|
| Status |
Public on Sep 17, 2024 |
| Title |
37 Planktonic M9 0.5%Glu Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
PHL628
|
| Organism |
Escherichia coli |
| Characteristics |
cell line: PHL628
cell type: planktonic
media type: M9
temperature: 37 °C
treatment: control
|
| Growth protocol |
PHL628 E coli cells were grown in either LB or M9 media supplemented with rhamnose or no additional sugar or 0.5% glucose, respectively. Cells were grown at 28 or 37 C for 48 h and harvested as biofilm cells or planktonic (swimming) cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAprotect (Qiagen) and Rneasy Plus kit (Qiagen). 1 µg or greater was sent for sequencing. rRNA removal by using Ribo-Zero Plus rRNA Depletion Kit (Illumina)
rRNA depleted samples were quantified and used for library preparation using the KAPA mRNA HyperPrep Kits (Roche). Following the library preparation, the final concentration of all of the libraries was measured using the Qubit dsDNA HS Assay Kit (Life Technologies), and the average library size was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-Seq data quality control, alignment, quantification, and statistics calculations were done using the workflow, using the reference genome and annotation of E. coli strain MG1655 from NCBI (genome sequence GenBank ID U00096.3; assembly ID GCA_000005845.2). Adapter sequences were trimmed with scythe v0.994, and low-quality ends were trimmed with sickle v1.33.5,17 HISAT2 v2.2.2.1 was used to align reads to the reference genome.20 Salmon v1.10.2 was used to quantify the expression of transcripts.35
Assembly: GCA_000005845
Supplementary files format and content: Tab-delimited text file of raw counts for each sample
|
| |
|
| Submission date |
Aug 08, 2024 |
| Last update date |
Sep 17, 2024 |
| Contact name |
Lisa Ryno |
| E-mail(s) |
lryno@oberlin.edu
|
| Organization name |
Oberlin College
|
| Department |
Chemistry and Biochemistry
|
| Street address |
119 Woodland St
|
| City |
Oberlin |
| State/province |
Ohio |
| ZIP/Postal code |
44074 |
| Country |
USA |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE274311 |
L-rhamnose globally changes the transcriptome of planktonic and biofilm Escherichia coli cells and modulates biofilm growth |
|
| Relations |
| BioSample |
SAMN43080171 |
| SRA |
SRX25638944 |
