|
| Status |
Public on Jan 04, 2017 |
| Title |
AdarEA_2 |
| Sample type |
SRA |
| |
|
| Source name |
head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: y, sc, AdarE374A
tissue: head
age: 3 day
|
| Growth protocol |
Heads were dissected from 3 day old male flies grown at 18C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), depleted of ribosomal RNA, and treated again using TURBO DNase.
Libraries produced using the KAPA RNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 75-bp cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
gene_expression.txt
|
| Data processing |
fastx_trimmer was used to trim the 76th base from reads.
Reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations.
Read counts were obtained using featureCounts from the Subread package.
DESeq2 was used to obtain gene expression levels.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: Normalized gene expression profiles for each sample in tab-delimited columns with a header in the first line.
|
| |
|
| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Billy Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
300 Pasteur Drive. Alway M303
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE86054 |
RNA-Seq of head tissue from Drosophila melanogaster Wild Type and AdarEA mutant |
| GSE86056 |
A-to-I RNA Editing in Drosophila |
|
| Relations |
| Reanalyzed by |
GSM3281823 |
| BioSample |
SAMN05645903 |
| SRA |
SRX2053339 |
