Journal: bioRxiv

Article Title: SomaScan Bioinformatics: Normalization, Quality Control, and Assessment of Pre-Analytical Variation

doi: 10.1101/2024.02.09.579724

Figure Lengend Snippet: Venn diagram showing the SOMAmer overlap (based on “SeqId” identifiers) between the 1.3K, 5K, 7K, and 11K SomaScan assays.

Article Snippet: For each human protein SOMAmer in the plasma 7K assay, we calculated the Spearman’s correlation between the fully normalized RFU values from the adat file provided by SomaLogic using external references (a file designated with the “hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.anmlSMP” suffix) and the full normalization described here using internal references (“hyb.msnCal.ps.cal.msnAll”).

Techniques:

Journal: bioRxiv

Article Title: SomaScan Bioinformatics: Normalization, Quality Control, and Assessment of Pre-Analytical Variation

doi: 10.1101/2024.02.09.579724

Figure Lengend Snippet: Distribution of Spearman’s correlation estimates for the 7,289 human protein SOMAmers in the 7K plasma SomaScan assay, calculated over nearly 1,800 human donor samples from the BLSA . For each SOMAmer, the correlation was calculated between the fully normalized RFU values from SomaLogic’s pipeline using external references and the full normalization described here using internal references.

Article Snippet: For each human protein SOMAmer in the plasma 7K assay, we calculated the Spearman’s correlation between the fully normalized RFU values from the adat file provided by SomaLogic using external references (a file designated with the “hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.anmlSMP” suffix) and the full normalization described here using internal references (“hyb.msnCal.ps.cal.msnAll”).

Techniques: Clinical Proteomics

Journal: bioRxiv

Article Title: dnaudit + pydnaweb: A lightweight text-based planning and documentation workflow for genetic cloning with automatic verification

doi: 10.1101/2025.05.31.657172

Figure Lengend Snippet: A . amplification of Fragment A by PCR; B . amplification of Fragment B containing the gRNA by PCR; C . amplification of Fragment C by fusion PCR; D . digestion of the Cas9 plasmid using the MssI restriction enzyme to generate the final Cas9 cassette; E . amplification of the dDNA cassette (GFP) by PCR; F . integration of the Cas9 cassette and Fragment C in the C. albicans HIS1 locus by homologous recombination.

Article Snippet: Finally, Fragment C was co-transformed into C. albicans SC5314 together with the appropriately digested CAS9 pADH99 plasmid (with MssI restriction enzyme; Addgene plasmid # 90979; ) and the donor DNA. dDNAs ( ) were amplified from the template CIp10–γmGFP (Addgene plasmid # 163119, 27) using the oligonucleotides dDNA_ATO1_GFP_Fw and dDNA_ATO1_GFP_Rv as forward and reverse primers, respectively ( Table S1 ).

Techniques: Amplification, Plasmid Preparation, Homologous Recombination

Journal: bioRxiv

Article Title: dnaudit + pydnaweb: A lightweight text-based planning and documentation workflow for genetic cloning with automatic verification

doi: 10.1101/2025.05.31.657172

Figure Lengend Snippet: The Cas9 endonuclease is guided by the gRNA to the target site within the ATO1 gene. The gRNA binds to the complementary DNA sequence, allowing Cas9 to introduce a double-strand break (DSB) at that locus (Figure S2). The donor DNA cassette containing the gene encoding GFP facilitates homology-directed repair (HDR), resulting in the insertion of the GFP sequence into the 3’ end of the ATO1 gene.

Article Snippet: Finally, Fragment C was co-transformed into C. albicans SC5314 together with the appropriately digested CAS9 pADH99 plasmid (with MssI restriction enzyme; Addgene plasmid # 90979; ) and the donor DNA. dDNAs ( ) were amplified from the template CIp10–γmGFP (Addgene plasmid # 163119, 27) using the oligonucleotides dDNA_ATO1_GFP_Fw and dDNA_ATO1_GFP_Rv as forward and reverse primers, respectively ( Table S1 ).

Techniques: Sequencing, Introduce