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Sample GSM8472230

Query DataSets for GSM8472230

Status

Public on Nov 05, 2024

Title

SARC_77_CSA_MES

Sample type

SRA

Source name

Tumour tissue

Organism

Homo sapiens

Characteristics

tissue: Tumour tissue
methylation-based molecular_classification_(sarc_v12.2_classifier): Mesenchymal chondrosarcoma

Extracted molecule

total RNA

Extraction protocol

RNA was extracted with RNeasy Kit (QIAGEN, Hilden, Germany; cat. ID: 74106) and quantified with High Sensitivity Qubit™ RNA Assay Kits (Invitrogen™, Waltham, MA, USA; cat. ID: Q32855).
Transcriptome assay was performed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, San Diego, CA, USA) and sequenced on the NextSeq550 or NOVAseqX (Illumina Inc, San Diego, CA, USA). Paired-end runs were sequenced in 74 cycles per read (2 X 74), with an average of 41.5 million reads per sample.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

NextSeq 550

Description

SARC_77

Data processing

Transcriptome raw data quality was verified with FASTQC . We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. Alinment against GRCh38.primary_assembly.genome.fa and assigned mapped reads from genomic RNA sequencing to genomic features were performed using Rsubread package (v 2.18.0)
Assembly: GRCh38
Supplementary files format and content: A csv file corresponding to gene count matrix containing assigned mapped reads from genomic RNA sequencing to genomic features

Submission date

Aug 19, 2024

Last update date

Nov 05, 2024

Contact name

Felipe Silva

E-mail(s)

[email protected]

Organization name

Boldrini

Street address

R. Márcia Mendes, 506