|
| Status |
Public on Aug 24, 2020 |
| Title |
succinate_terminal ileum [4171_9] |
| Sample type |
SRA |
| |
|
| Source name |
succinate_terminal ileum
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
treatment: succinate
tissue: terminal ileum
cell type: primary epithelial cells
|
| Growth protocol |
primary cells
|
| 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 Novaseq6000 with a 2x150 paired-end kit standard run
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4171-AS-9-TAATACAG-ATATTCAC_S125
|
| 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
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al. 2019 - BioRxiv) Biological read: read2 - 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
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Aug 29, 2020 |
| Contact name |
Ken Lau |
| E-mail(s) |
ken.s.lau@vanderbilt.edu
|
| Phone |
6159366859
|
| Organization name |
Vanderbilt University
|
| Department |
Cell and Developmental Biology
|
| Street address |
2215 Garland Ave. MRBIV10475
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE145829 |
Ileum/colon treated with succinate |
| GSE145830 |
Ileal single-cell analysis in the context of inflammation focused on tuft cells |
|
| Relations |
| BioSample |
SAMN14173728 |
| SRA |
SRX7794023 |
