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| Status |
Public on May 24, 2024 |
| Title |
mock 3 |
| Sample type |
SRA |
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| Source name |
Inflorescence meristem
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Inflorescence meristem
genotype: Columbia-0
developmental stage: two weeks after bolting
treatment: mock
time: 6 hours post-treatment
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| Treatment protocol |
Two weeks after bolting, inflorescence apexes of Arabidopsis 35S:LhG4:GR»HB21 (HB21 ind) plants were treated with dexamethasone, that allows the HB21 expression, or mock. 6-8 hours after treatment inflorescence apexes were collected removing all visible opened flowers.
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| Growth protocol |
Plants were grown at 21°C under long day conditions (16 h light, 8h night), in a 2:1:1 by vol. mixture of peat:perlite:vermiculite.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA for RNA-seq was obtained with the RNeasy Plant Mini Kit (QUIAGEN)
The cDNA libraries were built using the Novogene Company United procedure for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end sequencing (2 × 150 bp) was performed on a MiSeq (Illumina).
Reads were aligned to the reference genome of Arabidopsis thaliana available at the TAIR database (Lamesch et al., 2012) using TopHat (Trapnell et al., 2009) and Bowtie (Langmead et al., 2009) software.
The abundance estimation of the transcripts was performed using the RSEM package (Li and Dewey, 2011) and the differentially expressed transcripts (fragments per kilobase million value) were estimated using Cufflinks (Trapnell et al., 2010).
The sequences from DEG were annotated through BLAST search against the TAIR database
Assembly: Arabidopsis thaliana (TAIT10)
Supplementary files format and content: tab-delimited text file include tpm values for each sample
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| Submission date |
Dec 08, 2023 |
| Last update date |
May 24, 2024 |
| Contact name |
Vicente Balanzà |
| E-mail(s) |
vbalanza@ibmcp.upv.es
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| Organization name |
IBMCP (CSIC-UPV)
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| Department |
Development and hormonal action
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| Lab |
1,09
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| Street address |
Av de los Naranjos s/n
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| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46022 |
| Country |
Spain |
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| Platform ID |
GPL26208 |
| Series (1) |
| GSE249766 |
HB21 induction in Arabidopsis inflorescence apexes |
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| Relations |
| BioSample |
SAMN38735791 |
| SRA |
SRX22836399 |
| 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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