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| Status |
Public on Feb 28, 2014 |
| Title |
La Calamine 3 |
| Sample type |
SRA |
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| Source name |
La Calamine
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| Organism |
Noccaea caerulescens |
| Characteristics |
ecotype: La Calamine
origin: Zn/Pb mine spoil (calamine)
metal accumulation and tolerance: Assunção, A.G.L., et al. 2003. New Phytol. 159, 411-419.
tissue: pool of 12 root samples
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| Growth protocol |
hydroponic culture as described in Schat, H. et al. 1996. Evolution Int. J. O. Evolution 50, 1888–1895, except for GA and LC 10 µM Zn, for MP 2 µM Zn and 10 µM Ni
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| Extracted molecule |
total RNA |
| Extraction protocol |
The libraries were constructed following the SOLiD™ Total RNA-Seq Kit's (Whole Transcriptome library) protocol, Applied Biosystems Part Number 4452437 Rev A, 01/2010
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Description |
14_LC3
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| Data processing |
Counts: Sequence reads were obtained and mapped to the Arabidopsis (TAIR9) genome using SOLiD Bioscope software with default settings. Counts included.
Genome Build:
14_LC3_counts.txt: TAIR9
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| Submission date |
Feb 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pauliina Halimaa |
| Organization name |
University of Eastern Finland
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| Department |
Department of Biology
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| Street address |
Yliopisonranta 1 E
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platform ID |
GPL15250 |
| Series (1) |
| GSE35900 |
SOLiD sequencing of Noccaea (Thlaspi) caerulescens root transcriptomes from three contrasting ecotypes |
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| Relations |
| SRA |
SRX120303 |
| BioSample |
SAMN00790939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM877220_14_LC3_counts.txt.gz |
6.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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