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Sample GSM2438915 Query DataSets for GSM2438915
Status Public on May 04, 2017
Title Fc_2
Sample type SRA
Source name Fc
Organism Mus musculus
Characteristics strain: Lgr5-eGFP-IRES-CreER
tissue: small intestine
cell type: Lgr5-eGFP(+) cells
treatment: Ad Fc
condition: control intestinal stem cell population without perturbation
Treatment protocol in vivo adenoviral intravenous injection into mice followed by small intestine tissue harvest, dissociation and FACS isolation
Growth protocol in vivo modulation of Wnt versus R-spondin in mice
Extracted molecule total RNA
Extraction protocol epithelial cell preparation from proximal jejunum
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al.
Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting ( 5bp UMI tags were extracted from Read2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Submission date Dec 23, 2016
Last update date May 15, 2019
Contact name Kelley Yan
Organization name Columbia University
Department Medicine
Street address 650 W. 168th St., BB8-801B
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL19057
Series (1)
GSE92865 Single-cell RNA-seq of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin modulation in vivo
BioSample SAMN06177113
SRA SRX2442210

Supplementary file Size Download File type/resource
GSM2438915_Fc_2_mex_mm10_barcodes.tsv.gz 4.7 Kb (ftp)(http) TSV
GSM2438915_Fc_2_mex_mm10_matrix.mtx.gz 7.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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