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Sample GSM3611484 Query DataSets for GSM3611484
Status Public on Jul 07, 2020
Title A3 [RNA-Seq]
Sample type SRA
Source name primary thyroid tumor
Organism Homo sapiens
Characteristics tumor subtype: ATC
tissue: thyroid
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using the miRNeasy Isolation Kit (Quiagen) for miRNA and Total RNA isolation, according to the manufacturer's instructions from human tumor and non-transformed tissue.
500 ng of total RNA was depleted of ribosomal RNA using the RiboMinus kit (Life Technologies) according to the instructions of the manufacturer. Depleted RNA was then fragmented by addition of 5 fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min in a thermocycler followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier. Fragmented RNA was then reversed transcribed using random hexamer and Superscript III (Life Technologies). The second strand was synthesized using the TargetAmp kit (Epicentre) according to the instructions of the manufacturer. The final steps of library preparation, e.g. blunt end repair, adapter ligation, adapter fill-in and amplification were done according to Meyer and Kircher (2010, PMID: 20516186). The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 2x100 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiScanSQ
Description DE_Thyroid_totalRNA_all.csv
Data processing Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.4.2) with parameters -q 10 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg19 UCSC) using TopHat2 (v 2.0.12) with parameters -r 50 -p 6 -g 20 –b2-N 1
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -p -M -t exon -g gene_id and Ensembl gene annotations (GRCh 37.75)
Differential gene expression was assessed using R/edgeR (v 3.12.1) using TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including FPM, log2 fold change and false discovery rate values for each sample
Submission date Feb 18, 2019
Last update date Jul 07, 2020
Contact name Danny Misiak
Phone +49345573962
Organization name Martin Luther University Halle-Wittenberg
Department Molecular Cell Biology
Lab Hüttelmaier Lab
Street address Kurt-Mothes-Str. 3a
City Halle (Saale)
ZIP/Postal code 06120
Country Germany
Platform ID GPL15456
Series (2)
GSE126698 IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis [RNA-Seq]
GSE126729 IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis
BioSample SAMN10964454
SRA SRX5389981

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

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