|
| Status |
Public on Oct 26, 2023 |
| Title |
ISC/EB ATACseq H1 RNAi A |
| Sample type |
SRA |
| |
|
| Source name |
ISC/EB
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ISC/EB
cell type: Intestinal cells
genotype: esgts, UAS-GFP UAS H1 RNAi 1
treatment: H1 RNAi 1
time: 4 days induction at 29°C
|
| Treatment protocol |
For each replicate, 70 guts (control and H1 RNAi) were dissected in cold PBS, dissociated in elastase and FACS-sorted to isolate 50-100,000 GFP+ progenitor cells
|
| Growth protocol |
3-day old female flies with esgts, UAS-GFP (control) or esgts, UAS-GFP UAS-H1 RNAi 1 were kept at 18°C for 2 days and shifted to 29°C for 4 days on poor food to induce RNAi expression
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmented DNA purified with Qiagen Minelute Cleanup Kit
Tagmentation of DNA with Tn5 transposase from Illumina (#FC-121-1030)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bioinfo-pf-curie/ATAC-seq: v1.0.2 pipeline for ATAC-seq data processing developed by the Curie Bioinformatics Core facility was used (https://doi.org/10.5281/zenodo.7576558)
Raw reads were trimmed for adapters using trimgalore and aligned to the Drosophila melanogaster reference genome (dm6) using bowtie2
Duplicated reads were removed from the aligned results with Picard, and filtered to discard low mapping quality reads <20, aligned to mitochondrial chromosome reads as well as singleton reads.
Only valid pairs were considered. Read shifting was applied to account for Tn5 insertions (+ strand reads adjusted by 4 bp, and - strand reads adjusted by -5bp).
Peaks were called using MACS2 and Narrow peaks with q<0.01 were reported.
Assembly: dmelr6.28
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Feb 09, 2023 |
| Last update date |
Oct 26, 2023 |
| Contact name |
Allison Bardin |
| E-mail(s) |
allison.bardin@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE224963 |
Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification [ATAC-seq] |
| GSE224967 |
Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification |
|
| Relations |
| BioSample |
SAMN33228349 |
| SRA |
SRX19323548 |
