|
| Status |
Public on Jun 25, 2024 |
| Title |
H3K4me1_Pdgfra_R1 |
| Sample type |
SRA |
| |
|
| Source name |
OCT4-mCherry
|
| Organism |
Mus musculus |
| Characteristics |
cell line: OCT4-mCherry
cell type: nEnd
cut&tag antibody: H3K4me1, Abcam, ab8895
treatment: no treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
nEnd subpopulations were isolated by fluorescence activated cell sorting (FACS) based on OCT4-mCherry and PDGFRA-APC expression (Oct4+, douple positive (DP) and Pdgfra+) using a BD FACSAria III Cell Sorter
Library preparation according to the protocol detailed in Kaya-Okur et al. 2020 (Nature Protocols)
Cleavage Under Targets & Tagmentation (CUT&Tag)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H3K4me1_Pdgfra_consensus.bed
|
| Data processing |
Raw reads where processed with bcl2fastq (v 2.19.1)
Raw sequence reads were aligned to the mm10 reference genome (with Bowtie2)
quality filtered with samtools (v 1.12) flags (-b -F4 -q13)
Normalised bigwigs for visualisation was generated with bamCoverage (anaconda2 v 4.4.0) using binsize 5 and RPKM.
Peaks were called using SEACR (https://seacr.fredhutch.org/) for each population with population-specific IgG using the 'stringent' setting
Consensus peaks pr condition was defined as peaks present in at least 2 of 3 biological replicates, and these were combined to generate a counttable for downstream analysis (reads within defined peaks were counted using bedtools, v 2.26.0, coverage).
Assembly: mm10
Supplementary files format and content: bigWig, bed (except for IgG samples)
Library strategy: CUT&Tag
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
reNEW
|
| Lab |
Brickman
|
| Street address |
3B Blegdamsvej
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE232925 |
The primitive endoderm supports lineage plasticity to enable regulative development [CUT&Tag] |
| GSE232926 |
The primitive endoderm supports lineage plasticity to enable regulative development |
|
| Relations |
| BioSample |
SAMN35217570 |
| SRA |
SRX20440963 |
