|
| Status |
Public on Jul 14, 2021 |
| Title |
time_24_replicate_3 |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture
|
| Organism |
Nostoc sp. PCC 7120 = FACHB-418 |
| Characteristics |
strain: Nostoc sp. PCC 7120
time point (h): 24
|
| Treatment protocol |
Chloramphenicol 40 µg ml-1 was added to cultures at the beginning of the experiment
|
| Growth protocol |
Nostoc sp. PCC 7120 cultures were grown at 30ºC under continuous illumination (75 µE m-2 s-1) in BG11 medium ( Rippka, R. 1988 Methods Enzymol, 167, 3-27. ) supplemented with 10 mM NaHCO3. 1% (w/v) and bubbled with a mixture of CO2 and air (1% v/v).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by the hot phenol method as described in Luque et al. 2002 Mol Microbiol, 46, 1157-1167.
250 ng of total RNA from each culture were used to prepare libraries compatible with Illumina sequencing. Libraries were prepared using the Zymo-Seq RiboFree™ Total RNA Library Kit (Zymo, Cat. No. R3000) following the instructions of the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Genome_build: ASM970v1 available from https://www.ebi.ac.uk/ena/browser/view/GCA_000009705.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Oct 08, 2020 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Francisco José Romero-Campero |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Sevilla
|
| Department |
Institute for Plant Biochemistry and Photosynthesis
|
| Street address |
Americo Vespucio 49
|
| City |
Seville |
| ZIP/Postal code |
41092 |
| Country |
Spain |
| |
|
| Platform ID |
GPL29232 |
| Series (1) |
| GSE159215 |
Role of a cryptic tRNA gene operon in the recovery from translation stress |
|
| Relations |
| BioSample |
SAMN16395635 |
| SRA |
SRX9261229 |
