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| Status |
Public on Nov 23, 2023 |
| Title |
RNAseq, Williams 82, 8 hpi, control2 |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Glycine max |
| Characteristics |
tissue: shoot
genotype: Williams 82
treatment: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAGEN RNeasy Plant Mini Kit.
Library construction was performed at Novogene.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RNAseq_wm_8hc2
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| Data processing |
The quality of the sequenced reads was assessed using FastQC and the raw reads from the RNA-seq data were trimmed using Trimmomatic to remove adapters and low-quality reads
The trimmed reads were then aligned to the soybean reference genome, Williams 82 genome assembly v4.0 (Wm82.a4) using HISAT v2.2.1.
In addition, reads with multiple mapping matches were removed using COMEX 2 to retain uniquely mapped reads, and shortest alignments among multiple mapped reads or one alignment at random for each palindromic multiple mapping read if applicable.
The number of reads per gene for each sample was counted using HTSeq.
Assembly: Williams 82 genome assembly v4.0 (Wm82.a4)
Supplementary files format and content: Tab-delimited txt file including the HT-seq counts per gene for each sample.
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| Submission date |
Aug 16, 2023 |
| Last update date |
Nov 23, 2023 |
| Contact name |
Meixia Zhao |
| Organization name |
University of Florida
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| Street address |
1355 Museum Dr
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32611 |
| Country |
USA |
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| Platform ID |
GPL28801 |
| Series (2) |
| GSE240964 |
Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean [RNA-seq] |
| GSE240966 |
Transcriptomic and epigenetic responses unveil resistance mechanisms to Phytophthora sansomeana in soybean |
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| Relations |
| BioSample |
SAMN37004690 |
| SRA |
SRX21381592 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7713059_wm_8hc2.count.txt.gz |
223.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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