|
| Status |
Public on Aug 22, 2019 |
| Title |
Rag_SPIC_tet_DOX_BCLAF1_07 |
| Sample type |
SRA |
| |
|
| Source name |
pre-B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Rag -/- Abelson cells
passage: 10 to15
chip antibody: anti-BCLAF1 (A300-608A, Bethyl Laboratories)
|
| 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 |
| E-mail(s) |
bednarski_j@wustl.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN11166077 |
| SRA |
SRX5541115 |
