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Sample GSM3700780 Query DataSets for GSM3700780
Status Public on Aug 22, 2019
Title Input_Rag
Sample type SRA
Source name pre-B cells
Organism Mus musculus
Characteristics cell type: Rag -/- Abelson cells
passage: 10 to15
chip antibody: none
Extracted molecule genomic DNA
Extraction protocol For ChiP Seq: All cells were treated with imatinib for 48 hours. ChIP was performed using anti-PU.1, anti-FLAG anti-HA anti-BCLAF1, control rabbit IgG and control mouse IgG antibodies DNA was cross-linked with 2% formaldehyde for 10 min at room temp (1 x 106 cells/ml). Reaction was stopped with 125 M Glycine. Cells were lysed with NP-40 and nuclei were frozen in liquid nitrogen then lysed with SDS. DNA was fragmented by sonicating with 30-second pulses for 60 cycles using a Bioruptor.DNA fragmentation was in the range of 200-500 bp and was monitored by agarose gel electrophoresis. Immunoprecipitation was performed with anti-PU.1 anti-HA anti-BCLAF1 or control rabbit IgG and Protein A Dynabeads DNA was eluted, reverse cross-linked and then purified with QIAquick PCR purification kit. For ChIP-PCR analysis, PCR was performed. For ChIP-seq analysis, fragmented DNA was quantified using 2100 Bioanalyzer and DNA libraries were prepared using Illumina TruSeq. Sequencing was performed using an Illumina HiSeq 3000 by the Washington University Genome Technology Access Center.
DNA libraries were prepared using Illumina TruSeq
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
Data processing MACS version 2 for peak calling
bigwig to BED tool v0.1.0 in Galaxy V18.09.
Overlapping ChIP peaks by R package (GenomicRanges) and Bedtools V2.25.0
Motif discovery using HOMER2 and MEME-ChIP
ETS enrichment by rtfbs_db from CisBP for mouse.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ChiP seq samples
Submission date Apr 01, 2019
Last update date Aug 22, 2019
Contact name Jeffery J Bednarski
Phone (314) 286-2825
Organization name Washington University School of Medicine
Department Department of Pediatrics
Lab Bednarski Lab
Street address 660 S. Euclid Ave., Campus Box 8208
City St. Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
Platform ID GPL21493
Series (2)
GSE129124 RAG-mediated DNA breaks attenuate PU.1 activity in early B cells through activation of a SPIC-BCLAF1 complex [ChIP-Seq]
GSE129130 RAG-mediated DNA breaks attenuate PU.1 activity in early B cells through activation of a SPIC-BCLAF1 complex
BioSample SAMN11166078
SRA SRX5541116

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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