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| Status |
Public on Apr 06, 2021 |
| Title |
Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Seeds are the basis of agriculture, yet their full transcriptional complexity has remained unknown. Here, we employ single-nucleus RNA-sequencing to characterize developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the site of gene imprinting in plants, mediates the relationship between the maternal parent and embryo. We identify new cell types in the chalazal endosperm region, which interfaces with maternal tissue for nutrient unloading. We further demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. These data indicate imprinting in endosperm is heterogeneous and suggest that parental conflict, which is proposed to drive the evolution of imprinting, is fiercest at the boundary between filial and maternal tissues.
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| Overall design |
To identify cell/nuclei types and investigate imprinting dynamics within endosperm, single nucleus RNA-seq was performed using the Smart-seq2 method on seed nuclei, targeting either the 3C or 6C FANS peak in order to enrich for triploid endosperm (other seed tissues are diploid). A total of 1,664 libraries were sequenced, of which 64 were negative controls (no DNA in library prep or no cell sorted), 51 were made from two nuclei to test single-nuclei sorting accuracy, 112 failed QC checks (< 1,500 genes detected and/or <1,000 detected with 5+ reads), and the remaining 1,437 were high-quality single-nuclei libraries used in final analysis. The final dataset consists primarily of seeds derived from Col, Cvi reciprocal crosses at 4 days after pollination (DAP), although some nuclei were instead obtained from Col, Ler crosses and/or other timepoints.
Please note that the counts.txt files for the P17_10A, P21_10A, and P22_10A samples are identical as they are from negative controls that should not have any reads mapping to A. thaliana.
There are ~50 negative controls in the dataset, and most have at least one or two reads falling in a gene somewhere and so the processed data files (read counts per gene) aren't exactly the same, but the read counts in all three files are actually zero for all genes, so all three files are identical.
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| Contributor(s) |
Picard CL, Povilus RA, Williams BP, Gehring M |
| Citation(s) |
34059805 |
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| Submission date |
Aug 30, 2020 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Colette L Picard |
| E-mail(s) |
clpicard@ucla.edu
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| Organization name |
University of California - Los Angeles
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| Department |
Molecular, Cell and Developmental Biology
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| Lab |
Colette L Picard
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| Street address |
610 Charles E Young Dr East, Room 4045
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (2) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (1664)
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| Relations |
| BioProject |
PRJNA660263 |
| SRA |
SRP279357 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157145_CPM_total_expression.txt.gz |
23.0 Mb |
(ftp)(http) |
TXT |
| GSE157145_RAW.tar |
156.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE157145_norm_maternal_counts.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE157145_norm_paternal_counts.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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