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Sample GSM4547350 Query DataSets for GSM4547350
Status Public on Nov 01, 2020
Title Control input rep2
Sample type SRA
 
Source name Bone (tibia)
Organism Mus musculus
Characteristics strain: C57BL/6;129
tissue: tibia bone
developmental stage: E14.5
genotype: control
chip antibody: none
Treatment protocol Isolated tibias were trisected along the longitudinal axis and the tibial samples at the center (tibial midshaft) were used for ChIP-seq.
Growth protocol E14.5 embryos were collected by crossing H3f3b(K36M-flox/K36M-flox) mice with Prx1-Cre mice, and tibias were isolated .
Extracted molecule genomic DNA
Extraction protocol MNase-digested chromatin was used for ChIP-seq.
ULI-N-ChIP-seq protocol was used for ChIP-seq.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description Control_input.bw
Data processing Single-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore! with an option '-q 30'.
Reads from PCR duplicates were removed by using Samtools 'markdup' with an option '-r'.
After confirming reproducibility between replicates, they were merged by using 'divide_bam.py' in RSeQC and Samtools 'merge' so that each replicate data contributes equally to the merged file.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin using deepTools 'bamCompare'.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
 
Submission date May 11, 2020
Last update date Nov 01, 2020
Contact name Takashi Ishiuchi
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Epigenetics and Development
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL18480
Series (2)
GSE150351 A histone H3.3K36M mutation in mice causes imbalance of histone modifications and defects in chondrocyte differentiation [ChIP-seq]
GSE150353 A histone H3.3K36M mutation in mice causes imbalance of histone modifications and defects in chondrocyte differentiation
Relations
BioSample SAMN14892602
SRA SRX8327284

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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