 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 12, 2023 |
| Title |
cs_cage_root_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Triticum aestivum 12-days-old seedlings
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: 12-days-old seedlings
cultivar: Chinses Spring
age/tissue: 9-days root
|
| Treatment protocol |
No treatment applied
|
| Growth protocol |
Common wheat (Triticum aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C. The germinated seeds with residual endosperm were transferred to soil (1:1:3 mixture of vermiculite: perlite: peat soil) or Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The seedlings (above-ground parts) in soil were harvested after 9-day growth. The root in Hoagland solution were harvested after 9-day growth. The spikelets at booting stage (Feeke 10) were harvested. The fresh immature embryos (14days post anthesis) were isolated and either frozen in liquid nitrogen
For CAGE-seq，total RNA was treated with RQ1 DNase to remove DNA. The total RNA was treated with T4 polynucleotide kinase subsequently digested with Terminator 5´-Phosphate-Dependent Exonuclease to enrich the capped mRNA. Next, reverse transcription was performed with RT primer harboring a 3'-adaptor sequence and randomized hexamer. Subsequently, the 5’adaptor harboring three additional rG at the 3’terminus was added to the RT reaction to allow template switching and tagging of the 5’ adaptor. The cDNAs were treated with Exonuclease I to digest the primers, purified and amplified with PCR primers. The libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For CAGE-seq, only the R1 read were kept to mapping. Cutadaptwas applied to trim 3’ adaptor and 9 bases at the 5’end, used SortMeRNA to remove the reads originating from chloroplast, mitochondria and rRNA. Clean reads were mapped to the IWGSC (version 1.0) with Bowtie2 Only unique mapped reads were used for analysis. The 5′ coordinate of R1 reads was considered the position of the transcription start sites.
For ChIP-seq, Bisulfite-seq and RNA-seq, reads were trimmed with the Trim Galore and cutadapt. For RNA-sequencing, clean reads were aligned with HISAT2. SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly (version 1.1). For ChIP-seq data, clean reads were aligned with bwa program. The MACS2 was used to identify the peaks.
For Bisulfite-seq data, the clean reads were then aligned by the Bismark program. The extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low confidence positions whose methylation ratios were not recorded.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: CAGE-seq signal in each site were provided in bed file.
|
| |
|
| Submission date |
Mar 09, 2022 |
| Last update date |
Oct 12, 2023 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Biochemistry
|
| Lab |
Functional Epigenomics Group
|
| Street address |
2005 Songhu Road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE198284 |
Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development |
|
| Relations |
| BioSample |
SAMN26549890 |
| SRA |
SRX14424032 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5943592_cs_cage_root_rep1_unique_best.site_frq.bed.gz |
2.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
