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Sample GSM2230436

Query DataSets for GSM2230436

Status

Public on Jan 03, 2017

Title

VM_6.5w

Sample type

SRA

Source name

human fetus

Organism

Homo sapiens

Characteristics

cell type: NA
fetal region: Ventral Mesencephalon
embryonic age: 6 weeks, 5 days
antibody: none

Treatment protocol

none

Growth protocol

none

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 Embryo.Repeats.uniqID.UniqueReads.NOT.IN.EXON.final.txt

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