|
| Status |
Public on May 25, 2020 |
| Title |
Bulk Exponential Wild-Type E. coli |
| Sample type |
SRA |
| |
|
| Source name |
Liquid Culture
|
| Organism |
Escherichia coli |
| Characteristics |
library prep: Bulk
growth stage: Exponential
fixed: Yes
|
| Growth protocol |
Cells were diluted 1:100 or 1:50 into fresh media from an overnight culture and grown 2 hours (exponential) or 5 hours (stationary)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PETRI-seq libraries were subjected to in situ RT and ligations followed by cell lysis with detergent and proteinase K; Bulk libraries were prepared from fixed cells after lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
cDNA
prepared from the same cells as SB442
SB432_SB433_FC
|
| Data processing |
Barcode demultiplexing with cutadapt 1.18
UMIs extracted with UMI-tools version 0.5.5
Reads aligned with bwa version 0.7.17
Features called with featureCounts version 1.6.3
Final matrix generated by collapsing reads by UMI with a custom script in python 2.7.15
Genome_build: Genbank U00096; Genbank CP000255.1
Supplementary_files_format_and_content: tab-delimited txt
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
May 25, 2020 |
| Contact name |
Sydney B Blattman |
| E-mail(s) |
sb3292@columbia.edu
|
| Organization name |
Columbia University
|
| Lab |
Tavazoie Lab
|
| Street address |
1150 St. Nicholas Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE141018 |
Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing |
|
| Relations |
| BioSample |
SAMN14655909 |
| SRA |
SRX8151655 |
