|
| Status |
Public on Jul 30, 2024 |
| Title |
12132022_W62202315-V1-2_S558_R2C2_7H_S290 |
| Sample type |
SRA |
| |
|
| Source name |
human nasopharyngeal swab
|
| Organisms |
Homo sapiens; Severe acute respiratory syndrome coronavirus 2 |
| Characteristics |
tissue: human nasopharyngeal swab
bc run_id: 31
pipeline version: BC
|
| 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)
Other: RNAseq with limited amplicons.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt
|
| Data processing |
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
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 used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BC_count_table.txt; run31_R1BC_count_table.txt; run38_R1BC_count_table.txt; run46_R1BC_count_table.txt; run139_R1BC_count_table.txt; run141p3_R1BC_count_table.txt; run141p6_R1BC_count_table.txt
Supplementary files format and content: run27_R2BC_count_table.txt; run31_R2BC_count_table.txt; run38_R2BC_count_table.txt; run46_R2BC_count_table.txt; run139_R2BC_count_table.txt; run141p3_R2BC_count_table.txt; run141p6_R2BC_count_table.txt
Supplementary files format and content: run27_count_table.txt; run31_count_table.txt; run38_count_table.txt; run46_count_table.txt; run139_count_table.txt; run141p3_count_table.txt; run141p6_count_table.txt
Supplementary files format and content: run27_BC_pair_analysis_filenames.txt; run31_BC_pair_analysis_filenames.txt; run38_BC_pair_analysis_filenames.txt; run46_BC_pair_analysis_filenames.txt; run139_BC_pair_analysis_filenames.txt; run141p3_BC_pair_analysis_filenames.txt; run141p6_BC_pair_analysis_filenames.txt
|
| |
|
| Submission date |
May 01, 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 |
GPL28867 |
| Series (2) |
| GSE231415 |
Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population II |
| GSE231416 |
Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population |
|
| Relations |
| BioSample |
SAMN34502492 |
| SRA |
SRX20176764 |
