| Series | GSE49321 |
| Title | Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells |
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| Year | 2013 |
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| Country | Sweden |
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| Article | Sandberg 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 |
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| PMID | 24056875 |
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| Bio Project | BioProject: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA213629 |
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| Sra | SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRP028301 |
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| Overall Desgin | Cells of four different origins were profiled using commercial SMARTer and compared to five variants of an improved protocol (Smart-Seq2). |
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| Summary | Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells. |
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| Experimental Protocol | Lysis 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).
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| Data processing | All 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).
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| Platform | GPL11154;GPL13112 |
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| Public On | Public on Sep 01 2013 |
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Differential expression gene List between two groups.
