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Sample GSM6131742 Query DataSets for GSM6131742
Status Public on Sep 27, 2023
Title Seedling RNA-seq rep2
Sample type SRA
 
Source name leaf
Organism Oryza sativa
Characteristics ecotype: japonica
developmental stage: Seedling
Treatment protocol Calli were treated with different combinations of transformation treatments.
Growth protocol Plants derived derectly from seeds or regenerated from calli were cultivated until the tillering stage in an Academia Sinica greenhouse under natural light.
Extracted molecule total RNA
Extraction protocol RNA was isolated from leaves of transgenic rice under different treatment groups using RNeasy Plant mini kit (Qiagen) or Trizol for RNA-seq libraries. Genomic DNA was extracted from leaves by using a DNeasy Plant Mini Kit (Qiagen).
RNA-seq libraries were prepared following standard Illumina protocols according to manufacturer’s instructions. The fragmented DNA was then used for library preparation using Illumina's library preparation kits. Premethylated adapter ligated fragments were bisulfite converted using the EZ DNA methylation kit (Zymo Research). The BS-seq libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2500 (Illumina) sequencers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Seedling_2
Data processing Clean RNA-seq reads were mapped to the genome using Tophat.
Fragments per kilobase of transcript per million mapped reads (FPKM) was obtained to represent the gene expression level. Count table was generated using Cuffnorm and DEGs were identified using Cuffdiff. Genes with adjusted p-values <=0.05 and 1.5-fold difference in expression were considered differentially expressed.
BS-seq reads were aligned against the rice genome (MSU7) using BS Seeker2
BS Seeker2 post-processes the alignments to remove non-unique and low-quality mappings.
The DNA methylation level was calculated as ((#C)/(#C+#T)), each of which covered at least four reads for an accurate estimation
Assembly: MSU7
Supplementary files format and content: Processed data (CGmap) is in text format. column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
 
Submission date May 11, 2022
Last update date Sep 27, 2023
Contact name Ying-Chung Lin
E-mail(s) ycjimmylin@ntu.edu.tw
Organization name National Taiwan University
Department Life Science
Street address NO. 1, SEC. 4, ROOSEVELT RD., DA-AN DIST.
City Taipei
ZIP/Postal code 10617
Country Taiwan
 
Platform ID GPL19290
Series (1)
GSE202715 Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation
Relations
BioSample SAMN28189786
SRA SRX15232103

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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