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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 15, 2017 |
| Title |
Colon/K562, replicate 1 |
| Sample type |
SRA |
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| Source name |
colon/K562
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain/background: C57Bl6
mouse genotype/variation: WT
mouse cell type: Colonic epithelial cells
human cell line: K562
treatment: None
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| Treatment protocol |
None.
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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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| Description |
Epithelial enrichment
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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: *_colon_rnaseq.csv: Comma-delimited tables, with cells and genes, as columns and rows.
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| Submission date |
Aug 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ken Lau |
| E-mail(s) |
ken.s.lau@vanderbilt.edu
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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 |
GPL19415 |
| Series (1) |
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| Relations |
| BioSample |
SAMN07510118 |
| SRA |
SRX3096214 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2743164_rep1_colon_rnaseq.csv.gz |
4.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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