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Sample GSM4466726 Query DataSets for GSM4466726
Status Public on Apr 09, 2020
Title BCELL_PRDM15
Sample type SRA
 
Source name Primary mouse lymphoma
Organism Mus musculus
Characteristics tissue: Primary mouse lymphoma
cell type: B cells
genotype/variation: E mu-Myc transgenic
antibody: PRDM15 antibody
Treatment protocol Cells were fixed using 1% formaldehyde, collected in SDS lysis buffer and frozen for ChIP. Detailed experimental procedures can be found in the supplemental method section of the paper.
Growth protocol Lymphoma cells were maintained in B Cell growth meidum: 500ml DMEM (Hyclone #30022.01, DMEM with high glucose, with 4.0mM L-glutamine, without Sodium Pyruvate) +500ml IMDM (Lonza #12-722F) +10% FBS +Penicillin/streptomycin +0.1mM Asparagine +2mM L-glutamine +11ug IL7 +2.2ul B-mercaptoethanol +Non-essential amino acids (100uM each of Glycine, L-alanine, L-asparagine, L-aspartic acid, L-glutamic acid, L-proline, L-serine)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated cells and histone-DNA complexes were enriched using PRDM15 antibody. Antibody is an in-house produced rabbit polyclonal antibody against PRDM15.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Eu_MYC_IP_mm9_sorted
Data processing Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.8 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Peak calling was done using MACS 2.1.0 with the following configurations: -f BAM -g mm -B -q 0.01 --bw 300
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package
 
Submission date Apr 09, 2020
Last update date Apr 12, 2020
Contact name Julia Nanyi Zhao
E-mail(s) julia.zhao@icahn.mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Oncological Sciences
Lab Ernesto Guccione
Street address 1470 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL19057
Series (1)
GSE116905 Identification of PRDM15 Cistrome in Emu-Myc Lymphoma cells
Relations
BioSample SAMN14567702
SRA SRX8088918

Supplementary file Size Download File type/resource
GSM4466726_Eu_MYC_IP_mm9_sorted.bw 200.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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