|
| Status |
Public on Jul 22, 2020 |
| Title |
S. cerevisiae Aligned to C. albicans Genome |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
treatment: 42°C Heat Shock
|
| Treatment protocol |
Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.
|
| Growth protocol |
Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 12
Processed file required for samples 10 and 11 analysis. Contains genes misaligned to the wrong genome for use in species mixing.
|
| Data processing |
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.
Supplementary_files_format_and_content: Tab delimited raw count table with gene and barcode ids (Samples 3 and 4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Samples 14 and 15)
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Ryan Patrick Dohn |
| E-mail(s) |
dohnr@uchicago.edu
|
| Phone |
8479618001
|
| Organization name |
University of Chicago
|
| Department |
Department of Medicine
|
| Lab |
Basu
|
| Street address |
5841 S. Maryland Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE154515 |
mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces Cerevisiae and Candida Albicans |
|
| Relations |
| BioSample |
SAMN15545097 |
| SRA |
SRX8740237 |
