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Sample GSM2644345 Query DataSets for GSM2644345
Status Public on Jul 10, 2017
Title Original_Prox1_1
Sample type SRA
 
Source name small intestine
Organism Mus musculus
Characteristics cell type: Prox1-GFP(+) cells
treatment: none
condition: sorted Prox1+ cells from Prox1-GFP reporter mouse
Growth protocol primary cell isolates from reporter mice
Extracted molecule total RNA
Extraction protocol epithelial cell preparation from proximal jejunum of mice
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single-cell GEMs for the "Original Prox1_1" and "Orginal_Prox1_2" samples, which are two technical replicates. 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. 2017. The remainder of the libraries were made using the Chromium Single Cell Instrument to generate single-cell GEMs using the Chromium Single Cell 3' Gel Bead and Library Kit from 10x Genomics (#120235, 120234, 120236, 120262).
For the "Original_Prox1_1" and "Original_Prox1_2" samples, the sequencing libraries were loaded at 2.1 pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98 bp Read1, 14 bp I7 Index, 8 bp I5 Index and 5 bp Read2. Note that these libraries were generated before the official launch of GemCode Single Cell 3’ Gel Bead and Library Kit. Thus 5bp UMI was used (the official GemCode Single Cell 3’ Gel Bead contains 10 bp UMI). For the remainder of the samples, the sequencing libraries were loaded at 2.1 pM on an Illumina Hiseq4000 with 2 × 75 paired-end kits using the following read length: 26 bp Read1, 8 bp I7 Index and 98 bp Read2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description GemCode
Data processing The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). For the old Prox1+ samples, UMI=5 was used for the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bam: bam files of individual samples; mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome
 
Submission date May 30, 2017
Last update date May 15, 2019
Contact name Kelley Yan
E-mail ky2004@cumc.columbia.edu
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)
GSE99457 Injury-inducible stem cell potential of the intestinal enteroendocrine lineage: single-cell mRNA-seq profiling
Relations
BioSample SAMN07178030
SRA SRX2869993

Supplementary file Size Download File type/resource
GSM2644345_original_Prox1_1_mex_mm10_barcodes.tsv.gz 2.5 Kb (ftp)(http) TSV
GSM2644345_original_Prox1_1_mex_mm10_genes.tsv.gz 212.8 Kb (ftp)(http) TSV
GSM2644345_original_Prox1_1_mex_mm10_matrix.mtx.gz 3.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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