Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 643
Release date: May 21 2015
Last update date: Oct 26 2018
Access: Public
Computational protocol: CEL-Seq, STAR, HTSeq, Cufflinks, t-SNE, iGenomes, GEO
Dataset link Scalable Microfluidics for Single Cell RNA Printing and Sequencing

Experimental Protocol


A microfluidic device that pairs sequence-barcoded mRNA capture beads with individual cells was used to barcode cDNA from individual cells which was then pre-amplified by in vitro transcription in a pool and converted into an Illumina RNA-Seq library. Libraries were generated from ~600 individual cells in parallel and extensive analysis was done on 396 cells from the U87 and MCF10a cell lines and from ~500 individual cells with extensive analysis on 247 cells from the U87 and WI-38 cell lines. Sequencing was done on the 3'-end of the transcript molecules. The first read contains cell-identifying barcodes that were present on the capture bead and the second read contains a unique molecular identifier (UMI) barcode, a lane-identifying barcode, and then the sequence of the transcript.

Repositories


GEO

GSE66357

ArrayExpress

E-GEOD-66357

ENA

SRP055569

BioProject

PRJNA276634

Download


Contact


Peter Sims
Peter A Sims

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