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Sample GSM1841095 Query DataSets for GSM1841095
Status Public on Sep 15, 2015
Title JIA_E_SF_Run2
Sample type SRA
 
Source name Synovial Fluid
Organism Homo sapiens
Characteristics diagnosis: JIA patient
tissue: Synovial Fluid
cell type: CD4+CD45RO+ T cells
chip antibody: anti H3K27ac (ab4729; Abcam)
in vitro activation: no
Treatment protocol To activate HC cells, HC PBMC were cultured for 16h with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads)
Growth protocol CD4+CD45RO+ cells were sorted from HC peripheral blood mononuclear cells (PBMC), either in vitro activated or not, and JIA PBMC and synovial fluid mononuclear cells (SFMC).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and barcoded libraries were sequenced 75bp single-end on Illumina NextSeq500 sequencer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Run 2
Data processing Sample demultiplexing and read quality assessment was performed using BaseSpace (Illumina) software.
Reads were mapped to the reference genome (hg19) with Bowtie 2.1.0 using default settings.
SAM files were converted to BAM files using samtools version 0.1.19.
Peaks were called using MACS-2.1.0.
Enriched regions were identified compared to the input control using MACS2 callpeak --nomodel --exttsize 300 --gsize=hs -p 1e-9.
The mapped reads were extended by 300bp and converted to TDF files with igvtools-2.3.36
Differential binding analysis was performed using the R package DiffBind version 1.8.5. In DiffBind read normalization was performed using the TMM technique using reads mapped to peaks which were background subtracted using the input control.
BEDtools v2.17.0 was used for general manipulation of peak bed-files
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files
 
Submission date Jul 31, 2015
Last update date May 15, 2019
Contact name Janneke Peeters
E-mail(s) j.g.c.peeters-7@umcutrecht.nl
Organization name UMC Utrecht
Street address Heidelberglaan 100
City Utrecht
ZIP/Postal code 3584CX
Country Netherlands
 
Platform ID GPL18573
Series (2)
GSE71596 Epigenetic profiling of Juvenile Idiopathic Arthritits (JIA) patients
GSE71597 Epigenetic profiling and RNA-sequencing of Juvenile Idiopathic Arthritits (JIA) patients
Relations
BioSample SAMN03946187
SRA SRX1127411

Supplementary file Size Download File type/resource
GSM1841095_JIA_E_SF_Run2.bw 111.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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