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| Status |
Public on Apr 19, 2023 |
| Title |
h33 RNA seq1 |
| Sample type |
SRA |
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| Source name |
18-day-old seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 18-day-old seedling
cell type: somatic cells
genotype: hot3-3
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| Growth protocol |
16 hr light/8 hr dark, 23˚C
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from 18-day-old seedlings using TRI Reagent (MRC, TR118) according to the manufacturer’s instructions. 4 ug of DNase-treated total RNA was used for the construction of sequencing libraries.
Polyadenylated RNA isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) was subjected to RNA-seq library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
hot3-3 Seedling, rep1
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| Data processing |
Paired reads were trimmed by cutadapt v4.2 and then mapped to the Arabidopsis genome Araport11 using STAR v2.7.10b with parameters "--alignIntronMax 5000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Read pairs mapped to coding transcripts were counted by featureCounts v2.0.3 with parameters "-p --countReadPairs -B -C -O".
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt files containing gene accession, raw read counts, and gene length.
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| Submission date |
Jan 18, 2023 |
| Last update date |
Apr 19, 2023 |
| Contact name |
Chenjiang You |
| E-mail(s) |
chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
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| Organization name |
Fudan University
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| Street address |
2005 Songhu Rd
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL26208 |
| Series (2) |
| GSE223169 |
Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (RNA-Seq) |
| GSE223172 |
Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation |
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| Relations |
| BioSample |
SAMN32782809 |
| SRA |
SRX19062581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6940586_hot33_1.txt.gz |
175.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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