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| Status |
Public on Nov 22, 2021 |
| Title |
A6WD3 |
| Sample type |
SRA |
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| Source name |
probiotics isolated from human feces
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| Organism |
Bifidobacterium animalis |
| Characteristics |
growth: growth in MRSc medium at the stationary phase
source: feces
strain: Bifidobacterium animalis subsp. lactis A6
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using the TURBO DNA-free Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava 1.8 for base-calling and Phred score calculation
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: Bowtie2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
May 05, 2021 |
| Last update date |
Nov 22, 2021 |
| Contact name |
Hui Wang |
| E-mail(s) |
wanghui1201@cau.edu.cn
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| Organization name |
China Agricultural University
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| Street address |
No. 17 Tsing Hua East Road, HaiDian District
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| City |
Beijing |
| ZIP/Postal code |
100085 |
| Country |
China |
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| Platform ID |
GPL30086 |
| Series (1) |
| GSE173957 |
Growth phase-associated changes in the proteome and transcriptome of Bifidobacterium animalis subsp. lactis A6 |
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| Relations |
| BioSample |
SAMN19026188 |
| SRA |
SRX10787741 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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