GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7978813

Query DataSets for GSM7978813

Status

Public on Apr 02, 2024

Title

Input2

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