GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1937188

Query DataSets for GSM1937188

Status

Public on Jan 13, 2016

Title

Input Rhesus Brain ThalamicNuclei RM1

Sample type

SRA

Source name

Rhesus macaque female thalamic nuclei tissue

Organism

Macaca mulatta

Characteristics

tissue: Thalamic nuclei
gender: Female
age: 5
Cause of death: Euthanasia
postmortem delay: 0.5 hrs
experiment type: Input
chip antibody: none

Treatment protocol

Growth protocol

Extracted molecule

genomic DNA

Extraction protocol

Crosslink, Lyse and Immunoprecipitate
Illumina Truseq DNA library protocol

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NextSeq 500

Data processing

Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1
Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000
genome build: hg38, rheMac3, panTro4, mm10
processed data files format and content: txt files contain called peaks
processed data files format and content: narrowPeak files contain called peaks in BED format
processed data files format and content: bedGraph files contain treat pileup
processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format

Submission date

Nov 11, 2015

Last update date

May 15, 2019

Contact name

Menno P Creyghton

E-mail(s)

[email protected]

Organization name

Hubrecht Institute

Lab

Creyghton