|
| Status |
Public on May 08, 2024 |
| Title |
Homogalacturonan, KHP1, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Xylanibacter ruminicola KHP1
|
| Organism |
Xylanibacter ruminicola |
| Characteristics |
strain: KHP1
tissue: liquid culture
treatment: Homogalacturonan
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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
|
| |
|
| Submission date |
Mar 28, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Urška Murovec |
| E-mail(s) |
Urska.Murovec@bf.uni-lj.si
|
| Organization name |
Biotechnical Faculty
|
| Street address |
Jamnikarjeva 101
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN40648904 |
| SRA |
SRX24095482 |
