{
  "id": 348524,
  "title": "Question Regarding the Collected Data",
  "url": "/competitions/open-problems-multimodal/discussion/348524",
  "author_name": "",
  "post_date": "2022-08-28T20:12:28.522984900Z",
  "votes": 4,
  "comment_count": 1,
  "views": 0,
  "content": "<p>I have never worked with multiomics data before - so this is incredibly exciting! I have a very basic background in cellular biology and wanted to make sure I understood how the data was collected and the potential implications. I apologize in advance if some of these questions are very basic or nonsensical or have already been answered elsewhere (and I didn't see them)</p>\n<ol>\n<li>I am assuming that the cells from the 4 donors were placed on separate plates?</li>\n<li>The cells collected from the plates for measurement by Multiome or CITEseq are never returned (once measured, they are destroyed)?</li>\n<li>Are we assuming the CD34+ cells behave the same way in aggregate over time? In other words the data collected from cells on day 3 should be representative of all other cells on the plate on day 3?</li>\n<li>Is there reason to assume that RNA/Protein expression will change the plate environment?</li>\n<li>After being thawed, do the cells decay (thereby affecting expression patterns)?</li>\n</ol>\n<p>Thank you!</p>",
  "messages": [
    {
      "id": "1917535",
      "postDate": "08/28/2022 20:12:28",
      "content": "<p>I have never worked with multiomics data before - so this is incredibly exciting! I have a very basic background in cellular biology and wanted to make sure I understood how the data was collected and the potential implications. I apologize in advance if some of these questions are very basic or nonsensical or have already been answered elsewhere (and I didn't see them)</p>\n<ol>\n<li>I am assuming that the cells from the 4 donors were placed on separate plates?</li>\n<li>The cells collected from the plates for measurement by Multiome or CITEseq are never returned (once measured, they are destroyed)?</li>\n<li>Are we assuming the CD34+ cells behave the same way in aggregate over time? In other words the data collected from cells on day 3 should be representative of all other cells on the plate on day 3?</li>\n<li>Is there reason to assume that RNA/Protein expression will change the plate environment?</li>\n<li>After being thawed, do the cells decay (thereby affecting expression patterns)?</li>\n</ol>\n<p>Thank you!</p>",
      "rawMarkdown": "I have never worked with multiomics data before - so this is incredibly exciting! I have a very basic background in cellular biology and wanted to make sure I understood how the data was collected and the potential implications. I apologize in advance if some of these questions are very basic or nonsensical or have already been answered elsewhere (and I didn't see them)\n\n1. I am assuming that the cells from the 4 donors were placed on separate plates?\n1. The cells collected from the plates for measurement by Multiome or CITEseq are never returned (once measured, they are destroyed)?\n1. Are we assuming the CD34+ cells behave the same way in aggregate over time? In other words the data collected from cells on day 3 should be representative of all other cells on the plate on day 3?\n1. Is there reason to assume that RNA/Protein expression will change the plate environment?\n1. After being thawed, do the cells decay (thereby affecting expression patterns)?\n\nThank you!",
      "votes": null
    },
    {
      "id": "1917699",
      "postDate": "08/29/2022 01:58:08",
      "content": "<p>Hi <a href=\"https://www.kaggle.com/jjinho\" target=\"_blank\">@jjinho</a>! Thanks for your interest in the competition. And great you developed more interest in biology! Let me try to answer your questions:</p>\n<ol>\n<li>Yes! They are held completely separate.</li>\n<li>To measure a cell with the 10x Multiome kit or CITEseq, you have to lyse them, i.e. breakdown the cell membrane. So yes, they are not returned. Each cell is measured only at one time point. However, they cells that were not removed and remain in the plate keep growing.</li>\n<li>Yes, so you can assume the cells are taken out randomly from the plate (mathematically speaking, you sample uniformly from a population of cells).</li>\n<li>Cell media, i.e. the liquid the cells are surrounded and fed by, is exchanged on a daily basis. The effects of cell differentiation should be minor.</li>\n</ol>",
      "rawMarkdown": "Hi @jjinho! Thanks for your interest in the competition. And great you developed more interest in biology! Let me try to answer your questions:\n1. Yes! They are held completely separate.\n2. To measure a cell with the 10x Multiome kit or CITEseq, you have to lyse them, i.e. breakdown the cell membrane. So yes, they are not returned. Each cell is measured only at one time point. However, they cells that were not removed and remain in the plate keep growing.\n3. Yes, so you can assume the cells are taken out randomly from the plate (mathematically speaking, you sample uniformly from a population of cells).\n4.  Cell media, i.e. the liquid the cells are surrounded and fed by, is exchanged on a daily basis. The effects of cell differentiation should be minor.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 1917699,
      "author_name": "peterholderrieth",
      "author_url": "",
      "post_date": "08/29/2022 01:58:08",
      "content": "<p>Hi <a href=\"https://www.kaggle.com/jjinho\" target=\"_blank\">@jjinho</a>! Thanks for your interest in the competition. And great you developed more interest in biology! Let me try to answer your questions:</p>\n<ol>\n<li>Yes! They are held completely separate.</li>\n<li>To measure a cell with the 10x Multiome kit or CITEseq, you have to lyse them, i.e. breakdown the cell membrane. So yes, they are not returned. Each cell is measured only at one time point. However, they cells that were not removed and remain in the plate keep growing.</li>\n<li>Yes, so you can assume the cells are taken out randomly from the plate (mathematically speaking, you sample uniformly from a population of cells).</li>\n<li>Cell media, i.e. the liquid the cells are surrounded and fed by, is exchanged on a daily basis. The effects of cell differentiation should be minor.</li>\n</ol>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "1917535": "I have never worked with multiomics data before - so this is incredibly exciting! I have a very basic background in cellular biology and wanted to make sure I understood how the data was collected and the potential implications. I apologize in advance if some of these questions are very basic or nonsensical or have already been answered elsewhere (and I didn't see them)\n\n1. I am assuming that the cells from the 4 donors were placed on separate plates?\n1. The cells collected from the plates for measurement by Multiome or CITEseq are never returned (once measured, they are destroyed)?\n1. Are we assuming the CD34+ cells behave the same way in aggregate over time? In other words the data collected from cells on day 3 should be representative of all other cells on the plate on day 3?\n1. Is there reason to assume that RNA/Protein expression will change the plate environment?\n1. After being thawed, do the cells decay (thereby affecting expression patterns)?\n\nThank you!",
    "1917699": "Hi @jjinho! Thanks for your interest in the competition. And great you developed more interest in biology! Let me try to answer your questions:\n1. Yes! They are held completely separate.\n2. To measure a cell with the 10x Multiome kit or CITEseq, you have to lyse them, i.e. breakdown the cell membrane. So yes, they are not returned. Each cell is measured only at one time point. However, they cells that were not removed and remain in the plate keep growing.\n3. Yes, so you can assume the cells are taken out randomly from the plate (mathematically speaking, you sample uniformly from a population of cells).\n4.  Cell media, i.e. the liquid the cells are surrounded and fed by, is exchanged on a daily basis. The effects of cell differentiation should be minor."
  },
  "source": "meta"
}