|
| Status |
Public on Dec 05, 2019 |
| Title |
S2_RNAseq_2 |
| Sample type |
SRA |
| |
|
| Source name |
Neural strain cells
|
| Organism |
Methanococcus maripaludis |
| Characteristics |
strain: S2
genotype: wild type
growth period: mid-log phase
|
| Growth protocol |
The Methanococcus maripaludis strains were grew until mid-log phase and harvested
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 3 ug of total RNA was used for RNA-seq and 5 ug of total RNA was used for Term-seq .
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
S2_2
FPKM of RNA_seq.txt
|
| Data processing |
For RNA-seq raw reads of fastq format were firstly processed through in-house perl scripts to remove low quality reads and those containing adapter or ploy-N. The clean reads were mapped against predicted transcripts of the M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/) by using Bowtie2-2.2.3. HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and then the FPKM was calculated based on the gene length and mapped read counts.
Genome_build: M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample of RNA_seq. The TESs for each stain identified in duplicate and the average head reads (reads number of -1 site minus +1 site) and ratio1_1 (ratio of -1 site to +1 site) are listed in tab-delimited text files.
|
| |
|
| Submission date |
Dec 03, 2019 |
| Last update date |
Dec 06, 2019 |
| Contact name |
Lei Yue |
| E-mail(s) |
yuelei14@mails.ucas.edu.cn
|
| Organization name |
Chinese academy of science
|
| Department |
Institute if Microbiology
|
| Lab |
Anaerobes research group
|
| Street address |
NO.1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL27854 |
| Series (1) |
| GSE141346 |
RNA-seq and Term-seq of Methanococcus maripaludis wild-type strain S2 and aCPSF1 depletion strain â–˝aCPSF1 |
|
| Relations |
| BioSample |
SAMN13477372 |
| SRA |
SRX7266835 |
