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Sample GSM1481533 Query DataSets for GSM1481533
Status Public on Jan 01, 2015
Title proband
Sample type SRA
 
Source name blood
Organism Homo sapiens
Characteristics cell type: peripheral blood mono-nuclear cells
genotype: KLF1: W30X/R319fsX34
tissue: blood
Extracted molecule total RNA
Extraction protocol RNA was extracted from the peripheral blood mononuclear cell (PBMC) layer derived by Ficoll-paque extraction from 20 mL of whole blood. In the case of the proband, blood was drawn immediately prior to transfusion to enrich for endogenous nucleated erythroid cells and reticulocytes.
Beginning with 20 µg total RNA, the Ambion GLOBINclear™ kit (#AM1980, Life Technologies) was used to remove human alpha-globin and beta-globin mRNA. Ambion Dynabeads® mRNA DIRECT™ Micro Purification Kit (#61021, Life Technologies) was used to select the polyA+ (mRNA) fraction. ERCC control RNA from the Ambion ERCC RNA Spike-In Mix Kit (#4456740, Life Technologies) was added to estimate the amplification efficiency during library construction. Barcoded RNA-seq libraries were prepared using the Ion Total RNA-Seq Kit v2 (#4475936, Life Technologies) along with the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (#4475485, Life Technologies) for sequencing on the Ion Proton instrument (Life Technologies). Three barcoded libraries were sequenced on a single P1 chip such that approximately 20 million mapped reads were obtained for each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing Base calling was performed within Torrent_Suite version 4.0.1
Sequencing reads were aligned to the human genome (build hg19) using Tophat2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between samples was performed with Cuffdiff2 using option --max-bundle-frags 1000000000
Genome_build: hg19
Supplementary_files_format_and_content: comma separated variable file containing FPKM values for each sample
 
Submission date Aug 19, 2014
Last update date May 15, 2019
Contact name Graham William Magor
E-mail(s) gmagor@mmri.mater.org.au
Organization name Mater Research
Lab Cancer Genomics
Street address 37 Kent St
City Brisbane
State/province Queensland
ZIP/Postal code 4152
Country Australia
 
Platform ID GPL17303
Series (1)
GSE60514 KLF1 null neonates display hydrops fetalis and a deranged erythroid transcriptome
Relations
BioSample SAMN03000649
SRA SRX684324

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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