lulab.github.io

#Intranet Public Docs



Shared Data @ Bioinfo. Platform (from Lu Lab)

I. Licensed Data

Apply for access from NIH, get the signature of PI, and then you can obtain the data.

How to apply for access: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=pi_requests

/Share2/home/lulab1/TCGA

1. miRNA-seq (bam file, hg38)

miRNA-seq of these cancers: BRCA, COAD, ESCA, LIHC, LUAD, LUSC, PAAD, READ, STAD

/Share2/home/lulab1/TCGA/miRNA-Seq

2. RNA-seq (bam file, hg38)

RNA-seq of these cancers: BRCA, COAD, ESCA, LIHC, LUAD, LUSC, PAAD, READ, STAD

/Share2/home/lulab1/TCGA/RNA-Seq

3. TCGA-L3 (counts, FPKM, hg38)

counts and fpkm of these cancers: BRCA, COAD, ESCA, LIHC, LUAD, LUSC, READ, STAD

/Share2/home/lulab1/TCGA/TCGA_L3

II. Public Data

/Share2/home/lulab1/CCLE

1. CellLineAnnotation (tsv)

Cell Line Annotations

/Share2/home/lulab1/CCLE/CellLineAnnotation

2. RNAseq_Raw (bam, tsv)

RNAseq profiling of 1019 cell lines

/Share2/home/lulab1/CCLE/RNAseq_Raw

3. mRNA expression Array (gct,res)

Raw Affymetrix CEL files were converted to a single value for each probe set using Robust Multi-array Average (RMA) and normalized using quantile normalization

/Share2/home/lulab1/CCLE/mRNAexpressionGeneExpression

4. DNA Copy Number (gct, res)

Raw Affymetrix CEL files were converted to a single value for each probe set representing a SNP allele or a copy number probe.

/Share2/home/lulab1/CCLE/DNACopyNumberAffySNP

5. Oncomap mutations (maf)

The mutations were assessed in 33 genes (381 specific mutations) using Oncomap 3.0 core

/Share2/home/lulab1/CCLE/OncomapMutations

6. Hybrid capture sequencing (maf)

List of mutations and indels in 1651 genes, determined by targeted massively parallel sequencing.

/Share2/home/lulab1/CCLE/HybridCaptureSequencing

7. Pharmacological profiling (maf)

Pharmacologic profiles for 24 anticancer drugs across 504 cell lines.

/Share2/home/lulab1/CCLE/PharmacologicalProfiling