Elementolab/Datasets

From Icbwiki

Elementolab/

• mitocheck http://www.mitocheck.org/cgi-bin/mtc?query=MCG_0000592
• yeast HiC http://www.ncbi.nlm.nih.gov/sra?db=sra&cmd=Search&Term=SRP002120&itool=QuerySuggestion
• FAIRE-seq in Pf http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001451
• Zhao's nucleosome data http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/hgtcellnucleosomes.aspx
• NCI-60 gene expression data: http://discover.nci.nih.gov/datasets.jsp
• NCI-60 GI50 http://dtp.nci.nih.gov/dtpstandard/subsets/comp.jsp

or http://dtp.nci.nih.gov/dtpstandard/subsets/index.jsp or http://dtp.nci.nih.gov/docs/dtp_search.html

• NCI-60 bulk download http://dtp.nci.nih.gov/docs/cancer/cancer_data.html
• ChEMBL: a database of ca. 500,000 bioactive compounds, their quantitative properties and bioactivities http://www.ebi.ac.uk/chembldb/

B cells

• Various B cell arrays (CB, NB, memory, DLBCL, BL, cell lines, etc) from the Dalla-Favera group
  • sample labels
• DLBCL samples from DFCI (Monti et al)
  • GCB/ABC labels
  • Oxphos/BCR/HR labels
• DLBCL samples from Staudt lab (recent PNAS paper on CNV)
  • GCB/ABC labels
• DLBCL samples from Hummel et al, NEJM
  • GCB/ABC labels

In GEO

• centroblast vs centrocytes (CXCR4+ vs CXCR4-) http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE15271

Genomes (The assembly sequence in one file per chromosome)

• hg19 (Feb. 2009) http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.zip
• hg18 (Mar. 2006) http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip

Proteomes

• RefSeq NP ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/protein/

RNA-seq

• Chris Burge's RNAseq dataset http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12946

Hi-C

• http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199

Other

• Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra/

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