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Sample GSM3445834 Query DataSets for GSM3445834
Status Public on Oct 26, 2018
Title GS518_Spleen1.4_KO_Tregs_ATAC
Sample type SRA
 
Source name Treg cells
Organism Mus musculus
Characteristics tissue: Spleen
genotype: Blimp1deltaFoxp3
chip antibody: none
Treatment protocol The mice were immunized with MOG(35-55) and CFA at day 0. The mice received pertussis toxin at day0 and day2.
Growth protocol Animals were kept in a specific pathogen-free facility at the Technical University of Munich or at the Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. All experimental protocols were approved by the standing committee for experimentation with laboratory animals of the Bavarian state authorities or the animal ethics committee of the Walter and Eliza Hall Institute and carried out in accordance with the corresponding guidelines.
Extracted molecule genomic DNA
Extraction protocol The cells were isolated from the CNS at the peak of the disease. The cells were digested with collagenase and DNAse to obtain single cell suspensions
Nextera DNA Sample Prep Kit FC-121-1030
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Raw reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -S”
ATAC peaks over Input background were identified using Homer (Heinz et al., 2010) findPeaks.pl with option “-style factor”
Peaks from all samples replicates were merged using mergePeaks resulting in a unified Peak set
The peak list was filtered for promoter-associated peaks (distance to TSS < 1000bp) with bedtools
annotatePeaks was used to obtain coverage counts within 500 pb across peak centers
Differential ATAC peaks were determined with the DESeq2 result function and filtered for padj < 0.05. Genomic feature annotation of ATAC-seq peaks was done using annotatePeaks.
Transcription factor motif prediction was done with Homer findMotifsGenome.pl
bigWig files were generated from homer tag directories using makeBigWig.pl
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are in bigWig format and contain differential ATAC peaks for each sample
 
Submission date Oct 25, 2018
Last update date Oct 26, 2018
Contact name Thomas Korn
E-mail(s) thomas.korn@me.com
Phone 00498941405617
Organization name Technical University of Munich
Department Neurology
Lab Korn lab
Street address Ismaninger Str. 22
City Munich
State/province Bavaria
ZIP/Postal code 81675
Country Germany
 
Platform ID GPL18480
Series (1)
GSE121764 Blimp1 maintains regulatory T cell identity at sites of inflammation through epigenetic imprinting
Relations
BioSample SAMN10290944
SRA SRX4936151

Supplementary file Size Download File type/resource
GSM3445834_GS518_S1.4_m1.ucsc.bigWig 55.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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