|
| Status |
Public on Aug 31, 2020 |
| Title |
M63_11 |
| Sample type |
SRA |
| |
|
| Source name |
culture population
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
growth medium: M63
growth temperature: 37°C
growth phase: late exponential phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cell cultures were mixed with the ice cold phenol ethanol solution (phenol: ethanol = 1: 9), and centrifuged at 16,000g for 5 min at 4°C. The pelleted cells were stored at -80°C for future use. Total RNAs were extracted using an RNeasy mini kit (QIAGEN Cat#74104), in accordance to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample Preparation Guide, Part#15031047 Rev. E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using RTA.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.38.
Trimmed reads were mapped to reference genome with Bowtie v1.1.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTseq v0.10.0.
Genome_build: ASM75055v1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Bei-Wen Ying |
| E-mail(s) |
ying.beiwen.gf@u.tsukuba.ac.jp
|
| Phone |
81 29 853 6633
|
| Organization name |
University of Tsukuba
|
| Street address |
1-1-1 Tennoudai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8572 |
| Country |
Japan |
| |
|
| Platform ID |
GPL27123 |
| Series (1) |
| GSE136101 |
Escherichia coli transcriptome reorganization caused by nutritional changes |
|
| Relations |
| BioSample |
SAMN12613424 |
| SRA |
SRX6747284 |
