|
| Status |
Public on Jun 16, 2022 |
| Title |
sample.ginkgo.11588398 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
temperature: 37.0 celsius
timepoint: 5.0 hour
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Magjet RNA extraction kit (Thermo) according to manufacturer's instructions.
RNA quality was assessed using Tapestation (Agilent). KAPA RNA Hyperprep kit (Roche) was used for ribosomal RNA depletion and Illumina compatible library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
None
|
| Data processing |
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_IcaR_Gate/1
|
| |
|
| Submission date |
Jun 13, 2022 |
| Last update date |
Jun 28, 2022 |
| Contact name |
Joshua Urrutia |
| E-mail(s) |
jurrutia@tacc.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Texas Advanced Computing Center
|
| Lab |
Life Sciences Computing
|
| Street address |
10100 Burnet Rd
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78758 |
| Country |
USA |
| |
|
| Platform ID |
GPL26592 |
| Series (1) |
| GSE206047 |
Transcriptional Response to Inducers for E. coli and B. subtilis |
|
| Relations |
| BioSample |
SAMN29017962 |
| SRA |
SRX15693068 |
