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| Status |
Public on Jul 01, 2024 |
| Title |
H26.2 |
| Sample type |
SRA |
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| Source name |
pistachio hull (pericarp)
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| Organism |
Pistacia vera |
| Characteristics |
tissue: pistachio hull (pericarp)
sampling (growing_degree_days,_c): 1657
cultivar: Kerman
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| Extracted molecule |
total RNA |
| Extraction protocol |
At each time point pistachio fruit hull (exocarp) and shell (endocarp), and kernel (seed) tissue were separated, and flash frozen with liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as paired-end 150-bp reads on an Illumina Hiseq X Ten platform by IDseq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Quality and adapter trimming was done with Trimmomatic v0.39 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 v2.3.4.1 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v0.913
Assembly: Pistacia vera c.v. Kerman (BioProject PRJNA1049825)
Supplementary files format and content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads
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| Submission date |
May 10, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Barbara Blanco-Ulate |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, Davis
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| Department |
Plant Sciences
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| Lab |
Blanco Lab
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| Street address |
1 Shields Ave.
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL34465 |
| Series (1) |
| GSE267225 |
In a nutshell: pistachio genome and kernel development |
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| Relations |
| SRA |
SRX24523259 |
| BioSample |
SAMN41342281 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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