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Series GSE92332 Query DataSets for GSE92332
Status Public on Nov 06, 2017
Title A single-cell survey of the small intestinal epithelium
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To understand the diversity of cellular states within mouse intestinal epithelial tissue, we obtained whole intestines from wild type mice, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.
Overall design To understand normal tissue homeostasis, untreated cells were profiled, while to investiage the impact of enteric pathogens on epithelial cells, mice infected with both Salmonella Enterica and the parasitic worm H. polygyrus were profiled using both 3'-droplet-based and full length plate-based single-cell RNAseq. RANKL-mediated differentiation of organoid cultures were used to sequence the rare intestinal M cell, these were then compared to M cells obtained from the in vivo follicle associated epithelium (FAE).

Please note that the FAE_UMIcounts.txt file has been updated on May 7th 2020.
Contributor(s) Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garret WS, Shi HN, Rozenblatt-Rosen O, Yilmaz O, Xavier R, Regev A
Citation(s) 29144463, 30089906
Submission date Dec 13, 2016
Last update date May 10, 2020
Contact name Adam Haber
Organization name Harvard T. H. Chan School of Public Health
Street address 665 Huntington Ave, HSPH Building 1, Room 305
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (1957)
GSM2425828 Salmonella/H.poly Cell 1
GSM2425829 Salmonella/H.poly Cell 2
GSM2425830 Salmonella/H.poly Cell 3
BioProject PRJNA357261
SRA SRP095033

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE92332_AtlasFullLength_TPM.txt.gz 25.8 Mb (ftp)(http) TXT
GSE92332_EEC_UMIcounts.txt.gz 1.1 Mb (ftp)(http) TXT
GSE92332_FAE_UMIcounts.txt.gz 9.6 Mb (ftp)(http) TXT
GSE92332_LargeCellSort_UMIcounts.txt.gz 24.1 Mb (ftp)(http) TXT
GSE92332_Org_RANKL_UMIcounts.txt.gz 11.2 Mb (ftp)(http) TXT
GSE92332_RAW.tar 322.8 Mb (http)(custom) TAR (of MTX, TSV)
GSE92332_Regional_UMIcounts.txt.gz 21.2 Mb (ftp)(http) TXT
GSE92332_SalmHelmFullLength_TPM.txt.gz 6.4 Mb (ftp)(http) TXT
GSE92332_SalmHelm_UMIcounts.txt.gz 17.2 Mb (ftp)(http) TXT
GSE92332_SalmonellaInfect_UMIcounts.txt.gz 11.6 Mb (ftp)(http) TXT
GSE92332_Supplementary_files_format_and_content_readme.txt.gz 695 b (ftp)(http) TXT
GSE92332_atlas_UMIcounts.txt.gz 15.2 Mb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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