|
| Status |
Public on Mar 20, 2018 |
| Title |
ph505 mutant cells 3 |
| Sample type |
SRA |
| |
|
| Source name |
ph505 eye-antennal imaginal discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: FRT19A,ph505 / tubGal80,FRT19A; eyFlp, act>>gal4, UAS-GFP/+
tissue: ph505 eye-antennal tissue
facs-sorted cells: GFP+ (ph505 tumor cells)
experiment: 3
|
| Treatment protocol |
ph505 eye-antennal tissues were FACS-sorted based on GFP signal. GFP+ pool of cells correspond to ph505 tumor cells, while GFP- pool of cells correspond to wild-type surrounding cells.
|
| Growth protocol |
Flies were maintained on standard food at 25°C and 60% humidity, under a 12hr light: 12hr dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from FACS-sorted samples by using PicoPure RNA isolation kit, including a step of DNase treatment.
We prepared sequencing libraries according to Smart-Seq2 protocol. Two technical replicates per sample of a total of 11 samples, including 7 tumor and 4 control (22 libraries).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
tumor.3
This GEO Sample represents 2 technical replicates.
Processed data file: Counttable_collapsed.txt
|
| Data processing |
Adaptor clipping / Quality trimming with Trimmomatic (v0.30), parameters: ILLUMINACLIP:TruSeq2-SE.fa:2:30:10 TRAILING:3 LEADING:3 MINLEN:24
Alignment with STAR (v2.3.0e), parameters: default.
Duplicate removal with Picard Tools MarkDuplicates (v1.121), parameters: REMOVE_DUPLICATES=true
Counting of transcripts with HTSeq htseq-count (v0.6.1).
Importing counts for each sample, merging technical replicates with R (v3.1.0).
Genome_build: Drosophila melanogaster Apr. 2006 (BDGP R5/dm3) assembly (Release 5)
Supplementary_files_format_and_content: Counttable_collapsed.txt: Tab-delimited text file contains counts for each gene. Technical replicates collapsed into single columns.
|
| |
|
| Submission date |
Jul 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Renato Paro |
| Organization name |
ETH Zurich
|
| Department |
D-BSSE
|
| Street address |
Mattenstrasse 26
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE101463 |
An epigenetically-deregulated tumor state reveals a new role for embryonic transcription factors as cancer drivers |
|
| Relations |
| Reanalyzed by |
GSM3283810 |
| BioSample |
SAMN07352445 |
| SRA |
SRX3005917 |
