|
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.
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|
|
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
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|
|
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 |