|
| Status |
Public on Jun 15, 2021 |
| Title |
RNAseq.F_KD_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
3rd instar larval salivary gland
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: 3rd instar larval salivary gland
genotype/variation: Nub-Gal4 x Mtor RNAi
Sex: Female
|
| Treatment protocol |
UAS-Mtor RNAi induced with Nubbin-Gal4, control is Nubbin-Gal4.
|
| Growth protocol |
Fly larvae grown in standard conditions. Male or female salivary glands were dissected from wandering 3rd instar larva from appropriate crosses (control or Mtor RNAi induction).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Ambion) from salivary glands (10-12 animals per sample is sufficient) vortexed at 4°C for 2 h, extracted with ethanol precipitation, subsequently purified with PureLink RNA Kit columns (Invitrogen).
RNA-seq libraries were constructed using the dUTP method (Parkhomchuk et al., 2009).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
total RNA polyA-selected
RNAseq.read_count.txt
|
| Data processing |
RNA-Seq data were aligned against reference genome (dm3) using STAR (v2.3.0e) with default parameters and maximum fragment size of 2kb ("--alignMatesGapMax 2000"). The resulting files were filtered for concordant, primary alignments using SAMtools (v1.1). The enrichment of different genomic regions were analyzed using RSeQC (v3.0.1). Reads were assigned to RefSeq genes using featureCounts (v1.6.2) and differential expression between groups were analyzed using DESeq2.
TT-seq data were pre-processed in similar ways as RNA-seq. Visualization tracks were also generated in the same way. When assigning reads to RefSeq genes, we included the whole gene body instead of only coding regions. Differential expression between groups were analyzed again using DESeq2.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Yemin Lan |
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE155323 |
Correct dosage of X chromosome transcription is controlled by a nuclear pore component |
|
| Relations |
| BioSample |
SAMN15663435 |
| SRA |
SRX8841270 |
