|
| Status |
Public on Nov 01, 2016 |
| Title |
mRNA-seq_Col_clf_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling shoot
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 14 day old
tissue: seedling shoot
cultivar: Col
genotype: clf
|
| Growth protocol |
Wild-type hybrid was generated by crossing Arabidopsis thaliana ecotype Col and C24. clf hybrid was generated by crossing clf mutant in Col background (SALK_139371) and clf mutant in C24 background which was identified from our ethyl methanesulfonate mutant library. The mutation in clfC24 contained a G-to-A substitution at position 4196 of CDS, which generated a D-to-N amino acid substitution in the SET domain of CLF protein. Plants were grown on Murashige and Skoog plates containing 1% Sucrose. The shoots of 14-day-old seedlings were used for ChIP-seq and RNA-seq. All seedlings were grown under short-day condition (8 hours light at 22℃ and 16 hours dark at 18℃), unless otherwise indicated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatin immunoprecipitation experiment was performed following previously published procedure (Gendrel et al. 2005). Briefly, 1.5 g of shoots of 14-day-old plants were cross-linked by 1% formaldehyde in a vacuum, and then the samples were ground to fine powder in liquid nitrogen. Chromatin was immunoprecipitated with antibody against H3K27me3 (Millipore).Total RNA was extracted from shoots of 14-day-old Arabidopsis seedling using the Rneasy plant mini kit (Qiagen). mRNAs were extracted from the total RNAs by Dynabeads oligo(dT) (Invitrogen Dynal). First- and second-strand cDNAs were obtained using random hexamer primers and SuperScript II reverse transcriptase (Invitrogen).
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
polyA RNA isolated
|
| Data processing |
RNA-sequencing reads for Col and C24 were mapped to TAIR10 genome and SNP corrected C24 genome using Tophat software. For hybrid RNA sequencing data analysis, we aligned the reads to both of the TAIR10 genome and SNP corrected C24 genome. Reads were assigned to an allele based upon the highest quality alignment and were further used to calculated allelic expression divergence. ChIP-seq data was mapped to Arabidopsis genome using the similar methods as in RNA-seq. The only difference is that we use bowtie to map our ChIP-seq reads. MACS software with default parameters was used to call peaks representing enriched binding sites.llele based upon the highest quality alignment and were further used to calculated allelic expression divergence.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples, read counts for ChIP-seq samples
|
| |
|
| Submission date |
Oct 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mei Yang |
| E-mail(s) |
[email protected]
|
| Phone |
18010076165
|
| Organization name |
PKU
|
| Street address |
No.5 Yiheyuan Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL9062 |
| Series (1) |
| GSE62615 |
Natural variation of H3K27me3 modification between two Arabidopsis accessions and its inheritance in hybrid |
|
| Relations |
| BioSample |
SAMN03135277 |
| SRA |
SRX738358 |
