Rapid purification of DNA samples from dextran sodium sulfate (DSS) contaminants
Bibliographic record
Abstract
Dextran sodium sulfate (DSS) is widely used to model colonic inflammation and colorectal cancer. However, it is a potent inhibitor of DNA polymerase, necessitating its removal prior to downstream analysis. Currently, there is no robust, widely applicable method of removing DSS from DNA samples. Here, we demonstrate that cetyltrimethylammonium bromide (CTAB) buffer enables rapid and efficient removal of DSS from mouse stool DNA. In the absence of CTAB, DSS inhibited PCR reactions at concentrations of 136 nM and above. CTAB effectively removed DSS from DNA samples processed by both phenol-chloroform extraction and column cleanup kits. 700 μL of CTAB was able to remove up to 93 nmol (4 mg) of DSS after one round of cleanup, while two rounds removed up to 465 nmol (20 mg) of DSS. Purified genomic DNA was suitable for subsequent quantitative PCR analysis. • We established a protocol to remove sodium dextran sulfate (DSS) contamination from purified genomic DNA. • The purification method can be incorporated into a wide range of DNA extraction protocols. • Purified genomic DNA is of high quality and is suitable for subsequent quantitative PCR analysis.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.003 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".