|
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
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|
|
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 |