|
| Status |
Public on Oct 08, 2018 |
| Title |
RNA-seq of Escherichia coli strain 3 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq of Escherichia coli strain 3
|
| Organism |
Escherichia coli ATCC 8739 |
| Characteristics |
strain: ATCC 8739
|
| Treatment protocol |
NA
|
| Growth protocol |
The strain was streaked on nutrient broth (NB) agar plate from freezer stocks and grown at 37 °C for 24 h. Bacteria from a single colony were inoculated in 20 ml NB broth in 100 ml Erlenmeyer flask. The culture was grown in a 37 °C shaker for 16 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The extraction of total RNA from bacteria liquid culture was followed the invitrogen™ TRIzol reagent method (Thermo Fisher Scientific, 15596018). To determine the yield and quality of total RNA, Ultraviolet spectrophotometry (VASTECH, NV3000) method was used, followed by electrophoresis under an agarose EtBr gel. rRNA was removed from total RNA using Ribo-Zero rRNA Removal Kit (Illumina, MRZB12424) to purify mRNA
Strand Specific mRNA-seq library was generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, E7530L) following the manufacturer’s instructions. Index was added to each sample by NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (New England Biolabs, E7500L).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing was performed on Illumina Hiseq2500 with paired-end of 150bp.
The quality of sequencing data were assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Mapping to the reference of Escherichia coli ATCC8739 (NC_010468.1) was conducted by TopHat2.
Gene expressed value (FPKM) was called and normalized by EdgeR.
Genome_build: Escherichia coli ATCC8739 (NC_010468.1)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values of E3C_RNA
|
| |
|
| Submission date |
Jun 29, 2018 |
| Last update date |
Oct 08, 2018 |
| Contact name |
Jinsong Yan |
| E-mail(s) |
yanjsdmu@dmu.edu.cn
|
| Organization name |
Dalian Medical University
|
| Department |
Institute of Cancer Stem Cell
|
| Street address |
9 west section, Lvshun south road, Dalian, Liaoning Province, China
|
| City |
Dalian |
| ZIP/Postal code |
116044 |
| Country |
China |
| |
|
| Platform ID |
GPL25257 |
| Series (1) |
| GSE116453 |
Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing |
|
| Relations |
| BioSample |
SAMN09519151 |
| SRA |
SRX4325356 |
