|
| Status |
Public on Feb 22, 2019 |
| Title |
H2228_H1975_A549_H838_HCC827_Mixture_10X |
| Sample type |
SRA |
| |
|
| Source name |
lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
barcode coordinate: bases 1 to 16 on R1
umi coordinate: bases 17 to 26 on R1
|
| Growth protocol |
The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin. The cells were grown independently at 37C with 5% carbon dioxide until near 100% confluency.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cells were counted using Chamber Slide and rounghly 2 million cells from each cell line were mixed and processed by 10X. Three CEL-seq2 plates were sorted for the same sample.
following the standard 10X single cell RNA-seq document, using v2 chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq files were generated using Cellranger. All R1 files were concatenated and all R2 files were concatenated for processing with scPipe.
Sample filtered gene count matrix was generated using scPipe with ENSEMBL GRCh38p10 gene annotation. With scPipe, we processed the 5000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells.
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: barcodes.csv: Counts matrix with samples along the columns and genes along the rows
Supplementary_files_format_and_content: gene_count.csv: 5001 most abundant cell barcodes with cell ids, barcode sequence and counts
|
| |
|
| Submission date |
Feb 21, 2019 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Shian Su |
| E-mail(s) |
su.s@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Molecular Medicine
|
| Lab |
Ritchie Lab
|
| Street address |
1G Royal Parade
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE118767 |
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods |
| GSE126906 |
Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines 10X] |
|
| Relations |
| BioSample |
SAMN10985209 |
| SRA |
SRX5405937 |
