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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
NFE2L3ENSG000000503440.00792527511013556
POMPENSG000001329630.00797471161530507
ARHGDIBENSG000001113480.00832710412034496
INHBAENSG000001226410.00913960242409036
PKM20.00913960242409036
TPM2ENSG000001984670.00913960242409036
MRPL40ENSG000001856080.00944317951904235
NDUFA4ENSG000001890430.00944317951904235
GARSENSG000001061050.00944856820621367
UBBENSG000001703150.00944856820621367
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