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| Status |
Public on Apr 26, 2021 |
| Title |
P39.rep1 |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Zea mays |
| Characteristics |
tissue: seedling
genotype: P39
treament: Fresh
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
16,000 input nuclei per library (4 total libraries)
10X Genomics scATAC-seq v1.1
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ATAC
Genotype aggregated nuclei
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| Data processing |
Raw data processing with Cellranger
Cell genotyping with demuxlet
Peak calling with MACS2
Peaks filtered by empirical 0.001 FDR (using permuted background regions)
Genome_build: Zm-REFERENCE-NAM
Supplementary_files_format_and_content: NAM_lines_concatenated.ATAC.narrowpeak (column 1 = chromosome), (column 2 = start), (column 3 = end), (column 4 = peakID), (column 5 = -10*log10pvalue), (column 6 = NA), (column 7 = fold-change at peak summit), (column 8 = -log10pvalue at peak summit), (column 9 = -log10qvalue at peak summit), (column 10 = genotype), (column 11 = reference assembly)
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| Submission date |
Apr 26, 2021 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL25410 |
| Series (1) |
| GSE165787 |
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes |
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| Relations |
| BioSample |
SAMN18875571 |
| SRA |
SRX10682826 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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