NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7978811 Query DataSets for GSM7978811
Status Public on Apr 02, 2024
Title WT2_TET_GFP
Sample type SRA
 
Source name central nervous system
Organism Drosophila melanogaster
Characteristics tissue: central nervous system
genotype: w1118
Extracted molecule genomic DNA
Extraction protocol The central nervous systems from wild type (w11118), Tet null or Tet CD (catalytic dead) mutant third instar Drosophila melanogaster larvae were dissected in PBS. For RNA-seq, total RNA was extracted with Trizol. ChIP-seq were performed as described in Loubiere et al. (Bio Protocol 2017). CUT&RUN were performed as described in Ahmad et al. (PLoS Genet. 2019).
For RNA-seq, libraries were prepared using the Illumina TruSeq RNA Library Prep kit. For ChIP-seq and CUT&RUN, libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Novaseq 4000 polyA RNA reads were trimmed using cutadapt and checked with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Read counts were generated for each annotated gene using HTSeq-Count. RPKM (Reads Per Kilobase of exon per Megabase of library size) values were calculated using Cufflinks. Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
Genomic reads were aligned using bowtie2 on Drosophila genome (dm6 Ensembl realease 70)
The resulting reads were mapped to their respective reference genome using Bowtie2 (v2.4.2), reporting at most one hit for each read .
Assembly: Drosophila genome (dm6 Ensembl realease 70)
Supplementary files format and content: text file with RNA-seq RPKM expression per gene and condition
Supplementary files format and content: BigWig with read coverage per position across the genome.
 
Submission date Dec 18, 2023
Last update date Apr 02, 2024
Contact name yoan renaud
E-mail(s) yoan.renaud@uca.fr
Organization name igred
Street address place henri dunand
City clermont ferrand
ZIP/Postal code 63000
Country France
 
Platform ID GPL25244
Series (1)
GSE250415 Characterisation of TET function in drosophila larval central nervous system
Relations
BioSample SAMN38881080
SRA SRX22919658

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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