|
| Status |
Public on Oct 01, 2017 |
| Title |
N2_2 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
strain: PCC 6803
treatment: 4 hours nitrogen starvation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from Synechocystis cultures grown in ammonium and switched for 4 hours to nitrogen depleted conditions were extracted using PGTX 95 RNA extraction protocol described in (Pinto et al., 2009). Samples for RNA-seq were obtained simultaneously from same cultures used for chromatin immunoprecipitation experiments. The quantity and quality of total RNA were evaluated using RNA electropherograms (Agilent 2100 Bioanalyzer, Agilent Technologies)
RNA libraries were prepared for sequencing using standard Ion Torrent PGM Machine protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
The resulting reads were trimmed to remove adaptor sequences and low quality base-calls, and were aligned to the Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1) using Torrent Mapper version 3.0.1 with the parameters -n 4 -v stage1 map1 map2 map3.
Abundance measurement was calculated using the HTSeq Python script HTSeq-count v.0.6.0 (Anders et al., 2014) with the parameters -m intersection-strict -s n0 -i locus-tag -t gene
Genome_build: Synechocystis sp. PCC 6803 genome (NCBI Reference sequence: NC_000911.1)
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each Sample
|
| |
|
| Submission date |
Mar 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
joaquín Giner Lamia |
| E-mail(s) |
[email protected]
|
| Organization name |
CBGP-Universidad Politecnica de Madrid
|
| Department |
Biotecnologia
|
| Lab |
Evolutionary Computational Biology
|
| Street address |
Campus de Montegancedo
|
| City |
Pozuelo de Alarcón |
| State/province |
Madrid |
| ZIP/Postal code |
28223 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23246 |
| Series (2) |
| GSE97289 |
Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 [RNA-Seq] |
| GSE97291 |
Elucidating the direct target regulon of NtcA during the early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 |
|
| Relations |
| BioSample |
SAMN06672155 |
| SRA |
SRX2694286 |
