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| Status |
Public on Jun 30, 2020 |
| Title |
DP61 dCLCrV:GhSFT rep2 |
| Sample type |
SRA |
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| Source name |
DP61 dCLCrV:GhSFT_shoot apex at 15 dpi
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| Organism |
Gossypium hirsutum |
| Characteristics |
accession: domesticated day-neutral Delta Pine 61 (DP61)
virus inoculation: dCLCrV:GhSFT
genotype/variation: over-expressing GhSFT
tissue: Shoot apex (5 mm) harvested at 15 days post-inoculation
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| Treatment protocol |
Virus construction and inoculations were as described (McGarry et al., 2016).
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| Growth protocol |
Cotton was germinated in a 25°C growth chamber. At 4 days post-germination, seedlings remained uninoculated or the cotyledons were infiltrated with Agrobacterium tumefasciens GV3101 pMP90 harboring viral constructs. Following inoculations, plants were covered with a dome, incubated at room temperature overnight, and returned to the same 25°C growth chamber.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At 15 days post-inoculation, apices were excised from inoculated seedlings and uninoculated controls, fixed in acetone with vacuum-infiltration, and acetone changed twice before storing at 4°C. Acetone-dried apices were trimmed to 5 mm and expanding leaves were removed. Dried samples were frozen in liquid nitrogen, homogenized using a Retsch mill (Retsch GmbH, Haan, Germany), and RNA isolated by hot borate (Wan and Wilkins, 1994) followed by column clean-up (Zymo Research, Irvine, CA, USA).
2 µg of total RNA from uninoculated, dCLCrV:GhSFT-, and TRV:GhSP-infected DP61 and TX701 plants were used to prepare Illumina TruSeq Stranded mRNA libraries (Illumina, Inc., San Diego, CA, USA) as per the manufacturer's protocols, with three biological replicates per treatment per accession. Libraries were sequenced on a HiSeq2000 (the University of Texas Southwestern Genomics Core), and >30 million 50 bp single-end reads were obtained per replicate.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
DPCLCrV-SFT2_CAGATC_L005
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| Data processing |
Read quality was checked using FastQC.
Reads were aligned to the G. hirsutum JGI reference genome sequence using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Reads were aligned to the Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019) using the Tuxedo suite pipeline (TopHat v2.0.9 with Bowtie v2.1.0).
Gene FPKM (fragments per kilobase of exon model per million mapped fragments) values as normalized gene expression levels were calculated with Cufflinks v2.1.1.
Cuffdiff v2.1.1 was used to determine significant differences in gene expression between pair-wise comparisons using q ≤ 0.05 where q is the Benjamini-Hochberg correction to reduce false positives.
All of the above steps were conducted in the Discovery Environment at CyVerse.
Genome_build: G. hirsutum TX JGI assembly v.1.0 and annotation v.1.1 reference genome (Saski et al., 2017).
Genome_build: Gossypium hirsutum TM-1 genome CRI assembly v1_a1 reference genome (Yang et al., 2019).
Supplementary_files_format_and_content: Processed data file is a text file from the Cuffdiff output comparing FPKM values for each coding sequence across all treatments.
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| Submission date |
Jan 30, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Roisin C McGarry |
| Organization name |
University of North Texas
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| Department |
Dept. of Biological Sciences, BioDiscovery Institute
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| Street address |
1511 West Sycamore
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| City |
Denton |
| State/province |
TX |
| ZIP/Postal code |
76201 |
| Country |
USA |
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| Platform ID |
GPL16485 |
| Series (2) |
| GSE144545 |
SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures [GEO_SFT_SP] |
| GSE144546 |
SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures. |
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| Relations |
| BioSample |
SAMN13945892 |
| SRA |
SRX7651957 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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