|
| Status |
Public on Oct 26, 2023 |
| Title |
ISC/EB RNAseq 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 |
Crosses and adults were kept at 18°C, the GAL80 permissive temperature. 3 day old flies were shifted to 29°C for 1 day to induce Dam expression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation and purification was then performed with the Arcturus PicoPure RNA Isolation kit (Thermofisher)
RNA libraries were prepared with the Illumina Stranded mRNA Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D925T27
|
| Data processing |
Nextflow pipeline for RNA-seq data processing developed by the Curie Bioinformatics Core facility was used (https://doi.org/10.5281/zenodo.7443721)
FastQ files were generated with bcl2Fastq, demultiplexed and trimmed to remove adaptors using the Raw-QC and RNA-seq analysis pipelines
Reads were aligned to the Drosophila reference genome (dm6) to generate raw counts tables.
Assembly: dmelr6.28
Supplementary files format and content: tab-delimited text file include tpm values for each Sample
|
| |
|
| 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) |
| GSE224962 |
Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification [RNA-seq] |
| GSE224967 |
Chromatin state transitions in the Drosophila intestinal lineage reveal principles of cell type specification |
|
| Relations |
| BioSample |
SAMN33228252 |
| SRA |
SRX19323455 |
