|
| Status |
Public on Jul 15, 2024 |
| Title |
mice cecal content,F rep8 |
| Sample type |
SRA |
| |
|
| Source name |
cecal content of monocolonied Balb/c mice
|
| Organism |
Lactobacillus johnsonii |
| Characteristics |
tissue: cecal content of monocolonied Balb/c mice
cell type: Prokaryotic
|
| Treatment protocol |
For the in vitro transcriptomics, gnotobiotic Balb/c mice (F=8, M=2) were orally gavaged with 10^8 CFU of L. johnsonii MR1, grown over night under anaerobic conditions at 37 °C. Seven days after the oral gavage, the the cecal contents of the mice was harvest for in vivo bacterial transcriptomic analysis.
|
| Growth protocol |
L. johnsonii MR1 was grown over night anaerobically at 37 °Cs. For the in vitro samples, cells were subcultured the next day, grown anaerobically at 37 °Cs, and collected at exponential (5 hrs) and stationary phase (10hr) for RNA seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the in vitro samples, protease treament followed by RNA isolation was performed as per the bacterial RNA isolation protocol from Qiagen Rneasy Kit. For the in vivo samples, Trizol/Rneasy hybrid protocol by Mauricio Rodriguez-Lanetty was followed.
NEBNext Ultra II DNA library prep was used for cDNA library preperation.
RNA-seq. Sequencing was done using Novoseq, paired-end sequencing, with a sequencing depth of 33M reads per sample for in vitro samples and 150M reads per sample for in vivo samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
invivo_raw_counts.txt, S8
htseq count file
invivo_raw_counts.txt
|
| Data processing |
The sequencing quality of RNA reads was first assessed using FatsQC, version 0.11.8.
TrimGalore, version 0.6.7, was used to trim out adapter reads, as well as remove reads smaller than 90bp.
The reads were aligned to the L. johnsonii MR1 using Bowtie2 version 2.3.4.3 with default parameters for an end-to-end alignment. The resulting SAM files were converted to BAM files using SAMtools version 1.7.
The count matrix was generated using HtSeq, version 0.12.4, and counts were imported to R for differential gene expression analysis.
FPKM reads were generated, and differentially expressed genes were identified using DESeq2.
Assembly: L. johnsonii MR1 was used as the reference CP091981.1
Supplementary files format and content: tab-limited text file includes raw counts for each sample condition
|
| |
|
| Submission date |
Jul 09, 2024 |
| Last update date |
Jul 15, 2024 |
| Contact name |
Keerthikka Ravi |
| E-mail(s) |
krthkkrv@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular and Developmental Biology
|
| Lab |
Huffnagle lab
|
| Street address |
1105 N University st
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL34689 |
| Series (1) |
| GSE271801 |
in vitro and in vivo transcriptomics profile of Lactobacillus johnsonii MR1 |
|
| Relations |
| BioSample |
SAMN42383506 |
| SRA |
SRX25252495 |
