|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jun 26, 2024 |
Title |
HM-biolrep1 |
Sample type |
SRA |
|
|
Source name |
Mesophyll
|
Organism |
Gossypium hirsutum |
Characteristics |
tissue: Mesophyll
|
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
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
|
|
|
Submission date |
Jun 24, 2024 |
Last update date |
Jun 26, 2024 |
Contact name |
Brendan MORMILE |
E-mail(s) |
mormileb@umich.edu
|
Organization name |
University of Michigan
|
Street address |
211 redmond drive
|
City |
college station |
State/province |
Texas |
ZIP/Postal code |
77840 |
Country |
USA |
|
|
Platform ID |
GPL16485 |
Series (1) |
GSE270600 |
Activation of three targets by a TAL effector confers susceptibility to bacterial blight of cotton |
|
Relations |
BioSample |
SAMN42020255 |
SRA |
SRX25039125 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
|
|
|
|
|