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Dataset View [GSE38495]

Series	GSE38495
Title	Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Year	2012
Country	Sweden
Article	Sandberg 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
PMID	22820318
Bio Project	BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA170814
Sra	SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP014428
Overall Desgin	We 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.
Summary	We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells.
Experimental Protocol	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 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 processing	Alignment 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.
Platform	GPL10999;GPL11002;GPL13112;GPL15520
Public On	Public on Jul 22 2012

Cell Groups

Differential Expression Gene List

Embryonic stem cell_VS_LNCaP cell Embryonic stem cell_VS_NG2-sorted cell from blood Embryonic stem cell_VS_PC3 cell Embryonic stem cell_VS_Primary melanocyte Embryonic stem cell_VS_SKMEL5 cell Embryonic stem cell_VS_T24 cell Embryonic stem cell_VS_UACC257 cell LNCaP cell_VS_NG2-sorted cell from blood LNCaP cell_VS_PC3 cell LNCaP cell_VS_Primary melanocyte LNCaP cell_VS_SKMEL5 cell LNCaP cell_VS_T24 cell LNCaP cell_VS_UACC257 cell NG2-sorted cell from blood_VS_PC3 cell NG2-sorted cell from blood_VS_Primary melanocyte NG2-sorted cell from blood_VS_SKMEL5 cell NG2-sorted cell from blood_VS_T24 cell NG2-sorted cell from blood_VS_UACC257 cell PC3 cell_VS_Primary melanocyte PC3 cell_VS_SKMEL5 cell PC3 cell_VS_T24 cell PC3 cell_VS_UACC257 cell Primary melanocyte_VS_SKMEL5 cell Primary melanocyte_VS_T24 cell Primary melanocyte_VS_UACC257 cell SKMEL5 cell_VS_T24 cell SKMEL5 cell_VS_UACC257 cell T24 cell_VS_UACC257 cell

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