|
| Status |
Public on Jul 21, 2016 |
| Title |
Neat RNA Sequins Flat Mix |
| Sample type |
SRA |
| |
|
| Source name |
Neat RNA Sequins Flat Mix
|
| Organism |
synthetic construct |
| Characteristics |
molecule subtype: Neat RNA spike-in (no natural RNA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from K562 using TRIzol (Invitrogen). DNAse treatment was performed with TURBO DNase (Life Technologies) followed by a cleanup with RNA Clean and Concentrator-25 Kit (Zymo Research).
RNA was ribo-depleted using Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat) (Epicentre), libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed to remove standard Illumina adapter sequences using CutAdapt with Trim Galore wrapper script.
Reads were mapped using TopHat2 to genome co-index comprising hg38, ERCCs and our in silico chromosome.
Transcripts were assembled using StringTie, using reference annotations to calculate gene expression values (FPKMs).
Genome_build: hg38
Supplementary_files_format_and_content: GTF files for transcript assemblies, including quantitative expression values.
|
| |
|
| Submission date |
Jul 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Andrew Hardwick |
| E-mail(s) |
s.hardwick@garvan.org.au
|
| Phone |
+61401264672
|
| Organization name |
Garvan Institute of Medical Research
|
| Lab |
Transcriptomic Research
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE77072 |
Spliced synthetic genes as internal controls in RNA sequencing experiments. |
|
| Relations |
| BioSample |
SAMN05357556 |
| SRA |
SRX1897296 |
