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Sample GSM6801667

Query DataSets for GSM6801667

Status

Public on Dec 01, 2023

Title

A549 cells, replicate 1, scRNAseq

Sample type

SRA

Source name

lung cancer

Organisms

Homo sapiens; Mus musculus

Characteristics

cell type: lung cancer
tissue: lung cancer

Extracted molecule

total RNA

Extraction protocol

Mice were obtained from JiHui Laboratory Technology Co., Ltd. (China). All experimental protocols were approved by Shanghai University of Medicine and Health Sciences and mice were treated and sacrificed in accordance with the institutional guidelines for animal care. All mice were housed in a Specific Pathogen Free (SFP) environment at a suitable temperature (23±2 °C) and humidity (60±5 %) with a 12-h day/night cycle. 5 × 106 A549 cells were subcutaneously injected into the ventral flank of female nude mice (4 to 6 weeks old). After a few weeks，the tumors reached higher than 150 mm3 in volume calculated from the formula V = (length × width2)/2 using calipers, according to the report previously described(10). Mice were randomized into three groups gavaged through oral with vehicle (1% w/v CMC-Na, dissolved in sterile water), 7.5 mg/kg dacomitinib and 15 mg/kg dacomitinib, respectively. Mice were weighted and tumor sizes were measured every two or three days.
Single Cell preparation, library construction, sequencing and preliminary analysis were performed by Sinotech Genomics Co., Ltd. Shanghai, China. Each specimen was washed extensively in HyClone™ RPMI 1640 media, weighed, and enzymatically digested in 10 ml RPMI 1640 media supplemented with Collagenase type I (0.2 mg/mL，A004194, sangon, Shanghai, China), Collagenase type IV (0.2 mg/mL, A004186, sangon), Neutral Protease (0.1 mg/mL, A002100, sangon) and DNase I (0.01 mg/mL, B300065, sangon) for 1.5 h at 37°C with agitation. The mixture was strained consecutively through 70 μm and 40 μm cell strainers, washed twice in PBS, and centrifuged at 400 g for 5 minutes. After quenching digestion with excess RPMI-1640 medium, filtered single cell solutions were kept on ice until they were loaded into the BD Rhapsody system (BD, San Jose, CA) for single cell transcriptome isolation. The final library was generated using microbead-captured single cell transcriptome as the manufacturer’s protocol. The final cDNA library was generated from double strand full length cDNA by random priming amplification with the BD Rhapsody cDNA Kit (633773, BD Biosciences) and the BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (633774, BD Biosciences). All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) in the X Ten instrument (Illumina, San Diego, CA).

Library strategy

RNA-Seq

Library source

transcriptomic single cell

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

BD Rhapsody

Data processing

Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline.
Assembly: hg18,mm9
Supplementary files format and content: Tab-separated values files and matrix files

Submission date

Dec 07, 2022

Last update date

Dec 01, 2023

Contact name

Yu Yangziwei

E-mail(s)

212302491@st.usst.edu.cn

Phone

18116202232

Organization name

Shanghai University of Medicine and Health Science