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Sample GSM3057106

Query DataSets for GSM3057106

Status

Public on Mar 20, 2021

Title

6T_no_cas9_rep2

Sample type

SRA

Source name

HEK293T cell

Organism

Homo sapiens

Characteristics

cell line: HEK293T
tissue: Human embryonic kidney
treatment: PX330-GFP-noCas9-6T-sgRNA

Treatment protocol

HEK293T cells were seeded into 6-well plates one day prior to transfection, and transfected at 70-80% confluency using Polyethylenimine (PEI, Polysciences, Inc.USA) followed by the manufacturer’s protocol. For each well of a 6-well plate, 2 μg DNA and 6 μl PEI were used.

Growth protocol

HEK293T cell line was grown in Dulbecco’s modified Eagle’s Medium (DMEM, Thermo Fisher Scientific ,Waltham, USA) with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin at 37 °C in a 5% CO2 atmosphere.

Extracted molecule

polyA RNA

Extraction protocol

HEK293T cells were washed in ice-cold 1× PBS solution, and total RNA was isolated using Trizol according to the manufacturer’s instructions (Life Technologies, MA, USA). DNA was removed using the Ambion TURBO DNA-free Kit (Life Technologies, MA, USA). cDNA libraries were obtained using the VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina ® (Vazyme Biotech Co., Ltd., Jiangsu, China) from 1μg RNA following the manufacturer’s recommendations.
RNA libraries were prepared according to instructions of VAHTS mRNA-seq library prep kitfor illumina (Vazyme, NR601).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

NextSeq 550

Data processing

Sequencing reads were mapped to hg8 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression. Text files include normalized read counts, foldChange, pvalue ('cas9' represents the 'A' group, 'nocas9' represents the 'B' group).

Submission date

Mar 20, 2018

Last update date

Mar 20, 2021

Contact name

Zaijun Ma

E-mail(s)

[email protected]

Organization name

Chinese Academy Science

Street address

Qiuyue Road 26