single-cell RNA datasets¶

Available CARE snRNA-Seq data. This section reports most of the data related to RNA seq data analysis. lternatively, all the snRNA data be downloaded from the HTTP server.

Realease updates¶

Initial release for the CARE study (03/25/2020)

Bigwig tracks¶

Data files¶
File	Size	Last modified	RNA-Seq reads bigwig file
Adipocyte.snRNA.bw	11M	03/24/20	RNA-Seq reads bigwig file
Aggregate.snRNA.bw	497M	03/24/20	RNA-Seq reads bigwig file
Arterialar.Smooth_muscle.snRNA.bw	9.8M	03/24/20	RNA-Seq reads bigwig file
Atrial_cardiomyocyte.snRNA.bw	132M	03/24/20	RNA-Seq reads bigwig file
Endocardial.snRNA.bw	11M	03/24/20	RNA-Seq reads bigwig file
Endothelial.snRNA.bw	72M	03/24/20	RNA-Seq reads bigwig file
Fibroblast.snRNA.bw	112M	03/24/20	RNA-Seq reads bigwig file
Lymphocyte.snRNA.bw	7.3M	03/24/20	RNA-Seq reads bigwig file
Macrophage.snRNA.bw	34M	03/24/20	RNA-Seq reads bigwig file
Myofibroblast.snRNA.bw	6.4M	03/24/20	RNA-Seq reads bigwig file
Pericyte.snRNA.bw	38M	03/24/20	RNA-Seq reads bigwig file
Nervous.snRNA.bw	4.8M	03/24/20	RNA-Seq reads bigwig file
Ventricular_cardiomyocyte.snRNA.bw	266M	03/24/20	RNA-Seq reads bigwig file

Matrices¶

Different matrix formats are accessible for download. snRNA_Heart_data_matrix.mtx and snRNA_Heart_count_matrix.mtx are raw count and UMI matrices that goes along the barcode and features indexes snRNA_Heart_barcodes.tsv and snRNA_Heart_features.tsv. exprMatrix.tsv.gz is a more convenient matrix written as a tsv file with both indexes included:

zcat exprMatrix.tsv.gz|cut -f1,2,3,4,5,6|head
NF2_LA_AAACCCAAGACTAGAT NF2_LA_AAACCCAAGATAACGT NF2_LA_AAACCCAAGCATGTTC NF2_LA_AAACCCAAGCCTTCTC NF2_LA_AAACCCACAAAGCGTG
MIR1302-2HG     0.0     0.0     0.0     0.0     0.0
AL627309.1      0.0     0.0     0.0     0.0     0.0
AC114498.1      0.0     0.0     0.0     0.0     0.0
AL669831.5      0.0     0.0     0.0     0.0     0.0
FAM87B  0.0     0.0     0.0     0.0     0.0
LINC00115       0.0     0.0     0.0     0.0     0.0
FAM41C  0.0     0.0     0.0     0.0     0.0
AL645608.7      0.0     0.0     0.0     0.0     0.0
AL645608.1      0.0     0.0     0.0     0.0     0.0

Bed files¶
File	Size	Last modified	Description
snRNA_Heart_barcodes.tsv	810K	03/26/20	single-cell barcodes
snRNA_Heart_counts_matrix.mtx	460M	03/26/20	single cell count matrix in mtx format
snRNA_Heart_data_matrix.mtx	1.1G	03/26/20	single cell matrix in mtx format
snRNA_Heart_features.tsv	345K	03/26/20	feature index in tsv format
exprMatrix.tsv.gz	520M	03/30/20	matrix in tsv format including x and y indexes

Metadata¶

barcode metadata

Bed files¶
File	Size	Last modified	Description
snRNA_Heart_metadata.txt	16M	03/26/20	barcode metadata

Consensus¶

Bed files¶
File	Size	Last modified	Description
Normalized.gene.expression.by.cluster.snRNA.txt	6.1M	03/24/20	Consensus table for snRNA/snATAC integration