|
| Status |
Public on Mar 01, 2024 |
| Title |
cp2_5H3 |
| Sample type |
SRA |
| |
|
| Source name |
A2-165
|
| Organism |
Faecalibacterium prausnitzii |
| Characteristics |
strain: A2-165
genotype: WT
treatment: without calcium palmitate (CP2)/16h
|
| Treatment protocol |
The growth broth were supplied with/witout 0.01 mg/mL calcium palmitate
|
| Growth protocol |
F. prausnitzii A2-165 was cultured in YCFAG medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by acid phenol and chloroform/isoamyl alcohol extraction. The RNA cleanup was performed using a QIAgen kit according to the manufacturer’s recommendation (QIAGEN, German).
Then depletion of rRNA was performed using the Ribo-off kit for bacteria (Epicentre, Madison, WI, USA), followed by library construction for whole-transcriptome sequencing using BGI library prep kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
column cp2_5H3
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter- Quality limit: Q < 20 and length < 25 )
Trimmed sequence reads were filtered rRNA
Filtered sequence reads were mapped to F. prausnitzii A2-165 GCA_002734145.1 using STAR aligner
Read count extraction and normalization were performed using DESeq2
Assembly: GenBank assembly accession: GCA_002734145.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 21, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Hermie J.M. Harmsen |
| E-mail(s) |
h.j.m.harmsen@umcg.nl
|
| Organization name |
University Medical Center Groningen
|
| Street address |
Hanzeplein 1
|
| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9713GZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL33148 |
| Series (1) |
| GSE225701 |
Transcriptomic and lipidomic analyses unravel the responses of Faecalibacterium prausnitzii to calcium palmitate |
|
| Relations |
| BioSample |
SAMN33392698 |
| SRA |
SRX19452640 |
