Single-cell sequencing of enteroendocrine cells (EEs) in Drosophila midgut.

Experiment ID:SRP200614
Technology:scRNA-Seq
Description:Enteroendocrine cells (EEs) in the intestinal epithelium have important endocrine functions, yet this cell lineage exhibits great local and regional variations that have hampered detailed characterization of EE subtypes. Through single cell RNA-sequencing analysis, combined with a collection of neuropeptide/receptor knock-in strains, here we provide a comprehensive analysis of cellular diversity, spatial distribution and transcription factor (TF) code of EEs in adult Drosophila midgut. We identify 10 major EE subtypes that totally produced 14 different classes of hormone peptides. Each EE on average co-produces 2-5 different classes of hormone peptides. Functional screen with subtype-enriched TFs suggests a combinatorial TF code that controls EE cell diversity, with class-specific TFs Mirr and Ptx1that respectively define two major classes of EEs, and regional TFs such as Esg, Drm, Exex and Fer1that further define regional EE identity. Our single-cell data should greatly facilitate Drosophila modeling of EE differentiation and function. Overall design: FACS sort EE cells using CG32547-KI-GAL4> uas-GFP line and perform 10X genomics single cell sequencing. Raw data was further processed by Seurat algorithm and EE subtypes were visualized by generating a t-distributed stochastic neighborhood embedding (t-SNE) plot.
DOI:10.1016/j.celrep.2019.11.048
Source:SRP200614 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogasterscRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX5979983FBbt:00049284 adult enteroendocrine precursor cellEE progenitor cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired1710576711575313860047310683.5Browse results
SRX5979983FBbt:00058000 adult class I enteroendocrine cellclass I-ap EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600140911653.5Browse results
SRX5979983FBbt:00058001 adult anterior midgut class I enteroendocrine cellclass I-a EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired1710576711575313860066610980Browse results
SRX5979983FBbt:00058002 adult middle midgut class I enteroendocrine cellclass I-m EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600150011579Browse results
SRX5979983FBbt:00058003 adult posterior midgut class I enteroendocrine cellNAFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600155411657Browse results
SRX5979983FBbt:00058004 adult anterior midgut class II enteroendocrine cellclass II-a EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600130111517Browse results
SRX5979983FBbt:00058005 adult middle midgut class II enteroendocrine cellNAFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600168811693Browse results
SRX5979983FBbt:00058006 adult posterior midgut class II enteroendocrine cellclass II-p EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired17105767115753138600100211269.5Browse results
SRX5979983FBbt:00058200 adult class III enteroendocrine cellclass III EE cellFBbt:00003138 adult midgut (Drosophila)intestineFBdv:00007026 mature adult stage (fruit fly)adult stage 5-7 days oldfemaleNANANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq X TenTHREE_PRIMECELL0paired1710576711575313860030410076.5Browse results

Showing 1 to 9 of 9 entries

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