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| Status |
Public on Apr 07, 2023 |
| Title |
JA-2H |
| Sample type |
SRA |
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| Source name |
Root tips
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Root tips
genotype: Col-0
treatment: 2H 50µM Jasmonate
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| Extracted molecule |
total RNA |
| Extraction protocol |
6-day-old seedlings were transferred to 10 μM BAP-supplemented medium or an equal volume of DMSO as mock treatment and allowed to grow for 2 h. The root tips were then cut and incubated in protoplasting Solution B (1.5% (wt/vol) cellulysin and 0.1% (wt/vol) pectolyase in Solution A (600 mM mannitol, 2 mM MgCl2, 0.1% (wt/vol) bovine serum albumin, 2 mM CaCl2, 2 mM MES, 10 mM KCl, pH 5.5)) for approximately 1 h at room temperature. Cells were filtered through a 70 μm cell strainer and spun down at 200 g for 6 min, resuspended in Solution A, filtered through a 40 μm cell strainer and stained for live/dead using 4′,6-diamidino-2-phenylindole (DAPI) at 14 μM final concentration. Cells were sorted on a BD Aria II and protoplasts without the DAPI signal were selected for further analysis.
Sorted cells were centrifuged at 400 g at 4 °C and resuspended in Solution A to yield an estimated concentration of 1,000 cells per μl. Cellular suspensions were loaded on a Chromium Single Cell 3′ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) according to the manufacturer’s instructions. Sequencing libraries were loaded on an Illumina HiSeq4000 and sequenced following recommendations of 10X genomics
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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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| Description |
AGO002
10x Genomics
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| Data processing |
BCL files were demultiplexed using Cell Ranger mkfastq
FastQ files were processed using the Cell Ranger 3.1.0 count pipeline
Assembly: TAIR10.40
Supplementary files format and content: h5 files containing the count matrix (output from Cell Ranger)
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| Submission date |
Sep 07, 2022 |
| Last update date |
Apr 08, 2023 |
| Contact name |
Jana Roels |
| E-mail(s) |
jana.roels@vib.be, niels.vandamme@vib.be
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| Organization name |
VIB
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| Department |
VIB Single cell core
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| Street address |
Technologiepark-Zwijnaarde 71
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| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE212826 |
Gene expression profile of Arabidopsis root tip cells exposed to 2 hours of 50µM jasmonate |
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| Relations |
| BioSample |
SAMN30712193 |
| SRA |
SRX17466737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6553071_filtered_feature_bc_matrix.h5 |
31.7 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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