|
| Status |
Public on Sep 01, 2013 |
| Title |
Heart |
| Sample type |
SRA |
| |
|
| Source name |
Biochain:R-1234122-P
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: heart
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.
Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Normal tissue provided by Biochain
|
| Data processing |
Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.
Genome_build: hg18
Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format
|
| |
|
| Submission date |
Mar 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Morten Muhlig Nielsen |
| E-mail(s) |
morten.muhlig@clin.au.dk, muhligs@gmail.com
|
| Organization name |
Aarhus University
|
| Department |
Department of Molecular Medicine
|
| Street address |
Palle Juul-Jensens Bouleward 99
|
| City |
Aarhus |
| ZIP/Postal code |
DK-8200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE45326 |
Identification of expressed and conserved human non-coding RNAs |
|
| Relations |
| SRA |
SRX252506 |
| BioSample |
SAMN01984809 |
