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| Status |
Public on Jun 01, 2024 |
| Title |
captured mRNA-derived cDNA, 42-DAP seeds, rep 3, second experiment |
| Sample type |
SRA |
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| Source name |
developing seed
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| Organism |
Xanthomonas citri pv. fuscans |
| Characteristics |
tissue: developing seed
time: Day 42
cell type: bacteria
genotype: 7767-R pBBR1MCS-2::gfp6
treatment: spray inoculation of bean with 10^6 cfu/ml
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| Treatment protocol |
Bacteria were extracted by soaking seeds overnight in PBS containing 20% blocking agent (RNAlater, ThermoFisher scientific).
Macerates were centrifuged 15 min at 15,000 g and total RNAs were extracted from the pellet.
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| Growth protocol |
Bacterial suspension (106 cfu/ml) were spray-inoculated on bean at pre-flowering stage. Seeds of five plants were harvested and bulked to form a sample. Seeds were sampled 24, 35 and 42 days after pollination (DAP).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol at 65°C. Depending on RNA quality, 100 to 200 ng of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelectXT RNA Direct technology (Agilent) according to supplier instructions. Probes (120 nt) for bacterial mRNA capture were designed from annotated CFBP 7767 genomic sequence.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
42-3
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| Data processing |
Sequence reads were trimmed for adapter and low-quality sequence directly within Illumina NextSeq 550 software
Genomic sequence of strain CFBP 7767 was annotated using Eugene-PP and InterproScan results for structural and functional annotations, respectively.
Salmon was used to assign reads to predicted CFBP7767 mRNA.
Assembly: GCF_002759375.1 : Pacbio assembly of genomic sequence of CFBP 7767 (ASM275937v2: NZ_CP021012.1, NZ_CP021013.1, and NZ_CP021014.1) was used for alignment (Briand, M., Ruh, M., Darrasse, A., Jacques, M.-A., and Chen, N. W. (2021). Complete and Circularized Genome Sequences of 17 Xanthomonas Strains Responsible for Common Bacterial Blight of Bean. Microbiol Resour Announc 10, e00371-21).
Supplementary files format and content: tab-delimited text files (.sf) include count and TPM values for each sample
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| Submission date |
Mar 15, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Martial Briand |
| Organization name |
INRAE
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| Street address |
42, rue Georges Morel
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| City |
Beaucouzé |
| ZIP/Postal code |
49071 |
| Country |
France |
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| Platform ID |
GPL33255 |
| Series (2) |
| GSE227386 |
Xanthomonas citri pv fuscans transcriptomic changes during the contamination of Phaseolus vulgaris seeds |
| GSE227421 |
Molecular dialogue between Phaseolus vulgaris seed and Xanthomonas (Xcf) bacteria interactions during seed transmission |
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| Relations |
| BioSample |
SAMN33768497 |
| SRA |
SRX19680436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7099732_42_3.sf.gz |
77.3 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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