|
| Status |
Public on May 02, 2023 |
| Title |
S2-Grh_noCuSO4_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
genotype: S2-Grh
treatment: uninduced
|
| Treatment protocol |
Transcription factor expression was induced by adding CuSO4 to the cell culture media. For all induction experiments, cells were plated at 1×106 cells per mL. Experiments were performed with cells harvested 48 hours after induction.
|
| Growth protocol |
Drosophila S2 cells were cultured at 27°C in Schneider's medium supplemented with 10% fetal bovine serum and antibiotic/antimycotic.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
5×106 cells were harvested and resuspended in 800 µL Trizol (Invitrogen). RNA was purified using a chloroform extraction followed by a column-based Quick-RNA MiniPrep extraction (Zymo).
Poly-A-selected RNA sequencing (RNA-seq) libraries were prepared using the TruSeq RNA sample prep kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S2-Grh_noCuSO4.bw
S2-Grh_RNAseq_counts.tsv
|
| Data processing |
Raw reads were aligned to the Drosophila melanogaster (dm6) genome using HISAT2 version 2.1.0 with parameters -k 2 –very-sensitive.
Reads with a mapping quality score < 30 and reads aligning to the mitochondrial genome or unplaced scaffolds were discarded.
FeatureCounts (from Subread version 2.0) was used to assign aligned reads to genes (FlyBase gene annotation release r6.45).
The resultant table of read counts was used to perform differential expression analysis using DESeq2. Genes with an adjusted p-value < 0.05 and a fold change > 2 were considered differentially expressed.
Assembly: dm6
Supplementary files format and content: bigWig file: z-score normalized read depth of combined replicates.
Supplementary files format and content: RNAseq_counts.tsv: raw read counts that were used for downstream analysis. Gene length is included for convenient RPKM normalization.
|
| |
|
| Submission date |
Mar 21, 2023 |
| Last update date |
May 02, 2023 |
| Contact name |
Melissa M Harrison |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wisconsin Madison
|
| Department |
Biomolecular Chemistry
|
| Lab |
1135 Biochemical Sciences Bldg
|
| Street address |
420 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE227883 |
Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function [RNA-Seq] |
| GSE227884 |
Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function |
|
| Relations |
| BioSample |
SAMN33845373 |
| SRA |
SRX19742124 |
