|
| Status |
Public on Mar 24, 2024 |
| Title |
C24×Col-clf_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
genotype: hybrid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Trizol(Invitrogen, CA, USA). RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
Poly-A RNASeq library preparation and high-throughput sequencing were performed by Wuhan Frasergen Bioinformatics Co. Ltd and we used the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) to generate sequencing libraries, following the manufacturer’s recommendations.
Libraries were sequenced based on Novaseq 6000 guidelines (Illumina). Three biological replicates were performed for RNA-seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastp was used to filter low-quality reads from raw RNA-seq data.
We used STAR to map the filtered reads to TAIR10 genome reference.
The mapped file was filtered by Samtools to retain the unique mapping reads.
The differential expression genes between every two samples were analyzed using Cuffdiff.
Assembly: Tair10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 04, 2023 |
| Last update date |
Mar 24, 2024 |
| Contact name |
Xu Zhao Gao |
| E-mail(s) |
gaozx@pku.edu.cn
|
| Organization name |
Peking University
|
| Department |
College of Biological Sciences
|
| Lab |
Plant molecular genetics and agricultural biotechnology research laboratory
|
| Street address |
The Summer Palace Road No. 5
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE222132 |
Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids (clf) |
|
| Relations |
| BioSample |
SAMN32575289 |
| SRA |
SRX18924030 |
