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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 24, 2020 |
| Title |
G34 genotype replicate 3 - no salt stress |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Arundo donax |
| Characteristics |
tissue: Leaf
genotype: G34
treatment: Sample weekly irigated with water with no NaCl
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| Treatment protocol |
Water with no NaCl for CK samples, 250 mM NaCl for S3 samples, 420 mM NaCl for S4 samples
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| Growth protocol |
Weekly irrigation with water
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction with SpectrumTM Plant Total RNA Extraction kit (Sigma – Aldrich, St. Louis, MO).
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library was ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
G34_CK3
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| Data processing |
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
In the absence of a reference genome clean reads have been assembled using Trinity software (K 25, Kmer coverage 2). Corset software was used for hierarchical clustering
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq used for gene expression difference analysis
Genome_build: FASTA assembled sequences
Supplementary_files_format_and_content: Sample_annotation.xls: annotation result of genes expressed in each sample; FASTA assembled sequences: FASTA file containing sequences of assembled reads;
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| Submission date |
Oct 22, 2018 |
| Last update date |
Feb 25, 2020 |
| Contact name |
Angela Roberta Lo Piero |
| E-mail(s) |
rlopiero@unict.it
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| Phone |
+39-0957580238
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| Organization name |
University of Catania
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| Department |
Di3A
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| Lab |
Plant genetics
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| Street address |
Via S. Sofia 98
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| City |
Catania |
| State/province |
CT |
| ZIP/Postal code |
95123 |
| Country |
Italy |
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| Platform ID |
GPL25702 |
| Series (1) |
| GSE125104 |
Transcriptomic genotype-dependent response of Arundo donax L. under salt stress. |
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| Relations |
| BioSample |
SAMN10266239 |
| SRA |
SRX5250870 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3439150_G34_CK3_annotation.txt.gz |
16.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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