Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional profiling of esg+-midgut progenitor cells expressing esgRNAi or UAS-esg AND of whole midgut tissue from flies overexpressing UAS-esg in enterocyte (EC) cells

ABSTRACT: RNA-Seq of amplified mRNA from sorted esg+-midgut progenitor cells expressing esgRNAi or UAS-esg AND RNA-Seq of whole midgut tissue from flies overexpressing UAS-esg and UAS-esg+UAS-dIAP (+control empty vector RNAi, UAS-dIAP and w1118) using the MyoIA-Gal4ts EC-driver

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jerome Korzelius

PROVIDER: E-MTAB-2915 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Escargot maintains stemness and suppresses differentiation in Drosophila intestinal stem cells.

Korzelius Jerome J Naumann Svenja K SK Loza-Coll Mariano A MA Chan Jessica Sk JS Dutta Devanjali D Oberheim Jessica J Gläßer Christine C Southall Tony D TD Brand Andrea H AH Jones D Leanne DL Edgar Bruce A BA

The EMBO journal 20141008 24

Snail family transcription factors are expressed in various stem cell types, but their function in maintaining stem cell identity is unclear. In the adult Drosophila midgut, the Snail homolog Esg is expressed in intestinal stem cells (ISCs) and their transient undifferentiated daughters, termed enteroblasts (EB). We demonstrate here that loss of esg in these progenitor cells causes their rapid differentiation into enterocytes (EC) or entero-endocrine cells (EE). Conversely, forced expression of ...[more]

PMID: 25298397

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Project description:Purpose: We isolated Drosophila midgut cells : Delta+ intestinal stem cells (ISCs), Su(H)+enteroblasts (EBs), Esg+ cells (ISC+EB), Myo1A+Enterocytes (ECs), Pros+Enteroendocrine cells (EEs) and How+Visceral muscle cells (VM) from whole midguts to identify stem cell specific genes and study cell type specificities of midgut cells. We also isolated all the cell types from the 5 major regions (R1-R5) of the Drosophila midgut to study differences in cells in different regions. Methods: 3-7 day old female flies were dissected. Flies with GFP/YFP marking different cell types (using the GAL4-UAS system) were used to separate cells of the midgut.The midguts were dissociated with Elastase and FACS sorted using FACS AriaIII. RNA was extracted, amplified and sequenced. Whole midgut samples were sequenced on Illumina GAIIX and regional cell populations were sequenced on HiSeq2000. Methods:Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19). Methods: For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM). Results: More than 50% of the genome is expressed in the adult midgut (FlyAtlas- Chintapalli et al., 2007), of these genes about 50% (2457) were differentially expressed (DE) between all 4 cell types (ISCs, EBs, ECs and EEs) atleast 2 folds with 95% confidence Results: 159 genes that were specifically enriched in ISCs, 509 genes were specifically repressed in ISCs Conclusions: Our study represents the first detailed analysis of Drosophila intestinal cell transcriptomes, with biologic replicates, generated by RNA-seq technology.Our data facilitates comparative investigations of expression profiles of cells and reveals novel stem cell genes. Further region specific profiling adds precision to the analysis of variances in the midgut regions. We identify transcriptional regulators and regional transcription factors which modulate the midgut physiology. The dataset will be a great resource for hypothesis generation, tool building and fine tuned studies on the Drosophila midgut. mRNA profiles of Drosophila intestinal cells from whole midguts and midgut regions were generated by Deep Sequencing. Whole midgut profiles were generated in triplicates (Illumina GAIIx, 72 bp read length) and regional cell type profiles were genrated in duplicates (HiSeq 2000, 50bp read length).

Dataset Information

Transcriptional profiling of esg+-midgut progenitor cells expressing esgRNAi or UAS-esg AND of whole midgut tissue from flies overexpressing UAS-esg in enterocyte (EC) cells

Publications

Escargot maintains stemness and suppresses differentiation in Drosophila intestinal stem cells.

Similar Datasets

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