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| Status |
Public on Dec 31, 2020 |
| Title |
48hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep1 |
| Sample type |
SRA |
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| Source name |
48hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC
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| Organism |
Danio rerio |
| Characteristics |
developmental stage: 48h post fertilization
cell type: dorsal intermediate domain neural crest cell
genotype/variation: Foxc1KO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were purified by FACS-sorting. chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
FACS-sorted cells were centrifuged at 500 g for 20 m at 4 °C, and the pellet was suspended with 20 μL of lysis buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 0.2% N-P40) by pipetting 6-10 times to release the nuclei without purification. The cell lysate was then mixed with 30 μL reaction buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, and homemade Tn5 Transposase) by vortexing for 5 s. The reaction was incubated at 37°C for 20 minutes, followed by DNA purification using a Qiagen MinElute kit.
Libraries were amplified by PCR with indexed primers
DNA fragments are amplified by PCR for 5 cycles using NEBnext master mix, with primers containing various indexes. Additional cycles are determined by qPCR on 1/10 of the amplified libraries. After amplification, the libraries are cleaned using AMPURE beads, to only keep the fragments larger than 100bp. The libraries are pooled before sequencing.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter q value < 0.01.
Genome_build: danRer10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq
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| Submission date |
Sep 06, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Gage Crump |
| E-mail(s) |
gcrump@med.usc.edu
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| Phone |
323-442-2693
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| Organization name |
USC
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| Department |
Stem Cell
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| Lab |
Crump Lab
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| Street address |
1425 San Pablo St.
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platform ID |
GPL25922 |
| Series (1) |
| GSE157575 |
Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation |
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| Relations |
| BioSample |
SAMN16071175 |
| SRA |
SRX9085310 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4770939_48hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep1.narrowpeak.gz |
3.4 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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