|
| Status |
Public on Mar 28, 2016 |
| Title |
clf28 roots replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana_roots_clf-28 mutant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: roots
genotype: clf-28 mutant
age (weeks): 2
|
| Growth protocol |
Arabidopsis plant (Col-0 and clf-28) materials were grown under long day conditions at 22℃. Aerial samples (shoots) and roots were collected from two-week old plants that grew on MS plate. Inflorescences and siliques were collected from five-week old plants that grew in soil.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq strand-specific RNA sample Prep kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Single-end strand-specific RNA-seq
|
| Data processing |
FastaQ files of each sample were aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) of each TU were calculated using cuffdiff.
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks.
|
| |
|
| Submission date |
Sep 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jun Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Crop Science
|
| Department |
Chinese Academy of Agricultural Sciences
|
| Lab |
Jun Liu lab
|
| Street address |
1230 York Avenue
|
| City |
No.12 Zhongguancun South Street, Haidian |
| State/province |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE61545 |
Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis |
|
| Relations |
| BioSample |
SAMN03073873 |
| SRA |
SRX705991 |
