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Sample GSM3755476

Query DataSets for GSM3755476

Status

Public on Dec 20, 2019

Title

Marmoset_Cerebellum_Input

Sample type

SRA

Source name

Marmoset Cerebellum

Organism

Callithrix jacchus

Characteristics

chip antibody: none
tissue: Cerebellum

Extracted molecule

genomic DNA

Extraction protocol

TruSeq DNA sample preparation kit (Illumina)

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2000

Data processing

ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
RNA-seq: Sequencing reads were aligned using HISAT2 version 2.0.5. Reads that mapped to multiple locations and duplicate reads were removed using Samtools version 1.3.1. Reads in genes were counted using the featureCount function of the Rsubread package in R. The GTF file of Marmoset genes was obtained here: ftp://ftp.ensembl.org/pub/release-91/gtf/callithrix_jacchus.
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw; RNA-seq count values are in _RNAseq.txt;

Submission date

May 08, 2019

Last update date

Dec 20, 2019

Contact name

Menno P Creyghton

E-mail(s)

m.creyghton@hubrecht.eu

Organization name

Hubrecht Institute

Lab

Creyghton