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| Status |
Public on Dec 12, 2019 |
| Title |
TFAP2c HH9 rep1 |
| Sample type |
SRA |
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| Source name |
neural crest
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| Organism |
Gallus gallus |
| Characteristics |
tissue: neural crest
Stage: HH9
antibody: anti-AP2 gamma (abcam, ab218107)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neural plate border/neural crest dissections were performed on HH6/HH9 embryos (10 embryos/ 20 neural folds per experiment). Cells were dissociated in Accumax (Accutase, SCR006) cell dissociation solution for 20 minutes at RT under mild agitation. CUT&RUN experiments were carried out as described(Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: CUT&RUN
Base calling was performed using CASAVA 1.8
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18, and mapped to the galGal5 genome using Bowtie 2 v2.3.4.3 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Duplicate reads were marked using MarkDuplicates function of Picard tools v 2.0.4 and reads were filtered using samtools v1.9 -F 1804 -f 2
Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads
Genome_build: galGal5
Supplementary_files_format_and_content: bigwig files (scores represent enrichment normalized to 1x genome coverage)
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| Submission date |
Feb 21, 2019 |
| Last update date |
Dec 12, 2019 |
| Contact name |
Marcos Simoes-Costa |
| E-mail(s) |
simoescosta@cornell.edu
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| Organization name |
Cornell University
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| Department |
Molecular Biology and Genetics
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| Lab |
Simoes-Costa Lab
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| Street address |
526 Campus Rd
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| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL19787 |
| Series (1) |
| GSE126880 |
Heterodimerization of Tfap2 pioneer factors drives epigenomic remodeling during neural crest specification |
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| Relations |
| BioSample |
SAMN10984294 |
| SRA |
SRX5402888 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3616178_Tfap2c_HH9_1.bw |
174.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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