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| Status |
Public on Jul 08, 2024 |
| Title |
Seed early cotyledon 1 |
| Sample type |
SRA |
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| Source name |
seed
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| Organism |
Glycine max |
| Characteristics |
tissue: seed
strain: Merr. Cultivar 'Williams 82'
age: early stage
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were chopped and passed through a 30µm cell strainer. The filtered nuclei were purified by cell sorting using FACSAria II™ cell sorter (BD Biosciences). An average of 80-100,000 nuclei were collected for each sample, centrifuged, and re-suspended in phosphate buffered saline-bovine serum albumin 0.5%-RNA-inhibitor solution.
Libraries were performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The integration of the replicates and the processing of the data was generated in Seurat.
Assembly: Glycine_max_v2.1.52 From: http://ftp.ensemblgenomes.org/pub/plants/release-52/gtf/; http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/glycine_max/
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| Submission date |
Jun 13, 2023 |
| Last update date |
Nov 08, 2024 |
| Contact name |
Sergio Alan Cervantes-Perez |
| E-mail(s) |
[email protected]
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| Organization name |
University of Arizona
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| Department |
School of Plant Sciences
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| Lab |
Bucksch
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| Street address |
1140 E South Campus Dr
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| City |
Tucson |
| State/province |
Arizona |
| ZIP/Postal code |
85721 |
| Country |
USA |
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| Platform ID |
GPL28801 |
| Series (1) |
| GSE234864 |
Soybean cell atlas gene expression profile |
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| Relations |
| BioSample |
SAMN35725884 |
| SRA |
SRX20672422 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7476019_soybean_seed_early_cotyledon_sample1_barcodes.tsv.gz |
36.5 Kb |
(ftp)(http) |
TSV |
| GSM7476019_soybean_seed_early_cotyledon_sample1_features.tsv.gz |
400.8 Kb |
(ftp)(http) |
TSV |
| GSM7476019_soybean_seed_early_cotyledon_sample1_matrix.mtx.gz |
88.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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