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Dataset View [GSE38495]

SeriesGSE38495
TitleFull-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Year2012
CountrySweden
ArticleSandberg R,Schroth GP,Laurent LC,Loring JF,Khrebtukova I,Daniels GA,Faridani OR,Deng Q,Li R,Wang YC,Luo S,Ramsköld D.Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.Nature biotechnology.2012 Aug
PMID22820318
Bio ProjectBioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA170814
SraSRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP014428
Overall DesginWe generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells including putative circulating tumour cells.
SummaryWe assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells.
Experimental ProtocolcDNA was generated as described in the manual for SMARTer Ultra Low RNA Kit for Illumina sequencing marketed by Clontech. Then, a sequencing library was generated as described in Illumina's Ultra Low Input mRNA-Seq Guide.
cDNA was generated as described in the manual for SMARTer Ultra Low RNA Kit for Illumina sequencing marketed by Clontech. Then, a sequencing library was generated using the Epicentre Nextera sample preparation kit, with 5 min tagmentation at 55C with 0.25 ul transposase and 4 ul 5x HMW Nextera reaction buffer, then 35 ul of PB, then 88 ul SPRI XP beads.
Data processingAlignment by Bowtie (version 0.12.7, option –best) to genome and exon-exon junctions.; Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).; Conversion by samtools to bam format.; Conversion by bedtools to bed format.; Generation of RPKM (reads per kilobase and million mapped reads) values by rpkmforgenes.py available at http://sandberg.cmb.ki.se/rnaseq/.; Genome_build: mm9 for mouse; hg19 for human.; Supplementary_files_format_and_content: Bed12 format with uniquely aligned reads.; Supplementary_files_format_and_content: Tab-delimited plain text format with gene expression values in RPKM.
PlatformGPL10999;GPL11002;GPL13112;GPL15520
Public OnPublic on Jul 22 2012

Cell Groups

Differential Expression Gene List

KEGG GO Others   

Gene SymbolEnsembl IDFDR
ACVR2BENSG000001147390.00230718738048024
ALDH7A1ENSG000001649040.00230718738048024
IRF4ENSG000001372650.00230718738048024
MCAMENSG000000767060.00230718738048024
SPTBN1ENSG000001153060.00230718738048024
BNC2ENSG000001730680.00259301932943468
CD63ENSG000001354040.00268390130127684
LGALS3ENSG000001319810.00268390130127684
RBMS1ENSG000001532500.00268390130127684
RPL39LENSG000001639230.00268390130127684
Displaying 21-30 of 119 results.