|
| Status |
Public on Oct 09, 2019 |
| Title |
Intestinal progenitor cells, LBesgtsNRNAi1 |
| Sample type |
SRA |
| |
|
| Source name |
adult female intestinal progenitor cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: adult
gender: female
genotype: esgts/NRNAi
microbiome: L. brevis
cell type: intestinal progenitor cells
|
| Growth protocol |
adult virgin female drosophila were raised for 5 days at 25C, monoassociated with L brevis or L plantarum overnight (or kept germ free) then trasnferred to 29C for an additional 5 days before intestine dissection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Intestines were dissected and immediately placed in DEPC PBS on ice. After 100 guts per sample were collected for a replicate of three (approx. 2 hour dissection time) guts were dissociated into a single cell solution using elastase (1mg/mL) before running through the FACS machine. Small GFP+ cells were gated upon and selected for collection into DEPC PBS. The RNA was extracted from the progenitor cells using standard Trizol methods.
Library construction was performed at the Lunenfeld-Tanenbaum Research Facility (LTRI) using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Qualtiy control of raw reads with FastQC
Read trimming with Trimmomatic
Aligned to the Drosophila transcriptome using HISAT2
Conversion of BAM files to SAM files using Samtools
Counts for each sampek were determined with Rsubread then compiled into one document proir to differential analysis via edgeR
Genome_build: bdgp6
Supplementary_files_format_and_content: tab delimited files for raw counts (Rsubread output) and differential expression (edgeR output) for valid comparisons
|
| |
|
| Submission date |
Oct 08, 2019 |
| Last update date |
Oct 09, 2019 |
| Contact name |
Edan Foley |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Alberta
|
| Department |
MMI
|
| Lab |
6-59 HMRC
|
| Street address |
116st and 85ave
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2S2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23323 |
| Series (1) |
| GSE138555 |
RNASeq of Drosophila intestinal progenitor cells upon Notch knockdown or microbiome alterations |
|
| Relations |
| BioSample |
SAMN12992994 |
| SRA |
SRX6962960 |
