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| Status |
Public on Dec 25, 2022 |
| Title |
Ray-rep1 |
| Sample type |
SRA |
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| Source name |
SDX
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| Organism |
Populus trichocarpa |
| Characteristics |
cell type: Ray parenchyma cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from dissected cells was extracted using RNeasy Plant Mini Kit (QIAGEN, USA) and the mRNA was amplified using Arcturus® RiboAmp® HS PLUS RNA Amplification Kit (Applied Biosystems, USA)
RNA sequencing libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Cell_type_TPM_Ptr.txt
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| Data processing |
Details of data processing steps are provided in the manuscript.
Genome_build: Phytozome Populus trichocarpa genome v4.1, Phytozome Eucalyptus grandis genome v2.0, Liriodendron chinense genome (Chen et al., 2018), Trochodendron aralioides genome (Strijk et al., 2019)
Supplementary_files_format_and_content: For P. trichocarpa and L. chinense, the raw UMI counts of unfiltered (raw) and cellular (filtered) barcodes were generated using Cell Ranger (v5.0.1) including H5 files and tar archives containing sparse matrices (MTX files) and feature and barcode sequences (TSV files).
Supplementary_files_format_and_content: For E. grandis and T. aralioides, the raw UMI counts of unfiltered barcodes in TXT format were generated using the MARS-seq2.0 pipeline. The raw UMI counts of the barcodes with more than or equal to 100 UMI counts were then converted to H5 files for Cell Ranger.
Supplementary_files_format_and_content: For three SDX cell types of Populus trichocarpa, the TPM of each gene are in TXT format.
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| Submission date |
Jul 14, 2021 |
| Last update date |
Dec 25, 2022 |
| Contact name |
Ying-Chung Jimmy Lin |
| E-mail(s) |
ycjimmylin@ntu.edu.tw
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| Phone |
+886-2-33662509
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| Organization name |
National Taiwan University
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| Department |
Department of Life Science
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| Street address |
No. 1, Sec. 4, Roosevelt Rd.
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| City |
Taipei |
| ZIP/Postal code |
106319 |
| Country |
Taiwan |
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| Platform ID |
GPL26322 |
| Series (1) |
| GSE180121 |
Single-cell transcriptomics unveils xylem cell development and evolution |
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| Relations |
| BioSample |
SAMN20219569 |
| SRA |
SRX11449517 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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