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| Status |
Public on Jan 31, 2024 |
| Title |
nub>mRFP; ecd-RNAi rep 1 |
| Sample type |
SRA |
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| Source name |
Wing disc, L3
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Wing disc, L3
genotype: nub>mRFP; ecd-RNAi
treatment: ecd RNAi
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| Treatment protocol |
RNAi against ecd was driven in the nubbin domain of D. melanogaster larvae continuously until sample collection
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| Growth protocol |
Dosophila crosses were kept on a diet consisting of 0.8% agar, 8% cornmeal, 1% soymeal, 1.8% dry yeast, 8% malt extract and 2.2% sugar-beet syrup, supplemented with 0.625% propionic acid and 0.15% Nipagin, and maintained at 25 °C. Wing discs were collected from third-instar larvae 7 days after egg-laying
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, 150 WDs were dissected from third instar larvae in 1xPBS and snap-frozen in liquid nitrogen, and processed according to standard TRI Reagent protocol (Sigma Aldrich, #T9424) with DNase I treatment (Invitrogen, #AM2238).
For RNA sequencing, 2 μg of total RNA was used for library preparation (Illumina TruSeq Stranded total RNA Ribo-Zero). Pair-end sequencing (four biological replicates of each experimental group) at a read length of 100 bp was performed on an Illumina HiSeq 2000 machine.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
nrE3
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| Data processing |
Initial quality control of the raw data was performed using FastQC (RRID:SCR_014583).
Illumina sequencing adapters were removed from the sequencing reads with the cutadapt tool version 3.5 (Martin, 2011; RRID:SCR_011841)
For differential gene expression analysis, kallisto v0.46.1 (Bray et al., 2016; RRID:SCR_016582) was used for pseudoalignment of obtained reads to the complete Drosophila melanogaster transcriptome (BDGP6.28, Ensembl release 102) and transcript-level abundance quantification using 100 bootstrap samples.
Summarization of the obtained estimated counts to gene-level was performed using tximport v1.22.0 (Bray et al., 2015; RRID:SCR_016752).
Differential gene expression was determined using DESeq2 v1.34.0 (Love et al., 2014; RRID:SCR_015687).
Intron retention was analyzed using NxtIRFcore v1.2.1 (Wang and Ritchie 2022) and IRFinder v2.0.1 (Middleton et al., 2017)
Assembly: BDGP6.28, Ensembl release 104
Supplementary files format and content: csv: comma-separated table with DEseq2 normalized count
Supplementary files format and content: txt: tab-delimited table of DESeq2 results
Supplementary files format and content: tsv: per intron DESeq2 differential retention results
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| Submission date |
Sep 13, 2022 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Mirka Uhlirova |
| E-mail(s) |
mirka.uhlirova@uni-koeln.de
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| Organization name |
CECAD Research Center Cologne
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| Department |
Institute for Genetics
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| Lab |
Uhlirova Lab
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| Street address |
Joseph-Stelzmann Str. 26
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| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE213298 |
Xrp1 governs the stress response program to spliceosome dysfunction |
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| Relations |
| BioSample |
SAMN30839133 |
| SRA |
SRX17556934 |
| 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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