|
| Status |
Public on Mar 12, 2021 |
| Title |
sg646-2 [DHSM1_10] |
| Sample type |
SRA |
| |
|
| Source name |
WT U87 cells with control sgLOC646329
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: U87
clone background/id: WT
genotype/variation: sgLOC646329
|
| Treatment protocol |
sgRNA lentiviral transduction
|
| Growth protocol |
DMEM 10% FBS 1% Antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by Zymo Direct-zol RNA miniprep columns
Clontech SMARTer smRNA-Seq Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DHSM1_10_S10_L001
WT U87 cells with control sgLOC646329 replicate 2
|
| Data processing |
Quality assessment using fastqc, adapter and quality trimming using cutadapt
Alignment to reference genome and quantification (STAR 2.7)
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts matrix output of STAR
|
| |
|
| Submission date |
Apr 29, 2020 |
| 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 |
GPL20301 |
| Series (1) |
| GSE137048 |
miRNA-independent function of long noncoding pri-miRNA loci |
|
| Relations |
| BioSample |
SAMN14766819 |
| SRA |
SRX8202079 |
