|
| Status |
Public on Nov 29, 2017 |
| Title |
pH4_1h rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole transcriptome
|
| Organism |
Lacticaseibacillus rhamnosus GG |
| Characteristics |
ph: 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq RNA Sample Preparation Kit (Illumina) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Read data were aligned on the reference genome sequence.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Base-calling by the MiSeq platform
Alignment by Bowtie software
Using R packages for DEG analysis
Genome_build: Lactobacillus rhamnosus GG (ATCC 53103, RefSeq ID: NC_013198.1)
Supplementary_files_format_and_content: CSV file of normalized RPKM value from edgeR for every samples.
|
| |
|
| Submission date |
Nov 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
kucsbl submitter |
| E-mail(s) |
kucsbl.group@gmail.com
|
| Organization name |
Korea University
|
| Department |
Department of Biotechnology
|
| Lab |
Computational and Synthetic Biology Laboratory
|
| Street address |
Anamdong 5-ga, Seongbuk-gu
|
| City |
Seoul |
| State/province |
Seoul |
| ZIP/Postal code |
KS013 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24302 |
| Series (1) |
| GSE107337 |
RNA-seq analysis of Lactobacillus at acidic stress |
|
| Relations |
| BioSample |
SAMN08098216 |
| SRA |
SRX3422361 |
