IMPC phenotyping SOPs in JMC
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1 IMPC phenotyping SOPs in JMC Tissue Embedding and Block Banking IMPC_BLK_001 Purpose Collect and fix a standard list of tissues from the complete necropsy (see IMPC Gross Pathology & Tissue Collection SOP) Trim the fixed tissues into cassettes for processing Embed the tissues in paraffin in a standard orientation Experimental Design Minimum number of mutant animals: 2 mutant males + 2 mutant females Minimum age of animals: 16 weeks Procedure 1. The following 29 tissues are collected and wet fixed at necropsy (according to IMPC Gross Pathology & Tissue Collection SOP) Adrenal gland Heart Mammary gland Skin Thymus Brain Kidney Ovary Small intestine Thyroid Epididymis Large intestine Pancreas Spinal cord Trachea Esophagus Liver Prostate Spleen Urinary bladder Eye with optic nerve Lung Seminal vesicles Stomach Uterus Gall bladder Lymph node Skeletal muscle Testes 2. Trim the fixed tissue into labelled cassettes for processing according to Centre-specific SOP 3. Process the cassettes according to Centre-specific SOP 4. Embed the tissues in paraffin using the orientation below: Tissue Number of Tissue Pieces Embedding Orientation Brain Up to 5 Transverse or Mid-sagittal Eye with optic nerve 1 (per eye) Sagittal (optic nerve parallel to cassette surface) 1 (per eye) Sagittal (within skull) Spinal cord Up to 6 Cross Thymus 1 Flat Thyroid 1 (with trachea) Cross
2 Heart 1 Sagittal Trachea 1 (with thyroid) Cross Esophagus 1 Cross Lung Up to 5 Cross or Sagittal Liver Up to 2 Cross Gall bladder 1 (with liver) Cross Stomach Up to 2 Cross Small intestine 3 Cross (duodenum, jejunum, ileum) Large intestine 3 Cross (cecum, colon, rectum) Pancreas 1 Flat Spleen 1 Flat Kidney 2 Cross and Sagittal Adrenal gland At least 1 Cross or Sagittal Mammary gland At least 1 (with skin) Flat Lymph node At least 1 Flat Skin Up to 5 Cross on edge Skeletal muscle At least 1 Cross Urinary bladder 1 Flat Testes At least 1 Flat Epididymis At least 1 Flat Prostate 1 Flat Seminal vesicles At least 1 Flat Ovary At least 1 Flat Uterus 1 Flat Notes The age of the animals at which they undergo this procedure is an important data. It is, however, derived from the date of birth and the date of necropsy of the animal, the latter being a metadata parameter. Similar situation applies to the number of animals that a centre has submitted to this procedure it will also be derived and subject to quality control of the data. Parameters Version Type Increment Option Derived Unit Data Type Brain IMPC_BLK_010_001 Eye 1 with optic nerve (optic nerve parallel to cassette surface)
3 IMPC_BLK_011_001 Eye 2 with optic nerve (within skull) IMPC_BLK_012_001 Spinal cord IMPC_BLK_013_001 Thymus IMPC_BLK_014_001 Thyroid IMPC_BLK_015_001 Heart IMPC_BLK_016_001 Trachea IMPC_BLK_017_001 Esophagus IMPC_BLK_018_001 Lung IMPC_BLK_019_001 Liver IMPC_BLK_020_001 Gall bladder IMPC_BLK_021_001 Stomach IMPC_BLK_022_001 Small intestine IMPC_BLK_023_001 Large intestine IMPC_BLK_024_001 Pancreas IMPC_BLK_025_001 Spleen IMPC_BLK_026_001 Left Kidney IMPC_BLK_027_001 Right Kidney IMPC_BLK_028_001
4 Left Adrenal gland IMPC_BLK_029_001 Right Adrenal gland IMPC_BLK_030_001 Mammary gland IMPC_BLK_031_001 Lymph node IMPC_BLK_032_001 Skin IMPC_BLK_033_001 Skeletal muscle IMPC_BLK_034_001 Urinary bladder IMPC_BLK_035_001 Testes IMPC_BLK_036_001 Epididymis IMPC_BLK_037_001 Prostate IMPC_BLK_038_001 Seminal vesicles IMPC_BLK_039_001 Ovary IMPC_BLK_040_001 Uterus IMPC_BLK_041_001 Additional tissues IMPC_BLK_042_001 Metadata Version Type Increment Option Derived Unit Data Type Experimenter ID IMPC_BLK_003_ proceduremetadata TEXT Fixative IMPC_BLK_006_ proceduremetadata 10% neutral buffer formalin TEXT Tissue storage ID(s) 1.1 proceduremetadata TEXT
5 IMPC_BLK_007_001 Embedding medium IMPC_BLK_008_001 Date of sacrifice IMPC_BLK_001_001 Date of necropsy IMPC_BLK_002_ proceduremetadata Paraffin TEXT 1.0 proceduremetadata DATETIME 1.0 proceduremetadata DATETIME
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