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Sample GSM6342118

Query DataSets for GSM6342118

Status

Public on Jul 23, 2022

Title

RL-95-2 transfected with negative control of mimics

Sample type

SRA

Source name

endometrium

Organism

Homo sapiens

Characteristics

cell type: Endometrial cancer cell line
cell line: RL-95-2
transfection: negative control

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-T7 platform at Tsingke Biotechnology Co., Ltd..

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

DNBSEQ-T7

Data processing

Basecalls performed using CASAVA.
RNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

Submission date

Jul 18, 2022

Last update date

Jul 23, 2022

Contact name

Shanliang Zhong

E-mail(s)

slzhong@njmu.edu.cn

Organization name

The Affiliated Cancer Hospital of Nanjing Medical University

Street address

Baiziting 42