Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and diseasee. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Here, we deeply profiled lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development and integrated this resource to analyze the transcriptomes of single cells. While lncRNAs were generally detected at low levels in whole tissues, single cell transcriptomics revealed that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Furthermore, we used CRISRPi to show that LOC646329, a lncRNA enriched in radial glia but detected at low abundance in tissues, regulates cell proliferation. The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types. 16 Bulk Tissue Samples from GW13-23; 226 Single Cells from GW19.5-23.5 ------------------ bulk_tpm.polya.txt: bulk RNA-seq expression; using polyA full reference scell_ncounts.genes.thresh.txt: single cell RNA-seq expression; using polyA stringent reference; includes 50 GW16, GW21, GW21p3 cells previously analyzed (Pollen et. al. 2014) polya_RNA_stringent_ref.gtf: bulk RNA-seq polyA stringent transcriptome reference polya_RNA_full_ref.gtf: bulk RNA-seq polyA full transcriptome reference total_RNA_stringent_ref.gtf: bulk RNA-seq total stringent transcriptome reference total_RNA_full_ref.gtf: bulk RNA-seq total full transcriptome reference GW13_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal

Project description:Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. To achieve sustainable therapeutic benefit with targeted agents in mRCC, the effective target should focus on signaling pathways that are related to driver mutations occurred early in the clonal evolution of the disease and thus should be common to primary tumor and metastatic sites. Considering that extensive genetic heterogeneity may result in drug response variability among patients and treatment resistance, the tailored strategies for metastatic RCC is urgently needed. Here, we analyze single-cell RNA-seq (scRNA-seq) data from a matched primary RCC (pRCC) and lung metastasis (mRCC) to dissect ITH at the highest resolution to date with the objective of discovering the better therapeutic regimen. In order to identify successful clonal propagation from patient to PDX samples and understand pathogenesis from primary to metastatic RCC, we performed whole-exome sequencing (WES, n=4) and matched aCGH (n=4) on bulk tumor samples. And we utilized single-cell RNA sequencing (scRNA-seq) to model and dissect functional heterogeneity acroass primary and metastatic RCC tumors. We checked whether of capturing live one cell, not more cells, in microfluidics by fluorescent microscopic observation. To construct RNA sequencing libraries, we performed further quality controls including adequate quantities and qualities of amplified transcriptomes respectively from single cells. Tumor cells from the parental mRCC (n=34), PDX-mRCC (n=36) and PDX-pRCC (n=46) were finally analyzed in this study after filtering out poor quality cells.

Dataset Information

Sensitive, high-throughput single-cell RNA-Seq reveals within-clonal transcript-correlations in yeast populations

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets