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Sample GSM8207854

Query DataSets for GSM8207854

Status

Public on Apr 20, 2024

Title

PANC-1 cells, Control-rep3

Sample type

SRA

Source name

PANC-1

Organism

Homo sapiens

Characteristics

cell line: PANC-1
cell type: Pancratic cancer cells
treatment: none

Extracted molecule

total RNA

Extraction protocol

PANC-1 cells were pretreated with CAF-deirved Evs. The total RNA were extracted and sent for total RNA sequencing.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), mRNA with poly(A) is purified from 1μg total RNA using VAHTS® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) through two rounds of purification. Subsequently, mRNA fragment was interrupted using VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃ 8min and reversed transcription into cDNA which would use to synthesise U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand to ligase the indexed adapters which contains a T-base at the tail end. After UDG enzyme treatment of the U-labeled double-strand DNA, size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). Then the ligated products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 5 min; 12-17 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, and extension at 72℃ for 30 sec; final extension at 72℃ for 5 min. The average insert size of cDNA library was 280±80 bp. After purification by VAHTS® DNA Clean Beads (Vazyme,cat.N411-02, Nanjing, China), quality control of concentration and fragment size is performed by Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and Qubit assay tubes (Life, cat. 1604220, CA, USA). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 system (Illumina Corporation ， San Diego ， USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

LN_3

Data processing

Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
The expression level of mRNA were calculte using RSEM (RNA-Seq by Expectation Maximization) (v1.3.1) by normalized to FPKM (Fragments Per Kilobase Per Million reads)
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text file includes Fold change for samples

Submission date

Apr 15, 2024

Last update date

Apr 20, 2024

Contact name

Chonghui Hu

E-mail(s)

huchonghui@gdph.org.cn

Organization name

Guangdong Provincial People’s Hospital

Street address

NA Zhongshan 2nd Road, Guangzhou