|
| Status |
Public on Jul 30, 2019 |
| Title |
wildtype replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_cell culture
|
| Organism |
Methanosarcina mazei Go1 |
| Characteristics |
genotype/variation: wild type
growth condition: nitrogen limitation
growth stage: mid exponential growth phase
|
| Growth protocol |
Cells of M. mazei wild type and mutant strains were grown under nitrogen limitation and harvested at mid exponential growth phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using TRI reagent following the manufacturer´s protocol followed by DNaseI treatment and phenol-chloroform precipitation
For cDNA synthesis both RNA fractions were poly(A)-tailed using poly(A) polymerase. This was followed by treatment with TAP to remove the 5' PPP structures. Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNAs. First strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are part of the 3' sequencing adapter. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis. For Illumina sequencing, the cDNAs were pooled in approximately equimolar amounts.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FastQ quality trimming using FastX (version 0.0.13) and a cut-off value of 20
Fastq to fasta conversion using FastX FastX (version 0.0.13)
PolyA removal and sitze filtering by READemption 0.2.3
Read alignment using READemption 0.2.3 and segemehl 0.1.7
Coverage calculation using READemption 0.2.3
Genome_build: NC_003901.1
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
Jul 30, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
[email protected]
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22308 |
| Series (1) |
| GSE85456 |
sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1 |
|
| Relations |
| BioSample |
SAMN05559791 |
| SRA |
SRX2012143 |
