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Series GSE53386 Query DataSets for GSE53386
Status Public on Jun 16, 2015
Title Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We reported a new method of single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) to obtain single cell whole transcriptome analysis that covers both poly(A) plus and poly(A) minus RNA species. We built libraries of single mouse ESC , 10pg, 100pg and 1ng diluted mouse ES total RNA, single HEK293T cell and mouse early embryos before 4-cell stage. We analyzed these data using bioinformatics and find a good coverage of non-polyadenylated RNAs, circular RNA for example. to make a comparison,we also used mouse ES cells and HEK293T cells to build libraries using the protocol publish by F.Tang in 2009(sample name Tang2009_*). We also de novo assembled new genes in mouse ESCs and early embryo samples, further validated known and novel zygotic genes with a-Aminatine treated 2-cell embryos(sample name SUPeR-seq_a-AM_treated_2-cell*).
Overall design 3 Single mouse ES cells, 7 single HEK293T cells, 8 diluted mouse ES total RNA samples and 19 mouse embryo samples are performed using SUPeR-seq to evaluate its ability to detect genes in single RNAs and to cover poly(A)- RNA species.
Contributor(s) Fan X, Zhang X
Citation(s) 26201400
Submission date Dec 17, 2013
Last update date Nov 06, 2019
Contact name Xiaoying Fan
Organization name Peking University
Department College of Life Sciences
Lab Biodynamic Optical Imaging Center
Street address 5 Yiheyuan Road
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
Platforms (4)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (118)
GSM1290599 SUPeR-seq_ESC1
GSM1290600 SUPeR-seq_ESC2
GSM1290601 SUPeR-seq_ESC3
BioProject PRJNA231896
SRA SRP034543

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
GSE53386_RAW.tar 73.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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