 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 02, 2024 |
| Title |
B2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic neuroendocrine tumor, formalin-fixed paraffin-embedded
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic neuroendocrine tumor, formalin-fixed paraffin-embedded
grade: Grade 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the macrodisected 80 μm FFPE samples using RecoverAllTM Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, Waltham, MA, U.S.)
The libraries were constructed using the QiaSeq miRNA Library Kit by QIAGEN.
5 µl-s of isolate were used for each library. After library preparation, a Qubit 4 fluorimeter was used, to measure library concentrations, and to achieve equimolar pooling, then the NebNext Library Quant Kit (New England Biolabs) was utilised to measure the final pooled concentration before sequencing
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
fastq.gz files were uploaded to GeneGlobe (QIAGEN) for analysis, which performed adopter trimming, discarded low-quality reads, and aligned the results to GRCh38 using bowtie. Readcounts for miRNA were achived by mapping the results to miRBase v21.
Normalization, DeSeq2 and the neural network algorithm were then ran locally, using R.
Assembly: GRCh38, MirBase v21, piRNABank
Supplementary files format and content: .xlsx microRNA raw data count
|
| |
|
| Submission date |
Apr 24, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Bálint Kende Szeredás |
| E-mail(s) |
szeredasbalint@gmail.com
|
| Phone |
+36308628531
|
| Organization name |
Semmelweis University
|
| Department |
Department of Internal Medicine and Oncology - Department of Endocrinology
|
| Street address |
Korányi Sándor street 2/a
|
| City |
Nudapest |
| ZIP/Postal code |
1082 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE265752 |
MicroRNA expression profile of different grade pancreatic neuroendocrine tumors |
|
| Relations |
| BioSample |
SAMN41069948 |
| SRA |
SRX24353725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8228228_B2_S2_expression_values.xlsx |
324.3 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
