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| Status |
Public on May 07, 2024 |
| Title |
B. lactis |
| Sample type |
SRA |
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| Source name |
Culture
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| Organism |
Bifidobacterium animalis subsp. lactis |
| Characteristics |
tissue: Culture
cell type: bacterial cell
disease state: Sample control
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| Extracted molecule |
total RNA |
| Extraction protocol |
The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
BLACTIS
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| Data processing |
Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample
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| Submission date |
Feb 08, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Alex Martínez Ascensión |
| E-mail(s) |
alexmascension@gmail.com
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| Organization name |
Biogipuzkoa HRI
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| Street address |
P/ Doctor Begiristain
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| City |
Donostia |
| State/province |
Gipuzkoa |
| ZIP/Postal code |
20014 |
| Country |
Spain |
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| Platform ID |
GPL34172 |
| Series (1) |
| GSE255317 |
Study of microbial species in extracellular vesicles of sclerosis multiple patients |
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| Relations |
| BioSample |
SAMN39875252 |
| SRA |
SRX23571133 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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