 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 23, 2020 |
| Title |
CHON_H3K4me1_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CHON_H3K4me1
|
| Organism |
Homo sapiens |
| Characteristics |
msc donor: 2454e
cell type: differentiated chondrocytes
chip antibody: ChIP-seq grade polyclonal rabbit H3K4me1 (Diagenode, cat. no. C15410194)
differentiation time point: 14
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from hMSCs and differentiated chondrocytes were extracted using the Diagenode iDeal histone ChIP-seq kit (Diagenode SA, Ougrée, Belgium). Extracted chromatin was sonicated using a Diagenode Bioruptor Standard or Bioruptor Pico to an average size of 200-500bp, using 15 sonication cycles (30s on/30s off).
Replicate 1: Diagenode MicroPLEX v2 kit, replicate 2: NEBNext Ultra II kit (New England Biolabs, Hitchin, UK)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CHON_H3K4me1_merged_Rep2
|
| Data processing |
Quality control of sequencing reads was performed using FastQC (v.0.11.5).
Reads were aligned to the reference human genome hg38 using Bowtie2 (v.2.2.4)
MACS2 (v.2.1.0.2) was used to call broad peaks (parameters –broad and –no-model) using input samples as controls.
ChromHMM (v.1.12) was used to train a 16 state model
Genome_build: hg38
|
| |
|
| Submission date |
Mar 29, 2019 |
| Last update date |
Mar 25, 2020 |
| Contact name |
David Young |
| E-mail(s) |
david.young@ncl.ac.uk
|
| Organization name |
Newcastle University
|
| Street address |
Centre For Life
|
| City |
NEWCASTLE UPON TYNE |
| ZIP/Postal code |
NE1 3BZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE129031 |
Characterisation of epigenomic changes during chondrogenesis |
|
| Relations |
| BioSample |
SAMN11285831 |
| SRA |
SRX5599424 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3691959_CHON_H3K4me1_2454e.bigwig |
498.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
