Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 6
Release date: Oct 16 2013
Last update date: Nov 14 2017
Access: Public
Taxon: Homo sapiens
Computational protocol: InnateDB, BaseSpace, Bowtie, TopHat, edgeR, GEO, MARRAY
Dataset link Synthetic cationic peptide IDR-1018 modulates human macrophage differentiation

Experimental Protocol


RNA-seq was performed using the Illumina Genome Analyzer IIx platform. Monocytes were isolated from 3 healthy donors, and left unstimulated or stimulated for 4 hours with 20 μg/ml IDR-1018. For library preparation, 500 ng of total RNA was processed according to the Illumina TruSeq RNA sample preparation guide (Illumina catalogue number FC-122-1002). Briefly, mRNA was purified using poly-dT beads, followed by synthesis of the first and second cDNA strands, end repair addition of an poly-A overhang, and ligation of adapters and unique barcodes, as per the manufacturer’s instructions. DNA enrichment was carried out via a 15-cycle PCR. Following quantification, 8 pM of dsDNA was used for cluster generation on a CBOT instrument (Illumina, San Diego, CA). RNA sequencing was done on a GAIIx instrument (Illumina), performed as a single read run with 51 amplification cycles. Data processing was carried out in house, using CASAVA to convert raw data and demultiplex to FASTQ sequence files. Reads were aligned to the reference genome using TOPHAT, and then mapped to genes using the Bioconductor package GenomeRanges.

Repositories


GEO

GSE40131

ArrayExpress

E-GEOD-40131

ENA

SRP014856

BioProject

PRJNA172892

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Contact


Christopher Fjell

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