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Sample GSM6077219 Query DataSets for GSM6077219
Status Public on Nov 27, 2023
Title Total intestinal epithelial cell sample (Mouse_scRNA-seq)
Sample type SRA
 
Source name small intestine
Organism Mus musculus
Characteristics cell type: FACS sorted intestinal epitheilal cells (CD45-, EpCAM+)
tissue: small intestine
strain: Lgr5DTR-GFP
developmental stage: adult
Extracted molecule total RNA
Extraction protocol The intestine was washed, cut into 30 pieces of equal length, and incubated with media supplemented with 5mM EDTA and 10mM DTT at 37°C with 5% CO2. Cells were triturated, strained, washed, and labelled with barcodes unique to each segment using the MULTIseq method. The target population was FACS sorted.
10x libraries were prepared for sequencing using standard 10x genomics protocols adaoted for MULTIseq as described in McGinnis et al. Nat Methods 2019.
Chromium Single Cell 3'
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Chromium single cell data
Data processing 10x Genomics cellranger count used to produce the filtered gene count matrix files from fastq files
deMULTIplex v 1.0.2 was used to align MULTIseq barcodes and demultiplex the datasets from the "BAR" fastq files
Assembly: mouse mm10-3.0.0 reference (10x Genomics)
Supplementary files format and content: Matrix, barcodes, and features tables with raw gene counts for every gene and every sample
 
Submission date Apr 29, 2022
Last update date Nov 27, 2023
Contact name Rachel Klapper Zwick
E-mail(s) Rachel.Zwick@ucsf.edu
Organization name University of California, San Francisco
Lab Ophir Klein Lab
Street address 513 Parnassus Ave.
City San Francisco
ZIP/Postal code 94143
Country USA
 
Platform ID GPL24247
Series (2)
GSE201855 Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains [Mouse_scRNA-seq]
GSE201859 Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains
Relations
BioSample SAMN27622567
SRA SRX15048514

Supplementary file Size Download File type/resource
GSM6077219_IEC_barcodes.tsv.gz 38.9 Kb (ftp)(http) TSV
GSM6077219_IEC_features.tsv.gz 118.4 Kb (ftp)(http) TSV
GSM6077219_IEC_matrix.mtx.gz 90.4 Mb (ftp)(http) MTX
GSM6077219_IEC_mux_barcode_segment.tsv.gz 59.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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