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Sample GSM3103102 Query DataSets for GSM3103102
Status Public on Oct 01, 2018
Title Pax5 preB ChIP-seq
Sample type SRA
Source name RAG-/-µ+ pre-B cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Pre-B cells
Growth protocol Bone marrow and spleen cells were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females.
Extracted molecule genomic DNA
Extraction protocol For bone marrow subset purification we used B6 RAG-/- µ+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells.
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25 (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Confident peaks were called using MACS (version 1.4.2), with FDR<= 1% and the default p value (1E-5).
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: confident peaks (as called by MACS).
Submission date Apr 18, 2018
Last update date Oct 01, 2018
Contact name Salvatore Loguercio
Organization name TSRI
Department MB
Lab Balch
Street address 10550 North Torrey Pines Rd
City La Jolla
State/province California
ZIP/Postal code 92121
Country USA
Platform ID GPL13112
Series (2)
GSE113306 Epigenetic enhancer marks and transcription factor binding influence Vk gene rearrangement frequencies in pre-B cells and pro-B cells
GSE117804 Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vkappa Gene Rearrangement in Pre-B Cells and Pro-B Cells
BioSample SAMN08946940
SRA SRX3960589

Supplementary file Size Download File type/resource
GSM3103102_Pax5_preB-input_preB_macs_confident.bed.gz 236.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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