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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
GSTP1ENSG000000842078.18143592086792e-05
AMOTL2ENSG000001140190.000103475006099089
C12orf56ENSG000001853060.000103475006099089
S100A16ENSG000001886430.000103475006099089
ARHGAP11AENSG000001988260.000105463049337967
DKK1ENSG000001079840.000105463049337967
SEMA3AENSG000000752130.000152699323344353
METENSG000001059760.000169326815746953
RND3ENSG000001159630.000172852959293252
MEIS2ENSG000001341380.000176850380140934
Displaying 11-20 of 287 results.