Projects

Notebook entries grouped by the project: field. A project shows up here once it has a section below.

Cnidarian Stem Cells

Stem cells across cnidarians: single-cell RNA-seq of Acropora cervicornis and Pocillopora damicornis (all cells vs. ALDH+ libraries) and Nematostella vectensis.

Date Title Type
2026-05-07 Pdam 31298: Cell Ranger → GeneExt → CellBender run Analysis
2026-01-15 Obtaining sequences for HCR in Nvec Analysis
2024-04-24 CellRanger on Ehrens scRNAseq data Analysis
No matching items

Mnemiopsis Phagocytes

Functional characterization of putative immune cells in Mnemiopsis leidyi. GitHub repo

Dark Genes

Thermally responsive unannotated genes and single-cell atlases in Galaxea fascicularis and other corals. GitHub repo

Porites astreoides Genome

GitHub repo

Porites July Bleaching

Date Title Type
2022-08-12 PJB ITS2 Re-seq Analysis Analysis
2022-04-27 Old Tag-seq analysis for PJB Analysis
2022-03-21 20220319 PJB ITS2 re-seq Lab work
2021-11-09 ITS2 KW-AH-ES samples Lab work
2021-11-04 20211104 ITS2 Test set for KW-AH-ES samples Lab work
2021-10-22 HIAST2 alignment with Mansour transcriptome Analysis
2021-06-30 20210629 Total Protein Testing Lab work
2021-06-11 Airbrushing Protocol for Porites July Bleaching Project Lab work
2021-01-21 20210121 Nanodrop results on Tag-Seq samples Lab work
2020-12-03 20201202 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-12-03 20201203 Tag-Seq prep for Porites July Bleaching Experiment Lab work
2020-11-30 20201126 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-25 20201125 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-23 20201119 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-23 20201120 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-18 20201117 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-12 20201110 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-12 20201111 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-11-09 20201106 DNA RNA Extractions Porites July Bleaching Experiment and WGBS samples Lab work
2020-10-29 20201029 DNA RNA Extractions Porites July Bleaching Experiment and WGBS samples Lab work
2020-10-27 20201027 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-10-26 20201025 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-10-23 20201022 DNA RNA Extractions Porites July Bleaching Experiment Lab work
2020-10-20 20201020 Adult P.astreoides and AH test sample Metabolomic Extractions Lab work
2020-10-15 20201015 Adult P.astreoides Metabolomic Extractions Lab work
2020-10-14 20201013 Adult P.astreoides Metabolomic Extractions Lab work
2020-10-12 20201009 Adult P.astreoides Metabolomic Extractions Lab work
2020-10-09 20201008 Adult P.astreoides Metabolomic Extractions Lab work
2020-10-07 20201006 Adult P.astreoides Metabolomic Extractions Lab work
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Porites Thermal Transplant

GitHub repo

Date Title Type
2023-08-21 Epidiverse WBGS testing Analysis
2023-08-04 BisSNP Analysis Analysis
2023-03-15 EpiDiverse SNP Analysis Analysis
2022-11-21 Testing BS-SNPer on WGBS data Analysis
2022-10-18 Troubleshooting WGBS Scripts Troubleshooting
2021-11-16 Methylseq trimming test to remove m-bias Analysis
2021-10-21 NF-CORE Methylseq Thermal Transplant Analysis
2021-05-26 20210526 WGBS PicoMethyl-seq library re-amplification 2 Lab work
2021-05-12 20210512 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 8 Lab work
2021-05-10 20210510 WGBS PicoMethyl-seq library re-amplification Lab work
2021-05-06 20210506 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 7 Lab work
2021-05-04 20210504 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 6 Lab work
2021-04-29 20210428 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 5 Lab work
2021-04-27 20210426 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 4 Lab work
2021-04-23 20210422 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 3 Lab work
2021-04-16 Thermal Transplant WGBS PicoMethyl Protocol Lab work
2021-04-15 20210415 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 2 Lab work
2021-04-01 20210401 WGBS PicoMethyl-seq library prep for Thermal Transplant Trial 1 Lab work
2021-03-25 20210325 Thermal Transplant ITS2 Lab work
2021-03-10 20210309 Thermal Transplant ITS2 Lab work
2021-03-04 20210302 Thermal Transplant ITS2 Lab work
2021-02-18 Thermal Transplant ITS2 Test Lab work
2021-02-08 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 8 Lab work
2020-08-27 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 7 Lab work
2020-08-20 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 5 Lab work
2020-08-19 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 6 Lab work
2020-08-19 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 4 Lab work
2020-08-16 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 5 Lab work
2020-08-16 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 3 Lab work
2020-08-13 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 4 Lab work
2020-08-13 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Batch 2 Lab work
2020-08-12 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 3 Lab work
2020-08-12 DNA RNA Extractions on P. astreoides larvae - BEAD BEATING Lab work
2020-08-07 DNA Extractions for adult homogenates of Porites Thermal Transplant Batch 2 Lab work
2020-08-06 DNA Extractions for adult homogenates of Porites Thermal Transplant Lab work
2020-08-06 DNA-RNA extractions Porites Thermal Transplant Larvae BATCH 1 Lab work
2020-08-05 DNA-RNA Extractions Porites astreoides homogenates, larvae, and adult fragments Lab work
2020-07-31 DNA-RNA-Extraxtion-Thermal-Transplant-Porites-Homogenates Lab work
2020-07-30 DNA-RNA-Extractions-Thermal-Transplant-Porites-and-Geoduck Lab work
2020-01-13 DNA RNA Extractions Thermal Transplant ADULT AND LARVAE Trial 4 Lab work
2019-12-05 DNA RNA Extractions Thermal Transplant Porites LARVAE Trial 1 Lab work
2019-12-05 DNA RNA Extractions Thermal Transplant Porites Trial 3 Lab work
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 1 Lab work
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 2 Lab work
2019-12-04 DNA RNA Extractions Thermal Transplant Porites Trial 2 Lab work
No matching items

Symbiont Integration

Porites Nutrition

Astrangia Nutrition

Date Title Type
2019-05-15 Citrate Synthase for A. poculata nutrition experiment Lab work
2019-05-15 SAM ELISA Kit for A. poculata nutrition experiment Lab work
2019-04-18 Astrangia Nutrition DNA Extractions Lab work
No matching items
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