Metadata template

This repository provides a version-controlled template for metadata tracking and submission for the Odomlab2.0.

Changelog

2021-05-12 - Version 2021-05.1

Changes

• New fields:
  • GENOTYPE - needed for ArrayExpress /ENA submission, typically this is wild type, if not working with GMO
  • TISSUE - important if your SAMPLE_TYPE is not indicating the tissue, fill this field
  • IMAGING_DATASET_ID - ID/Label to reference imaging dataset e.g. for Spatial Transcriptomics
• Removed redundant fields:
  • BARCODE_I7
  • BARCODE_I5
  • use BARCODE_I5_SEQ and BARCODE_I7_SEQ instead this is required for ILSe
• Please note that CAST/Ej is not a species. For SPECIES enter Mus musculus and specify the STRAIN CAST/Ej
• Website to get info and spreadsheets: https://odomlab2.github.io/metadata-submission/
• Columns may be sorted according to category, rather than by point-of-use

2020-11-05

Added fields to Chip-Seq:

• ANTIBODY
• ANTIBODY_LOT_NUMBERwq
• ANTIBODY_TARGET

2020-10-27

Major Changes

Most importantly, I added two fields:

• INDIVIDUAL_REF_ID
• INDIVIDUAL_REF_DB

The following fields were renamed

• LIBRARY_PREP_KIT -> LIB_PREP_KIT
• SAMPLE_ID -> SAMPLE_NAME_GPCF
• BIOMATERIAL_ID -> SAMPLE_TYPE

How to use:

The purpose of these is to provide a clear reference point to the animals used. Thus, at the DKFZ, the INDIVIDUAL_REF_ID is the ANIMAL_NUMBER from the MOVI database or the spreadsheet-dump located at

"T:/Animals/Animal numbers MOVI "

In this case INDIVIDUAL_REF_DB would be set to "MOVI"

For CRUK-originated samples, the animal numbers (column: "MOUSE ID" are listed in the following spreadsheet:

T:/FREEZER -80/Freezer 2- Cambridge samples/Cambridge sample inventory lists/190307_harvested_tissue_mouse2.xlsx

In this case INDIVIDUAL_REF_DB would be set to "ODOM_TISSUE_DB".

The field "LIB_PREP_KIT" is used by OTP to select adapter sequences for trimming of RNAseq reads. Please check in your previous submission, if the library preparation kit that are using is registered in OTP (odcf-service@dkfz.de) or tell the ODCF which kit you have used and which adapter it contains.

Minor changes

• Modified description banners in the bottom. It should be more clear now, that all fields are mandatory to fill out, not only those for ILSE.

Versioning

This repository used calendar-versioning (https://calver.org/) according to the following scheme:

YY.0M-minor

Accordingly, the first version released in October, 2020 is tagged: 20.10-1