Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Albert de la Chapelle
PROVIDER: E-GEOD-83520 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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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
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2015-11-02 | E-GEOD-59043 | biostudies-arrayexpress
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2015-10-29 | E-GEOD-63426 | biostudies-arrayexpress
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Project description:Long noncoding RNAs (lncRNAs) are a major transcriptional output of the mammalian genome, yet their functions are poorly characterized. In this experiment, we used RNA interference (RNAi) and locked nucleic acid antisense oligonucleotides (LNAs) to deplete the lncRNAs LINC00899 and C1QTNF1-AS1 (C1) in HeLa cells. Both of these lncRNAs are of interest as their depletion results in mitotic delay, suggesting a role in mitotic progression. After depletion of each lncRNA with RNAi or LNAs, we performed high-throughput RNA sequencing and tested for differential expression compared to negative control samples (using control siRNAs or negative control LNAs) to identify downstream regulatory targets of each lncRNA. We generated 3-4 replicates for each condition, spread across multiple batches and experiments. Samples with the same batch number were treated at roughly the same time (within the same month), while the experiment number is nested within batch and refers to cells treated on the same day. Samples were pooled and sequenced across multiple lanes, yielding 8-9 technical replicates per sample.
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