 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 30, 2024 |
| Title |
cotyledon seed, replicate 1, scRNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
cotyledon stage seed cells
|
| Organism |
Glycine max |
| Characteristics |
tissue: cotyledon stage seed cells
genotype: Williams 82
|
| Growth protocol |
Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Fresh cotyledon stage seeds were hand chopped in lysis buffer (15mM Tris pH7.5, 20mM NaCl, 80mM KCl, 0.5mM Spermine, 5mM 2-ME, 0.05% Triton X-100, 80U/ml RNase inhibitor (Roche, 3335399001)), then filtered through 40um and 20um nylon mesh. Nuclei were diluted with 3 volumes cold wash buffer (20mM MES pH5.4, 0.4M Mannitol, 20mM KCl, 0.1% BSA, 80U/ml RNase inhibitor), and resuspended in 1ml cold wash buffer. DAPI-stained nuclei were counted on a hemocytometer, spun again and resuspended to achieve a target concentration of 3500 nuclei/ul.
Library was constructed using 10,000 nuclei, following 10X Genomics protocol for Chromium Next GEM Single Cell Multiome ATAC+Gene expression v1 assay.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calls were processed into fastq files using Illumina bcl2fastq v2.20.0.422.
Raw files were analyzed by 10X Genomics Cell Ranger ARC v1.0, using a custom soybean reference ( built using genome version Wm82.a2.v1).
Single-cell feature counts were generated using the "count" function.
Ambient RNA contamination was removed using the R package SoupX v1.6.1 with default parameters and the resulting snRNA count matrix was imported in Seurat v4.1.1 for downstream analyses.
Assembly: Wm82.a2.v1
Supplementary files format and content: SoupX_filtered_matrix.mtx contains detected, cell-associated barcodes in Matrix Market Exchange (MEX) format. The matrix elements are the number of UMIs associated with a feature (row) and a barcode (column), after ambient RNA contamination was removed using SoupX. The TSV files correspond to the gene IDs and cellular barcodes.
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains the features detected (genes and peaks) in rows, while the columns consist of all cell-associated barcodes. The format is the Hierachical Data Format (H5).
Supplementary files format and content: atac_fragments.tsv.gz and atac_peaks.bed are fragments created by two separate transposition events and the genomic intervals having local enrichment of transposase cut-sites, respectively, in BED format.
|
| |
|
| Submission date |
Sep 13, 2023 |
| Last update date |
Sep 30, 2024 |
| Contact name |
John Harada |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California
|
| Department |
Plant Biology
|
| Lab |
Harada lab
|
| Street address |
One Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE243174 |
Single-cell Multiomic profiling of soybean cotyledon-stage seeds |
|
| Relations |
| BioSample |
SAMN37387550 |
| SRA |
SRX21773690 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7780242_SoupX_filtered_matrix.mtx.gz |
87.9 Mb |
(ftp)(http) |
MTX |
| GSM7780242_barcodes.tsv.gz |
34.2 Kb |
(ftp)(http) |
TSV |
| GSM7780242_genes.tsv.gz |
255.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
