|
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 (http://software.10xgenomics.com/single-cell/overview/welcome). 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 |
E-mail(s) |
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) |
GSE92865 |
Single-cell RNA-seq of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin modulation in vivo |
|
Relations |
BioSample |
SAMN06177113 |
SRA |
SRX2442210 |