|
| Status |
Public on Dec 05, 2018 |
| Title |
2: rfpC_WL |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Chlorogloeopsis fritschii PCC 9212 |
| Characteristics |
genotype: rfpC knockout mutant
antibiotic: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested, immediately frozen in liquid nitrogen, and stored at -80 oC. Total RNA was extracted with phenol and further purified with High Pure RNA Isolation Kit (Roche, Indianapolis,IN). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, Inc.)
Library was generated by using the TruSeq Stranded mRNA Kit with skipping of poy(A) selection (Illumina, Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Mapping against the Chlorogloeopsis fritschii PCC 9212 genome was performed using the BWA software package using modified scripts to accommodate the Illumina sequences as shown in Li and Durbin (2009). Bioinformatics 25, 1754-1760.
The resulting alignment files were further analyzed with self-developed scripts modified from Ludwig and Bryant (2011). Frontiers in Microbiology 2, 41. to extract expression levels for each gene.
Supplementary_files_format_and_content: Tab-delimited text files including reads of each gene in each sample. Locust tags are searchable on the JGI/IMG website.
|
| |
|
| Submission date |
Dec 04, 2018 |
| Last update date |
Dec 05, 2018 |
| Contact name |
Donald Ashley Bryant |
| E-mail(s) |
dab14@psu.edu
|
| Organization name |
The Pennsylvania State University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
403
|
| Street address |
Althouse
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL25893 |
| Series (1) |
| GSE123329 |
Chlorogloeopsis sp. PCC 9212 wild type and mutants in response to erythromycin and light colors |
|
| Relations |
| BioSample |
SAMN10519745 |
| SRA |
SRX5095209 |
