|
| Status |
Public on Dec 19, 2017 |
| Title |
C29-Form-R2 |
| Sample type |
SRA |
| |
|
| Source name |
Hyperthermophilic archeaon
|
| Organism |
Thermococcus paralvinellae |
| Characteristics |
carbon source: Formate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were resuspended in TRIzol (Invitrogen) and total RNA was extracted using a Direct-zol RNA extraction kit (Zymo). RNA quantity was determined with Qubit fluorometry. RNA integrity was checked by a bioanalyzer and a Nanodrop spectrometer. Genewiz sequencing facilities performed rRNA removal, library construction, multiplexing and sequence the RNA with HiSeq2500, 2×100 Paired-End.
RNA libraries were prepared for sequencing using standard Illumina protocols by Genewiz Sequencing Facilities.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Formate
|
| Data processing |
Basecalls performed using Illumina CASAVA software
Sequenced reads were trimmed for adaptor sequence
Alligned to T. paralvinellae genome using STAR_2.5.1b
FeatureCounts (Liao et al., 2014) was used to assign aligned sequence reads to genomic features
Transcript per Million (TPM) were reported
Genome_build: NZ_CP006965.1 Refseq NCBI
Supplementary_files_format_and_content: tab-delimited text files include raw count or TPM values for each Sample
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Begum D. Topcuoglu |
| E-mail(s) |
topcuoglu.begum@gmail.com
|
| Organization name |
University of Massachusetts
|
| Department |
Microbiology
|
| Lab |
James F. Holden Lab
|
| Street address |
336 North Pleasant St., Apt:3B
|
| City |
Amherst |
| State/province |
MA |
| ZIP/Postal code |
01002 |
| Country |
USA |
| |
|
| Platform ID |
GPL23684 |
| Series (1) |
| GSE101078 |
Differential expression analysis of a hyperthermophilic archeaon Thermococcus paralvinellae upon hydrogen stress |
|
| Relations |
| BioSample |
SAMN07339302 |
| SRA |
SRX2993628 |
