|
| Status |
Public on Oct 24, 2015 |
| Title |
uqc4 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
physiology: Normal
character: Heat Susceptible
ecotype: Col 0
RNAi mutant: Wild Type
|
| Growth protocol |
Arabidopsis plants were grown under green house conditions at 21°C and relative humidity of 50-60%. Roots are harvested and used for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total rna was isolated using Trizol reagent and enriched with 50% PEG and 0.1% Nacl for small rna isolation. The RNA bands of corresponding size ranging between 15-30 nucleotides were gel purified. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The adapter sequences were trimmed and low quality sequences were filtered using FastX tool kit [http://hannonlab.cshl.edu/fastx_toolkit/], then mapped to Arabidopsis genome using bowtie [http: //bowtie.cbcb.umd.edu.] with parameters -a -v 0.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample
|
| |
|
| Submission date |
Dec 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dinesh Gupta |
| Organization name |
ICGEB
|
| Department |
Structural and Computational Biology
|
| Lab |
Bioinformatics
|
| Street address |
Aruna Asaf Ali Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL9302 |
| Series (2) |
| GSE53687 |
3’ and 5’ end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs [Arabidopsis thaliana] |
| GSE53688 |
3' and 5' end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs |
|
| Relations |
| BioSample |
SAMN02486629 |
| SRA |
SRX399678 |
