|
| Status |
Public on Aug 24, 2015 |
| Title |
PTC15 - small RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Thyroid tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Thyroid tumor
diagnosis: Papillary Thyroid Carcinoma
sequenced molecule: small RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Surgically removed tissues were quickly frozen in liquid nitrogen until analysis. The samples were snap frozen on dry ice and stored at -80°C. Total RNA was extracted with TRIzol solution (Invitrogen), and the integrity of RNA was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). All samples were collected with the informed consent of the patients and the experiments were approved by the Hospital Research Ethics Committee at Hospital Universitario La Paz.
Illumina® TruSeq® Small RNA & Illumina® TruSeq® Stranded mRNA
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Second data set. Patient #15 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data
|
| Data processing |
small RNAseq. STEP: Preprocessing. Illumina Small-RNA Adapter sequences were removed from raw reads using cutadapt software (v1.2.1), retrieving reads with lenghts from 17nt to 34 nt.
small RNAseq. STEP: Alignment. Remaining reads were aligned against human genome (hg19) using Bowtie algorithm (v.0.12.7; parameters: -n 0 -l 17 –best).
RNAseq. STEP: Alignment. Reads were aligned against human genome (hg19) using TopHat algorithm (v.2.0.4; parameters: --bowtie --segment-length 20 --genome-read-mismatches 2 –read-mismatches 2 --segment-mismatches 1 --max-multihits 5 --library-type fr-firststrand )
STEP: Counting tags. Counts of mapped reads in genomic locations (microRNA/exons respectively) were obtained using Htseq-count software (v0.5.4; intersection-nonempty mode; hg19 and miRBase v20)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each microRNA/gene for (Htseq-count output).
|
| |
|
| Submission date |
Jun 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Javier Perales-Paton |
| E-mail(s) |
javier.perales@bioquant.uni-heidelberg.de
|
| Organization name |
Heidelberg University
|
| Department |
Faculty of Medicine
|
| Lab |
Institute for Computational Biomedicine
|
| Street address |
Im Neuenheimer Feld 267
|
| City |
Heidelberg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE63511 |
The miR-146b-3p/PAX8/NIS Regulatory Circuit Modulates the Differentiation Phenotype and Function of Thyroid Cells During Carcinogenesis |
|
| Relations |
| BioSample |
SAMN03769214 |
| SRA |
SRX1055545 |
