E-MTAB-2797
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA177791
PROVIDER: E-MTAB-2797 | ExpressionAtlas | 2016-10-24
REPOSITORIES: ExpressionAtlas
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Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/ Strand specific RNA-Seq data E-MTAB-1585 was normalized and subtracted control from knockdown to generate tracks that more clearly displayed the unusual pattern of RNA expression caused by knockdown of 7SK. The following wig files were generated from multiple samples (i.e.raw data files), as indicated in the 'readme.txt' file. 7sk_3p_KD_norm.wig: 7SK 3P Knockdown normalized 7sk_3p_KDF_norm.wig: 7SK 3P Knockdown normalized (Forward) 7sk_3p_KDR_norm.wig: 7SK 3P Knockdown normalized (Reverse) 7sk_5p_KD_norm.wig: 7SK 5P Knockdown normalized 7sk_5p_KDF_norm.wig: 7SK 5P Knockdown normalized (Forward) 7sk_5p_KDR_norm.wig: 7SK 5P Knockdown normalized (Reverse) 7sk_Control_norm.wig: 7SK Control normalized 7sk_ControlF_norm.wig: 7SK Control normalized (Forward) 7sk_ControlR_norm.wig: 7SK Control normalized (Reverse) 7sk_3p_KDF-ControlF.wig: 7SK 3P Knockdown-Control (Forward) 7sk_3p_KDR-ControlR.wig: 7SK 3P Knockdown-Control (Reverse) 7sk_5p_KDF-ControlF.wig: 7SK 5P Knockdown-Control (Forward) 7sk_5p_KDR-ControlR.wig: 7SK 5P Knockdown-Control (Reverse)
2013-09-19 | E-GEOD-50860 | biostudies-arrayexpress
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
2016-03-28 | E-GEOD-71315 | biostudies-arrayexpress
Project description:Transposon-based construction of strand-specific RNA-seq libraries
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