|
| Status |
Public on Jun 14, 2023 |
| Title |
1291_AS_1_Coffey: cell viability enrichment |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
prep: inDrop scRNA-seq
genotype: WT
tissue: colon
|
| Growth protocol |
primary cells, cell lines grown in standard conditions of C02 and DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse epithelial cell suspensions were obtained by EDTA chelation 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 using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were limited to the number denoted in the accompanying manuscript (Deronisha et al., 2023)
NextSeq: Technical read: Read 2 -UMI/Cell barcodes are positioned exactly as in (Klein et al., 2015) Biological read: read1 -transcript
NovaSeq:Technical read: Read1 - UMI/cell barcodes are positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - transcript
Assembly: Mouse: GRCm38.85; Human: GRCh38.p7
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows
|
| |
|
| Submission date |
Jun 09, 2023 |
| Last update date |
Aug 06, 2023 |
| 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 |
GPL19057 |
| Series (1) |
| GSE234620 |
A contamination focused approach for optimizing the single-cell RNA-seq experiment |
|
| Relations |
| BioSample |
SAMN35688819 |
| SRA |
SRX20650209 |
