|
| Status |
Public on Sep 01, 2023 |
| Title |
ganglioid culture, DIV4_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Enteric nervous system
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Enteric nervous system
cell type: Enteric glial culture
genotype: Sox10CreER/tdT
|
| Treatment protocol |
Neurogenic EGC cultures were established from Sox10Cre|tdT mice (24 hours after a single dose of tamoxifen injection at 100 μg/g of body weight).
|
| Growth protocol |
Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crude nuclei were isolated using IGEPAL solution from 50,000 FACS sorted tdTomato cells after 4 days in vitro.
Nuclei were subjected to tagmentation using the Illumina Nextera Tn5 transposase following published protocol with some modifications. Transposition was carried out at 37°C for an hour instead of the recommended 30mins for all samples processed. DNA fragments were purified using Qiagen MinElute PCR kit and subjected to PCR amplifications using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) and appropriate barcoded primers as described. Amplified fragments were further purified using AMPure XP Beads (Beckman Coulter) according to manufacturer’s recommendation to remove unamplified primers before sequencing. The resulting ATAC libraries were quantified using the GloMax multi-detection system (Promega) and size distribution assayed using a TapeStation D1000 ScreenTape (Agilent). The libraries were then pooled (4 nM) for sequencing and loaded onto the HiSeq 4000 (Illumina) for paired end 100 bp reads sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DIV4_60.mSm_peaks.annotatePeaks.txt
DIV4_60.mSm_peaks.broadPeak
DIV4_60.mSm_peaks.gappedPeak
DIV4_60.mSm_peaks.txt
|
| Data processing |
Reads from ATAC-Seq fastq files were aligned to the Ensembl GRCm38 genome, peaks mapped and quantified using the nextflow atacseq pipeline version 1.0dev (https://nf-co.re/atacseq).
Assembly: hg38
Supplementary files format and content: NF-core ATAC-seq pipeline MACS output
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Vassilis Pachnis |
| E-mail(s) |
Vassilis.Pachnis@crick.ac.uk
|
| Phone |
+442037961556
|
| Organization name |
The Francis Crick Institute
|
| Department |
Development and Homeostasis of the Nervous System Laboratory
|
| Lab |
Pachnis
|
| Street address |
1 Midland Road
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE241522 |
A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia (bulk ATAC-seq data from ganglioid cultures) |
|
| Relations |
| BioSample |
SAMN37124096 |
| SRA |
SRX21466906 |
