|
| Status |
Public on Mar 03, 2017 |
| Title |
ATACseq_animal3_50hpf |
| Sample type |
SRA |
| |
|
| Source name |
S. purpuratus embryos_50 hpf
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
aminal id: animal 3
developmental stage: Embryo
age: 50 hpf
|
| Growth protocol |
Grown at 15C in 0.45 micron filtered sea water
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were dissociated to individual cells and nuclei prepared. 500,000 cells were used in the transposition reaction following which the transposed genomic DNA was extracted and purified.
To amplify transposed DNA, the following reaction was prepared: 10 ul Transposed DNA, 15 ul of PCR master mix (Illumina, Nextera DNA 24 sample prep kit), 5 ul of PCR primer cocktail, 5 ul of each Index primer to be used (Illumina, Nextera 96 sample Index kit).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality of each read sample at each time point were analyzed. ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.2.5 with maximum fragment length of 2000 (-X 2000); other parameters used were default. Filter aligned reads with MAPQ score < 30
duplicate fragments were then removed using Picard.
MACS2 (Zhang et al., 2008) was used for peak calling with the parameters –g dm –nomodel –nolambda –extsize 239 –keep-dup all.
Jbrowse is used for visulization of predicted ATACseq peaks (http://www.echinobase.org/Echinobase/jbrowse/index.html?data=data_atac_sp)
Genome_build: assembly Spur_3.1; https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.3
Supplementary_files_format_and_content: BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue.
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Andrew Cameron |
| E-mail(s) |
parulk@caltech.edu
|
| Organization name |
California Institute of Technology
|
| Department |
Biology and Biological Engineering
|
| Lab |
Center for Computational Regulator Genomics
|
| Street address |
Caltech 1200 EAST CALIFORNIA BOULEVARD
|
| City |
PASADENA |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL20965 |
| Series (1) |
| GSE95651 |
Whole genome developmental time course of Tn5 transposon accessible chromatin patterns in sea urchin embryos |
|
| Relations |
| BioSample |
SAMN06472839 |
| SRA |
SRX2610878 |
