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| Status |
Public on Jul 27, 2023 |
| Title |
eBW4, scRNAseq |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organisms |
Pseudomonas aeruginosa; Escherichia coli; Bacillus subtilis |
| Characteristics |
cell type: bacterial cells
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| Treatment protocol |
Cells were treated for each experiment as described in M3-Seq.
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| Growth protocol |
Cells were grown in LB media for 90 minutes, then treated with antibiotics or phage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were fixed in formaldehyde overnight, washed 2x, permeabilized using lysozyme, then washed 2x more. Cells then underwent an in-situ RT for r1 indices, after which the cells were pooled. Cells were then loaded onto the 10X scATAC platform. Following droplet generation, emulsions were broken, cells were lysed, and processed according to the M3-Seq protocol.
Briefly, RNA was stripped from DNA using RNase H, followed by second strand synthesis using random primers. Following second strand synthesis, DNA library was tagmented, amplified, and then in vitro transcribed. The library was rRNA-depleted, and then reverse transcribed using a P5-specific primer. The final library was amplified and indexed using indexing primers.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
M3-Seq
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| Data processing |
The demultiplexing, alignment, and data processing were performed from the raw basecalls using custom scripts here: https://github.com/brwaang55/m3seq_scripts . Raw basecall files were converted into a single ended bam file as loaded here.
Assembly: B. subtilis 168 (assembly ASM904v1, assembly accession GCF_000009045.1); E. coli MG1655 (assembly ASM584v2, assembly accession GCF_000005845.2); E. coli Nissle (assembly ASM71459v1, assembly accession GCF_000714595.1).
Supplementary files format and content: *.csv: Comma-separated gene name files, cell annotation files, and matrix files.
Supplementary files format and content: bw_scifi*.samples.csv include demultiplexing information (barcodes, etc.).
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| Submission date |
May 08, 2023 |
| Last update date |
Jul 27, 2023 |
| Contact name |
Bruce Wang |
| E-mail(s) |
bw21@princeton.edu
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| Organization name |
Prinnceton University
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| Street address |
Lewis Thomas Lab
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
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| Platform ID |
GPL33391 |
| Series (1) |
| GSE231935 |
Massively-parallel Microbial mRNA Sequencing (M3-Seq) reveals heterogenous behaviors in bacteria at single-cell resolution |
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| Relations |
| BioSample |
SAMN34998525 |
| SRA |
SRX20253198 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7306273_bw_scifi9_1_all_samples.csv.gz |
4.5 Kb |
(ftp)(http) |
CSV |
| GSM7306273_bw_scifi9_1_samples.csv.gz |
1.6 Kb |
(ftp)(http) |
CSV |
| GSM7306273_bw_scifi9_2_samples.csv.gz |
1.6 Kb |
(ftp)(http) |
CSV |
| GSM7306273_cell_index_scifi10_BS168_USA300_25.csv.gz |
624.3 Kb |
(ftp)(http) |
CSV |
| GSM7306273_cell_index_scifi10_MG1655_25.csv.gz |
725.5 Kb |
(ftp)(http) |
CSV |
| GSM7306273_cell_index_scifi9_BS168_USA300_25.csv.gz |
593.2 Kb |
(ftp)(http) |
CSV |
| GSM7306273_cell_index_scifi9_MG1655_25.csv.gz |
586.2 Kb |
(ftp)(http) |
CSV |
| GSM7306273_expression_filtered_scifi10_BS168_USA300_25.csv.gz |
7.9 Mb |
(ftp)(http) |
CSV |
| GSM7306273_expression_filtered_scifi10_MG1655_25.csv.gz |
7.1 Mb |
(ftp)(http) |
CSV |
| GSM7306273_expression_filtered_scifi9_BS168_USA300_25.csv.gz |
11.0 Mb |
(ftp)(http) |
CSV |
| GSM7306273_expression_filtered_scifi9_MG1655_25.csv.gz |
8.1 Mb |
(ftp)(http) |
CSV |
| GSM7306273_gene_index_scifi10_BS168_USA300_25.csv.gz |
58.9 Kb |
(ftp)(http) |
CSV |
| GSM7306273_gene_index_scifi10_MG1655_25.csv.gz |
36.4 Kb |
(ftp)(http) |
CSV |
| GSM7306273_gene_index_scifi9_BS168_USA300_25.csv.gz |
58.9 Kb |
(ftp)(http) |
CSV |
| GSM7306273_gene_index_scifi9_MG1655_25.csv.gz |
36.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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