|
| Status |
Public on Jan 01, 2020 |
| Title |
Control Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Control Replicate 3
|
| Organism |
Escherichia coli |
| Characteristics |
experimental condition: control
|
| Treatment protocol |
Planktonic (control) or biofilm (experiment)
|
| Growth protocol |
Total RNA was extracted from a five days old slide biofilms which were transferred to a fresh LB Miller broth daily. As planktonic cells we used cells detached from the biofilm from the last, 5th day passage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted RNAs were processed with Illumina’s Ribozero bacteria kit to deplete of rRNA
Illumina’s TruSeq stranded RNA LT kit was used for Library construction.
Samples were run on 1x75 chip on Illumina Nextseq 500 machine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control Replicate 3
|
| Data processing |
Raw Nextseq data quality checked and filtered
Hisat2 alignments to E. coli C reference
Stringtie counts of gene features
Deseq2 Analysis of differential abundance
Genome_build: ASM207922v1
Supplementary_files_format_and_content: Stringtie results, diff_exp_genes_padj.tsv
|
| |
|
| Submission date |
Jan 15, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Joshua P Earl |
| E-mail(s) |
jpe39@drexel.edu
|
| Organization name |
Drexel University College of Medicine
|
| Department |
Microbiology and Immunology
|
| Lab |
Ehrlich
|
| Street address |
245 N. 15th St.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19102 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE125110 |
Complete genome sequence of Escherichia coli C - old model organism with a new application in biofilm research |
|
| Relations |
| BioSample |
SAMN10748819 |
| SRA |
SRX5251271 |
