|
| Status |
Public on Mar 16, 2021 |
| Title |
BW25113 slyA Mutant_ECMS2_1 |
| Sample type |
SRA |
| |
|
| Source name |
E coli BW25113 slyA Mutant
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
genotype: slyA Mutant
age: overnight log phase growth
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Each strain of E coli BW25113 and E coli BW25113 slyA Mutant were grown to log phase (16hrs) overnight in Nutrient broth at 37 degree celcius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy minikit (Qiagen), and residual DNA was digested using the RNase-free DNase kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQC used to examine quality of raw reads
Trimmomatic was used to trim the Illumina specific adaptors and primers
STAR Aligner was used to index and align the reads to the BW25113 reference genome
HTSeq was used to count the numbers of times that the gene reads aligned to the reference
DESeq2 was used to compare the difference in the number of times the genes showed up in each sample
Genome_build: Genbank Reference sequence CP009273.1 was used in the indexing and alignment step
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
processed data files contains data for 121 genes and contains the following:
__alignment_not_unique 1808510
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 17, 2021 |
| Contact name |
Derrick Scott |
| Organization name |
Delaware State University
|
| Street address |
1200 n dupont hwy
|
| City |
dover |
| State/province |
Delaware |
| ZIP/Postal code |
19901 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE168963 |
Transcriptome RNA Sequencing Data Set of Differential Gene Expression in Escherichia Coli BW25113 SlyA Wild Type and Mutant Strains |
|
| Relations |
| BioSample |
SAMN18315613 |
| SRA |
SRX10348174 |
