Data Access

Broadly Consented Data Downloads

We provide access to broadly consented Fiber-seq data that can be used by researchers for various genomic studies.

Available Datasets

Our broadly consented datasets include the following samples:

• CHM1: Complete hydatidiform mole cell line
• CHM13: Complete hydatidiform mole cell line (GRCh38 alignment)
• CHM13_DSA: CHM13 data aligned against the DSA (T2Tv2.0)
• GM12878: Lymphoblastoid cell line from Coriell Cell Repository
• HG002: Human genome reference sample (Ashkenazi Jewish trio son)
• K562: Chronic myelogenous leukemia cell line

All samples are processed with FIRE (Fiber-seq Inferred Regulatory Elements).

Data Formats

All datasets are provided in standard formats:

• Fiber-seq CRAM files: Primary data format containing m6A calls and nucleosome positions
• Processed FIRE outputs: Summary statistics, peaks, and aggregated results

Download Instructions

Browse Available Data

You can explore all available samples using the AWS CLI:

aws s3 ls --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/

Download Data

To download specific samples or datasets, use the AWS CLI with the following pattern:

aws s3 sync --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/[SAMPLE_NAME]/ ./[LOCAL_DIRECTORY]/

For example, to download CHM13 data:

aws s3 sync --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/CHM13/ ./CHM13_data/

Data Use Guidelines

When using our broadly consented data, please:

• Cite the original studies and data contributors