|
| Status |
Public on Jul 28, 2020 |
| Title |
Ras/Src HSD Mid rep4 |
| Sample type |
SRA |
| |
|
| Source name |
body wall muscle
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: day 14
tumor-type: Ras/Src HSD
tissue: body wall muscle
|
| Treatment protocol |
N.a
|
| Growth protocol |
Cultures were carried out on Bloomington semi-defined medium (https://bdsc.indiana.edu/information/recipes/germanfood.html) and contained sucrose (0.15 M and 1.0 M in CD and HSD, respectively) as the only purified sugar source. Ingredients were obtained from; Agar (Fisher Scientific; BP2641-1), Brewer’s Yeast (MP Biomedicals; 903312, Lot: BCBN0171V), Yeast Extract (Sigma-Aldrich; 70161), Peptone (Sigma-Aldrich; 82303), Sucrose (Fisher Scientific; S/8560/63), Magnesium sulfate hexahydrate (Fluka; 00627), Calcium chloride dihydrate (Sigma-Aldrich; 223506), Propionic acid (Sigma-Aldrich; P1386), p-Hydroxy-benzoic acid methyl ester (Sigma-Aldrich; H5501). Larvae were raised up until the indicated time point after egg laying at which point the relvant tissue was dissected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from pooled dissected tissue was extracted with the QIAGEN RNeasy Mini Kit.
RNA-seq libraries were prepared from a minimum of 10ng of total RNA using the Illumina Truseq mRNA stranded library prep kit (Illumina, San Diego, USA) according to the manufacturer’s protocol. Library quality was checked on a Bioanalyser HS DNA chip and concentrations were estimated by Qubit measurement.
Libraries were pooled in equimolar quantities and sequenced on a Hiseq2500 using paired end 100bp reads. At least 35 million reads passing filter were achieved per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_12_Ras.Src.HSD14
|
| Data processing |
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to dm3 whole genome using tophat2 (2.0.11) with parameters --library-type fr-firststrand -p 8
Gene annotations were obtained from Ensembl Drosophila genome (dm3). Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: dm3
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample
|
| |
|
| Submission date |
Nov 05, 2019 |
| Last update date |
Dec 04, 2020 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE139955 |
Transcriptome analysis of dissected muscle tissue from whole-animal Drosophila melanogaster tumour models across a time course. |
| GSE139958 |
Systemic muscle wasting drives tumourigenesis |
|
| Relations |
| BioSample |
SAMN13207412 |
| SRA |
SRX7101383 |
