|
| Status |
Public on Sep 08, 2020 |
| Title |
OP_MM565 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Methanosarcina mazei Go1 |
| Characteristics |
genotype: MM565 overproduction
|
| Treatment protocol |
-
|
| Growth protocol |
Cells of M. mazei vector control strain and MM565 overproducing strain were grown under optimal growth conditions (with puromycin in the media) 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
cDNA libraries for Illumina sequencing were constructed by vertis Biotechnologie AG, Germany (http://www.vertis‐biotech.com/) as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size‐fractionation step prior to cDNA synthesis. In brief, equal amounts of RNA samples were poly(A)‐tailed using poly(A) polymerase. Then, the 5'PPP structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5 ́‐phosphate of the RNA. First‐strand cDNA was synthesis by an oligo(dT)‐adapter primer and the M‐MLV reverse transcriptase. In a PCR‐based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20‐30 ng/μl. A library‐specific barcode for multiplex sequencing was part of a 3'‐sequencing adapter.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
[read trimming / clipping] cutdapt
[read mapping] READemption 0.3.5
[gene quantification ] READemption 0.3.5
[coverage calcutation] READemption 0.3.5
[differential gene expression analysis] DESeq2 1.6.3
Genome_build: NC_003901.1
Supplementary_files_format_and_content: Gene-wise read quantifications and nucleotide wise read coverages
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
Sep 08, 2020 |
| 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 |
GPL28591 |
| Series (1) |
| GSE151372 |
MM_0565 orchestrates CRISPR-based immunity in Methanosarcina mazei by transcriptional regulation of components essential for the adaptation |
|
| Relations |
| BioSample |
SAMN15047728 |
| SRA |
SRX8417153 |
