NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4379922 Query DataSets for GSM4379922
Status Public on Dec 07, 2021
Title Chd1[WT/WT]_1
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 SAMN14292002
SRA SRX7849517

Supplementary file Size Download File type/resource
GSM4379922_WT_1.txt.gz 118.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap