|
| Status |
Public on Nov 01, 2020 |
| Title |
H3.3K36M H3K27me3 ChIP-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone (tibia)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6;129
tissue: tibia bone
developmental stage: E14.5
genotype: H3.3K36M
chip antibody: H3K27me3 (Diagenode, #C15410069, lot A1824D)
|
| 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 |
K36M_input-normalized-H3K27me3.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 |
SAMN14892606 |
| SRA |
SRX8327281 |
