 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 09, 2014 |
| Title |
Stem(S) |
| Sample type |
SRA |
| |
|
| Source name |
Stem(S)
|
| Organism |
Solanum tuberosum |
| Characteristics |
cultivar: Kufri Chandramukhi
tissue: Stem(S)
age: 45 days old
|
| Growth protocol |
The plantlets of Solanum tuberosum (cv. Kufri Chandramukhi) were raised in vitro on MS medium and maintained under the 16hr light/8 hr dark photoperiod conditions at 22°C. The leaves, stem and root were collected from 45 days old whole in vitro grown potato plantlets and immediately frozen in liquid nitrogen, subsequently stored at -80°C until used. These in vitro grown plantlets were then potted and grown under natural field conditions, during the period of November-January, in the net house at the Department of Botany, University of Delhi, India. Mature plants started to tuberize after 35 days and tissues from the four early developmental stages of tuberization were harvested, according to size, from these naturalized plants, frozen in liquid nitrogen and stored at -80°C until used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the above mentioned tissues (0.2 grams each) using TRI reagent (Sigma, USA) as per the manufacturer’s instructions. The quality and quantity of RNA isolates was verified on denaturing agarose gel and by optical density (OD) measurement respectively.
Small RNA libraries for each tissue type were prepared independently using an Illumina Small RNA sample prep kit (Illumina, U.S.A), according to manufacturer’s instructions. Briefly, small RNAs (20-40 nt) were separated on 15% denaturing polyacrylamide gel and purified. Next, small RNAs were ligated with the 5’ and 3’adapters sequentially, eluted and gel purified. The 5’and 3’ligated small RNAs were reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, U.S.A) and PCR amplified with Phusion DNA Polymerase. The quality and quantity of cDNA library was assessed using Agilent Bioanalyzer (Agilent Technologies, U.S.A). Small RNA library preparation and their high-throughput sequencing was performed using an Illumina Genome Analyzer IIx (Illumina, U.S.A) at DBT-funded High Throughput Sequencing Facility at University of Delhi South Campus, India.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 2
small RNA profiling
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The removal of poor quality sequences and trimming of adaptor sequences from the raw sequence data was carried out using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/) . Sequences, smaller than 16 nt and larger than 30 nt were also removed. High quality trimmed sequences (16-30 nt in length, reads with no N, no more than 4 bases with quality score <10 and no more than 6 bases with quality score <13) were mapped onto plant t/rRNAs sequences from “Rfam” (excepted miRNAs), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95. The matched sequences were removed from downstream analysis. UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) was also used to remove any t/rRNA matchouts .
The unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) and default criteria were used to predict potato-specific and conserved miRNAs in potato. The read were aligned to the potato reference genome (PGSC DM assembly version 3) (http://potatogenomics.plantbiology.msu.edu/) with no mismatch.
Genome_build: PGSC DM assembly version 3
Supplementary_files_format_and_content: The .txt files report abundance measurements.
|
| |
|
| Submission date |
Nov 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Amar Kumar |
| E-mail(s) |
akumar23j@gmail.com
|
| Phone |
+91-11-27662609
|
| Organization name |
University of Delhi
|
| Department |
Botany
|
| Street address |
Chatra Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110007 |
| Country |
India |
| |
|
| Platform ID |
GPL15787 |
| Series (1) |
| GSE52599 |
Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing |
|
| Relations |
| BioSample |
SAMN02418739 |
| SRA |
SRX381123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1272351_Processed_STEM.txt.gz |
59.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
