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Sample GSM7676089 Query DataSets for GSM7676089
Status Public on Oct 18, 2023
Title Control GSK343 Rep3
Sample type SRA
 
Source name B16-F10 melanoma cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: WT
treatment: 5 uM GSK343
molecule type: rRNA-depleted RNA
Treatment protocol DMSO or 5 uM GSK343 for 4 days
Growth protocol B16-F10 cells (3e5) were treated with either DMSO or 5 uM GSK343 for 4 days in DMEM (Wisent) supplemented with 10% (v/v) FBS, 100 IU penicillin, 100 ug/mL streptomycin, 2 mM glutamine. Culture medium was changed daily with fresh vehicle or GSK343.
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: 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.
Assembly: mm10
Supplementary files format and content: csv: count table of gene expression; txt: count table of repetitive element expression
 
Submission date Aug 02, 2023
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)
GSE198232 Cytosolic pattern recognition receptors respond to EZH2-inhibition induced viral mimicry response that eliminates splenic B cells
GSE239879 Cytosolic PRRs are required to upregulate interferon gene expression upon EZH2 inhibition with GSK343 in B16-F10 melanoma cells [RNA-seq]
Relations
BioSample SAMN36807642
SRA SRX21223015

Supplementary file Size Download File type/resource
GSM7676089_NTC_G3.csv.gz 219.3 Kb (ftp)(http) CSV
GSM7676089_NTC_G3_fraction_counts.txt.gz 8.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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