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| Status |
Public on Feb 14, 2024 |
| Title |
stress_1 |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Abies koreana |
| Characteristics |
stress: drought stress
treatment: YPD broth with 250 microg/mL Tween-20
age: three-years-old
genotype: wild type
tissue: seedlings
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| Treatment protocol |
After adjusting the optical density of the AK-10 culture to 0.8, Tween-20 was added to a final concentration of 250 µg/mL. This mixture was foliar-sprayed onto seedlings three times: 7 d before, 4 d before, and 4 d after the initiation of drought stress. A control treatment was YPD broth with 250 µg/mL Tween-20.
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| Growth protocol |
Three-year-old A. koreana seedlings were obtained, and maintained in a greenhouse at 25 ± 5°C with daily watering. Drought stress was simulated by withholding water. The AK10 treatment was performed by culturing in yeast extract peptone dextrose (YPD) broth for 24 h at 25°C under constant agitation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
After surface sterilization with 70% ethanol and rinsing, 1 g of leaf tissue was ground in liquid nitrogen and homogenized in 15 mL of extraction buffer (100 mM Tris-HCl, 2% CTAB, 30 mM ethylenediaminetetraacetic acid, 2 M NaCl, 0.05% spermidine, 2% polyvinylpolypyrrolidinone, 2% 2-mercaptoethanol, and 1.5 mg/mL proteinase K). After incubation at 42°C for 90 min and chloroform-isoamyl alcohol extraction, RNAs were precipitated with 10 M LiCl, washed with ethanol, and resuspended in diethylpyrocarbonate-treated water.
Using the TruSeq RNA Sample Preparation Kit (Illumina, CA, USA), 1 µg of total RNAs was processed to produce cDNA libraries. These libraries were sequenced on a HiSeq 2000 platform (Illumina) by Macrogen (Seoul, Korea), generating 101-bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Korean fir seedlings under the drought stress state
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| Data processing |
Raw fastq.gz reads were refined using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Raw fastq.gz reads were refined by eliminating sequences with suboptimal quality scores. A bespoke Python script ensured the alignment of the forward and reverse reads.
Curated reads were mapped to the reference genome using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Using SAMtools, we converted the mapping outcome from SAM to BAM format and sorted it according to genomic coordinates.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Pseudotsuga menziesii GCA_001517045.1
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample
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| Submission date |
Nov 21, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Jungwook Park |
| E-mail(s) |
jjuwoogi@pusan.ac.kr
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| Organization name |
Pusan National University
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| Department |
Microbiology
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| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
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| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
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| Platform ID |
GPL33945 |
| Series (1) |
| GSE248350 |
RNA-seq based in vivo transcriptomes of Korean fir (Abies koreana) with enhanced drought tolerance by Aureobasidium pullulans AK10 |
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| Relations |
| BioSample |
SAMN38344913 |
| SRA |
SRX22592798 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7911909_stress_1_rpkm.txt.gz |
12.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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