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Sample GSM6265720 Query DataSets for GSM6265720
Status Public on Dec 01, 2023
Title Third instar CNS, gWT1
Sample type SRA
 
Source name central nervous system
Organism Drosophila melanogaster
Characteristics tissue: central nervous system
developmental stage: third instar larvae
genotype: w1118
Extracted molecule genomic DNA
Extraction protocol Third instar CNS were dissected in ice cold PBS. Samples 1-6: Tissues were crushed in lysis buffer (100 mM Tris-HCl pH9, 1 mM EDTA, 1% SDS), digested with RNAse A for 15 min at room temperature and 30 min at 65°C, before being incubated with 4 volumes of 3.2 M LiCl, 0.9 M KAc for 30 min at 4°C. After centrifugation at 12000 g for 20 min at 4°C, the supernatant was extracted with phenol-chloroform-isoamyl alcohol and DNA was precipitated with isopropanol. Samples 7-11:RNAs were extracted with Qiagen RNeasy Plus Micro kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Samples 1-6: libraries were prepared using a SMRTbell Express 2 Template prep kit. Samples 7-11: library preparation was performed using Kapa Biosystems library preparation kit.
Samples 1-6: SMRT-seq. Samples 7-11: RNA-seq
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Sequel
 
Description WT_fusion_all.xlsx
Sample 1
Data processing Illumina Hiseq2500 reads were trimmed using Trimmomatic 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
SMRT-seq reads were aligned using pbmm2 tool (https://github.com/PacificBiosciences/pbmm2) on Drosophila genome (dm6 Ensembl realease 70)
6mA detection was performed on every samples and on merged ones with IpdSummary tool from KineticTools (http://github.com/PacificBiosciences/kineticsTools) applying following parameters: --identify m6A --numWorkers 16 --pvalue 0.01 --identifyMinCov 5 –methylFraction
Assembly: Drosophila genome (dm6 Ensembl release 70)
Supplementary files format and content: text file with RNA-seq expression
Supplementary files format and content: Excel file with 6mA detected localization and scores
 
Submission date Jun 24, 2022
Last update date Dec 01, 2023
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 GPL28354
Series (1)
GSE206852 Analysis of gene expression in the Drosophila larval central nervous system
Relations
BioSample SAMN29329796
SRA SRX15887424

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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