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| Status |
Public on Dec 01, 2016 |
| Title |
Pmin input DNA |
| Sample type |
SRA |
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| Source name |
Pooled embryos
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| Organism |
Patiria miniata |
| Characteristics |
developmental stage: hatched blastula
age: 30 hpf
chip antibody: none
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| Growth protocol |
Approximately 100,000 embryos (1 x 10^8 cells) were cultured in artificial seawater at 15 °C until mesenchyme blastula stage (S. purpuratus, approximately 24 hpf) or hatched blastula stage (P. miniata, approximately 30 hpf.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryo samples were fixed in 1% formaldehyde in PBS for 10 minutes at room temperature, and fixation was stopped by addition of 0.125 M glycine. Samples were pelleted and flash-frozen. Chromatin was extracted using standard protocols, except that shearing was achieved by enzymatic digestion rather than sonication. Micrococcal nuclease (Cell Signaling Technology) and digestion was performed according to the manufacturer’s SimpleChIP® instructions. Chromatin immunoprecipitation was performed using standard protocols with 50 µg of fragmented chromatin and 10 µg of custom antibody for each Tbr ortholog.
Sequencing libraries were prepared from total (input) and immunoprecipitated chromatin using standard Illumina TruSeq ChIP library preparation protocols (Yale Center for Genome Analysis).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to either the Spur_3.1 or Pmin_1.0 draft genome assembly using bowtie v2.2.2 and the following paramters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
Alignments were filtered with samtools v0.1.19 to only include alignments with MAPQ >1. Furthermore, for Patiria miniata, any alignments that overlap predicted RTE2 retroelements were masked from downstream peak calling analyses.
Peaks were called using MACS2 v2.1.0 with the following parameters, for sea urchin -g 8e+8 -m 5 50 -q 0.05 , and for sea star -g 8e+8 --bw 250 -m 10 50 -p 1e-5.
Genome_build: Spur_3.1 and Pmin_1.0
Supplementary_files_format_and_content: For each species, a bed file is supplied reporting the position and statistics associated with each macs2 called peak. In addition, bedgraph files showing sequence tag pileups in treatment and control samples are provided for each.
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| Submission date |
Nov 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory Cary |
| Organization name |
Carnegie Mellon University
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| Department |
Biological Sciences
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| Street address |
4400 Fifth Ave
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
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| Platform ID |
GPL22676 |
| Series (2) |
| GSE89862 |
Genome-wide detection of Tbrain binding sites during early development in both sea urchin (S. purpuratus) and sea star (P. miniata) |
| GSE89865 |
Genome-wide use of high and low affinity Tbrain transcription factor binding sites during echinoderm development |
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| Relations |
| BioSample |
SAMN06017618 |
| SRA |
SRX2349181 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2391749_PmTbr_macs_control_lambda.bedgraph.gz |
308.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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