biospecimen non human template
Template for Biospecimen_non_Human [Source]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| specimenAge | The subject's age at the time of specimen extraction is the individual's age (since birth) at the time a given specimen was extracted. Measured as age in years. Other, Unknown, Not collected, Not applicable | True | STRING | ManifestColumn | |||
| specimenSource | Indicate the biological area of the specimen | True | STRING | ManifestColumn | |||
| specimenType | Type of biological material comprising the Specimen | True | STRING | ManifestColumn | blood,Cerebrospinal Fluid (CSF),Not applicable,Not collected,Not specified,organoid,plasma,saliva,serum,sputum,stool,swabs,tissue,Unknown,urine | ||
| tissueVolume | The volume of the tissue sample. Measured in microliters. | True | STRING | ManifestColumn | |||
| Component | False | ||||||
| Filename | False | ||||||
| cellType | Indicate the cell type. | True | STRING | sage.annotations-experimentalData.cellType-0.0.9 | ManifestColumn | A549, arachnoid, astrocytes, B-lymphocytes, CD138+, CD8+ T-Cells, CNON, dopaminergic neurons, Embryonic stem cells, epithelial, epithelial-like, fibroblast, GABAergic neurons, glia, GLUtamatergic neurons, immune cell, iPSC, iPSC-derived astrocytes, iPSC-derived glia, iPSC-derived neuron, iPSC-derived neuronal progenitor cell, iPSC-derived telencephalic organoids, lymphoblast, lymphoblastoid cell line, macrophages, meningioma, microglia, monocytes, monocyte-derived microglia, NCX NES, NeuN-, NeuN+, neural progenitor cell, neuron, oligodendrocyte, peripheral blood mononuclear cell, polygonal, round, schwann, Schwann cell precusor, schwannoma, SH-SY5Y, Not collected, Not specified, Not applicable, Other, Unknown | |
| fastingState | Was individual fasting when the sample was taken (true/false)? | True | STRING | sage.annotations-experimentalData.fastingState-0.0.2 | ManifestColumn | FALSE,Not applicable,Not collected,Not specified,TRUE,Unknown | |
| isPostMortem | Was the sample taken after death (true/false)? | True | STRING | sage.annotations-experimentalData.isPostMortem-0.0.2 | ManifestColumn | TRUE, FALSE | |
| nucleicAcidSource | Specifies the type of nucleic acid (DNA, RNA, Pooled, etc.) found in a sample. | True | STRING | sage.annotations-ngs.nucleicAcidSource-0.0.3 | ManifestColumn | bulk cell,bulk nuclei,mitochondria,Not applicable,Not collected,Not specified,single cell,single nucleus,sorted cells,sorted nuclei,Unknown | |
| organ | Indicate the organ the specimen is from | True | STRING | sage.annotations-experimentalData.organ-0.0.4 | ManifestColumn | blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown | |
| samplingAge | The calculated age of the sample, measurement is determined or coded by the data contributor.Other,Unknown, Not collected, Not applicable | True | STRING | sage.annotations-experimentalData.samplingAge-0.0.2 | ManifestColumn | ||
| specimenID | Identifying string linked to a particular sample or specimen, provide by the data contributor | True | STRING | sage.annotations-experimentalData.specimenID-0.0.2 | ManifestColumn | ||
| tissue | Indicate the tissue the specimen is from | True | STRING | sage.annotations-experimentalData.tissue-0.0.11 | ManifestColumn | amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain | |
| tissueWeight | The mass of the tissue specimen. Measured in mg. | True | STRING | sage.annotations-experimentalData.tissueWeight-0.0.2 | ManifestColumn | ||
| assay | The analysis or technology used to generate the data in this file | True | STRING | sage.annotations-experimentalData.assay-0.0.26 | ManifestColumn | 10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway, Not collected, Not specified, Not applicable, Other, Unknown | |
| individualID | Identifying string linked to the individual or animal being studied, provided by the data contributor | True | STRING | sage.annotations-experimentalData.individualID-0.0.2 | ManifestColumn |