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| Status |
Public on Dec 01, 2024 |
| Title |
Gastric Mucin Oligosaccharides replicate 1 |
| Sample type |
SRA |
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| Source name |
bacterial
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| Organism |
Erysipelotrichaceae bacterium DSM 116809 |
| Characteristics |
cell type: bacterial
genotype: wild type
treatment: 10mg/ml gastric mucin oligosaccharides
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| Treatment protocol |
At substrate-respective growth densities, cells were pelleted, resuspended in 1 mL of RNAprotect (Qiagen) and frozen at -80C until extraction.
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| Growth protocol |
Hoskinsella mucinolytica DSM116809 was grown in biological replicate 5ml cultures to mid-log phase under anaerobic conditions at 37ºC on Depleted Medium (DM) containing either N-acetylgalactosamine, N-acetylglucosamine and cellobiose at 5mg/ml or gastric mucin oligosaccharides at 10mg/ml.
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| Extracted molecule |
other |
| Extraction protocol |
Samples were thawed and treated with 500 uL buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA at pH 8), 210 uL of 20% SDS and 500 uL phenol:choloroform:isoamyl alcohol (125:24:1, pH 4.3) followed by bead beating for 3 minutes and centrifugation. Aqueous phase samples were subjected to a second phenol:choloroform:isoamyl alcohol mix and centrifugation prior to being precipitated with isopropanol, pellets resuspended, treated with DNaseI (NEB), and re-precipitated. Pellets were retained and resuspended in ultra pure water. Total RNA was confirmed to be DNA free (<0.5ng/ul) via quantitative PCR using universal 16S rRNA primers. If sequenced at the University of Michigan, rRNA was depleted with the MICROBExpress Bacterial mRNA Enrichment Kit (ThermoFisher). If sequenced at SeqCenter, total RNA was directly submitted.
Samples were multiplexed for sequencing on the Illumina NovaSeq platform at both the University of Michigan Advanced Genomics Core and SeqCenter.
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| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fastq files were analyzed in SeqMan NGen 17 software (DNA Lasergene suite) and averaged RPKM, fold change and p-values exported by ArrayStar software.
Assembly: UGRO018.gff; awaiting genome submission
Supplementary files format and content: xlsx file contains locus tags, gene annotations, avg RPKM for each substrate, fold changes and significance (p-values).
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| Submission date |
May 16, 2024 |
| Last update date |
Dec 01, 2024 |
| Contact name |
Nicholas Pudlo |
| E-mail(s) |
[email protected]
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| Organization name |
University of Michigan
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| Street address |
1150 W. Medical Center Dr.
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| City |
Ann Arbor |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL34484 |
| Series (1) |
| GSE267699 |
A novel, butyrate-producing Gram-positive bacterium from the human gut, Hoskinsella mucinolytica, selectively targets N-acetylhexosamine sugars in host mucins |
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| Relations |
| BioSample |
SAMN41426977 |
| SRA |
SRX24585304 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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