|
| Status |
Public on Dec 07, 2021 |
| Title |
Chd1[WT/WT]_3 |
| Sample type |
SRA |
| |
|
| Source name |
head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: wildtype
tissue: head
Sex: female
age: 10 d
|
| Treatment protocol |
Flies were snap frozen and decapitated. Heads were used for RNA isolation
|
| Growth protocol |
Virgin female flies were selected and kept at 25°, 60% humidity, 12/12 hour day/night cycle on standard cornmeal food until 10 days old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from snap frozen samples with TRI reagent following the manufacturer's protocol
Sequencing library construction was performed by BGI Corp for sequencing with the DNA nanoballs (DNB) system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The whole workflow was performed according to "RNA-seq workflow: gene-level exploratory analysis and differential expression"; https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
Transcript abundances were estimated using Salmon with the Drosophila melanogaster GCF_000001215.4_Release_6_plus_ISO1_MT_rna.fna.gz transcriptome downloaded from NCBI.
Estimates were imported into R using the package tximport.
DEseq2 was used to estimate differential expression between the sample groups.
Genome_build: Release 6 plus ISO1 MT
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: excel spreadsheet ".xlsx" file contains DEseq2 results for contrasts Chd1[-/-] vs Chd1[WT/WT] and Chd1[-/-] vs elav-Gal4>UAS-Chd1.
|
| |
|
| Submission date |
Mar 04, 2020 |
| Last update date |
Dec 07, 2021 |
| Contact name |
Ingo Bauer |
| Organization name |
Medical University of Innsbruck
|
| Department |
Institute of Molecular Biology
|
| Street address |
Innrain 80-82
|
| City |
Innsbruck |
| State/province |
Tirol |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL26560 |
| Series (1) |
| GSE146392 |
Gene expression profiling on heads of Drosophila chromodomain helicase DNA binding protein 1 (CHD1) deletion mutants |
|
| Relations |
| BioSample |
SAMN14292000 |
| SRA |
SRX7849519 |
