|
| Status |
Public on Oct 18, 2023 |
| Title |
Mutant-B-DMSO Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Ifih1/Ddx58/cGAS triple mutant
cell type: MACS-purified splenic B cells
treatment: DMSO
|
| Treatment protocol |
DMSO or 0.5 uM GSK343 for 48 hours
|
| Growth protocol |
Splenic B cells were purified from 6-8 week old mice using MACS and CD43 microbeads (Miltenyi biotec). The cells were treated with either DMSO or 0.5 uM GSK343 (5x10^6 cells/mL) for 48 hours in RPMI (Wisent) supplemented with 10% (v/v) FBS, 100 IU penicillin, 100 ug/mL streptomycin, 2 mM glutamine, 55 uM 2-BME, 2ng/mL BAX and 2ng/mL IL-4 (BioLegend).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Monarch Total RNA Miniprep kit (NEB T2010S)
Libraries were prepared with VAHTS Total RNA-seq library prep kit (GeneBio Systems, NR603-01), following the manufacturer's recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calls and demultiplexing were performed using bcl2fastq
Gene expression analysis: Reads were mapped to mm10 with STAR/2.7.8a and GENCODE VM22 comprehensive gene annotation. SAM files were converted to BAM, sorted and indexed with samtools/1.12. Reads aligned to gene annotations were counted with htseq-count/0.11.0 using default settings. Count tables were imported into Rstudio using R/3.6.3. Differential gene expression analysis was performed with edgeR/3.28.1.
Repetitive element expression analysis version 1: Reads were mapped to mm10 with bowtie2/2.3.3.1 using default settings. Unique and multimapped reads were separated using RepEnrich2. RepEnrich2 was used to count the number of reads aligning to each repName element in a custom repeat annotation file. The annotation was generated by removing low complexity and simple repeat repClass elements from Repeat Masker table downloaded from UCSC Table Browser. Any element overlapping mm10 blacklist coordinates (ENCODE) was also removed. Count tables were imported into Rstudio using R/3.6.3. Differential gene expression analysis was performed with edgeR/3.28.1.
Repetitive element expression analysis version 2: Reads were mapped to mm10 with STAR/2.5.2b using previously described settings (see citation in paper). Mapped reads overlapping with features in RepeatMasker track (mm10) were counted using FeatureCounts/2.0.3. Count tables were imported into Rstudio using R/3.6.3. Differential gene expression analysis was performed with edgeR/3.28.1.
Assembly: mm10
Supplementary files format and content: csv: count table of gene expression; txt: count table of repetitive element expression (Repenrich2); table: count table of repetitive element expression (STAR and featureCounts)
|
| |
|
| Submission date |
Mar 08, 2022 |
| Last update date |
Oct 18, 2023 |
| Contact name |
Frederick Andrew Dick |
| E-mail(s) |
fdick@uwo.ca
|
| Organization name |
Western University
|
| Department |
Pathology
|
| Lab |
A4-VRL LRCP
|
| Street address |
790 Commissioners Road E
|
| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A 4L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE198159 |
Cytosolic PRRs are required to upregulate inflammatory gene expression upon EZH2 inhibition with GSK343 |
| GSE198232 |
Cytosolic pattern recognition receptors respond to EZH2-inhibition induced viral mimicry response that eliminates splenic B cells |
|
| Relations |
| BioSample |
SAMN26527263 |
| SRA |
SRX14410460 |
