|
| Status |
Public on Jul 03, 2020 |
| Title |
B. subtilis PY79 (OD0.5-OD6.0) |
| Sample type |
SRA |
| |
|
| Source name |
Bacillus Genetic Stock Center (BGSC)
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
replicate: 2
|
| Treatment protocol |
For heat shock, 47C for 8 minutes.
|
| Growth protocol |
Liquid LB medium at 37C with shaking, starting from diluted overnight culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were fixed in cold formaldehyde overnight, permeabilized with Tween-20 and Lysozyme, then subjected to in-situ polyadenylation, reverse transcription and barcode ligation reactions. After barcoding, cells were lysed with proteinase K and barcoded cDNA was extracted on streptavidin beads
Barcoded cDNA bound to streptavidin C1 beads had a 3' adapter appended through template switching, followed by qPCR amplification and fragmentation with WGS Fragmentation Mix (Enzymatics). Adapters for Illumina sequencing were then appended by the final round of PCR.
SPLiT-seq, first barcode records sample identity
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: microSPLiT
The data preprocessing and alignment was performed using a modified SPLiT-seq pipeline (https://github.com/Alex-Rosenberg/split-seq-pipeline). Modifications: using STAR with the splicing isoform detection swiwwe usededt the hioutghoutest-scored multimapping re. We also keptwening a ctional count based on the number igninggood alignments, since bacterial genomes are known to contain overlapping CDSs.
Genome_build: ASM904v1.45 and ASM80076v1.37 from EnsemblBacteria
Supplementary_files_format_and_content: Cell by gene matrix (with cells above threshold 200 UMI/cell); Gene names; Cell annotations (barcode and well for heat shock data, OD for B.subtilis growth curve). For B. Subtilis growth curve, only mRNA are included in the cell-by-gene matrix.
Supplementary_files_format_and_content: For the heat-shock data, barcodes in wells 1-24 belong to heat-shocked cells and in wells 25-48 belong to control cells.
|
| |
|
| Submission date |
Jun 06, 2020 |
| Last update date |
Jul 04, 2020 |
| Contact name |
Anna Kuchina |
| Organization name |
University of Washington
|
| Department |
Electrical and Computer Engineering
|
| Lab |
Georg Seelig
|
| Street address |
185 Stevens Way, Paul Allen Center – Room AE100R
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL28092 |
| Series (1) |
| GSE151940 |
Microbial single-cell RNA sequencing by split-pool barcoding |
|
| Relations |
| BioSample |
SAMN15154359 |
| SRA |
SRX8485152 |
