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| Status |
Public on Dec 25, 2022 |
| Title |
Tar SDX cells_batch2 |
| Sample type |
SRA |
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| Source name |
SDX protoplasts
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| Organism |
Trochodendron aralioides |
| Characteristics |
cell type: SDX cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
SDX protoplasts were isolated into individual wells of the prepared 384-well plates using cell sorter.
Single-cell sequencing libraries were generated following the MARS-seq2.0 protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Details of data processing steps are provided in the manuscript.
Assembly: Phytozome Populus trichocarpa genome v4.1, Phytozome Eucalyptus grandis genome v2.0, Trochodendron aralioides genome (Strijk et al., 2019)
Supplementary files format and content: For P. trichocarpa, 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 P. trichocarpa, 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.
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| Submission date |
Jun 10, 2022 |
| 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 |
GPL30393 |
| Series (1) |
| GSE180121 |
Single-cell transcriptomics unveils xylem cell development and evolution |
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| Relations |
| BioSample |
SAMN28979461 |
| SRA |
SRX15676562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6234947_MARS-seq_UMItable_Tar_batch2.tar.gz |
13.7 Mb |
(ftp)(http) |
TAR |
| GSM6234947_Tar_batch2_UMI_filtered100.h5 |
3.2 Mb |
(ftp)(http) |
H5 |
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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