|
| Status |
Public on Dec 31, 2022 |
| Title |
vGlut_INTACT_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
VAChT:VGlut split-Gal4/UAS-UNC84
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: VAChT:VGlut split-Gal4/UAS-UNC84
cell type: Neuronal Nuclei
genotype: VAChT:VGlut split-Gal4/UAS-UNC84
treatment: None
time: 10 Day Old
|
| Growth protocol |
Crosses were reared and standard yeast/cornmeal-agar food to an age of 10 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Flies were snap frozen and ~0.2ml of fly heads were collected by sieving. Fly heads were homogenized according to the mini-INTACT protocol, and RNA was extracted using Trizol. Poly(A) RNA was isolated using the Poly(A)-purist kit.
RNA libraries for RNA-seq were prepared using NEXTFLEX Rapid Directional qRNA-Seq kit according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastp
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default settings and overlap analysis
UMItools
UMIs were extracted and appended to reads with UMItools, and later deduplicated with UMItools after STAR alignment
STAR
Reads were mapped to dm6 using STAR and the following settings: --outFilterMismatchNoverLmax 0.06 --outFilterMatchNmin 15 --outFilterMultimapNmax 1 --outSJfilterReads Unique --alignMatesGapMax 25000
FeatureCounts
A count table was produced using FeatureCounts
DESeq2
Differential expression was conducted using DESeq2
Assembly: dm6
Supplementary files format and content: tab-delimited text file consists of a non-normalized count table, with one column per experiment
|
| |
|
| Submission date |
Dec 28, 2022 |
| Last update date |
Jan 03, 2023 |
| Contact name |
Albert Dayuan Yu |
| E-mail(s) |
adyu@brandeis.edu
|
| Phone |
8579917778
|
| Organization name |
Brandeis University
|
| Department |
Molecular and Cell Biology
|
| Lab |
Rosbash Lab
|
| Street address |
415 South St.
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02453 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE221859 |
RNA profile of nuclei isolated from neurons coexpressing VAChT and VGlut or VAChT and VGAT |
|
| Relations |
| SRA |
SRX18787580 |
| BioSample |
SAMN32330465 |
