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Dataset View [GSE49321]

SeriesGSE49321
TitleImproved Smart-Seq for sensitive full-length transcriptome profiling in single cells
Year2013
CountrySweden
ArticleSandberg R,Winberg G,Sagasser S,Faridani OR,Björklund ÅK,Picelli S.Smart-seq2 for sensitive full-length transcriptome profiling in single cells.Nature methods.2013 Nov
PMID24056875
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA213629
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP028301
Overall DesginCells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2).
SummaryImproved Smart-Seq for sensitive full-length transcriptome profiling in single cells.
Experimental ProtocolLysis buffer from the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' (Clontech).; We prepared sequencing libraries according to the optimized Smart-Seq2 protocol, variants of Smart-Seq2 and using the standard Smart-Seq procedure ('SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech).
Data processingAll reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013).; Non-uniquely mapped reads were removed.; Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).; Genome_build: GRCh37; Supplementary_files_format_and_content: Gene expression values (tab-delimited text file).
PlatformGPL11154;GPL13112
Public OnPublic on Sep 01 2013

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
NGFRAP11.56256478228087e-26
PFN2ENSG000000700874.76053074138155e-26
PLS3ENSG000001020242.27085152360725e-23
SIX1ENSG000001267782.72241243906637e-21
CSRP2ENSG000001751838.36645470448472e-21
SPG20ENSG000001331042.38348842765127e-20
ALDH7A1ENSG000001649042.68733960830248e-20
TMEM237ENSG000001557552.68733960830248e-20
CDH2ENSG000001705581.2419660277217e-19
NT5C3L2.01523503030039e-19
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