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Sample GSM5664243 Query DataSets for GSM5664243
Status Public on Nov 03, 2021
Title Normoxia 3 Cell
Sample type SRA
Source name HEK293 cells
Organism Homo sapiens
Characteristics cell line: HEK293
sample type: Cells
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 theTRIzolâ„¢ (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
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
BioSample SAMN22822392
SRA SRX12879405

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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