Datasets
Raw data download
Raw fast5 files stay at the original repositories. This page collects the accession for each dataset and a direct link to the raw archive of every sample so you can skip the repository browsers.
The accession links lead to the original NCBI/EBI records with full metadata. Accessions starting with PRJEB or PRJNA resolve at the EBI European Nucleotide Archive; those starting with SRP at the NCBI Sequence Read Archive. The raw data column links straight to the fast5 archive of each sample.
If a link does not start downloading in the browser, copy the link address and fetch it from a terminal instead. Archives range from a few GB to several hundred GB; use a resumable downloader:
curl -L -C - -O "https://ftp.sra.ebi.ac.uk/vol1/run/ERR276/ERR2764782/10xpolyA.tar.gz"
# or
wget -c "https://ftp.sra.ebi.ac.uk/vol1/run/ERR276/ERR2764782/10xpolyA.tar.gz"Raw data by sample
| Dataset | Published | Accession | Species | Type | Sample | Raw data (fast5) |
|---|---|---|---|---|---|---|
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 10xpolyA | 10xpolyA.tar.gz |
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 15xpolyA | 15xpolyA.tar.gz |
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 30xpolyA | 30xpolyA.tar.gz |
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 60xpolyA | 60xpolyA.tar.gz |
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 80xpolyA | 80xpolyA.tar.gz |
| ont_ployA_standard | 2018-09 | PRJEB28423 | Synthetic | RNA | 100xpolyA | 100xpolyA.tar.gz |
| eGFP_polyA_DNA | 2019-06 | PRJEB31806 | Synthetic | cDNA | dna_rep1_sqklsk108_flipflop | dna_rep1_sqklsk108_flipflop.tar.gz |
| eGFP_polyA_DNA | 2019-06 | PRJEB31806 | Synthetic | cDNA | dna_rep2_sqklsk109_flipflop | dna_rep2_sqklsk109_flipflop.tar.gz |
| eGFP_polyA_RNA | 2019-06 | PRJEB31806 | Synthetic | RNA | rna_rep1_sqkrna001_plus_rt | rna_rep1_sqkrna001_plus_rt.tar.gz |
| eGFP_polyA_RNA | 2019-06 | PRJEB31806 | Synthetic | RNA | rna_rep2_sqkrna001_plus_rt | rna_rep2_sqkrna001_plus_rt.tar.gz |
| eGFP_polyA_RNA | 2019-06 | PRJEB31806 | Synthetic | RNA | rna_rep3_sqkrna002_minus_rt | rna_rep3_sqkrna002_minus_rt.tar.gz |
| lambda_phage | 2021-03 | PRJNA926802 | lambda phage | DNA | VER5940 | single_fast5_lambdaphage.tar.1 |
| NA12878 | 2019-06 | PRJEB23027 | Homo sapiens | DNA | FAB42828 | FAB42828-288548394_Multi_Fast5.tar Raw fast5 page |
| NA12878 | 2019-06 | PRJEB23027 | Homo sapiens | DNA | FAF04090 | FAF04090-3842965088_Multi_Fast5.tar Raw fast5 page |
| NA12878 | 2019-06 | PRJEB23027 | Homo sapiens | DNA | FAF09968 | FAF09968-3439856925_Multi_Fast5.tar Raw fast5 page |
| curlcake | 2019-07 | PRJNA511582 | Synthetic | RNA | m6A-mod-rep1 | RNAAB090763.fast5.tar.gz.3 |
| curlcake | 2019-07 | PRJNA511582 | Synthetic | RNA | m6A-mod-rep2 | RNA081120182.fast5.tar.gz.2 |
| curlcake | 2019-07 | PRJNA511582 | Synthetic | RNA | non-mod-rep1 | RNAAB089716.fast5.tar.gz.4 |
| curlcake | 2019-07 | PRJNA511582 | Synthetic | RNA | non-mod-rep2 | RNA081120181.fast5.tar.gz.2 |
| scBY4741_m5C | 2021-06 | PRJNA563591 | Synthetic | RNA | m5C_modified | RNA010220191_m5C_fast5.tar.gz.1 |
| scBY4741_hm5C | 2021-06 | PRJNA548268 | Synthetic | RNA | hm5C_modified | RNA080420191_5hmC_fast5.tar.gz.1 |
| scBY4741_pU | 2021-02 | PRJNA549001 | Synthetic | RNA | pU_modified | pU.tar.4 |
| hct116 | 2021-04 | PRJEB44348 | Homo sapiens | RNA | HCT-WT-rep1 | SGNex_Hct116_directRNA_replicate3_run1.tar.gz AWS |
| hct116 | 2021-04 | PRJEB44348 | Homo sapiens | RNA | HCT-WT-rep2 | SGNex_Hct116_directRNA_replicate3_run4.gz AWS |
| hct116 | 2021-04 | PRJEB44348 | Homo sapiens | RNA | HCT-WT-rep3 | SGNex_Hct116_directRNA_replicate4_run3.tar.gz AWS |
| hek293t_wt | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-WT-rep1 | HEK293T-WT-rep1.tar.gz |
| hek293t_wt | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-WT-rep2 | HEK293T-WT-rep2.tar.gz |
| hek293t_wt | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-WT-rep3 | HEK293T-WT-rep3.tar.gz |
| hek293t_ko | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-Mettl3-KO-rep1 | HEK293T-Mettl3-KO-rep1.tar.gz |
| hek293t_ko | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-Mettl3-KO-rep2 | HEK293T-Mettl3-KO-rep2.tar.gz |
| hek293t_ko | 2021-01 | PRJEB40872 | Homo sapiens | RNA | HEK293T-Mettl3-KO-rep3 | HEK293T-Mettl3-KO-rep3.tar.gz |
| mESCs_eligos | 2020-10 | PRJNA497103 · SRP166020 | Mus musculus | RNA | mESCs_Mettl3_WT | mESCs_Mettl3_WT_fast5.tar.gz.1 |
| mESCs_eligos | 2020-10 | PRJNA497103 · SRP166020 | Mus musculus | RNA | mESCs_Mettl3_KO | mESCs_Mettl3_KO-ref_fast5.tar.gz.1 |
| ecoli_eligos | 2020-08 | PRJNA497103 · SRP166020 | Escherichia coli | RNA | IVT_Inosine | IVT_Inosine_fast5.tar.gz.1 |
| ecoli_eligos | 2020-08 | PRJNA497103 · SRP166020 | Escherichia coli | RNA | IVT_m5C | IVT_m5C_fast5.tar.gz.1 |
| ecoli_eligos | 2020-08 | PRJNA497103 · SRP166020 | Escherichia coli | RNA | IVT_m6A | IVT_m6A_fast5.tar.gz.1 |
| ecoli_eligos | 2020-08 | PRJNA497103 · SRP166020 | Escherichia coli | RNA | IVT_normalA | IVT_normalA_fast5.tar.gz.1 |
| ecoli_eligos | 2020-08 | PRJNA497103 · SRP166020 | Escherichia coli | RNA | IVT_normalC | IVT_normalC_fast5.tar.gz.1 |
| dinopore_ivt | 2023-01 | SRP363295 | Synthetic | RNA | gBlock_pureI | 20200322_gBlock2_pureI.fast5.tar.gz.1 |
| dinopore_ivt | 2023-01 | SRP363295 | Synthetic | RNA | gBlock_G | 20200322_gBlock2_G.fast5.tar.gz.1 |
| dinopore_xenopus | 2022-04 | SRP363295 | Xenopus lavies | RNA | rep3_stage1_20200812 | 20200812_xenopus_rep3_stage1_withRT.tar.gz |
| dinopore_xenopus | 2022-04 | SRP363295 | Xenopus lavies | RNA | rep3_stage1_20201005 | 20201005_xenopus_rep3_stage1_withRT.tar.gz |
| dinopore_xenopus | 2022-04 | SRP363295 | Xenopus lavies | RNA | rep3_stage9_20200812 | 20200812_xenopus_rep3_stage9_withRT.tar.gz.2 |
| dinopore_xenopus | 2022-04 | SRP363295 | Xenopus lavies | RNA | rep3_stage9_20201008 | 20201008_xenopus_rep3_stage9_withRT.tar.gz.2 |
After downloading
Place the raw archive under 1_raw_signal/ of the dataset directory and follow the preprocessing pipeline. If you only need the processed results, the processed dataset on Zenodo already contains the outputs of every pipeline step.