|
| Status |
Public on Jul 30, 2024 |
| Title |
synthetic control group 1 |
| Sample type |
SRA |
| |
|
| Source name |
synthetic control
|
| Organism |
synthetic construct |
| Characteristics |
tissue: synthetic control
sample type: synthetic control
pipeline.version: preclinical
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sparseq_control_data_GEOver.txt
|
| Data processing |
Samples sequenced using Illumina NextSeq, MiSeq, and MiniSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were developed to track and quantify key mutations within samples and to aggregate data.
Final anaylsis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1)
Supplementary files format and content: positive sample text file [sparseq_sample_data_GEOver.txt] has 63036 patient samples with bowtie alignment counts and variant analysis pipeline results
Supplementary files format and content: negative control text file [sparseq_negative_data_GEOver.txt] has 1928 negative human samples with bowtie alignment counts
Supplementary files format and content: non-patient control text file [sparseq_control_data_GEOver.txt] has 2886 total synthetic control samples with bowtie alignment counts
Library strategy: RNAseq with limited amplicons.
|
| |
|
| Submission date |
Feb 10, 2023 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Jeff Wrana |
| Organization name |
Lunenfeld-Tanenbaum Research Institute
|
| Street address |
600 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1X5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19424 |
| Series (2) |
| GSE224951 |
Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population I |
| GSE231416 |
Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population |
|
| Relations |
| BioSample |
SAMN33241491 |
| SRA |
SRX19330473 |
