|
| Status |
Public on Sep 09, 2021 |
| Title |
exp031020 RBD rep 5 |
| Sample type |
SRA |
| |
|
| Source name |
bulk yeast cell culture
|
| Organism |
Komagataella phaffii |
| Characteristics |
transgene: SARS-Cov2 receptor binding domain
|
| Treatment protocol |
Cells were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and resuspended in fresh media with 3% methanol to induce recombinant gene expression.
|
| Growth protocol |
Cell were harvested after 18 h of production at 3 mL plate scale. Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified according to the Qiagen RNeasy kit (cat #74104) and RNA quality was analyzed to ensure RNA Quality Number >6.5.
3'DGE Nextera
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
phaffi_plus_transgenes_031020.fa.gz
dalvie031020_intCt.txt.gz
dalvie031020_l2cpm.txt.gz
|
| Data processing |
MiSeq sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative per unique molecular identifier using a custom script. Gene expression was quantified using salmon (version 1.3.0, Patro et al., 2017) using the indicated Komagataella transcriptomes plus transgenes as selective alignment targets. The resulting counts were summarized to the gene level using tximport (version 1.12.3) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.26.8, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space for visualization.
Genome_build: Komagataella phaffi WT (PRJNA304977) with indicated transcriptomes
Supplementary_files_format_and_content: phaffi_plus_transgenes_020821.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: phaffi_plus_transgenes_031020.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: dalvie020821_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie020821_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie031020_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_031020.fa.gz target
Supplementary_files_format_and_content: dalvie031020_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_031020.fa.gz target
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
Sep 09, 2021 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
charliew@mit.edu
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL30002 |
| Series (1) |
| GSE172054 |
Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice |
|
| Relations |
| BioSample |
SAMN18740758 |
| SRA |
SRX10600446 |
