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| Status |
Public on Jun 30, 2020 |
| Title |
TJ rep1 |
| Sample type |
SRA |
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| Source name |
meristems from juvenile TX701 seedlings
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| Organism |
Gossypium hirsutum |
| Characteristics |
accession: wild photoperiodic Texs 701 (TX701)
tissue: meristem
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| Treatment protocol |
Apices from DP61 and TX701 cotton were harvested at different developmental stages. Apices were fixed in acetone, and meristems and flanking leaves were dissected with the aid of a SMZ 1500 stereomicroscope (Nikon, Melville, NY, USA). The developmental stages from which meristems were harvested included: (1) monopodial main stem from juvenile DP61; (2) monopodial main stem from juvenile TX701; (3) adult monopodial main stem from TX701 grown under non-inductive long days (plants were not flowering); (4) monopodial lateral branches from TX701 grown under non-inductive long days (plants were not flowering); (5) adult monopodial main stem from TX701 grown under inductive short days after the transition to reproductive growth (plants had flowering sympodial branches); and (6) adult sympodial fruiting branches from TX701 grown under inductive short days (flowering sympodial branches). Abbreviations are as follows: D = DP61; T = TX701; DJ/TJ = juvenile meristems; DJL/TJL = immature leaves flanking DJ/TJ meristems; TL20/TS20 = meristem from the branch at node 20 of TX701 plants grown under long (L) or short (S) days; TL20L/TS20L = immature leaves flanking the TL20/TS20 meristems; TLM/TSM = monopodial main stem meristem from mature TX701 plants grown under long (L) or short (S) days; TLML/TSML = immature leaves flanking the TLM/TSM meristems.
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| Growth protocol |
Plants were grown under 16 h/8 h long (L) or 10 h/14 h short (S) days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot borate (Wan and Wilkins, 1994) followed by column-purification (Zymo Research, Irvine, CA, USA), and mRNA amplified (one-round) with TargetAmp Amplification Kit (Epicenter, Madison, WI, USA). Amplified mRNA was quantified by bioanalyzer (Agilent, Santa Clara, CA, USA), and 125 ng used to prepare Illumina TruSeq mRNA stranded libraries (Illumina, Inc., San Diego, CA, USA).
125 ng of amplified mRNA was used to prepare Illumina TruSeq mRNA stranded libraries (Illumina, Inc., San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
TJ1_AGTCAA_L002
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| Data processing |
Read quality was checked using Fastqc.
Reads were aligned to the G. hirsutum TX JGI assembly v.1.0 and annotation v.1.1 reference genome (Saski et al., 2017) 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.
Genome_build: Gossypium 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: Text file of Cuffdiff output comparing FPKM values for each coding sequence across all samples.
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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) |
| GSE144544 |
SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures [meristems] |
| 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 |
SAMN13945928 |
| SRA |
SRX7652117 |
| 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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