|
| Status |
Public on Jul 06, 2022 |
| Title |
H3K27Ac, OEPs, ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
otic epibranchial progenitors (OEPs)
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: OEPs
Stage: ss8-9
chip antibody: anti-H3K27Ac (Abcam, ab4729)
|
| Treatment protocol |
NA
|
| Growth protocol |
Embryos were grown in ovo at 38°C until reaching the desired stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
200 pieces of OEP tissue per sample were manually dissected. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared following standard protocols. Briefly, tissue was dissociated in nuclei expulsion buffer, cells were then pelleted, washed in PBS and snap-frozen. Crosslinked chromatin was fragmented by sonication and immunoprecipitated following Nano-ChIP protocol using antibodies for H3K27ac, H3K27me3, H3K4me3. Adaptors and primers for NEBNext library preparation kit (Illumina, E6040S) were used to prepare library following NanoChIP protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Data was processed and aligned using the NF-core ChIPseq v1.2.0 pipeline (doi: 10.5281/zenodo.2634132).
Reads were trimmed using Trim Galore! Reads were aligned using BWA. Broad peaks were called using MACS2 with an effective genome size of 1.05e9.
Genome_build: galgal6
Supplementary_files_format_and_content: broadPeak
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
Jul 06, 2022 |
| Contact name |
Andrea Streit |
| Organization name |
Kings College London
|
| Department |
Centre for Craniofacial & Regenerative Biology
|
| Street address |
Guys Hospital, Great Maze Pond
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22626 |
| Series (2) |
| GSE168083 |
Sox8 reprograms ectoderm into ear vesicles and associated neurons [ChIP-seq] |
| GSE168089 |
Sox8 reprogram ectoderm into ear vesicles and auditory neurons |
|
| Relations |
| BioSample |
SAMN18108864 |
| SRA |
SRX10207139 |
