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| Status |
Public on Apr 21, 2023 |
| Title |
Gbi48L_biol rep 1 |
| Sample type |
SRA |
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| Source name |
cotyledons
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| Organism |
Gossypium bickii |
| Characteristics |
tissue: cotyledons
time: 48-hours after imbibition
treatment: under light
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA was used for cDNA library construction with the NEBNext Ultra RNA Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform. Illumina short paired-end reads produced previously were trimmed using Trimmomatic (v.0.36) with default parameters. The high-quality reads were aligned to the G. bickii genome using HISAT2 (v.2.0.4). The counts of reads aligned to each transcript were calculated with HTSeq (v.0.6.0) software, and fragments per kilobase of transcript per million mapped fragments were used to estimate the expression level of each gene.
Assembly: Gossypium bickii (G1) genome JZU_v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Feb 05, 2023 |
| Last update date |
Apr 21, 2023 |
| Contact name |
Yue SUN |
| E-mail(s) |
[email protected]
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| Organization name |
Zhejiang University
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| Street address |
Yuhangtang Rd
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL33091 |
| Series (2) |
| GSE224574 |
Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq] |
| GSE224635 |
Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii |
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| Relations |
| BioSample |
SAMN33098882 |
| SRA |
SRX19286940 |
| 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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