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Sample GSM7441199 Query DataSets for GSM7441199
Status Public on Jun 07, 2023
Title Adult intestinal esg+ cells, scute overexpression batch2, rep2
Sample type SRA
 
Source name Adult midgut
Organism Drosophila melanogaster
Characteristics tissue: Adult midgut
cell type: esg-positive cells
genotype: esg-Gal4, UAS-GFP, tub-Gal80[ts], UAS-scute
treatment: temperature switch 18>29C
Treatment protocol Switched to 29ºC in normal food for 2 days prior to dissection.
Growth protocol Flies maintained at 18ºC in normal food until adulthood.
Extracted molecule total RNA
Extraction protocol We dissected 100 midguts/genotype in triplicate and for each sample 20,000–40,000 cells were sorted into RNAse-free 1× PBS with 5 mM EDTA. RNA was isolated using the Arcturus PicoPure™ RNA Isolation Kit.
The entire amount of isolated RNA was used as input for RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit. Two hundred nanograms of amplified aRNA was used as input for RNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 2x150bp
Data processing map with `--readFilesCommand zcat --outMultimapperOrder Random --outSAMmultNmax 1 --runMode alignReads --outSAMtype BAM Unsorted --quantMode GeneCounts`
index with `bamtools index -in aligned.bam -out indexed.bam`
sort with `bamtools sort -out sorted.bam -in indexed.bam`
count reads per gene with `featureCounts -T 8 -p -C -F GTF -t exon -g gene_id ...`
Assembly: FB2019_03 Dmel Release 6.28
Supplementary files format and content: .featurecounts files contain the mapping of reads to each gene in plain text (tab-delimited)
Supplementary files format and content: .summary files contain summary statistics of the mapping in plain text
 
Submission date Jun 02, 2023
Last update date Jun 07, 2023
Contact name Joaquin de Navascues Melero
E-mail(s) j.denavascues@essex.ac.uk
Organization name University of Essex
Department School of Life Sciences
Street address Wivenhoe Park
City Colchester
State/province Essex
ZIP/Postal code CO4 3SQ
Country United Kingdom
 
Platform ID GPL25244
Series (1)
GSE234019 Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation in the Drosophila adult intestine
Relations
BioSample SAMN35574003
SRA SRX20581253

Supplementary file Size Download File type/resource
GSM7441199_SCUTE2.featurecount.summary.txt.gz 283 b (ftp)(http) TXT
GSM7441199_SCUTE2.featurecount.txt.gz 833.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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