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Sample GSM3688718 Query DataSets for GSM3688718
Status Public on Mar 28, 2019
Title esggal4NREG80_RNAi_Kis3_F
Sample type SRA
 
Source name intestine
Organism Drosophila melanogaster
Characteristics cell type: intestinal stem cells (ISC)
genotype: esg-gal4ts NREGal80>UAS_RNAi_KIS
tissue: adult intestine
Growth protocol Crosses and adults were kept at 18°C, the GAL80 permissive temperature. 3 day old flies were shifted to 29°C for 2 days to induce RNAi expression
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from FACS sorted ISC of 100 females dissected midguts via Arcturus PicoPure RNA isolation Kit and amplified using Arcturus RiboAmp HS plus Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Using the damidseq_pipeline reads in fastq files were aligned to the Drosophila melanogaster reference genome version 6 using bowtie2 and alignments were extended to 300 nucleotides or the first GATC site, whichever occurred first.
GATC sites in mappable regions read coverage was counted using bedtools coverage and GATC sites with fewer than 5 counts on average were discarded.
The remaining GATC sites were split into control counts and DamID fusion counts and tested for statistically significant differences using DESeq2, which also estimates a variance stabilized log2 fold enrichment values for each GATC site
Peaks were called by merging 2 or more consecutive significant GATC sites (adjusted p-value < 0.01, log2 fold change > 0). Genes were classified as bound by a protein if 2 consecutive GATC sites within the gene body were occupied with an adjusted p-value < 0.01.
RNA Pol II occupancy was determined by considering mean ratios (Dam-RNA Pol II/Dam-only) across annotated transcripts using “polii.gene.call” script and false discovery rates (FDR) were assigned. Genes with an FDR < 0.01 were used as genes active in ISC.
Reads were quasi-mapped against the Drosophila reference transcriptome fasta using Salmon.
Differential gene expression testing was performed using tximportData, RUVseq.
Genes with an adjusted p-value < 0.01 were considered differentially expressed.
Genome_build: Flybase, release 6.13
 
Submission date Mar 27, 2019
Last update date Mar 28, 2019
Contact name Marius van den Beek
E-mail(s) m.vandenbeek@gmail.com
Phone +33156246580
Organization name Institut Curie
Department GENETICS AND DEVELOPMENTAL BIOLOGY
Lab STEM CELLS AND TISSUE HOMEOSTASIS
Street address 11-13 rue Pierre et Marie Curie, Equipe Bardin/UMR3215/Batiment BDD
City Paris cedex 05
State/province Ile-de-France
ZIP/Postal code 75005
Country France
 
Platform ID GPL25244
Series (1)
GSE128941 Stem cell proliferation is kept in check by the chromatin regulators Kismet/CHD7/CHD8 and Trr/MLL3/4
Relations
BioSample SAMN11266367
SRA SRX5582285

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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