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| Status |
Public on May 28, 2021 |
| Title |
B73_seedling_rep1 |
| Sample type |
SRA |
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| Source name |
B73_seedling
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| Organism |
Zea mays |
| Characteristics |
genotype: B73
developmental stage: V1
tissue: Seedling
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| Extracted molecule |
total RNA |
| Extraction protocol |
16,000 nuclei were used to construct each library via nuclei lysis, wash, and centrifugation steps.
10X Genomics scRNA-seq Chromium Next GEM Single Cell 3' v3.1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
cellranger count (v4.0.0)
filter barcodes with less than 1000 UMIs and 500 expressed genes
filter barcodes below 1 standard deviation from the mean fraction of nuclear derived UMIs
filter barcodes above 1 standard deviation from the mean fraction of mitocondrial and chloroplast derived UMIs
Genome_build: B73 AGP v4
Supplementary_files_format_and_content: Binary triplet matrix format of geneIDs (column 1), nuclei ID (column 2), and UMI counts (column 3)
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| Submission date |
May 27, 2021 |
| Last update date |
May 28, 2021 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
[email protected]
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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) |
| GSE155178 |
A cis-regulatory atlas of maize single cells |
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| Relations |
| BioSample |
SAMN19370142 |
| SRA |
SRX11007102 |
| 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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