|
| Status |
Public on Mar 18, 2019 |
| Title |
C2C12_Cells_DMSO_Replicate_3_12h |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 cells, DMSO, 12h treatment
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
agent: DMSO
replicate: 3
|
| Treatment protocol |
C2C12 cells were incubated with the indicated drugs at concentrations of 500 nM (JQ1 & LP99) or 2 µM (GSK2801, BAZ2ICR & BSP) for 12 h before they were harvested for extraction of total RNA
|
| Growth protocol |
C2C12 mouse myoblast cells were grown in DMEM containing 20% FBS. 0.3x106 cells were seeded and allowed to grow for 36 hrs before switching to differentiation media (DMEM containing 2% horse serum, 10 µg/ml insulin and 10 µg/ml Transferrin)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using PureLinkTM RNA kit as per the manufacturer’s protocol.
|
| Label |
Biotin
|
| Label protocol |
Mouse RNA samples were processed using the Affymetrix GeneChip WT PLUS Reagent kit, the manual target preparation for GeneChip whole transcript expression arrays
|
| |
|
| Hybridization protocol |
Labelled ss-cDNA were hybridised to the Affymetrix Clariom™ S Assay HT, mouse -24 Array Plate
|
| Scan protocol |
Processing was carried out on the Affymetrix GeneTitan platform and analysed using the Affymetrix Expression console software
|
| Description |
Gene expression data from C2C12 mouse myoblast cells treated with DMSO (replicate 3) for 12h
|
| Data processing |
Raw CEL data were processed in R (v.3.5.1) using Bioconductor (v.3.7) and the oligo package (v.1.44). Quality controls were carried out using the arrayQualityMetrics package (v.3.36.0) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. On this basis one of the three arrays treated with BSP was considered to be an outlier and was discarded (sample 'BSP_rep3', file 'BSP_rep3.CEL'), with the rest of the analysis performed without taking it into account. Background correction and normalization were carried out employing the Robust Multichip Array (RMA) method implemented in the oligo package. Data were filtered using the genefilter package (v.1.62.0) employing the nsFilter function and an interquartile range (IQR) cut-off of 0.28 (or >log(1.2), determined by the midpoint of the shortest interval containing half of the data. Probe sets that did not have an Entrez gene identifier were also removed. From the 29129 features available on the Clariom S Mouse HT chip, 14538 remained after filtering. A linear model was applied employing the limma package (v.3.36.2) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Genes were considered differentially expressed if the adjusted P-value, calculated using the Benjamini–Hochberg method in order to minimize false discovery rate, was less than 0.05 and the mean level of expression was greater than 1.5-fold. Data were annotated using the clariomsmousehttranscriptcluster.db annotation data (https://www.bioconductor.org/packages/release/data/annotation/html/clariomsmousehttranscriptcluster.db.html).
Clariom_S_Mouse_HT.r1.pgf (from http://www.affymetrix.com/Auth/analysis/downloads/lf/xta/Clariom_S_Mouse_HT/Clariom_S_Mouse_HT_TAC_Analysis.r1.zip)
Clariom_S_Mouse_HT.na36.mm10.transcript.csv (from http://www.affymetrix.com/Auth/analysis/downloads/na36/xta/Clariom_S_Mouse_HT.na36.mm10.transcript.csv.zip)
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| |
|
| Submission date |
Jul 24, 2018 |
| Last update date |
Mar 18, 2019 |
| Contact name |
Panagis Filippakopoulos |
| E-mail(s) |
panagis.filippakopoulos@gmail.com
|
| Organization name |
Oxford University
|
| Department |
Nuffield Department of Medicine
|
| Lab |
Structural Genomics Consortium
|
| Street address |
ORCRB - Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7DQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24242 |
| Series (1) |
| GSE117612 |
A Chemical Toolbox for the Study of Bromodomains and Epigenetic Signaling |
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