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Sample GSM2225091 Query DataSets for GSM2225091
Status Public on Jul 21, 2016
Title Neat RNA Sequins Mix A
Sample type SRA
 
Source name Neat RNA Sequins Mix A
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 SAMN05357554
SRA SRX1897294

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record
Processed data provided as supplementary file

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