|
| Status |
Public on Oct 12, 2021 |
| Title |
Supermere_P1 |
| Sample type |
SRA |
| |
|
| Source name |
Supermere
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DiFi
cell type: Colorectal cancer cells
compartment: extracelluar nanoparticle
molecule subtype: small RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total small RNA was extracted from pelleted cells or extracellular samples using the miRNeasy Mini Kit (QIAGEN, 217004) according to the manufacturer’s protocol.
Total RNA from each sample was taken into small RNA library preparation protocol using Automated NEXTflex® Small RNA-Seq Kit v3 (Bioo Scientific, PerkinElmer) for Illumina® Libraries on PerkinElmer® Scilone® G3 NGS workstation according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Index78-Bioo_miRNA_i5_Index78_SL406248
|
| Data processing |
Reads were processed using the TIGER informatics pipeline doi: 10.1080/20013078.2018.1506198
Reads were trimmed to remove adapter sequences with Cutadapt v2.5
Reads were aligned to GRCh37 using Bowtie1 v1.2.3
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw gene count matrix
|
| |
|
| Submission date |
Mar 07, 2021 |
| Last update date |
Oct 12, 2021 |
| Contact name |
Marisol Ramirez |
| E-mail(s) |
marisol.a.ramirez@vumc.org
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Center for Quantitative Sciences, Department of Biostatisticss
|
| Street address |
2220 Pierce Avenue, 571 Preston Research Building
|
| City |
NASHVILLE |
| State/province |
TENNESSEE |
| ZIP/Postal code |
37232-6848 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE168416 |
Supermeres, a new functional extracellular nanoparticle replete with disease biomarkers and therapeutic targets |
| GSE168418 |
Supermeres, a new functional extracellular nanoparticle replete with disease biomarkers and therapeutic targets |
|
| Relations |
| BioSample |
SAMN18201898 |
| SRA |
SRX10254360 |
