|
| Status |
Public on Nov 02, 2022 |
| Title |
Atg6D_2: Atg6D/+ repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole third instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genetic bkg: w118
genotype: Atg6-/+
tissue: whole third instar larvae
|
| Growth protocol |
Larvae were raised on standard food at 25C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from third instar wandering larvae using the Qiagen RNeasy Kit
RNA libraries were prepared for sequencing using strand specific standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
RNA-sequencing reads were aligned against fruit fly reference genome dm6 using Hisat2 (version 2.1.0)
The FPKM values were determined by Cufflinks (v2.2.1)
The differential expression was analzyed by limma with the FPKM values as input
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample obtained from cufflinks output
|
| |
|
| Submission date |
May 22, 2018 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Julie Zhu |
| E-mail(s) |
[email protected]
|
| Phone |
5088565377
|
| Organization name |
UMass Medical School
|
| Department |
Molecular Cellular and Cancer Biology
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE114790 |
Next generation sequencing to determine changes in Drosophila Atg6 mutant larval transcriptome |
|
| Relations |
| BioSample |
SAMN09238503 |
| SRA |
SRX4116158 |
