|
| Status |
Public on Nov 03, 2021 |
| Title |
Normoxia 1 EV |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
sample type: Extracellular Vesicles
treatment: Normoxia
cell type: Human Embryonic Kidney Cell line
|
| Treatment protocol |
HEK293 cells were transfected with 4EC1 plasmid using Lipofectamine 3000 (ThermoFisher, Waltham, USA) for 48 hours and transferred to Hypoxia chamber for 24 hrs for RNA collection.
|
| Growth protocol |
HEK293 cells were grown in DMEM(Gibco,New York, USA) supplemented with 10% FBS(Gibco,New York, USA) on tissue culture plates cultured to about 80% confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular RNA was extracted using theTRIzol™ (Thermo Fisher, Waltham, USA) after treatment and extracellular RNA was isolated using ExoRNeasy midi kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
Long RNA libraries were contructed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio USA, Cat # - 634413) by following the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Long RNAs
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2
DESeq2 v1.30.1 was used to generate normalized read counts for each of the transcripts across each sample.
Genome_build: Homo Sapiens GRCh38/hg38
Supplementary_files_format_and_content: Processed data files are csv files containing DESeq2 normalized read counts.
|
| |
|
| Submission date |
Nov 01, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Guoping Li |
| E-mail(s) |
gli21@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
CVRC
|
| Lab |
Dr. Saumya Das
|
| Street address |
Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE186954 |
TRACE-seq: A transgenic system for unbiased loading of mRNA into extracellular vesicles allowing non-invasive transcriptome profiling of living cells |
|
| Relations |
| BioSample |
SAMN22822388 |
| SRA |
SRX12879409 |
