|
| Status |
Public on Oct 23, 2018 |
| Title |
AK250_RydC_rep2_10min |
| Sample type |
SRA |
| |
|
| Source name |
overexpression of small RNA RydC
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12 substr. MG1655
genotype: rydC +/+
|
| Growth protocol |
Cells were grown in LB broth at 37 degrees Celsius for 1 hour 30 min and then RNA extracted after 10 min of RydC induction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the hot phenol method and ribosomal RNA removed using the Ribozero Bacteria kit (Illumina, CA)
Strand-specific librares were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'; DNA libraries for RNA-Seq were prepared with the Library Construction kit from Kapa Biosystems
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Libraries were quantitated by qPCR, pooled in equimolar concentration, and each pool sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq2000
TruSeq SBS sequencing kit version 3 was used
Fastq files were generated with Casava 1.8.2
Supplementary_files_format_and_content: files were analyzed using Rockhopper, where outputs include tab-delimited files with differentially expressed genes, non-codiing RNAs, and operons.
NC_000913_transcripts.txt: function of gene, start/stop for transcripts, expression levels, and q-value measuring differential expression between two experimental conditions
NC_000913_operons.txt: multi-gene operons
summary.txt: % of successfully aligned reads
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Oct 23, 2018 |
| Contact name |
Alisa Margaret King |
| E-mail(s) |
amking4@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Microbiology
|
| Lab |
Dr. Carin K. Vanderpool
|
| Street address |
601 S Goodwin Ave Room C211
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE121595 |
Next Generation Sequencing Facilitates Putative Target Identification for the Small RNA RydC |
|
| Relations |
| BioSample |
SAMN10267405 |
| SRA |
SRX4912070 |
