|
| Status |
Public on May 03, 2013 |
| Title |
M. kandleri sRNAs + Tris-HCl pH8.8 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured organism
|
| Organism |
Methanopyrus kandleri AV19 |
| Characteristics |
protocol: sRNAs + Tris-HCl pH8.8
|
| Growth protocol |
Methanopyrus kandleri was grown in the Archaeenzentrum Regensburg (H. Huber, M. Thomm, K. Stetter) in a 300 l fermenter as described (Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB et al. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proceedings of the National Academy of Sciences of the United States of America 99(7): 4644-4649.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by SDS-lysis of the cell pellet and phenol/chloroform extraction and small RNAs were purified from total RNA using the MirVana RNA extraction kit (Ambion). Specific sample treatment protocols were followed as described in the samples section. The RNAs were treated with poly(A) polymerase to add a poly-A tail that was used for cDNA synthesis and were prepared with an Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001). Libary preparation and sequencing on an Illumina HiSeq2000 sequencer was performed at the Max-Planck Genomecentre Cologne.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
total small RNA (<200 bases)
Sample 5
10 µg of M. kandleri sRNA was incubated in a buffer containing 170 mM Tris-HCl pH 8.8 37° C for 3 hours to facilitate deacetylation of tRNA molecules
|
| Data processing |
Illumina Software CASAVA1.8 was used for basecalling and removal of adaptor sequences
Sequencing reads were trimmed ((i) removal poly-A tails, (ii) removal of sequences using a quality score limit of 0.05)) and mapped to the reference genome (GenBank: NC_003551) with CLC Genomics Workbench 6.0 (CLC Bio, Aarhus, Denmark). A total of 83338855 reads with an average length of 61 nt were obtained after trimming. The following mapping parameters were employed (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.5, similarity: 0.8). Reads below 15 nt were removed.
CLC Genomics Workbench 6.0 was utilized to determine the coverage for the individual RNA molecules.
GenBank: NC_003551
Genome_build: ASM718v1
Supplementary_files_format_and_content: tab-delimited text file including the coverage of mapped sequence reads at single nucleotide resolution for the M. kandleri genome.
|
| |
|
| Submission date |
Mar 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lennart Randau |
| E-mail(s) |
lennart.randau@mpi-marburg.mpg.de
|
| Organization name |
MPI for terrestrial microbiology
|
| Street address |
Karl-von-Frisch Strasse 10
|
| City |
Marburg |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16769 |
| Series (1) |
| GSE44979 |
Methanopyrus kandleri small RNA analysis |
|
| Relations |
| SRA |
SRX247373 |
| BioSample |
SAMN01942132 |
