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Status |
Public on Apr 02, 2024 |
Title |
CD3 |
Sample type |
SRA |
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Source name |
central nervous system
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Organism |
Drosophila melanogaster |
Characteristics |
tissue: central nervous system genotype: Tet CD
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Extracted molecule |
polyA RNA |
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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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Submission date |
Dec 18, 2023 |
Last update date |
Apr 02, 2024 |
Contact name |
yoan renaud |
E-mail(s) |
yoan.renaud@uca.fr
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Organization name |
igred
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Street address |
place henri dunand
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City |
clermont ferrand |
ZIP/Postal code |
63000 |
Country |
France |
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Platform ID |
GPL25244 |
Series (1) |
GSE250415 |
Characterisation of TET function in drosophila larval central nervous system |
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Relations |
BioSample |
SAMN38881045 |
SRA |
SRX22919677 |
Supplementary data files not provided |
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