|
| Status |
Public on Sep 26, 2016 |
| Title |
RsaFa rep2 |
| Sample type |
SRA |
| |
|
| Source name |
RsaFa
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
strain: NA1000
genotype: delta_rsaFa
|
| Growth protocol |
Cultures were grown to early log phase in PYE (peptone, yeast extract) rich media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and immediately added to ice-cold ethanol containing 5% (vol/vol) water-saturated phenol (pH 6.6). Total RNA was isolated using hot phenol and phenol/chloroform extractions.
5 ug of total RNA was treated with the ScriptSeq Complete Kit - Bacteria from Epicentre, an Illumina company (Cat# BB1224) for ribosomal RNA depletion and library generation with ScriptSeq Index Primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing data was mapped to the C. crescentus NA1000 reference genome sequence (GenBank accession number NC_011916.1) using Bowtie v1.1.1 with parameters -t -S -m 1
HTSeq-0.6.1p1 was used to quantify the number of counts per genomic feature
the counts per genomic feature output was converted to a .bam file, sorted, and indexed using samtools-0.1.19
RSeQC-2.3.9 was used to normalize the counts data and generate .wig files
Genome_build: GenBank accession number NC_011916.1
Supplementary_files_format_and_content: .wig files were generated using RSeQC-2.3.9. Values were normalized to 200,000,000. Each sample has a forward and reverse wig file associated with it. The first line of the wig files was modified for successful loading into the genome browser Mochiview.
|
| |
|
| Submission date |
Jun 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
K. Wesley Overton |
| Organization name |
Lawrence Livermore National Laboratory
|
| Department |
Biosciences and Biotechnology Division
|
| Street address |
7000 East Avenue
|
| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94550 |
| Country |
USA |
| |
|
| Platform ID |
GPL22063 |
| Series (1) |
| GSE83526 |
Two outer membrane proteins contribute to Caulobacter crescentus cellular fitness by preventing intracellular S-layer protein accumulation |
|
| Relations |
| BioSample |
SAMN05272550 |
| SRA |
SRX1865270 |
