|
| Status |
Public on May 05, 2024 |
| Title |
gmjmj1920-2 leaf RNA-seq, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Glycine max |
| Characteristics |
tissue: Leaf
cell type: somatic cells
genotype: jmj19 jmj20
|
| Growth protocol |
12 hr light/12 hr dark, 25˚C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from 17-day-old leaves using RN38 Reagent (Aidlab Biotechnologies Co.,Ltd) 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired reads were trimmed by cutadapt v4.2 and then mapped to the soybean genome Wm82.a2 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: Wm82.a2.v1
Supplementary files format and content: Tab-delimited txt files containing gene accession, raw read counts, and gene length.
|
| |
|
| Submission date |
May 07, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Chenjiang You |
| E-mail(s) |
chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
|
| Organization name |
Fudan University
|
| Street address |
2005 Songhu Rd
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL28801 |
| Series (2) |
| GSE231885 |
Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean [RNA-seq] |
| GSE231886 |
Histone demethylases JMJ19 and JMJ20 interact with LUX2 to mediate flowering time and adaptation in soybean. |
|
| Relations |
| BioSample |
SAMN34993645 |
| SRA |
SRX20249459 |
