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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 24, 2020 |
| Title |
wt1 |
| Sample type |
SRA |
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| Source name |
wild type_terminal ileum
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
tissue: terminal ileum
cell type: primary epithelial cells
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| Growth protocol |
primary cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. 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 |
1238-AS-1-GCCAAT_S1
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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 (the filtering code available at: https://github.com/KenLauLab/scRNAseqQC).
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
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 |
Feb 24, 2020 |
| Last update date |
Aug 29, 2020 |
| 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 |
GPL19057 |
| Series (2) |
| GSE145827 |
WT/AtohKO/TNFdARE Ileum |
| GSE145830 |
Ileal single-cell analysis in the context of inflammation focused on tuft cells |
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| Relations |
| BioSample |
SAMN14173621 |
| SRA |
SRX7794003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4336558_counts_1238_1.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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