|
| Status |
Public on Mar 12, 2021 |
| Title |
u87_ont_grch38 |
| Sample type |
SRA |
| |
|
| Source name |
U87
|
| Organism |
Homo sapiens |
| Characteristics |
clone: WT
|
| Treatment protocol |
Transfection using Lipofectamine RNAiMAX and collected at the respective time-point
|
| Growth protocol |
DMEM 10% FBS 1% Antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by Zymo Direct-zol RNA miniprep columns
Illumina TruSeq Stranded mRNA and Nanopore Direct RNA Sequencing protocol for the nanopore sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Description |
Oxford Nanopore direct RNA-Sequencing of U87 RNA
|
| Data processing |
Quality assessment, adapter and quality trimming using fastp (0.13.1)
Alignment to reference genome (hisat2 2.1.0)
Gene expression quantification (featureCounts 1.5.0)
Differential gene expression analysis (DESeq2 1.22, R 3.5)
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Counts matrix output of featureCounts
|
| |
|
| Submission date |
Sep 06, 2019 |
| Last update date |
Mar 12, 2021 |
| Contact name |
David Wu |
| Organization name |
UCSF
|
| Lab |
Dan Lim
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE137048 |
miRNA-independent function of long noncoding pri-miRNA loci |
|
| Relations |
| BioSample |
SAMN12710135 |
| SRA |
SRX6814961 |
