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IHEC / epiATLAS-metadata-harmonization

IHEC metadata merging and cleanup
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Markers column: link to protocol extraction #3

Closed GFrosi closed 2 years ago

GFrosi commented 3 years ago

43 EpiRR related to Blueprint (ex: IHECRE00000071) had a link in the “marker” column that was erased. However, the corresponding protocols page (https://www.blueprint-epigenome.eu/index.cfm?p=7BF8A4B6-F4FE-861A-2AD57A08D63D0B58) is referring to “CD4 naive cells” so “CD4+” and perhaps “CD45RO+” also mentioned in the protocol could be added as “markers”

daniel-rico commented 3 years ago

IHECRE00000071 is actually an anti-inflammatory macrophage (M2): the protocol from the three type of macrophages (M0, M1 and M2) is here: https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/UCAM_BluePrint_Macrophage.pdf @GFrosi , could you give the 43 EpiRR IDs to check all of them please? We can find the right markers and put them (instead of the link)

GFrosi commented 3 years ago

Hi @daniel-rico ,

Thanks for your reply. Here are the 43 EpiRR IDs. If you need something else, please just let me know.

IHECRE00000008.3 IHECRE00000013.3 IHECRE00000016.3 IHECRE00000019.3 IHECRE00000039.3 IHECRE00000043.3 IHECRE00000045.3 IHECRE00000055.3 IHECRE00000059.3 IHECRE00000060.3 IHECRE00000071.3 IHECRE00000079.3 IHECRE00000082.3 IHECRE00000084.3 IHECRE00000091.3 IHECRE00000099.3 IHECRE00000113.3 IHECRE00000121.3 IHECRE00000126.3 IHECRE00000129.3 IHECRE00000150.3 IHECRE00000151.3 IHECRE00000154.3 IHECRE00000158.3 IHECRE00000161.3 IHECRE00000174.3 IHECRE00000177.3 IHECRE00000184.3 IHECRE00000195.3 IHECRE00000255.2 IHECRE00000269.2 IHECRE00000303.2 IHECRE00000312.2 IHECRE00000318.2 IHECRE00001289.1 IHECRE00001293.1 IHECRE00001299.1 IHECRE00001384.1 IHECRE00001391.1 IHECRE00001398.1 IHECRE00001510.1 IHECRE00001555.1 IHECRE00001558.1

daniel-rico commented 3 years ago

Fantastic, thanks a lot!

Juliana will review them.

Cheers, Daniel

Pronouns: he/him On 23 Aug 2021, 16:22 +0200, GFrosi @.***>, wrote:

Hi @daniel-rico , Thanks for your reply. Here are the 43 EpiRR IDs. If you need something else, please just let me know. IHECRE00000008.3 IHECRE00000013.3 IHECRE00000016.3 IHECRE00000019.3 IHECRE00000039.3 IHECRE00000043.3 IHECRE00000045.3 IHECRE00000055.3 IHECRE00000059.3 IHECRE00000060.3 IHECRE00000071.3 IHECRE00000079.3 IHECRE00000082.3 IHECRE00000084.3 IHECRE00000091.3 IHECRE00000099.3 IHECRE00000113.3 IHECRE00000121.3 IHECRE00000126.3 IHECRE00000129.3 IHECRE00000150.3 IHECRE00000151.3 IHECRE00000154.3 IHECRE00000158.3 IHECRE00000161.3 IHECRE00000174.3 IHECRE00000177.3 IHECRE00000184.3 IHECRE00000195.3 IHECRE00000255.2 IHECRE00000269.2 IHECRE00000303.2 IHECRE00000312.2 IHECRE00000318.2 IHECRE00001289.1 IHECRE00001293.1 IHECRE00001299.1 IHECRE00001384.1 IHECRE00001391.1 IHECRE00001398.1 IHECRE00001510.1 IHECRE00001555.1 IHECRE00001558.1 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

juearcilaga commented 3 years ago

Neutrophils CD16+

Monocyte derived Macrophage CCR7, CD25, CD14, CD40 CD206, CD36, CD45

Monocytes CD14, CD42b, CD64, CD45

Cord Blood Progenitor Populations Hematopoietic Stem Cell (HSC) Multipotent Progenitor (MPP) Common Lymphoid Progenitor (CLP) Common Myeloid Progenitor (CMP) Megakaryocyte-Erythroid Progenitor (MEP) Granulocyte-Macrophage Progenitor (GMP)

naive CD4 CD4, CD45RA

GFrosi commented 3 years ago

Thanks Juliana,

however our "mission" is only to report the markers used or validated for each of these EpiRR (not the ones that are expected); could you complete the "marker" column of the following table when appropriate? If you are not sure we'll simply keep a blank (as most of the samples anyway).

Thanks a lot again.

EpiRR | biomaterial_type | tissue_type | cell_type| markers IHECRE00000008.3 | primary cell culture | venous blood | macrophage | IHECRE00000013.3 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000016.3 | primary cell culture | venous blood | macrophage | IHECRE00000019.3 | primary cell culture | cord blood | inflammatory macrophage | IHECRE00000039.3 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000043.3 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00000045.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (resting) | IHECRE00000055.3 | primary cell culture | cord blood | alternatively activated macrophage | IHECRE00000059.3 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000060.3 | primary cell culture | cord blood | macrophage | IHECRE00000071.3 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000079.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | IHECRE00000082.3 | primary cell culture | venous blood | macrophage | IHECRE00000084.3 | primary cell culture | venous blood | macrophage | IHECRE00000091.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | IHECRE00000099.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (resting) | IHECRE00000113.3 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00000121.3 | primary cell culture | cord blood | macrophage | IHECRE00000126.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (proliferating) | IHECRE00000129.3 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000150.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | IHECRE00000151.3 | primary cell culture | cord blood | macrophage | IHECRE00000154.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | IHECRE00000158.3 | primary cell culture | cord blood | conventional dendritic cell | IHECRE00000161.3 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00000174.3 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00000177.3 | primary cell culture | venous blood | macrophage | IHECRE00000184.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (proliferating) | IHECRE00000195.3 | primary cell culture | cord blood | inflammatory macrophage | IHECRE00000255.2 | primary cell culture | cord blood | conventional dendritic cell | IHECRE00000269.2 | primary cell culture | cord blood | alternatively activated macrophage | IHECRE00000303.2 | primary cell | venous blood | adult endothelial progenitor cell | IHECRE00000312.2 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00000318.2 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00001289.1 | primary cell culture | cord blood | inflammatory macrophage | IHECRE00001293.1 | primary cell culture | venous blood | inflammatory macrophage | IHECRE00001299.1 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00001384.1 | primary cell culture | cord blood | alternatively activated macrophage | IHECRE00001391.1 | primary cell culture | venous blood | alternatively activated macrophage | IHECRE00001398.1 | primary cell culture | venous blood | macrophage | IHECRE00001510.1 | primary cell | venous blood | adult endothelial progenitor cell | IHECRE00001555.1 | primary cell | venous blood | adult endothelial progenitor cell | IHECRE00001558.1 | primary cell culture | cord blood | conventional dendritic cell |

juearcilaga commented 3 years ago

IHECRE00000303.2 | primary cell | venous blood | adult endothelial progenitor cell |   IHECRE00001510.1 | primary cell | venous blood | adult endothelial progenitor cell |   IHECRE00001555.1 | primary cell | venous blood | adult endothelial progenitor cell |   IHECRE00000013.3 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD45 IHECRE00000039.3 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD46 IHECRE00000055.3 | primary cell culture | cord blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD47 IHECRE00000059.3 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD48 IHECRE00000071.3 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD49 IHECRE00000129.3 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD50 IHECRE00000269.2 | primary cell culture | cord blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD51 IHECRE00000312.2 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD52 IHECRE00001299.1 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD53 IHECRE00001384.1 | primary cell culture | cord blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD54 IHECRE00001391.1 | primary cell culture | venous blood | alternatively activated macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD55 IHECRE00000158.3 | primary cell culture | cord blood | conventional dendritic cell |   IHECRE00000255.2 | primary cell culture | cord blood | conventional dendritic cell |   IHECRE00001558.1 | primary cell culture | cord blood | conventional dendritic cell |   IHECRE00000126.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (proliferating) IHECRE00000184.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (proliferating) IHECRE00000045.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (resting) |   IHECRE00000099.3 | primary cell culture | cord blood | endothelial cell of umbilical vein (resting) |   IHECRE00000019.3 | primary cell culture | cord blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD55 IHECRE00000043.3 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD56 IHECRE00000113.3 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD57 IHECRE00000161.3 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD58 IHECRE00000174.3 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD59 IHECRE00000195.3 | primary cell culture | cord blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD60 IHECRE00000318.2 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD61 IHECRE00001289.1 | primary cell culture | cord blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD62 IHECRE00001293.1 | primary cell culture | venous blood | inflammatory macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD63 HECRE00000008.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD63 IHECRE00000016.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD64 IHECRE00000060.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD65 IHECRE00000082.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD66 IHECRE00000084.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD67 IHECRE00000121.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD68 IHECRE00000151.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD69 IHECRE00000177.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD70 IHECRE00001398.1 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD71 IHECRE00000079.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | Lin-CD34+CD38+IL-3Ra-CD45RA- IHECRE00000091.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | Lin-CD34+CD38+IL-3Ra-CD45RA- IHECRE00000150.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | Lin-CD34+CD38+IL-3Ra-CD45RA- IHECRE00000154.3 | primary cell | cord blood | megakaryocyte-erythroid progenitor cell | Lin-CD34+CD38+IL-3Ra-CD45RA-

The information about the markers comes from the documentation of the protocols: Blueprint Epigenome - Protocols (blueprint-epigenome.eu). Macrophages are derived from monocytes, they used the marker before inducing their differentiation in M0, M1 and M2 (https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/UCAM_BluePrint_Macrophage.pdf).

I couldn't find information about the markers of endothelial cells and dendritic cells

juearcilaga commented 2 years ago

Hello Juliana,

Do you think we can assume the positive symbol for the Markers that you described on git? Or should we just keep the markers with this description? (e.g Lin-CD34+CD38+IL-3Ra-CD45RA-

Thanks a lot for your help!

Gabriella Frosi

juearcilaga commented 2 years ago

Hi Gabriella,

In the columns where the markers do not have a symbol, we can assume positive (According to what Daniel and I interpret from the Blueprint's protocol). In the columns where there are negative symbols, I spoke to Daniel, and we think it is important to keep that information. This example (e.g Lin-CD34+CD38+IL-3Ra-CD45RA-) Could be something like : Lin-, CD34+, CD38+, IL3RA-, CD45RA-. Separating the markers with commas and eliminating from the name IL-3 the (-) symbol to avoid confusion with the negative symbol. Daniel says that replacing the negative and positive symbols for "neg" and "pos" is another alternative if ambiguities persist.

Thank you very much

Juliana

GFrosi commented 2 years ago

Thanks a lot Juliana and Daniel,

I will perform the updates.

Cheers

Gabriella Frosi

GFrosi commented 2 years ago

Another question @juearcilaga ,

In this example:

IHECRE00000008.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD63 IHECRE00000016.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD64 IHECRE00000060.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD65 IHECRE00000082.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD66 IHECRE00000084.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD67 IHECRE00000121.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD68 IHECRE00000151.3 | primary cell culture | cord blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD69 IHECRE00000177.3 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD70 IHECRE00001398.1 | primary cell culture | venous blood | macrophage | CCR7, CD25, CD14, CD40,CD206, CD36, CD71

The last marker is always incremented by one (CD63, CD64, CD65...CD71). Is it correct? The same pattern occurred with the EpiRR associated with "inflammatory macrophage". Could you just confirm it?

Best

juearcilaga commented 2 years ago

Hi @GFrosi,

You are totally right, that is a mistake I made. Should be CCR7+, CD25+, CD14+, CD40+ ,CD206+, CD36+, CD45+ in all. https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/UCAM_BluePrint_Macrophage.pdf (Antibodies for Macrophage purity check)

Thank you very much

GFrosi commented 2 years ago

Thanks for your reply @juearcilaga!