linc-FISH catalog datasets list
Dataset-1 Candidate transcripts information
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Candidate set trait table
Candidate set trait table – sub table
Classic examples
mRNA-set1
mRNA-set2
Oligo design table
Dataset-2 Two color validation and full probe set counts
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Two color validation- classification (1=valid, 2=invalid, 3= no signal)
Two color validation- valid cell type pairs tab delimited file
Cells eliminated from analysis
Zip file containing for each lincRNA all the raw intensity data for the full probe set and the two
color probe sets (for every cell imaged provides the raw intensity values and nuclear localization
information)
Dataset3 – Single cell analysis of the validate set
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Image analysis summary table
Localization pattern classification table – for each lncRNA-cell pair
Mitotic cell analysis – summary table
Correlation with CCNA2 cell analysis – summary table
Divergent neighbors analysis – summary table
Dataset 4 – RNA-Seq abundance estimation
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Expression submatrix across 30 tissues – including only transcripts in this study
Expression submatrix HeLa/hLF/hFF- including only transcripts in this study
RNA-Seq sample source and IDs
GTF/BED of all candidates and transcripts in this study
ID mappings
Zip file containing GTF files and cuffdiff output gene abundance estimation matrices
1. refAnnotation.hg19.gtf - GTF used for abundance estimate. This was generated by a
Cuffmerge of : all UCSC genes (28Aug2012), and the lincRNA and TUCP annotation from
Cabili et al. 2011 and all transripts imaged in this study.
2. refAnnotation.hg19.bed
3. KellyTissues_refAnnot_gene_exp.gct - Expression matrix across 30 tissues/cells for all
genes in the refAnnotation.hg19.gtf . Generated by a Cuffdiff2 run on tissues/cells specified
in Dataset4.
4. lincFISHCells_refAnnot_gene_exp.gct - Expression matrix across HeLa/hLF/hFF for all
genes in the refAnnotation.hg19.gtf . Generated by a Cuffdiff2 run on tissues/cells specified
in Dataset4.
5. lncRNA_FISH_transcriptSet.gtf – gtf of all transcript used in this study
6. lncRNA_FISH_transcriptSet_IDMap.txt – ID map transcript used in this study and
Refseq/Cabili et al. 2011 IDs.
7. lncRNA_FISH_transcriptSet_vs_refAnnotation_IDMap – ID mapping between transcripts
used in this study and the corresponding unique ID in the refAnnotation. gtf used for
transcriptome abundance estimate