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| Status |
Public on Feb 09, 2017 |
| Title |
root_10uM_PO4_B2 |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Zea mays |
| Characteristics |
line: B73
organ: root
organ: whole root system
treatment: 10 uM soil phosphate
age: 21 days
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| Growth protocol |
Maize plants, inbred line B73, were grown for 21 days in a tube-based system supplied with Hoagland solution (Hoagland and Broyer 1936) containing the standard 1000 uM (+P) or a modified 10 uM (-P) concentration of KH2PO4. The concentration of potassium was maintained constant by addition of KCl as required.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was frozen and ground in liquid nitrogen. Total RNA was isolated using the PureLink RNA Mini Kit (Ambionby Life Technologies, CA, USA).
Up to 4ug of total RNA was fragmented, converted to cDNA and enriched by PCR according to the Illumina TruSeq RNA SamplePrep v2 protocol (Illumina, Inc., CA, USA) The libraries were confirmed in agarose gels and quantified using the microplate based PicoGreen® dsDNA quantification assay (Molecular Probes Inc., OR, USA) and Agilent Bioanalyzer system. Illumina’s barcodes were used to pool 10 samples per lane. The pools were quantitated by qPCR, using the Library Quantification kit (Kapa Biosystems, Inc., MA, USA) with the CFX Connect Real-Time PCR Detection System (Bio-rad, CA, USA) and sequenced by the Illumina HiSeq 2500 system using a TruSeq SBS sequencing kit version 3.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls were analysed with Casava 1.8.2 (Illumina, Inc., CA, USA).
Sequenced reads were mapped to the transcripts file of the B73 maize genome, version 284_6a from Phytozome 10, using bowtie2 version 2.2.4 with the parameters --very-sensitive and -a.
Individual SAM output files were used as input for the eXpress software (http://bio.math.berkeley.edu/eXpress/index.html), version 1.5.1, using default parameters.
Genome_build: 6a (Phytozome 10)
Supplementary_files_format_and_content: txt, tab delimited, eXpress output files
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| Submission date |
Dec 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruairidh Sawers |
| E-mail(s) |
rsawers@langebio.cinvestav.mx
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| Organization name |
LANGEBIO-CINVESTAV
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| Street address |
Km 9.6 Lib. N. Car. Irapuato-Leon
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| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36821 |
| Country |
Mexico |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE63779 |
The maize genome encodes novel members of the purple acid phosphatase (PAP) subgroup Ia |
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| Relations |
| BioSample |
SAMN03247912 |
| SRA |
SRX793136 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1557009_B73_R_10_B2_params.xprs.txt.gz |
85.1 Kb |
(ftp)(http) |
TXT |
| GSM1557009_B73_R_10_B2_results.xprs.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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