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Series GSE71315 Query DataSets for GSE71315
Status Public on Mar 28, 2016
Title Single cell analysis of long non-coding RNAs in the developing human neocortex
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary 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.
 
Overall design 16 Bulk Tissue Samples from GW13-23; 226 Single Cells from GW19.5-23.5
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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
 
Contributor(s) Liu JS, Nowakowski T, Pollen A, Lui J, Kriegstein A, Aaron D, Daniel L
Citation(s) 27081004
Submission date Jul 24, 2015
Last update date May 15, 2019
Contact name John Liu
E-mail(s) john.liu@ucsf.edu
Organization name UCSF
Street address 35 Medical Center Way
City SAN FRANCISCO
State/province California
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (242)
GSM1832344 GW13_1_polya
GSM1832345 GW14.5_1_polya
GSM1832346 GW16_1_polya
Relations
BioProject PRJNA290888
SRA SRP061549

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71315_GW13_1_polya_minus.bw 109.6 Mb (ftp)(http) BW
GSE71315_GW13_1_polya_plus.bw 112.2 Mb (ftp)(http) BW
GSE71315_GW13_1_total_minus.bw 356.3 Mb (ftp)(http) BW
GSE71315_GW13_1_total_plus.bw 373.8 Mb (ftp)(http) BW
GSE71315_GW14.5_1_polya_minus.bw 153.2 Mb (ftp)(http) BW
GSE71315_GW14.5_1_polya_plus.bw 157.7 Mb (ftp)(http) BW
GSE71315_GW14.5_1_total_minus.bw 462.8 Mb (ftp)(http) BW
GSE71315_GW14.5_1_total_plus.bw 486.3 Mb (ftp)(http) BW
GSE71315_GW16_1_polya_minus.bw 134.4 Mb (ftp)(http) BW
GSE71315_GW16_1_polya_plus.bw 135.8 Mb (ftp)(http) BW
GSE71315_GW16_1_total_minus.bw 362.2 Mb (ftp)(http) BW
GSE71315_GW16_1_total_plus.bw 378.4 Mb (ftp)(http) BW
GSE71315_GW16_2_polya_minus.bw 160.8 Mb (ftp)(http) BW
GSE71315_GW16_2_polya_plus.bw 165.0 Mb (ftp)(http) BW
GSE71315_GW16_2_total_minus.bw 354.9 Mb (ftp)(http) BW
GSE71315_GW16_2_total_plus.bw 370.9 Mb (ftp)(http) BW
GSE71315_GW21_1_polya_minus.bw 121.6 Mb (ftp)(http) BW
GSE71315_GW21_1_polya_plus.bw 124.5 Mb (ftp)(http) BW
GSE71315_GW21_1_total_minus.bw 361.7 Mb (ftp)(http) BW
GSE71315_GW21_1_total_plus.bw 374.8 Mb (ftp)(http) BW
GSE71315_GW21_2_polya_minus.bw 159.2 Mb (ftp)(http) BW
GSE71315_GW21_2_polya_plus.bw 163.6 Mb (ftp)(http) BW
GSE71315_GW21_2_total_minus.bw 415.0 Mb (ftp)(http) BW
GSE71315_GW21_2_total_plus.bw 433.2 Mb (ftp)(http) BW
GSE71315_GW23_1_polya_minus.bw 134.9 Mb (ftp)(http) BW
GSE71315_GW23_1_polya_plus.bw 138.2 Mb (ftp)(http) BW
GSE71315_GW23_1_total_minus.bw 371.1 Mb (ftp)(http) BW
GSE71315_GW23_1_total_plus.bw 384.3 Mb (ftp)(http) BW
GSE71315_GW23_2_polya_minus.bw 127.8 Mb (ftp)(http) BW
GSE71315_GW23_2_polya_plus.bw 131.4 Mb (ftp)(http) BW
GSE71315_GW23_2_total_minus.bw 343.8 Mb (ftp)(http) BW
GSE71315_GW23_2_total_plus.bw 358.2 Mb (ftp)(http) BW
GSE71315_bulk_tpm.polya.txt.gz 3.0 Mb (ftp)(http) TXT
GSE71315_polya_RNA_full_ref.gtf.gz 36.7 Mb (ftp)(http) GTF
GSE71315_polya_RNA_stringent_ref.gtf.gz 36.2 Mb (ftp)(http) GTF
GSE71315_scell_ncounts.genes.thresh.txt.gz 6.0 Mb (ftp)(http) TXT
GSE71315_total_RNA_full_ref.gtf.gz 37.3 Mb (ftp)(http) GTF
GSE71315_total_RNA_stringent_ref.gtf.gz 36.2 Mb (ftp)(http) GTF
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Raw data are available in SRA
Processed data are available on Series record

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