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| Status |
Public on May 08, 2024 |
| Title |
Glucose, TF13, biol rep 2 |
| Sample type |
SRA |
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| Source name |
Segatella bryantii TF1-3
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| Organism |
Segatella bryantii |
| Characteristics |
strain: TF1-3
tissue: liquid culture
treatment: Glucose
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| Extracted molecule |
total RNA |
| Extraction protocol |
Strains were grown in liquid minimal or modified DSMZ medium 330 containing different substrates, until they reached OD value of 0.3-0.5. 1.5 mL of each triplicate was removed and immediately combined with 3 mL of RNAprotect bacteria reagent (Qiagen). RNA was purified using RNeasy Mini Kit (Qiagen) with the on-column DNase treatment. The quantity of the isolated RNA was determined using Spark 10M multifunctional microplate reader with Quant-iTTM RNA Assay Kit (Thermo Scientific).
Illumina stranded TruSeq RNA library incl bacterial ribodepletion or NEBNext Ultra Directional RNA library prep kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
fastQC, Trimmomatic v0.39, BWA tool 0.7.17-r1188, FeatureCounts 2.0.0, R 4.1.2
Assembly: SPAdes genome assembler v3.15.3
Supplementary files format and content: raw counts for each sample
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| Submission date |
Mar 28, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Urška Murovec |
| E-mail(s) |
Urska.Murovec@bf.uni-lj.si
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| Organization name |
Biotechnical Faculty
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| Street address |
Jamnikarjeva 101
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| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
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| Platform ID |
GPL34345 |
| Series (1) |
| GSE262719 |
Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in two ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1 |
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| Relations |
| BioSample |
SAMN40648884 |
| SRA |
SRX24095518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8174449_GLU02_TF13_fc.txt.gz |
41.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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