lincRNA-FISH catalog

Localization and Abundance Analysis of Human lincRNAs at Single Cell and Single Molecule Resolution

Long noncoding RNAs (lncRNAs) have emerged as key players in different cellular processes and are required for diverse functions in vivo. However, fundamental aspects of lincRNA remain poorly characterized, including their subcellular localization, abundance and variation at a single cell resolution.  Here, we used single molecule, single-cell RNA fluorescence in situ hybridization (RNA FISH) to survey 61 long intergenic noncoding RNAs (lincRNAs) and catalog their abundance and cellular localization patterns in three human cell types. Our lincRNA set was chosen by a variety of properties such as conservation and tissue specific expression across a spectrum of expression abundance. We find that lncRNAs have diverse sub-cellular localization patterns ranging from strictly nuclear localization to almost exclusive cytoplasmic localization, with the majority localized primarily in the nucleus. We observed that the low abundance of lncRNAs as measured in bulk cell populations cannot be explained by high expression in a small subset of ‘jackpot’ cells. Simultaneous analysis of lncRNAs and mRNAs from corresponding divergently transcribed loci showed that divergent lincRNAs do not present a distinct localization pattern and are not always co-regulated with their neighbor. Overall, our study highlights important differences and similarities between lncRNAs and mRNAs. The rich set of localization patterns we observe suggest a broad range of potential functions for lncRNA.

View lncRNA FISH images with OMERO https://omero.broadinstitute.org/ (user: lincFISHGuest  pasword:welcome )

You can biew images by setting the viewer options on top left to FISHScreenMembers/MoranCabili. To view an image, select the thubmnail and double click, an enlarged image window will open with "rendering detailes" on the left. You can edit rendering of RGB colors to better view spots over dapi. Setting “rendering details” of each color to the full range is the desired default. 

Download raw image file (zipped by lncRNA name) from our FTP site (Username :lincFISHguest Password: welcome)

Download supplamentry data from here:

 lincFISH_catalog_datasetKey (docx)

Dataset-1 Candidate transcripts information (xls)

                   a. SuppDataset1- Fasta seq used to designed probe sets(zip)

Dataset-2 Two color validation and full probe set counts (xls)

                   a. SuppDataset2- raw intensity data for full probe sets(zip)

                   b. SuppDataset2- raw intensity data for 2-color probe sets(zip)

Dataset3 – Single cell analysis of the validate set (xls)

Dataset 4 – RNA-Seq abundance estimation (xls)

                  a. SuppDataset4- transcripts files RNA-Seq expression matrices(zip)