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| Status |
Public on May 04, 2017 |
| Title |
scFv_DKK1c_1 |
| Sample type |
SRA |
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| Source name |
scFv_DKK1c
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| Organism |
Mus musculus |
| Characteristics |
strain: Lgr5-eGFP-IRES-CreER
tissue: small intestine
cell type: Lgr5-eGFP(+) cells
treatment: Ad scFv-DKK1c
condition: Wnt GOF
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| Treatment protocol |
in vivo adenoviral intravenous injection into mice followed by small intestine tissue harvest, dissociation and FACS isolation
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| Growth protocol |
in vivo modulation of Wnt versus R-spondin in mice
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Dec 23, 2016 |
| 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 |
GPL19057 |
| Series (1) |
| GSE92865 |
Single-cell RNA-seq of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin modulation in vivo |
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| Relations |
| BioSample |
SAMN06177116 |
| SRA |
SRX2442221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2438926_scFv_DKK1c_1_mex_mm10_barcodes.tsv.gz |
4.9 Kb |
(ftp)(http) |
TSV |
| GSM2438926_scFv_DKK1c_1_mex_mm10_matrix.mtx.gz |
7.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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