|
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 |