Towards a complete understanding of personal biology
From personal genome to phenome.
PGP1 — a human reference you can actually useconsented cells, deposited data, no restriction on use, even commercial.
- Zerorestrictions on useOpen consentamong the few human cell lines consented for any use, even commercial
- 1,017recordsVast multi-omics8 omics · 59 assay types · 14 cell types from one person
- 19research groupsWorked on by leading labs19.4 TB of data deposited in ENCODE, GEO, SRA and 4DN
Data produced byAppleton · Colossal Biosciences176Bernstein · Broad101Lewis · University of California, San Diego36Estrada · Baylor College of Medicine28Campbell · Yale University28Myers · HAIB23Mortazavi · UCI14Snyder · Stanford14Chen-Plotkin · University of Pennsylvania12Stamatoyannopoulos · UW11+9 more
Navigating PGP1’s personal reference genome architecture
Manuscriptin preparationData releasereleased
Telomere-to-Telomere Accurate and Gapless Genome Assembly
Complete, accurate, and annotated to the base.
- Complete and highly accurate. Every chromosome telomere to telomere, completely gapless. QV 71, one error in 13 Mb.
- Annotated beyond genes. Genes and lncRNAs, the repeat classes — segmental duplications, satellite arrays including the centromeres — and the regulatory elements, cCREs and CpG islands: the ground a functional genomics study starts from.
- Minimal error, every base of it shown. Confirmed structural error in unique sequence: 1.7 ppm, each call a track you can open. Quality report →
- Sequence & genes
- Genes — protein-coding, with isoforms
- lncRNA — long non-coding transcripts
- Regulation
- CpG islands — CGIs
- cCREs — candidate cis-regulatory elements
- Repeat structure
- Repeats — interspersed repeats
- Satellite arrays — including the centromere
- Segmental duplications — large, near-identical copies
- Assembly quality
- Erroneous regions — where the assembly is uncertain0.08% flagged
1.7 ppm confirmed error in unique sequence10,408 bp, HiFi ∩ ONT ÷ 5.95 Gb
Tracing one person into a lineage of cells and its multi-omics
1The person
hu43860C27 records · 8 layers
2Lines established
LCL, EBV-transformed B-lymphocyte7GM20431 · blood, age 51WGS · in situ Hi-C · intact Hi-Cfibroblast, untransformed143GM23248 · skin punch, age 55ChIP-Seq · Hi-C · RNA-Seq · +20 more3Reprogrammed
iPSC542GM23338 · reprogrammed from GM23248ChIP-Seq · RNA-Seq · ATAC-Seq · +22 more4Differentiated into 11
neural118
mesoderm108
crest and surface72
1The person
2Lines established
3Reprogrammed
4Differentiated into 11
blood
skin
LCL, EBV-transformed B-lymphocyte7GM20431 · blood, age 51WGS · in situ Hi-C · intact Hi-C
LCL, EBV-transformed B-lymphocyteGM20431
blood, age 51 · from hu43860C
7records · 195 files · 2.1 TB
Raw 124 · 788 GBProcessed 71 · 1.3 TB
genome 4 · epigenome 3
- Assays
- WGS 4 · in situ Hi-C 2 · intact Hi-C 1
- Labs
- Aiden · Baylor 2 · Ren · UCSD 1
- Obtain
- Coriell GM20431 · RRID:CVCL_7659
Open the line →
fibroblast, untransformed143GM23248 · skin punch, age 55ChIP-Seq · Hi-C · RNA-Seq · +20 more
fibroblast, untransformedGM23248
skin punch, age 55 · from hu43860C
143records · 2,032 files · 7.2 TB
Raw 269 · 2.5 TBProcessed 1,763 · 5.1 TB
genome 18 · variants 1 · transcriptome 21 · epigenome 103
- Assays
- ChIP-Seq 45 · Hi-C 28 · RNA-Seq 14 · +20 more
- Labs
- Estrada · Baylor College of Medicine 28 · Bernstein · Broad 16 · +8 more
- Obtain
- Coriell GM23248 · RRID:CVCL_F183
Open the line →
iPSC542GM23338 · reprogrammed from GM23248ChIP-Seq · RNA-Seq · ATAC-Seq · +22 more
iPSCGM23338
reprogrammed from GM23248
542records · 4,165 files · 4.5 TB
Raw 1,265 · 1.2 TBProcessed 2,900 · 3.4 TB
genome 11 · transcriptome 94 · epigenome 437
- Assays
- ChIP-Seq 345 · RNA-Seq 70 · ATAC-seq 34 · +22 more
- Labs
- Appleton · Colossal Biosciences 40 · Bernstein · Broad 26 · +9 more
- Obtain
- Coriell GM23338 · RRID:CVCL_F182
Open the line →
what the card edge shows
genometranscriptomeepigenomeclinome
neural118
- bipolar neuron31Histone ChIP-Seq · TF ChIP-Seq · +9 morebipolar neuronneuraldifferentiated from GM23338 (iPSC) · edge inferred31records · 1,617 files · 2.6 TBRaw 221 · 364 GBProcessed 1,396 · 2.3 TBtranscriptome 6 · epigenome 25
- Assays
- Histone ChIP-seq 13 · TF ChIP-seq 7 · Control ChIP-seq 3 · +8 more
- Labs
- Bernstein · Broad 16 · Myers · HAIB 8 · +4 more
- Made by
- Church Lab · Harvard Medical SchooliNGN — inducible NGN1/NGN2, four days of doxycycline
- Paper
- Busskamp et al., 2014 · Mol Syst Biol
Open → - neuron28RNA-Seq · Non-coding RNA profiling by array · +1 moreneuronneuraldifferentiated from GM23338 (iPSC) · edge inferred28records · 42 files · 49.3 GBRaw 22 · 38.2 GBProcessed 20 · 11.1 GBtranscriptome 27 · epigenome 1
- Assays
- RNA-Seq 18 · Non-coding RNA profiling by array 9 · PRO-cap 1
- Labs
- Lewis · University of California, San Diego 27 · Yu · Cornell 1
- Made by
- Busskamp, Lewis & ChurchiNGN — inducible NGN1/NGN2 in PGP1 iPSCs
- Paper
- Busskamp et al., 2014 · Mol Syst Biol
Open → - astrocyte26RNA-Seq · Mint-ChIP-Seq · +9 moreastrocyteneuraldifferentiated from GM23338 (iPSC) · edge inferred26records · 354 files · 813 GBRaw 217 · 631 GBProcessed 137 · 182 GBtranscriptome 13 · epigenome 13
- Assays
- RNA-Seq 10 · Mint-ChIP-seq 6 · DNase-seq 2 · +8 more
- Labs
- Appleton · Colossal Biosciences 10 · Bernstein · Broad 9 · +5 more
- Made by
- Church Lab · Harvard Medical Schooltranscription-factor conversion, machine-guided
- Paper
- Appleton et al., 2025 · Cell Rep
Open → - brain organoid19Mint-ChIP-Seq · DNase-seq · +3 morebrain organoidneuraldifferentiated from GM23338 (iPSC) · edge inferred19records · 1,451 files · 1.4 TBRaw 864 · 245 GBProcessed 587 · 1.1 TBepigenome 19
- Assays
- Mint-ChIP-seq 12 · DNase-seq 3 · Control Mint-ChIP-seq 2 · +2 more
- Labs
- Bernstein · Broad 16 · Stamatoyannopoulos · UW 3
- Made by
- Arlotta Lab · Harvard Universitydorsal forebrain organoids, 180 days
- Paper
- Velasco et al., 2019 · Nature
Open → - glutamatergic neuron14Mint-ChIP-Seq · Control ChIP-Seq · +7 moreglutamatergic neuronneuraldifferentiated from GM23338 (iPSC) · edge inferred14records · 342 files · 372 GBRaw 170 · 96.5 GBProcessed 172 · 276 GBtranscriptome 3 · epigenome 11
- Assays
- Mint-ChIP-seq 6 · Control ChIP-seq 1 · Control Mint-ChIP-seq 1 · +6 more
- Labs
- Bernstein · Broad 9 · Mortazavi · UCI 2 · +3 more
- Made by
- Church Lab · Harvard Medical Schoolexcitatory cortical neurons, cryopreserved
- Paper
- not recorded at the archive
Open →
mesoderm108
- NK cell52RNA-SeqNK cellmesodermdifferentiated from GM23338 (iPSC) · edge inferred52records · 52 files · 15.9 GBRaw 52 · 15.9 GBtranscriptome 52
- Assays
- RNA-Seq 52
- Labs
- Appleton · Colossal Biosciences 52
- Made by
- Church Lab · Harvard Medical Schooltranscription-factor conversion, computer-guided
- Paper
- Jung et al., 2021 · Nat Commun
Open → - cardiomyocyte28RNA-Seqcardiomyocytemesodermdifferentiated from GM23338 (iPSC) · edge inferred28records · 28 files · 49 GBRaw 28 · 49 GBtranscriptome 28
- Assays
- RNA-Seq 28
- Labs
- Campbell · Yale University 28
- Made by
- Campbell Lab · Yale UniversityGiWi protocol (CHIR99021 / IWP4), lactate selection
- Paper
- Shen et al., 2022 · Stem Cell Reports
Open → - endothelial cell14Mint-ChIP-Seq · Control ChIP-Seq · +7 moreendothelial cellmesodermdifferentiated from GM23338 (iPSC) · edge inferred14records · 270 files · 278 GBRaw 126 · 84.9 GBProcessed 144 · 193 GBtranscriptome 3 · epigenome 11
- Assays
- Mint-ChIP-seq 6 · Control ChIP-seq 1 · Control Mint-ChIP-seq 1 · +6 more
- Labs
- Bernstein · Broad 9 · Mortazavi · UCI 2 · +3 more
- Made by
- Church Lab · Harvard Medical Schoolendothelial cells, cryopreserved
- Paper
- not recorded at the archive
Open → - microglia14RNA-Seqmicrogliamesodermdifferentiated from GM23338 (iPSC) · edge inferred14records · 14 files · 5.2 GBRaw 7 · 5.2 GBProcessed 7 · 15.8 MBtranscriptome 14
- Assays
- RNA-Seq 14
- Labs
- Chen-Plotkin · University of Pennsylvania 12 · Appleton · Colossal Biosciences 2
- Made by
- Chen-Plotkin Lab · University of PennsylvaniaiPSC-derived microglia (iMicroglia)
- Paper
- Carceles-Cordon et al., 2026 · Neuron
Open →
crest and surface72
- mammary epithelial cell36RNA-Seqmammary epithelial cellcrest and surfacedifferentiated from GM23338 (iPSC) · edge inferred36records · 33 files · 24.7 GBRaw 33 · 24.7 GBtranscriptome 36
- Assays
- RNA-Seq 36
- Labs
- Appleton · Colossal Biosciences 36
- Made by
- Church Lab · Harvard Medical Schooltranscription-factor conversion, computer-guided
- Paper
- Jung et al., 2021 · Nat Commun
Open → - melanocyte36RNA-Seqmelanocytecrest and surfacedifferentiated from GM23338 (iPSC) · edge inferred36records · 36 files · 83.4 GBRaw 36 · 83.4 GBtranscriptome 36
- Assays
- RNA-Seq 36
- Labs
- Appleton · Colossal Biosciences 36
- Made by
- Church Lab · Harvard Medical Schooltranscription-factor conversion, computer-guided
- Paper
- Jung et al., 2021 · Nat Commun
Open →
27records · 8 layers
Mapping every assay across the cell lineage
| Cell lineage | Genome | Methylation | ChIP-seq | Accessibility | 3D genome | RNA-seq | Small RNA | Proteome | Microbiome | Clinical | Other |
|---|---|---|---|---|---|---|---|---|---|---|---|
| the personhu43860C | the person · Genome & variantshu43860C 3records · 57 files · 14.7 GB
Browse these 3 records → | the person · DNA methylationhu43860C 1records · 1 files · 19.5 MB
Browse these 1 records → | the person · RNA-seqhu43860C 2records · 2 files · 28.3 MB
Browse these 2 records → | the person · Proteomehu43860C 2records · 2 files · 3.6 MB
Browse these 2 records → | the person · Microbiomehu43860C 1records · 1 files · 5.1 MB
Browse these 1 records → | the person · Clinical & imaginghu43860C 18records · 18 files · 119 MB
Browse these 18 records → | |||||
| fibroblastGM23248 | fibroblast · Genome & variantsGM23248 8records · 18 files · 428 GB
Browse these 8 records → | fibroblast · DNA methylationGM23248 9records · 118 files · 2.2 TB
Browse these 9 records → | fibroblast · ChIP-seqGM23248 61records · 1,192 files · 1.2 TB
Browse these 61 records → | fibroblast · Chromatin accessibilityGM23248 3records · 168 files · 307 GB
Browse these 3 records → | fibroblast · 3D genomeGM23248 35records · 147 files · 2.5 TB
Browse these 35 records → | fibroblast · RNA-seqGM23248 17records · 277 files · 446 GB
Browse these 17 records → | fibroblast · Small & non-coding RNAGM23248 5records · 70 files · 23 GB
Browse these 5 records → | fibroblast · UnclassifiedGM23248 5records · 42 files · 69.8 GB
Browse these 5 records → | |||
| iPSCGM23338 | iPSC · Genome & variantsGM23338 1records · 1 files · 22.8 GB
Browse these 1 records → | iPSC · DNA methylationGM23338 1records · 2 files · 27.4 MB
Browse these 1 records → | iPSC · ChIP-seqGM23338 390records · 3,080 files · 2.8 TB
Browse these 390 records → | iPSC · Chromatin accessibilityGM23338 44records · 423 files · 960 GB
Browse these 44 records → | iPSC · RNA-seqGM23338 77records · 497 files · 601 GB
Browse these 77 records → | iPSC · Small & non-coding RNAGM23338 19records · 108 files · 85.7 GB
Browse these 19 records → | iPSC · UnclassifiedGM23338 10records · 54 files · 22 GB
Browse these 10 records → | ||||
| NK cell | NK cell · RNA-seq 52records · 52 files · 15.9 GB
Browse these 52 records → | ||||||||||
| mammary epithelial cell | mammary epithelial cell · RNA-seq 36records · 33 files · 24.7 GB
Browse these 36 records → | ||||||||||
| melanocyte | melanocyte · RNA-seq 36records · 36 files · 83.4 GB
Browse these 36 records → | ||||||||||
| bipolar neuron | bipolar neuron · DNA methylation 1records · 2 files · 27.4 MB
Browse these 1 records → | bipolar neuron · ChIP-seq 23records · 1,217 files · 1.9 TB
Browse these 23 records → | bipolar neuron · Chromatin accessibility 1records · 156 files · 303 GB
Browse these 1 records → | bipolar neuron · RNA-seq 3records · 184 files · 355 GB
Browse these 3 records → | bipolar neuron · Small & non-coding RNA 3records · 58 files · 49.2 GB
Browse these 3 records → | ||||||
| cardiomyocyte | cardiomyocyte · RNA-seq 28records · 28 files · 49 GB
Browse these 28 records → | ||||||||||
| neuron | neuron · RNA-seq 19records · 42 files · 49.3 GB
Browse these 19 records → | neuron · Small & non-coding RNA 9records · 0 files · 0 B
Browse these 9 records → | |||||||||
| astrocyte | astrocyte · ChIP-seq 9records · 225 files · 125 GB
Browse these 9 records → | astrocyte · Chromatin accessibility 3records · 51 files · 78.4 GB
Browse these 3 records → | astrocyte · RNA-seq 13records · 64 files · 609 GB
Browse these 13 records → | astrocyte · Small & non-coding RNA 1records · 14 files · 1.6 GB
Browse these 1 records → | |||||||
| brain organoid | brain organoid · ChIP-seq 16records · 1,389 files · 1.3 TB
Browse these 16 records → | brain organoid · Chromatin accessibility 3records · 62 files · 69.6 GB
Browse these 3 records → | |||||||||
| endothelial cell | endothelial cell · ChIP-seq 9records · 157 files · 172 GB
Browse these 9 records → | endothelial cell · Chromatin accessibility 1records · 60 files · 57.4 GB
Browse these 1 records → | endothelial cell · RNA-seq 3records · 45 files · 45.8 GB
Browse these 3 records → | endothelial cell · Small & non-coding RNA 1records · 8 files · 2.6 GB
Browse these 1 records → | |||||||
| glutamatergic neuron | glutamatergic neuron · ChIP-seq 9records · 233 files · 252 GB
Browse these 9 records → | glutamatergic neuron · Chromatin accessibility 2records · 71 files · 97.3 GB
Browse these 2 records → | glutamatergic neuron · RNA-seq 2records · 30 files · 20.8 GB
Browse these 2 records → | glutamatergic neuron · Small & non-coding RNA 1records · 8 files · 2 GB
Browse these 1 records → | |||||||
| microglia | microglia · RNA-seq 14records · 14 files · 5.2 GB
Browse these 14 records → | ||||||||||
| LCLGM20431 | LCL · Genome & variantsGM20431 4records · 4 files · 45.7 GB
Browse these 4 records → | LCL · 3D genomeGM20431 3records · 191 files · 2 TB
Browse these 3 records → |