Swate template CIMR - Sample preparation
CIMR, Sampling, extraction, Metabolomics
v1.0.0 released on 01/01/0001
145 Downloads
Template Content
Building Blocks + example values
| Input [Source Name] | Parameter [replicate] | Term Source REF (EFO:0000683) | Term Accession Number (EFO:0000683) | Parameter [metabolism quenching method] | Term Source REF (DPBO:0000010) | Term Accession Number (DPBO:0000010) | Parameter [sample wash method] | Term Source REF (DPBO:0000170) | Term Accession Number (DPBO:0000170) | Parameter [sampling time measurement datum] | Term Source REF (OBI:0001508) | Term Accession Number (OBI:0001508) | Parameter [sample storage] | Term Source REF (DPBO:0000011) | Term Accession Number (DPBO:0000011) | Parameter [Drying Method] | Term Source REF (NCIT:C112923) | Term Accession Number (NCIT:C112923) | Parameter [grinding] | Term Source REF (CHMO:0001652) | Term Accession Number (CHMO:0001652) | Parameter [cell lysis] | Term Source REF (OBI:0302894) | Term Accession Number (OBI:0302894) | Parameter [Specimen Relocation] | Term Source REF (NCIT:C164367) | Term Accession Number (NCIT:C164367) | Parameter [Method of extraction (attribute)] | Term Source REF (SNOMED:260707002) | Term Accession Number (SNOMED:260707002) | Parameter [concentration adjustment] | Term Source REF (DPBO:0000171) | Term Accession Number (DPBO:0000171) | Parameter [extract cleanup] | Term Source REF (DPBO:0000172) | Term Accession Number (DPBO:0000172) | Parameter [extract storage] | Term Source REF (DPBO:0000173) | Term Accession Number (DPBO:0000173) | Output [Sample Name] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | Liquid Nitrogen | NCIT | https://bioregistry.io/NCIT:C68796 | roots washed with water | 2025-04-15, 12 pm to 1 pm | -80 °C freezer, 1 week | lyophilization, 2 days | 1 min in Retsch mill with 2 metal balls | buffer-based lysis | shipped on dry ice for 24 h | 1 ml ice-cold methanol (MeOH) per 6 mg lyophilized tissue, two extractions combined, CHCl3/MeOH (2/1, v/v) followed by 10% trichloroacetic acid extraction | Dried under nitrogen, resolubilized in H2O | ultrafiltration | C | http://purl.obolibrary.org/obo/C_24097 | - 20 °C freezer, 1 week |
Release Notes
Currently Work in Progress 🚧Versions
| Version | Name | Release on |
| 1.0.0 | CIMR - Sample preparation | 01/01/0001 |