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| Status |
Public on Oct 08, 2022 |
| Title |
RS_rep1 |
| Sample type |
SRA |
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| Source name |
Bacterial culture with resistant starch
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| Organism |
Bifidobacterium adolescentis |
| Characteristics |
strain: P2P3
genotype: wild type
conditions: 0.5% resistant starch
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| Growth protocol |
B. adolescentis P2P3 was anaerobically incubated in 50 mL of CM broth containing each carbon substrateds (0.5% GLC, SS, GRS, and RS) at 37'C with constant shaking. At the initial stationary phase, the cells were kept on ice to stop the growth.
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 ml of each culture centrifuged and total RNA was prepared using RNeasy Midi kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Austin, TX, USA) was used to remove bacterial rRNA from the total RNA samples.
Eight libraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq4000 instrument.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by featureCounts tool in the Subread package.
Counted values were normalised in the RPKM method.
Genome_build: Bifidobacterium adolescentis P2P3 GCF_003856735.1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Oct 08, 2019 |
| Last update date |
Oct 08, 2022 |
| Contact name |
Jungwook Park |
| E-mail(s) |
jjuwoogi@pusan.ac.kr
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| Organization name |
Pusan National University
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| Department |
Microbiology
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| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
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| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
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| Platform ID |
GPL27584 |
| Series (1) |
| GSE138588 |
Transcriptome analysis of Bifidobacterium adolescentis P2P3 cultivated with resistant starch |
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| Relations |
| BioSample |
SAMN12994701 |
| SRA |
SRX6965452 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4113973_RS1.txt.gz |
34.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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