|
| Status |
Public on Mar 04, 2015 |
| Title |
rfaH_37_2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Yersinia enterocolitica |
| Characteristics |
strain: Y11
growth phase: logarithmic phase
genotype/variation: rfaH mutant
temperature: 37°C
|
| Growth protocol |
Overnight cultures were diluted in fresh sterile LB broth and incubated at either 22°C or 37°C with vigorous shaking till the OD = 0.6 was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using the SV Total RNA Isolation System (Promega). The qualities of the isolated RNA, as well as the rRNA profiles were determined using Bioanalyzer (Agilent).
The ribosomal RNA was removed using Ribo-ZeroTM rRNA Removal Kit for Gram-negative Bacteria (Epicentre); RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Clean and merge reads using the adapter sequences and discarding the shortest ones; TOOL=SeqPrep; VERSION=v0.4-5-gb62f433; PARAMETERS=-f reads_1.fq -r reads_2.fq -1 reads_adapterClean_1.fq.gz -2 reads_adapterClean_2.fq.gz -s reads_adapterClean_pairedSingle.fq.gz -L 35 -y I -A CTGTCTCTTATAC -B CTGTCTCTTATAC
Filter out reads with homopolymers (>70% read length) and trim the bases at the end of the read with lower quality values (<20); TOOL=At-home perl script; PARAMETERS=--quality_threshold 20 --homopolymer_threshold 70
Filter reads aligning to rRNA or tRNA; TOOL=bowtie2; VERSION=2.1.0; PARAMETERS=-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -k 20 --local --score-min L,-0.6,-0.6
Alignment of the reads to reference genome; TOOL=Tophat2; VERSION=v2.0.8b; PARAMETERS= --bowtie1 --mate-inner-dist NNN --mate-std-dev NN -G organism.gtf --library-type fr-secondstrand --no-discordant
Estimation of gene FPKM values; TOOL=Cufflinks; VERSION=v2.0.2; PARAMETERS=--library-type fr-secondstrand --frag-bias-correct genome.fa -b genome.fa --GTF organism.gtf
Genome_build: NCBI GenBank | FR729477 | Yersinia enterocolitica subsp. palearctica Y11.
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM values for each sample separately
|
| |
|
| Submission date |
Mar 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Päivi Saavalainen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
TRIMM
|
| Street address |
Haartmaninkatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19851 |
| Series (1) |
| GSE66516 |
Role of RfaH in Yersinia enterocolitica O:3 |
|
| Relations |
| BioSample |
SAMN03387157 |
| SRA |
SRX897372 |
