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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 23, 2018 |
| Title |
Replicate 2 |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Mus musculus |
| Characteristics |
treatment: none
cell type: epithelial enrichment
strain: C57Bl6
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| Growth protocol |
primary cells/cell line mix
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNAse dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths
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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 |
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis, and barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows
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| Submission date |
May 04, 2018 |
| Last update date |
Feb 27, 2020 |
| Contact name |
Ken Lau |
| E-mail(s) |
[email protected]
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| Phone |
6159366859
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| Organization name |
Vanderbilt University
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| Department |
Cell and Developmental Biology
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| Street address |
2215 Garland Ave. MRBIV10475
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE114044 |
Colonic single-cell RNA-seq experiment |
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| Relations |
| Reanalyzed by |
GSM4363334 |
| BioSample |
SAMN09070527 |
| SRA |
SRX4042029 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3131536_colon_bio2.csv.gz |
3.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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