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| Status |
Public on Jul 10, 2017 |
| Title |
Lgr5-eGFPneg_1 |
| Sample type |
SRA |
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| Source name |
small intestine
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| Organism |
Mus musculus |
| Characteristics |
cell type: Lgr5-eGFP(-) cells
treatment: none
condition: sorted cells from Lgr5-eGFP reporter mouse
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| Growth protocol |
primary cell isolates from reporter mice
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Chromium, v2
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| 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
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| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kelley Yan |
| E-mail(s) |
ky2004@cumc.columbia.edu
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| Organization name |
Columbia University
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| Department |
Medicine
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| Street address |
650 W. 168th St., BB8-801B
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE99457 |
Injury-inducible stem cell potential of the intestinal enteroendocrine lineage: single-cell mRNA-seq profiling |
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| Relations |
| BioSample |
SAMN07178048 |
| SRA |
SRX2869997 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2644349_Lgr5eGFP_neg_1_mex_mm10_barcodes.tsv.gz |
4.7 Kb |
(ftp)(http) |
TSV |
| GSM2644349_Lgr5eGFP_neg_1_mex_mm10_genes.tsv.gz |
212.8 Kb |
(ftp)(http) |
TSV |
| GSM2644349_Lgr5eGFP_neg_1_mex_mm10_matrix.mtx.gz |
5.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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