|
| Status |
Public on Sep 24, 2015 |
| Title |
cell line R4 at P9 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila cell line R4 at Passage P9
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: R4
passage: 9
|
| Treatment protocol |
samples were collected from cells cultured in 25 cm2 T flasks
|
| Growth protocol |
cells cultured in Schneider's media supplemented with 10% FBS (fetal bovine serum) and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation using TRIzol reagent.5 micrograms of long RNA species from each sample were depleted from rRNAs using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Epicentre)
RNA libraries were prepared for sequencing starting from 50ng of rRNA-depleted RNAs following the manufacturer's instructions (Script-Seq v2 RNA-Seq; Epicentre)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to the Drosophila melanogaster genome (BDGP release 5/dm3) and annotated using TopHat (v1.4.1) and a custom Bowtie index (Bowtie v0.12.8) based on Drosophila annotated transcripts from Flybase release dmel-r5.43
We determined read counts using Bedtools
Genome_build: Drosophila melanogaster genome (BDGP release 5/dm3)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary-Lee Dequeant |
| E-mail(s) |
mdequeant@genetics.med.harvard.edu, fagegalt@cshl.edu, Greg.Hannon@cruk.cam.ac.uk, perrimon@receptor.med.harvard.edu
|
| Phone |
617-432-6855
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Norbert Perrimon
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE73353 |
Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq] |
| GSE73354 |
Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization |
|
| Relations |
| Reanalyzed by |
GSM3276774 |
| BioSample |
SAMN04103723 |
| SRA |
SRX1278010 |
