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Status |
Public on May 08, 2024 |
Title |
Starch, KHP1, biol rep 1 |
Sample type |
SRA |
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Source name |
Xylanibacter ruminicola KHP1
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Organism |
Xylanibacter ruminicola |
Characteristics |
strain: KHP1 tissue: liquid culture treatment: Starch
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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 |
GPL34344 |
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 |
SAMN40648909 |
SRA |
SRX24095479 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8174424_ST001_fc.txt.gz |
42.2 Kb |
(ftp)(http) |
TXT |
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