|
| Status |
Public on Jun 29, 2015 |
| Title |
Bt_IgActl_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mid-log phase culture
|
| Organism |
Bacteroides thetaiotaomicron |
| Characteristics |
strain: VPI-5482
mab: JC63.1
od600 at harvest: 0.598
|
| Treatment protocol |
Cultures were grown to early log phase (OD600 ~0.1) and antibody or PBS (carrier control) was added to each culture tube. Tubes were then incubated until cultures reached OD600 0.5-0.7, when they were harvested into RNAprotect (Qiagen).
|
| Growth protocol |
Cells were grown to mid-log phase in TYG medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were extracted using acidic phenol:chlorophorm:isoamyl alcohol (125:24:1, pH 4.5). rRNA was removed using Ribo-zero.
Illumina adapters were ligated to the DNA with T4 DNA ligase and cDNAs were size-selected by 2% agarose gel electrophoresis. PCR of the adapter-ligated product was performed , and samples were pooled in equal proportion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample name: Bt_RNA_Seq_B_25
|
| Data processing |
Short read alignment with Bowtie v1.1.0.
Removal of rRNA and intergenic reads.
Differential expression analysis with DESeq2 package in R version 3.1.2.
Genome_build: ASM1106v1 (NC_004663)
Supplementary_files_format_and_content: Raw counts.
|
| |
|
| Submission date |
Jan 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph D Planer |
| E-mail(s) |
planerj@wusm.wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pathology
|
| Street address |
4444 Forest Park Ave
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63112 |
| Country |
USA |
| |
|
| Platform ID |
GPL19723 |
| Series (2) |
| GSE65449 |
Characterizing the interactions between a naturally-primed IgA and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [RNA-Seq] |
| GSE65456 |
Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice |
|
| Relations |
| BioSample |
SAMN03322496 |
| SRA |
SRX860747 |
