM of β-mercaptoethanol)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA using the Qiagen-DNeasy Blood &Tissue Kit according to the supplier's instructions (Qiagen, Hilden, Germany). This included a proteinase K digestion at 55C overnight. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
5hmC level in mouse embryonic stem cells knocked out for LSH
|
| Data processing |
Library strategy: hMeDIP-Seq
The BWA software was used to map reads on mouse genome (NCBI 37; UCSC mm9). Reads not uniquely mapped to the reference genome were discarded.
sam files were converted into bam and sorted using samtools (version 1.3.1)
Duplicates reads (i.e. mapping to the same location) were removed using Picardtool MarkDuplicates (version 1.64)
For visualisation, bam were converted into bedgraph using bamTobw tool (https://github.com/YangLab/bamTobw)
Genome_build: NCBI 37; mm9
Supplementary_files_format_and_content: bedGraph file containing hmC enrichment profile across mm9 genome
|
| |
|
| Submission date |
Feb 05, 2018 |
| Last update date |
Feb 21, 2021 |
| Contact name |
Maud de Dieuleveult |
| E-mail(s) |
maud.dedieuleveult@gmail.com
|
| Organization name |
Free University of Brussels
|
| Lab |
Laboratory of Cancer Epigenetics
|
| Street address |
Route de Lennik 808
|
| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE110129 |
The chromatin remodeler Lsh modulates genome-wide cytosine hydroxymethylation |
|
| Relations |
| BioSample |
SAMN08466552 |
| SRA |
SRX3648122 |
