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Status |
Public on Dec 01, 2023 |
Title |
Third instar CNS, gWT1 |
Sample type |
SRA |
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Source name |
central nervous system
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Organism |
Drosophila melanogaster |
Characteristics |
tissue: central nervous system developmental stage: third instar larvae genotype: w1118
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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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Sequel |
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Description |
WT_fusion_all.xlsx Sample 1
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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
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Submission date |
Jun 24, 2022 |
Last update date |
Dec 01, 2023 |
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 |
GPL28354 |
Series (1) |
GSE206852 |
Analysis of gene expression in the Drosophila larval central nervous system |
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Relations |
BioSample |
SAMN29329796 |
SRA |
SRX15887424 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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