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| Status |
Public on Nov 14, 2020 |
| Title |
Bcel_InWAX rep2 |
| Sample type |
SRA |
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| Source name |
Bacterial cells
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| Organism |
Bacteroides cellulosilyticus |
| Characteristics |
strain: DSM 14838
carbon source: insoluble wheat arabinoxylan
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| Treatment protocol |
Different carbon sources
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| Growth protocol |
The defined medium was composed of sodium chloride (15 mM), dipotassium hydrogen phosphate (5 mM), monopotassium hydrogen phosphate (5 mM), sodium bicarbonate (9.5 mM), cysteine hydrochloride (4 mM), magnesium (II) chloride heptahydrate (0.1 mM), calcium (II) chloride dihydrate (54 µM), iron (II) sulphate heptahydrate (1.4 µM), hemin chloride (1.9 µM), vitamin K3 (5.8 µM), vitamin B12 (7.3 nM), and appropriate carbon source (Xylose:Arabinose or Insoluble wheat arabinoxylan) (5 mg/mL).
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| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were rapidly mixed with RNAprotect bacterial reagent and collected by centrifugation, as described by the manufacturer and used for subsequent RNA extraction. RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Contaminating DNA was removed in-column using NEB DNase I (Ipswich, MA), and the quality of the RNA was assessed by using a Bioanalyzer 2100 with a RNA 6000 Nano Assay Reagent kit from Agilent (Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Standard Illumina 4000 protocol was used for base calling
Sequenced reads were trimmed for adaptor sequence, and trimmed based bellow quality score of 30 using Trimmomatic
Reads were aligned to the genome using BowTie2. Reads mapping to gene features were counted using htseq-count based on Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765-1786, (2013).
Differential expression analysis was performed using the edgeR package in R and the TMM method was used for library normalization
Genome_build: Bacteroides cellulosilyticus DSM 14838
Genome_build: Bacteroides intestinalis DSM 17393
Genome_build: Bacteroides oleiciplenusYIT 12058
Supplementary_files_format_and_content: tab-delimited table containing raw counts and edgeR tab-delimited table comparissons of each species in the two different growth carbon sources
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| Submission date |
Nov 13, 2020 |
| Last update date |
Nov 15, 2020 |
| Contact name |
Gabriel Vasconcelos Pereira |
| E-mail(s) |
[email protected]
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| Phone |
2179795483
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| Organization name |
University of Michigan
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| Street address |
1150 West Medical Center Drive
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL29414 |
| Series (1) |
| GSE161471 |
Next generation sequencing (NGS) allows identification of differentially regulated genes during Bacteroides growth on xylose:arabinose and insoluble wheat arabinoxylan |
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| Relations |
| BioSample |
SAMN16793845 |
| SRA |
SRX9506078 |
| 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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