 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 24, 2024 |
| Title |
SBC318 |
| Sample type |
SRA |
| |
|
| Source name |
MG1655
|
| Organism |
Escherichia coli |
| Characteristics |
cell type: MG1655
genotype: hipA7-pWJ445 (pTet-dCas9)
treatment: hipA7 lag abx
treatment: 2-day semisolid outgrowth after overnight (lag)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1456)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Barcode demultiplexing with custom python script
Remove flanking constant sequences with cutadapt 1.18
Reads aligned with bwa version 0.7.17
Features called with custom python scripts that check for PAM sequence
processed data files format and content: excel file with five tabs: sample overview, log2FC, p-value, significance (1=enriched, -1=depleted; FDR=0.1) and n_positions (number of crRNAs included per gene)
Assembly: Genbank U00096
|
| |
|
| Submission date |
Aug 23, 2024 |
| Last update date |
Aug 24, 2024 |
| 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) |
| GSE229435 |
Identification and genetic dissection of convergent persister cell states |
|
| Relations |
| BioSample |
SAMN43323629 |
| SRA |
SRX25816397 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
