|
| Status |
Public on Feb 23, 2021 |
| Title |
Nicd OE-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
intestinal progenitor cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: midgut
cell type: intestinal progenitor cells
age: adult stage day 7
genotype: Nicd overexpressed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Drosophila midgut were removed and digested using Elastase (Sigma, cat. no. E0258). About 10000 ISCs labeled with green fluorescent protein (GFP) were sorted using FACSAria II cell sorter (Becton Dickinson) and RNA was harvested using the Arcturus PicoPure RNA isolation kit (Applied Biosystems). The RNA was then amplified using Arcturus RiboAmp HS PLUS RNA ampliļ¬cation kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using STAR v2.6.1a_08-27 with default parameters
DESeq2 was used for relative quantitation of genes expression and differential expression analysis.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample
|
| |
|
| Submission date |
May 09, 2019 |
| Last update date |
Feb 23, 2021 |
| Contact name |
huanwei huang |
| E-mail(s) |
hhw2436@gmail.com
|
| Organization name |
NIBS
|
| Street address |
7 Science Park Rd., ZGC life science park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE130942 |
Transcriptome profiling of Drosophila wild type and ttk-RNAi, dpn overexpressed, Nicd overexpressed and seq&Nicd overexpressed intestinal progenitor cells |
| GSE130943 |
Tramtrack safeguards tissue identity of Drosophila intestinal stem cells by preventing neuroblast-like program activation and neuroendocrine tumors |
|
| Relations |
| BioSample |
SAMN11607967 |
| SRA |
SRX5809935 |
