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Sample GSM6758045

Query DataSets for GSM6758045

Status

Public on Dec 01, 2022

Title

L03_25, WT, TPC_OL9, biol rep 3

Sample type

SRA

Source name

HEK293A

Organism

Homo sapiens

Characteristics

cell line: HEK293A
cell type: human embryonic kidney cells
genotype: WT
treatment: TPC_OL9

Treatment protocol

Cells were treated for 5-5,5 hours with following agents: 1) No treatment, 2) 0.1% DMSO, 3) 100 nM (for WT HEK293) or 50 nM (for PARP1-KO HEK293) Tpc + 0.1% DMSO, 4) 5 μM OL9-119 solved in 0.1% DMSO, 5) 100 nM (for WT HEK293) or 50 nM (for PARP1-KO HEK293) Tpc + 5 μM OL9-119.

Growth protocol

Cells were grown in DMEM/F12 medium supplemented with 1×GlutaMAX, 100 c.u./ml penicillin and 100 mg/ml streptomycin, in the presence of 10% fetal bovine serum in a 5% CO2 atmosphere.

Extracted molecule

polyA RNA

Extraction protocol

RNA was isolated with the Trizol according to the manufacturer instructions.
RNA were enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module, libraries were prepared with MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd., China)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MGISEQ-2000RS

Description

L03_25

Data processing

Quality control of raw reads were performed using FastQC v0.11.9
Sequence reads were aligned to hg38 human genome using STAR v 2.7.8.
Quantification of reads was also performed using STAR, option –quantMode GeneCounts
Quality control of aligment were performed using module infer_experiment.py of RSeQC v4.0.0, module CollectRnaSeqMetrics from Picard v2.26.6
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

Submission date

Nov 28, 2022

Last update date

Dec 01, 2022

Contact name

Maxim Ri

E-mail(s)

maxim.ree@gmail.com

Organization name

LLC AcademGene

Street address

Lavrenteva st. 6