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Your search keyword '"McDonough, Samantha"' showing total 13 results
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13 results on '"McDonough, Samantha"'

1. Additional file 4 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 4. Correlation of pre-capture library concentration with bioinformatics metrics for all samples excluding FFzn controls.

Published
2022
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2. Additional file 2 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 2. Evaluation of sample size on the calculation of sample wise median correlation.

Published
2022
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3. Additional file 3 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 3. Pair-wise scatter plot among pre-sequencing lab metrics and post sequencing bioinformatics metrics.

Published
2022
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4. Additional file 7 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 7. A decision tree model to predict QC pass/fail based on DV50.

Published
2022
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5. Additional file 5 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 5. Evaluation of false positives based on FFPE and FFzn replicates.

Published
2022
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6. Additional file 6 of Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

Author

Liu, Yuanhang, Bhagwate, Aditya, Winham, Stacey J., Stephens, Melissa T., Harker, Brent W., McDonough, Samantha J., Stallings-Mann, Melody L., Heinzen, Ethan P., Vierkant, Robert A., Hoskin, Tanya L., Frost, Marlene H., Carter, Jodi M., Pfrender, Michael E., Littlepage, Laurie, Radisky, Derek C., Cunningham, Julie M., Degnim, Amy C., and Wang, Chen

Abstract

Additional file 6. Pair-wise scatter plot among pre-sequencing lab metrics and DV50/100/200 metrics.

Published
2022
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7. Additional file 2 of E-cigarette-induced pulmonary inflammation and dysregulated repair are mediated by nAChR α7 receptor: role of nAChR α7 in SARS-CoV-2 Covid-19 ACE2 receptor regulation

Author

Qixin Wang, Sundar, Isaac K., Dongmei Li, Lucas, Joseph H., Thivanka Muthumalage, McDonough, Samantha R., and Rahman, Irfan

Abstract

Additional file 2 Table S1. Sub-chronic e-cig exposure using PG with or without nicotine altered blood gas but not hematology. Table S2. Sub-chronic e-cig exposure using PG with nicotine increased pro-inflammatory cytokines in BALF.

Published
2020
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8. Additional file 1 of E-cigarette-induced pulmonary inflammation and dysregulated repair are mediated by nAChR α7 receptor: role of nAChR α7 in SARS-CoV-2 Covid-19 ACE2 receptor regulation

Author

Qixin Wang, Sundar, Isaac K., Dongmei Li, Lucas, Joseph H., Thivanka Muthumalage, McDonough, Samantha R., and Rahman, Irfan

Abstract

Additional file 1 Figure S1. Sub-chronic e-cig with PG + Nic exposure increased cotinine levels in mouse serum. Mice were exposed to e-cig with or without nicotine for 30 days, and blood was collected through submandibular venipuncture following the final exposure. Cotinine levels were measured in serum samples from WT and nAChR α7 KO mice exposed to PG or PG with nicotine by ELISA (Cat# CO096D, Calbiotech), (n = 3–10/group). Figure S2. Sub-chronic e-cig exposure decreased exercise capacity in nAChR α7 KO mice. Mice were exposed to e-cig with or without nicotine for 30 days, and treadmill for exercise ability measurements were performed before the day of sacrifice, after the last exposure. The running distance and running time for nAChR α7 global KO and WT mice (A and B, respectively) and nAChR α7 lung epithelial cell-specific floxed/Cre-CC10 KO mice (C and D, respectively) were recorded separately. (n = 3–6/group), (*P

Published
2020
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10. Additional file 6: of Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

Author

Bhagwate, Aditya, Yuanhang Liu, Winham, Stacey, McDonough, Samantha, Stallings-Mann, Melody, Heinzen, Ethan, Davila, Jaime, Vierkant, Robert, Hoskin, Tanya, Frost, Marlene, Carter, Jodi, Radisky, Derek, Cunningham, Julie, Degnim, Amy, and Wang, Chen

Subjects
mental disorders, 3. Good health
Abstract

Table showing expected versus observed variant allelic frequency in positive control samples (HD) (DOCX 18 kb)

11. Additional file 3: of Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

Author

Bhagwate, Aditya, Yuanhang Liu, Winham, Stacey, McDonough, Samantha, Stallings-Mann, Melody, Heinzen, Ethan, Davila, Jaime, Vierkant, Robert, Hoskin, Tanya, Frost, Marlene, Carter, Jodi, Radisky, Derek, Cunningham, Julie, Degnim, Amy, and Wang, Chen

Subjects
3. Good health
Abstract

Table showing substitution frequency distributions for all the study samples (DOCX 15 kb)

12. Additional file 6: of Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

Author

Bhagwate, Aditya, Yuanhang Liu, Winham, Stacey, McDonough, Samantha, Stallings-Mann, Melody, Heinzen, Ethan, Davila, Jaime, Vierkant, Robert, Hoskin, Tanya, Frost, Marlene, Carter, Jodi, Radisky, Derek, Cunningham, Julie, Degnim, Amy, and Wang, Chen

Subjects
mental disorders, 3. Good health
Abstract

Table showing expected versus observed variant allelic frequency in positive control samples (HD) (DOCX 18 kb)

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