Dataset features

Specifications


Dataset type: Other
Number of samples: 31
Release date: Jun 1 2016
Last update date: Oct 24 2018
Access: Public
Chemicals: Nucleotides
Dataset link Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay

Experimental Protocol


The study consists of two separate MPRA experiments, a 78,958 oligo (79k study) and a 7,500 oligo library (7.5k). For each library we processed independent transfections into two lymphoblastoid cell lines; in total we completed 5 replicates of NA12878 and 3 replicates of NA19239. For the 79k library we also performed 5 replicate transfections into the hepatocarcinoma cell line HepG2. Raw data is provided as Illumina reads of the 20 bp barcode from the RNA extracted 24 hours post transfection as well as from the plasmid library used for transfection. We also provide oligo/barcode combinations from the ∆gfp vector in the form of a tab delimited file containing the raw sequence reads of the barcode (column 1) and genomic sequence (column 2). Processed count files are unnormalized counts for each oligo acquired by summing all barcode matches together for each replicate.

Repositories


GEO

GSE75661

ArrayExpress

E-GEOD-75661

ENA

SRP066967

BioProject

PRJNA305000

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