Standard file formats for data submission

On this page, you’ll find the standard files and formats agreed upon by the ATLAS-D2K Consortium for data submissions:

Table of contents:

• General file format requirements
  • Sequencing formats
  • High resolution image formats
  • Thumbnail formats
  • Video formats
• Mandatory assets for data submission (detailed)
  • Sequencing data
  • H\&E data
  • IHC/Immunofluorescence data
  • In-situ Hybridization (ISH) Specimen
  • Antibodies
  • Protocols

General file format requirements

Here are the general file formats the ATLAS-D2K Center request for the following types of data to provide the most reproducibility and best user experience.

Sequencing formats

• .fastq
• .bam

High resolution image formats

These are in order of desirability:

• Native file formats: CZI, LIF, LSM, VSI, Panaroma

• OME-TIF, TIFF

• JPG, PNG, GIF

Thumbnail formats

• General: The thumbnail should highlight the area of interest in your original image. It is usually displayed on the general search page to provide quick impression of the original images.
• Resolution: Make the height and width of the thumbnail 150 pixels and around 72 DPI.
• File format: .png, .jpeg (Note: These are browser-supported image formats)

Video formats

• .mp4
• .avi

Mandatory assets for data submission (detailed)

Sequencing data

For RNA-Seq, CHIP-Seq, ATAC-Seq and scRNA-seq data:

H&E data

IHC/Immunofluorescence data

In-situ Hybridization (ISH) Specimen

Antibodies

Protocols