Annotare Submission Guidelines for Sequencing-Based Spatial Transcriptomics

ArrayExpress accepts sequencing-based spatial transcriptomics datasets. These guidelines describe how to prepare and submit such data using Annotare.

Imaging-based spatial data are not accepted. Please submit imaging-based spatial datasets to the BioImage Archive.

Please refer to the general Annotare submission guide for detailed submission instructions.

---

Scope and Data Routing

Raw data files are brokered to the European Nucleotide Archive (ENA), while ArrayExpress archives metadata, images, and processed data.

Human Data and Consent

Data derived from human samples that could potentially lead to donor identification may be submitted only if consent for public data release has been obtained.

In such cases, submissions may consist of processed data only. The submission must still provide sufficient metadata and protocols to allow interpretation of the dataset.

General Principles

The goal of an ArrayExpress submission is to ensure that users can understand and reproduce the dataset without referring to an associated publication. All relevant metadata, protocols, and processed outputs should therefore be included.

Annotare Template Selection

For spatial transcriptomics submissions, please select the “Single cell sequencing” template in Annotare. This template allows submission of more than two files per sample and captures the required experimental metadata.

Recommended Metadata for Spatial Transcriptomics

Annotare will automatically require core metadata based on the selected experimental model. For spatial transcriptomics, we strongly recommend including the additional sample attributes listed below.

Sample-Level Metadata (Required for Spatial Data)

• Sample ID
  A unique identifier for the biological specimen used in the experiment.
• Slide ID
  A unique identifier for the glass slide or cartridge on which the tissue section was mounted.
• Sampling site
  The precise anatomical location from which the tissue was obtained, preferably using a standardized anatomical ontology.
• Specimen with known storage state
  Method used to preserve the tissue prior to processing (e.g. fresh frozen, FFPE).
• Section thickness
  Thickness of the tissue section mounted on the slide, reported in micrometers (µm).
• Permeabilization time

Optional (If Relevant)

• Position on slide
  Description of where the capture area is located on the slide.

Library Information

In the Single-cell library information tab:

• Specify the library construction method (e.g. 10x Visium v2).
• If “Other” is selected, provide full details in the Nucleic acid library construction protocol.

Protocol Requirements

Please provide all required protocols. In addition, spatial transcriptomics submissions should include a Dissection protocol describing:

Sample Preparation

• Fixation
• Sectioning / slicing
• Permeabilization

Sample Imaging

• Microscopy instrument
• Magnification
• Microscopy technique
• Imaging setup

Data Processing

In the normalization / data transformation protocol, please specify the version of the downstream analysis software.

File Requirements

Raw Data (Required unless restricted human data)

• FASTQ files
• BAM files

Processed Data (Required)

• High-resolution image of the tissue section
• Processed cell/spot count matrix
• Barcode coordinates file
• For Visium data: barcode_mappings.parquet