|
| Status |
Public on Apr 03, 2013 |
| Title |
3 day old root tip tissue (Root tip) |
| Sample type |
SRA |
| |
|
| Source name |
3 day old root tip tissue (Root tip)
|
| Organism |
Medicago truncatula |
| Characteristics |
cell type: meristenatic root cells
cultivar: Jemalong A17
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole RNA was extracted using the 'Trizol' method. The small RNA component was isolated using a standard precipitation method after the addition of 6 µl 50% PEG (MW 8000) and 7.5 µl 4M NaCl
Small RNA libraries were constructed using a modified version of ‘Preparing Samples for Small RNA Sequencing Using Alternative v1.5 Protocol’ (Part # 15002615 Rev. A, February 2009, Illumina, San Diego, CA, USA). Variations to this protocol were; 200-300 ng low molecular weight RNA was used. 3' and 5' adaptors were ligated in separate reactions. The 3' adaptor ligation was carried out for 2.5 h at 22 oC and the 5' adaptor ligation was carried out for 1 h at 22 oC and then overnight at 4 oC.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Distal 3mm of three day old root containing the root apical meristem and root cap.
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Adaptor trimming and genome alignment was perform using Novoalign v2.07.18
Read collation was performed using a custom PERL script
Read count normalisation was performed using EdgeR
Duplex energy calculations were done using the RNAduplex module of ‘Vienna RNA package’
Individual miRNA hairpin structures were produced using Mfold-quikfold (RNA 3.0, linear)
Genome_build: MedtrA17_3.5 (Medicago truncatula 3.5.1)
Supplementary_files_format_and_content: All_seqs_Planta_normalised1.txt file containing normalised read counts of published sequences
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
rod eyles |
| E-mail(s) |
rod.eyles@anu.edu.au
|
| Organization name |
Australian National University
|
| Street address |
Linnaeus Way
|
| City |
Canberra |
| ZIP/Postal code |
0200 |
| Country |
Australia |
| |
|
| Platform ID |
GPL15815 |
| Series (1) |
| GSE45726 |
microRNA profiling of root tissues and root forming explant cultures in Medicago truncatula |
|
| Relations |
| SRA |
SRX258983 |
| BioSample |
SAMN01997266 |
