|
| Status |
Public on May 11, 2013 |
| Title |
[E-MTAB-1222] polyA+_testis_7060321 |
| Sample type |
SRA |
| |
|
| Source name |
polyA+_testis_7060321
|
| Organism |
Homo sapiens |
| Characteristics |
material type: organism part
organismpart: testis
Sex: male
biosourcetype: frozen sample
biosourceprovider: Clontech
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns.
PCR_amplification | 5' and 3' RACE reactions were performed in 12.5 ul volume independently with brain and testis polyA+ RNA with the SMART RACE amplification kit (Clontech) using manufacturer's instructions. 7.5ul of each of the 400 lncRNA targets were pooled respecting tissues and directionality of the RACE reaction (5' and 3' RACE) and purified with the QIAquick kit (Quiagene) as described for RT-PCR-seq experiments (Howald et al. 2012). A set of 25 control reactions targeting full-length annotated transcripts were RACEd in parallel as positive controls. 1.5ul of these controls were pooled with the other reactions prior to library preparation.
sequencing | Libraries were prepared following the Rapid Library Preparation Method Manual for GS FLX+ Series / XL+ Kit. The emulsion PCRs (emPCRs) for the library titrations and the sequencing reactions were prepared according to the emPCR Method Manual â Lib-L LV for GS FLX+ Series - XL+. Sequencing was performed on a GS FLX+ Instrument following the Sequencing Method Manual for GS FLX+ Series / XL+ Kit. Sequencing images were analyzed with the Roche 454 Shotgun-pipeline and Amplicons-pipeline programs. Two FastQ files were generated, one per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
454 GS FLX |
| |
|
| Description |
Performer: Andalusian Human Genome Sequencing Centre
|
| Data processing |
processed data not provided
|
| |
|
| Submission date |
May 09, 2013 |
| Last update date |
May 15, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9186 |
| Series (1) |
| GSE46635 |
[E-MTAB-1222] GENCODE Batch VIII a: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing |
|
| Relations |
| SRA |
ERX145716 |
| SRA |
ERX145712 |
| SRA |
ERX145717 |
| SRA |
ERX145713 |
