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Sample GSM5561952 Query DataSets for GSM5561952
Status Public on Sep 14, 2021
Title A549 268
Sample type SRA
 
Source name NSCLC
Organism Homo sapiens
Characteristics tumour type: Lung adenocarcinoma
cell type: Epithelial
Treatment protocol Untreated
Growth protocol Upon purchase, cells were stored at -80ºC freezer and then thawed just before directly loading to C1 HT mRNA-seq IFCs.
Extracted molecule total RNA
Extraction protocol Individual cells were captured in chambers of Fluidigm HT mRNA-seq IFC. Total RNA extraction and preamplification of synthesized cDNAs were performed in Fluidigm C1 systems using the script of 'mRNA Seq HT:RT & Amp (1912x)’.
A total of 1,600 3'-end enriched scRNA-seq libraires (400 libraries per cell line) were constructed using Nextera XT index Kit v2 Set A/B and Nextera XT DNA library preparation kits.
3'-end enriched scRNA-seq using Fluidigm C1 system
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 268
Data processing Basecalling performed using Real-Time Analysis (RTA) version 2.0
Fluidigm mRNA Sequencing High Throughput Demultiplexer Script (https://www.fluidigm.com/software) and Geneious Prime 2019.2.1 (https://www.geneious.com) were used to demultiplex.
BBDuk Trimmer (a part of Bestus Bioinformatics Tools; RRID:SCR_016968) was used for quality trimming.
HISAT2 (RRID:SCR_015530) was used for read mapping to align processed reads to human reference genome (GRCh38.p13; NIH).
FeatureCounts (A part of Subread; RRID:SCR_009803) was used to count aligned reads per gene.
Genome_build: Human reference genome (GRCh38.p13; NIH)
Supplementary_files_format_and_content: Fastq containing 3'-end enriched scRNA-seq reads at single-end read
 
Submission date Sep 07, 2021
Last update date Sep 14, 2021
Contact name Paola Marignani
E-mail(s) pmarigna@dal.ca
Phone 1 902 494 6033
Organization name Dalhousie University
Department Biochemistry & Molecular Biology
Lab 9F1
Street address 5850 College Street, Tupper Medical Building
City Halifax
State/province Nova Scotia
ZIP/Postal code B3H 1X5
Country Canada
 
Platform ID GPL18573
Series (1)
GSE183590 Single-cell RNA sequencing for the identification of early-stage lung cancer biomarkers from circulating blood
Relations
BioSample SAMN21310459
SRA SRX12033698

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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