|
| Status |
Public on Nov 15, 2015 |
| Title |
mir-11 KO(w-) biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
3rd instar larval eye disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 3rd instar larval
tissue type: eye disc
stock: mir-11 KO (w-)
|
| Treatment protocol |
Different genotypes were compared: Canton S, mir-11 KO(w-), mir-11~998 RMCE-1 and mir-11~998 RMCE-2
|
| Growth protocol |
Flies were cultured on standard medium at 25 degrees Celcius
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
Library construction was performed using standard Illumina protocols; Illumina HiScanSQ Instrument; Total RNA directional; incl. rRNA depletion
Single end 50 bp sequencing 2-lane flowcell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
30-50 discs/sample
|
| Data processing |
Control software: HiSeq Control Software 2.2.38
Primary Analysis: RTA 1.18.61.0
Secondary Analysis: CASAVA-1.8.2
Read Quality Assessment and Filtering was done with FastQC program
TopHat2 was used for mapping of reads. "featureCount" of SubRead package was used to count the reads of exons for each gene abundance measurement. (Ensembl gene v.77)
Genome_build: D. melanogaster ENSEMBL (v77)
Supplementary_files_format_and_content: tab-delimited text files include absolute count values for each sample
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Truscott |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Frolov lab
|
| Street address |
900 S Ashland Ave, room 2356
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE73946 |
RNA Seq analysis of unchecked miR-998 expression in Drosophila melanogaster 3rd instar larval eye discs |
|
| Relations |
| Reanalyzed by |
GSM3277245 |
| BioSample |
SAMN04160964 |
| SRA |
SRX1331544 |
