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Status |
Public on Mar 17, 2021 |
Title |
Bifidobacterium longum W13R transcriptom sequence 3 |
Sample type |
SRA |
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Source name |
Bifidobacterium longum W13R total RNA
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Organism |
Bifidobacterium longum |
Characteristics |
strain: W13R
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing library. RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200-300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, Paired-end libraries were sequenced by Illumina NovaSeq 6000 sequencing (150bp*2.).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
LR20I10FP6_Clean_Data
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Data processing |
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic) Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters. To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05. To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05. Genome_build: Bifidobacterium_W13; https://www.ncbi.nlm.nih.gov/assembly/GCF_004936435.1 Supplementary_files_format_and_content: tab-delimited text files include gene count for each Sample
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Submission date |
Jan 03, 2021 |
Last update date |
Mar 17, 2021 |
Contact name |
Tang jiao |
E-mail(s) |
xutingtingga@sina.com
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Phone |
15536096530
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Organization name |
Tianjin University Of Science and Technology
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Street address |
Binhai new area
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City |
Tianjin |
ZIP/Postal code |
300450 |
Country |
China |
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Platform ID |
GPL29554 |
Series (1) |
GSE164163 |
Analysis of EPS structure and transcriptome expression difference of Bifidobacterium longum W13 and W13R |
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Relations |
BioSample |
SAMN17205490 |
SRA |
SRX9771103 |
Supplementary data files not provided |
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Raw data are available in SRA |
Processed data are available on Series record |
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