|
Status |
Public on Jul 06, 2022 |
Title |
Input, OEPs, ChIPseq |
Sample type |
SRA |
|
|
Source name |
otic epibranchial progenitors (OEPs)
|
Organism |
Gallus gallus |
Characteristics |
cell type: OEPs Stage: ss8-9 chip antibody: none
|
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 |
SAMN18108865 |
SRA |
SRX10207138 |