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Sample GSM2230416 Query DataSets for GSM2230416
Status Public on Jan 03, 2017
Title hNES-WT-2
Sample type SRA
Source name hNES cell culture
Organism Homo sapiens
Characteristics cell type: iPS-derived neural progenitor cells
genotype: WT
Treatment protocol Cells were transduced with an MOI 1 and allowed to expand 10days prior to FACS (FACSAria, BD sciences). GFP+ cells were snap frozen before isolation of RNA.
Growth protocol AF22 (iPS-derived, hNES) were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 supplement (1x, Thermo Fisher Scientific), B27 (0.05x, Invitrogen) , EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). Cells were grown on NuncTM T25 or T75 flasks pre-coated with Poly L-Ornithine (15µg/ml, Sigma) and Laminin (2mg/ml, Sigma). Cells were passaged every 2-3 days using TryplLETM Express enzyme (Life Technologies) and Defined Trypsin Inhibitor (Life Technologies) and plated at a density of 6x104 per cm2. 
Extracted molecule polyA RNA
Extraction protocol miRNeasy Micro Kit (Qiagen)
KAPA stranded RNA-seq with RiboErase kit. 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Processed data in
Data processing RNA-seq reads were mapped to the human genome assembly hg38 using STAR aligner v4.1. For mRNA analysis, default parameters were used. For analysis of retrotransposons we used the --outFilterMultimapNmax 1 to only report uniquely mapping reads
ChIP-seq reads were mapped to the human genome assembly hg38 using Bowtie2 with --very-sensitive. All alignments with MAPQ < 10 were discarded.
ChIP-seq peaks were called with MACS2 normalizing against IN. H3K9me3 peaks were called using --broad, TRIM28 peaks were called with default parameters. A cutoff of -q 0.05 was used for both data sets.
mRNA and non-coding RNAs were quantified using the subread package FeatureCounts (--primary) and iGenome NCBI annotation. Retrotransposons were quantified using the RepeatMasker track from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-Seq: Matrix of quantification of non-exonic retroelements using featureCounts.
Supplementary_files_format_and_content: ChIP-Seq: Bed files with called peaks.
Submission date Jul 11, 2016
Last update date May 15, 2019
Contact name Per Brattas
Organization name Lund University
Lab Clinical Genomics
Street address Sölvegatan 17
City Lund
ZIP/Postal code 221 84
Country Sweden
Platform ID GPL21290
Series (1)
GSE84259 TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells
BioSample SAMN05372133
SRA SRX1925738

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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