|
| Status |
Public on Oct 01, 2011 |
| Title |
HS2336 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Histophilus somni |
| Characteristics |
strain: 2336
|
| Treatment protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's protocol. Total RNA preparations were treated with RNase-free DNAse (Invitrogen; Carlsbad, CA). We used the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and determined the RIN of total RNA to be greater than 8. MICROBExpress Kit (Ambion) that specifically removes rRNAs was used for mRNA enrichment. Small RNAs (i.e., tRNA and 5S rRNA) are not removed with this enrichment step (confirmed by Bioanalyzer).
|
| Growth protocol |
H. somni 2336 was propagated on three TSA-blood plates for 16 hr till a fresh lawn of cells was visible. The plates were washed with brain heart infusion (BHI) broth and the culture was adjusted to an OD620nm=0.8, supplemented with RNAprotect reagent, and cells harvested by centrifugation and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used 100 ng enriched mRNA with Illumina mRNA-Seq sample preparation kit (Illumina,San Diego, CA) for library construction following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Perl script was written to convert Illumina reads into fastq format. Solexa fastq format was then converted to Sanger fastq format using the script 'fq_all2std.pl' from MAQ. All the reads in sanger fastq format were mapped to the Histophilus somni 2336 genome sequence (GenBank Accession number. CP000947) using the alignment tool Bowtie allowing for a maximum of two mismatches. The reads that map to more than one location were discarded. Samtools was used for data format conversion into SAM/BAM format and to generate alignment results in a pileup format. Subsequent analysis was performed using in house perl scripts.
|
| |
|
| Submission date |
May 26, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Ranjit Kumar |
| E-mail(s) |
rk228@msstate.edu
|
| Phone |
6623257706
|
| Organization name |
MSU
|
| Department |
Dept of Basic Science
|
| Lab |
Mark Lawrence
|
| Street address |
240 Wise Center Drive,PO Box 6100
|
| City |
starkville |
| State/province |
MS |
| ZIP/Postal code |
39762 |
| Country |
USA |
| |
|
| Platform ID |
GPL13659 |
| Series (1) |
| GSE29578 |
RNA-Seq based transcriptional map of bovine respiratory disease pathogen 'Histophilus somni 2336' |
|
| Relations |
| BioSample |
SAMN02198295 |
