 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 07, 2020 |
| Title |
P2 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
primary thyroid tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tumor subtype: PTC
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
DE_Thyroid_totalRNA_ATC_others_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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN10964426 |
| SRA |
SRX5390008 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
