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Sample GSM7109883 Query DataSets for GSM7109883
Status Public on Mar 22, 2023
Title bulk_wing_discs_Rn1_2_ctrl
Sample type SRA
 
Source name wing imaginal disc
Organism Drosophila melanogaster
Characteristics tissue: wing imaginal disc
developmental stage: third instar larvae
cell type: epithelial and mesenchymal cells
genotype: rnts>; UAS-mCD8-ChRFP, rn-Gal4, tub-Gal80ts
treatment: none
Treatment protocol Expression of the Xrp1 short isoforn was induced by temperature shift from 22 to 29°C
Growth protocol Larvae were raised at 22 oC and shifted to 29°C on day 7 AEL
Extracted molecule polyA RNA
Extraction protocol Wing imaginal discs (120 WDs for rnts>, 160 WDs for rnts>Xrp1-S) were dissected 48h later in PBS and flash-frozen in liquid nitrogen. Total RNA was isolated according to standard TRI Reagent protocol (Sigma Aldrich, #T9424), followed by DNase I treatment (Invitrogen, #AM2238) and repurification as described in (Mundorf and Uhlirova, 2016)
RNAseq libraries were prepared according to TruSeq stranded mRNA sample preparation guide (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Sequencing data were mapped using STAR with default parameters and no multimapping reads (outFilterMultimapNmax = 1) on FlyBase r6.35 reference genome (sjdbOverhang = 99, genomeSAindexNbases = 12)
Gene counts were obtained using htseq-count with default parameters on gene symbols GFF file (r6.35)
Assembly: dm6
Supplementary files format and content: HTSeq-count output for each RNA sample (control and Xrp1-S) comprising gene count information as TSV format.
 
Submission date Mar 21, 2023
Last update date Mar 22, 2023
Contact name Stein Aerts
Organization name VIB-KU Leuven
Department Department of Human Genetics / VIB Center for Brain and Disease Research
Lab Laboratory of Computational Biology
Street address Herestraat 49
City Leuven
State/province Flemish-Brabant
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL30203
Series (2)
GSE205401 Shared enhancer gene regulatory networks between wound and oncogenic programs
GSE227858 Shared enhancer gene regulatory networks between wound and oncogenic programs [RNA]
Relations
BioSample SAMN33845366
SRA SRX19742028

Supplementary file Size Download File type/resource
GSM7109883_WID_2a0d1a_RNA_lib_bulk_wing_discs_Rn1_2_ctrl_S10.count.txt.gz 61.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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