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| Status |
Public on Nov 08, 2018 |
| Title |
V1 (TRIGL-BDS-EUCGR) |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Tristaniopsis glauca |
| Characteristics |
tissue: leaf
leaf age: Young leaf
rust phenotype: infected
sampling site: natural field
bioanalyzeur rna concentration ng/µl: 114
rrna ratio [25s/18s]: 3.4
rin: 8.4
illumina adaptator: 22
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| Treatment protocol |
Liquid nitrogen conservation
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| Extracted molecule |
total RNA |
| Extraction protocol |
CTAB RNA extraction protocol
Illumina Truseq RNA Sample Preparation Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V1_CGTACG_L003
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| Data processing |
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (Hisat 2.04)
Differential Gene Expression analysis of infected V1, V2, V6 and V7 (considered as susceptible) versus healthy V3 and V4 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:7], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: GCF_000612305.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample and logFC, Pvalue and FDR for each gene
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| Submission date |
Nov 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Laurent Maggia |
| E-mail(s) |
laurent.maggia@cirad.fr
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| Organization name |
Cirad
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| Department |
BIOS
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| Lab |
AGAP
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| Street address |
TA A-108 / 03 Av. Agropolis
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| City |
montpellier |
| ZIP/Postal code |
34398 Cedex 5 |
| Country |
France |
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| Platform ID |
GPL24254 |
| Series (2) |
| GSE106740 |
Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-EUCGR] |
| GSE106750 |
Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) |
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| Relations |
| BioSample |
SAMN08007241 |
| SRA |
SRX3380993 |
| 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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