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| Status |
Public on Jun 28, 2021 |
| Title |
Sample_T3 RNA-seq |
| Sample type |
SRA |
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| Source name |
Tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: MPNST
genotype: PRC2 mutant
patient diagnosis: MPNST
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from fresh frozen surgical specimens using TRIzol (Cat# 10296010 Invitrogen) and purified using the RNeasy Mini Kit (Cat# 74106 Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2
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| Submission date |
Dec 04, 2019 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Ayush T Raman |
| E-mail(s) |
aayushraman09@gmail.com
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| Organization name |
Broad Institute of MIT and Harvard
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| Department |
Epigenomics Program
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE141438 |
RNA-seq dataset for MPNST patient tissue samples |
| GSE141439 |
Epigenomic reprogramming due to PRC2 functional loss induces an aggressive de-differentiated neural crest-like phenotype in MPNST |
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| Relations |
| BioSample |
SAMN13477652 |
| SRA |
SRX7267169 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4202887_Sample_T3ReadsPerGene.out.tab.gz |
165.5 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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