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| Status |
Public on Jun 26, 2024 |
| Title |
HM-biolrep3 |
| Sample type |
SRA |
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| Source name |
Mesophyll
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| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: Mesophyll
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Spectrum Plant Total RNA Kit (Sigma-Aldrich) and 1 μg of purified RNA was used for construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kit following the manufacturer’s protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Trimmomatic tool was used to preprocess raw RNA-seq reads by performing quality filtering and trimming of low-quality bases from sequencing reads to ensure that only high-quality reads were used for alignment and assembly.
The alignment of RNA-seq reads to the G. hirsutum (AD1) TM-1 genome was executed using HISAT2, employing an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini index.
Transcriptional assembly was conducted using StringTie, which reconstructed full-length transcripts from aligned reads while estimating their abundance and quantifying gene expression levels.
Differential gene expression was analyzed using Cuffdiff, a component of the Cufflinks suite, which facilitated the comparison of transcript abundances between different treatments.
Genes were considered differentially expressed if they demonstrated a log2 fold expression change >1 and an adjusted p-value < 0.05.
Assembly: G. hirsutum (AD1) TM-1 genome was used for the RNA-seq read alignment
Supplementary files format and content: Excel file includes transcript abundances, log2 fold expression changes, p-values, and gene annotations
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| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Brendan MORMILE |
| E-mail(s) |
mormileb@umich.edu
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| Organization name |
University of Michigan
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| Street address |
211 redmond drive
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| City |
college station |
| State/province |
Texas |
| ZIP/Postal code |
77840 |
| Country |
USA |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE270600 |
Activation of three targets by a TAL effector confers susceptibility to bacterial blight of cotton |
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| Relations |
| BioSample |
SAMN42020253 |
| SRA |
SRX25039127 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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