|
| Status |
Public on Jul 30, 2012 |
| Title |
K. pneumoniae TSS 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cells at mid-log phase (OD600nm 0.5)
|
| Organism |
Klebsiella pneumoniae |
| Characteristics |
strain: MGH78578
strategy: TSS-Seq
genome build: K. pneumoniae MGH78578 reference genome and 5 plasmids (NC_009648, NC_009649, NC_009650, NC_009651, NC_009652, NC_009653)
|
| Treatment protocol |
The cell culture was treated with the RNAprotect reagent (Qiagen).
|
| Growth protocol |
E. coli K12 MG1655 and K. pneumoniae MGH78678 was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
The amplified cDNA libraries from two biological replicates for each E. coli and K. pneumoniae were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome and K. pneumoniae MGH78578 genome with 5 plasmids, respectively, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 50% of the strongest signal upstream of an annotated gene were considered as multiple TSSs.
|
| |
|
| Submission date |
Feb 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
dkim@unist.ac.kr
|
| Organization name |
UNIST
|
| Department |
Department of Chemical Engineering
|
| Lab |
Systems Biology Lab
|
| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15233 |
| Series (2) |
| GSE35821 |
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq] |
| GSE35822 |
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling |
|
| Relations |
| SRA |
SRX119993 |
| BioSample |
SAMN00789127 |
