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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 17, 2023 |
| Title |
HEK293 cells, βarrestin1/2 KO, basal, biol rep 2 |
| Sample type |
SRA |
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| Source name |
βarrestin1/2 knock out
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: embryonic
genotype: {beta}arrestin1/2 knock out
treatment: incubation with vehicle
time: 1 h
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| Treatment protocol |
Cells were seeded in poly-D-lysine coated 6 well-plates and transfected with wild type β2AR plasmid. The following day, the cells were serum starved overnight. After 48 hours of transfection, the cells were incubated with 1 μM isoproterenol or vehicle for 1 h.
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| Growth protocol |
HEK293 wild type, β-arrestin1/2 KO and Gαs KO cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (D6429, Sigma) supplemented with 10% fetal bovine serum (FBS) (F2442, Sigma) and 1% penicillin/streptomycin (A5955, Sigma) and maintained in humidified atmosphere with 5% CO2 at 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
After stimulus, the cells were washed with PBS, total RNA was isolated with a RNeasy Mini Kit (74104, Qiagen) including an on-column DNase I digestion and quantified using a Nanodrop ND-1000 (Thermo Scientific).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
beta arrestin1/2 KO cells basal 2
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| Data processing |
The quantification of transcripts was calculated using Salmon (version 1.7.0), which provides accurate expression estimates.
The differential gene expression analysis including quality control, model fitting, and hypothesis testing was conducted using DESeq2.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: CSV file containing merged count values from all quant.sf files generated by Salmon. NOTE: Aligned against spliced transcripts
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| Submission date |
Oct 12, 2023 |
| Last update date |
Oct 17, 2023 |
| Contact name |
Valeria Burghi |
| E-mail(s) |
valeburghi@gmail.com
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| Organization name |
University of California San Diego
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| Department |
Pharmacology
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| Street address |
3855 Health Sciences Drive, Room 2345
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| City |
La Jolla |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE245270 |
β2-adrenergic receptor transcriptional response in HEK293 wild type, β-arrestin1/2 KO and Gαs KO cells upon isoproterenol stimulation. |
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| Relations |
| BioSample |
SAMN37799517 |
| SRA |
SRX22079875 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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