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Sample GSM4728472 Query DataSets for GSM4728472
Status Public on Mar 27, 2024
Title Suv39h1, Suv39h2 double knock-out LaminB1 ChIP replicate 1
Sample type SRA
Source name Thymus
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype: Suv39h1-/y Suv39h2-/-
gender: Male
cell type: CD4+CD8+ double positive thymocytes
Extracted molecule genomic DNA
Extraction protocol Flow cytometrically sorted DP thymocyte cells (CD45.2+CD19-CD4+CD8+) were fixed in 1% formaldehyde. Chromatin was Mnase digested then immunoprecipitated using anti-LaminB1 antibody. Chromatin was reverse cross-linked and purified using Zymo ChIP clean and concentrator kit.
Libraries were prepared using Illumina TruSeq DNA kit. Libraries were sequenced on an Illumina NextSeq 500 to produce paired-end 81bp reads.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing The replicates FASTQ files were merged, then reads were aligned to the mouse genome (mm10) with Rsubread.
Bam files were sorted with Rsamtools and duplicate reads were removed with MarkDuplicates from Picard tools.
WCE samples were down sampled to the size of the ChIP libraries (~53 million reads) using DownsampleSam from Picard tools.
The Enriched Domain Detector (EDD) tool ( was used to call LADs on the bam files using the WCE to the corresponding ChIP (WT: gap penalty 4.79 and bin size 6 kbp, KO: gap penalty 9.1 and bin size 8 kbp). This produced two BED files of peaks, one or control mice and one the DKO mice.
Genome_build: mm10
Supplementary_files_format_and_content: Bed format file containing LADs called by EDD (a tab-delimited text file specifying genomic regions by chromosome name, start position, end position).
Submission date Aug 14, 2020
Last update date Mar 27, 2024
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platform ID GPL19057
Series (2)
GSE156293 LaminB1 ChIP-seq of DP thymocytes from wildtype and Suv39h1 and Suv39h2 double knockout mice
GSE156297 RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice
BioSample SAMN15824103
SRA SRX8949749

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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