|
| Status |
Public on Nov 23, 2021 |
| Title |
N3 |
| Sample type |
SRA |
| |
|
| Source name |
primary thyroid tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tumor subtype: NT
subtype info: non-malignant human thyroid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 30 micrograms of primary tumor tissue using the Qiagen ALLprep tumour protocol with miRNeasy kits. 500 ng of total RNA was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer.
The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 50 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. Demultiplexing of raw reads, adapter trimming and quality filtering was done according to Stokowy et al. (PMID: 24625073).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Unstranded single-end reads with 51 bp in length were trimmed for adaptor and low quality sequences using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 16 –trim-n
Trimmed reads were mapped to the human genome (hg38 UCSC) using Bowtie2 (v 2.2.6) with parameters -p 6 -N 1 –un-gz
Mapped reads were summarized using featureCounts (v 1.6.3) with parameters -s 0 -T 6 -t miRNA -g ID and MirBase (v 22) annotations
Normalized gene expression was achieved using R/edgeR (v 3.28) by applying TMM normalization of read counts
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including TMM normalized abundance measurements (CPM, counts per million mapped reads) for each sample and differential expression information between tumor subtypes (log fold changes, p-values, FDR-values)
|
| |
|
| Submission date |
Oct 12, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Danny Misiak |
| E-mail(s) |
danny.misiak@medizin.uni-halle.de
|
| 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 (1) |
| GSE185719 |
MiRNA Deregulation Distinguishes Anaplastic Thyroid Carcinoma (ATC) and Supports Upregulation of Oncogene Expression |
|
| Relations |
| BioSample |
SAMN22225107 |
| SRA |
SRX12576769 |
