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| Status |
Public on May 01, 2017 |
| Title |
WT_singlecell_RNA-seq |
| Sample type |
SRA |
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| Source name |
semi-in-vivo of wild type pollen tubes
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| Organism |
Arabidopsis thaliana |
| Characteristics |
pollen tube: tissue
developmental stage: 300-400 um outside of the style
genotype: wild type
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| Treatment protocol |
About 500-600 double mutant pollen grains were hand-picked under a stereoscopic microscope and pollinated on a single stigma (emasculated for 36 hours) and cut together with the style. When the SIV PTs grew about 300-400 μm outside of the style, they were cut from the end of the style with tiny scissors (VANNAS, 8.5 cm, STR) under a stereo microscope.
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| Growth protocol |
pollen tubes were growed on the solid pollen germination medium (SPGM), which10% sucrose, 0.01% boric acid, 5 mM CaCl2, 5 mM KCl, 1 mM MgSO4 and pH=7.5.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Pollen tubes cut from two independent stigmas were pooled and directly placed into cell lysis buffer [0.45 μL 10×PCR buffer II, 0.27 μL 25 mM MgCl2, 0.225 μL 10% NP40, 0.225 μL 0.1 M DTT, 0.045 μL SUPERase-In (20 U/μL, Ambion), 0.045 μL RNase inhibitor (40 U/μL, Ambion), 0.125 μL 0.5 μM V1-T24 Primer, 0.09 μL 2.5 mM dNTP Mix, add H2O to 4.45 μL] and lysed by vortexing. The lysed solution was used to generate the cDNA libraries.
The cDNA libraries follow the Smart-seq2 protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Tophat (version 2.0.14) was used to map the Arabidopsis thaliana genome
Cufflinks (version 2.2.1) was used to normalize and verify expression level (FPKM: Fragments Per Kilobase of exon model per Million mapped fragments) of the two samples
Genome_build: Arabidopsis thaliana genome of TAIR10 version
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for two samples
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| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
huang jiaying |
| E-mail(s) |
1584030896@qq.com
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| Phone |
13011277622
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| Organization name |
Peking University
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| Department |
School of life science
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| Lab |
Qu Lijia
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| Street address |
Yiheyuan Road
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| City |
Bei Jing |
| ZIP/Postal code |
010 |
| Country |
China |
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| Platform ID |
GPL21785 |
| Series (1) |
| GSE98145 |
Sperm cells are passive cargo of the pollen tube in plant fertilization |
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| Relations |
| BioSample |
SAMN06828999 |
| SRA |
SRX2762987 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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