|
| Status |
Public on Mar 01, 2022 |
| Title |
NT12393_1 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli strain culture
|
| Organism |
Escherichia coli |
| Characteristics |
strain: DE-COMM-4021
growth condition: LB media
|
| Growth protocol |
Samples were grown in LB media until an O.D. concentration of about 0.2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (QIAGEN) followed by Dnaze treatment
Samples were subject ro rRNA depletion prior to library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
batch: Galardini_HC3HYBGX9
|
| Data processing |
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the NC_000913.3 E. coli K-12 genome’s transcripts using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files starting with the “kallisto_” prefix contain the transcripts counts
|
| |
|
| Submission date |
Feb 04, 2019 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Pedro Beltrao |
| Organization name |
EMBL-EBI
|
| Street address |
Wellcome Genome Campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE126081 |
Transcriptome profiling in an Escherichia coli strain collection |
|
| Relations |
| BioSample |
SAMN10871939 |
| SRA |
SRX5332438 |
