|
| Status |
Public on Oct 09, 2019 |
| Title |
non-neural crest_8-10ss rep1 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
FoxD3_Nc1_Citrine NEGATIVE neural crest isolated by FACS
|
| Organism |
Gallus gallus |
| Characteristics |
developmental stage: stage 8-10ss
tissue: neural crest
isolation_method: FAC sorted for FoxD3_NC1_Citrine NEGATIVE cells
amplification: Illumina Nextera DNA kit
|
| Treatment protocol |
Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion. We collected ~300 and ~600 NC cells per embryo at 5-6ss and 8-10ss respectively.
|
| Growth protocol |
Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FAC-sorted cells were lysed (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and tagmented using Illumina Nextera DNA kit (FC-121-1030) for 30mins at 37°C. Tagmented DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix for 11 cycles. Tagmentation efficiency was assessed using Agilent Tapestation. Three biological replicates were obtained for each stage.
Libraries were prepared using Illumina Nextera DNA kit and sequenced on Illumina Illumina NextSeq 500 using 40bp paired end reads
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-seq_counts.txt
|
| Data processing |
Reads were mapped using Bowtie -m 2 (v.1.0.0) to galGal4. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Peak calling was performed using MACS2, de novo motif search was performed using Homer (v.4.7)
Genome_build: galGal4
Supplementary_files_format_and_content: read counts (txt file)
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Oct 09, 2019 |
| Contact name |
Tatjana Sauka-Spengler |
| E-mail(s) |
tatjana.sauka-spengler@imm.ox.ac.uk
|
| Organization name |
MRC Weatherall Institute of Molecular Medicine
|
| Department |
University of Oxford
|
| Lab |
Sauka-Spengler lab
|
| Street address |
Radcliffe Department of Medicine
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE121318 |
Reconstruction of the global neural crest gene regulatory network in vivo [ATAC-seq] |
| GSE121527 |
Reconstruction of the global neural crest gene regulatory network in vivo |
|
| Relations |
| BioSample |
SAMN10246560 |
| SRA |
SRX4892189 |
