NOFIC AICS Collaborative Project

This page presents plans for data generation by participating labs on the Joint 4DN-AICS Collaborative Project. It will be updated regularly with links to data and exploration tools with upcoming data releases.

4DN Network Members can get more information about the project at the internal 4DN wiki.

Data Generation Plans

AssaySourceLabStatusStructureGene/ProteinFPNotes
DNAse-Hi-C4D NucleomeMurryReleasedFour cardiomyocyte differentiation time points
Repli-seq4D NucleomeGilbertReleased
Hi-C4D NucleomeDekkerReleased
Micro-C4D NucleomeDekkerReleased
Single cell Hi-C4D NucleomeShendureReleased
Single cell Hi-C4D NucleomeRenReleased
PLAC-seq4D NucleomeRenPartially releasedH3K4me3, CTCF, H3K27Ac, (PolII)
ChIA-PET4D NucleomeRuanReleasedCTCF, PolII
RNA-seqENCODEYin ShenUnder review at ENCODE DCC
ATAC-seqENCODEYin ShenData Generated, Being Submitted
pcHi-CSong et. alYin Shen Available
ATAC-seqSong et. alYin ShenAvailable
RNA-seqSong et. alYin ShenAvailable
CUT&RUNSong et. alYin ShenAvailable
PhasingSong et. alYin ShenAvailablehg19 only
scRNA-seqFriedman et.alJoseph Powell and Nathan PalpantAvailable
scRNA-seqFriedman et.alJoseph Powell and Nathan PalpantAvailable
ImagingAICSImaging data availableNuclear laminaLamin B1mEGFP, mTagRFP-T
ImagingAICSCell line availableDual-nuclear lamina/ERLaminB1/Sec61BmEGFP/mTagRFPtdata available Summer 2020
ImagingAICSImaging data availableNucleolus - DFCFBLmEGFP
ImagingAICSImaging data available Nucleolus - GCNPM1mEGFP
ImagingAICSCell line availableNuclear poreNUP153mEGFPdata available Summer 2020
ImagingAICSCell line availableHistonesH2BmEGFPdata available Summer 2020
ImagingAICSCell line availableParaspecklesFUSmEGFP
ImagingAICSCell line availableCohesin complexSMC1AmEGFPdata available Summer 2020
ImagingAICSCell line availableTranscription factorSOX-2mEGFP
ImagingAICSCell line availableDual-nucleolarFBL/NPM1mEGFP/mTagRFPtdata available Summer 2020
ImagingAICSCell line available - soonTriple-nucleolarFBL/NPM1/UBTFmEGFP/mTagRFPt/Halo
ImagingAICSClonal QC - pausedTelomeresTERF2mEGFP
ImagingAICSCell line availableSpecklesSONmEGFPdata available Summer 2020
ImagingAICSClonal QC - pausedHeterochromatinCBX1mEGFP
ImagingAICSClonal QC - pausedTranscription factorOCT-4mEGFP
ImagingAICSMixed population - pausedTranscription repressorCTCFmEGFP
ImagingAICSClonal QC - pausedReplication complexPCNAmEGFP
ImagingAICSClonal QC - pausedTranscriptional complexRNA Pol IImEGFP
ImagingAICSClonal QC - pausedPolycomb repressorEZH2mEGFP

Data on allencell.org

  • To find more information about the nuclear lines as part of the Allen Cell Collection visit our Cell Catalog
  • To download data from our Cell Feature Explorer, select the protein name(s) that are shown in the left panel, and hit the download button next to the # of cells.

Reference Data Sets

  Shared Analysis Products

Analysis Title File Format Generated From Description Provider
Noble Lab analyses - submitted 2020-05-06
Embeddings of WTC-11 snHi-C based on contact decay profile 4DNFIGLS3JZN zip 4DNESF829JOW, 4DNESJQ4RXY5 Embeddings of snHi-C data (c28 and c6 combined); GRCh37; includes contact decay profile (bin size 500kb, range 0-100Mb), cosine similarity matrix as well as 2D MDS embedding; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 snHi-C based on scHiCluster 4DNFI488OK8H zip 4DNESF829JOW, 4DNESJQ4RXY5 Embeddings of snHi-C data (c28 and c6 combined); GRCh37; includes output from scHiCluster (bin size 500kb, retain cells with >=10 contacts in each chromosomes), cosine similarity matrix as well as 2D MDS embeddings; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 snHi-C based on HiCRep 4DNFIHM5K63H zip 4DNESF829JOW, 4DNESJQ4RXY5 Embeddings of snHi-C data (c28 and c6 combined); GRCh37; includes similarity matrix calculated based on HiCRep (bin size 500kb, smoothing parameter h=1, max distance 4Mb) and 2D MDS embeddings; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 sciHi-C based on contact decay profile 4DNFIHA69V3Y zip 4DNES5R3NDIU, 4DNESHQOY22T Embeddings of sciHi-C data (R6 and R7 combined); GRCh38; includes contact decay profile (bin size 500kb, range 0-100Mb), cosine similarity matrix as well as 2D MDS embedding; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 sciHi-C based on scHiCluster 4DNFIKTK5Z1U zip 4DNES5R3NDIU, 4DNESHQOY22T Embeddings of sciHi-C data (R6 and R7 combined); GRCh38; includes output from scHiCluster (bin size 500kb, retain cells with >=10 contacts in each chromosomes), cosine similarity matrix as well as 2D MDS embeddings; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 sciHi-C based on HiCRep 4DNFIPX8D8DX zip 4DNES5R3NDIU, 4DNESHQOY22T Embeddings of sciHi-C data (R6 and R7 combined); GRCh38; includes similarity matrix calculated based on HiCRep (bin size 500kb, smoothing parameter h=1, max distance 4Mb, a background of 0.00001 is added to each contact map to get more stable HiCRep calculation) and 2D MDS embeddings; processed May 06, 2020. William Noble, UW
Embeddings of WTC-11 scRNAseq based on seurat 4DNFIS9Z64DX zip E-MTAB-6687 Embeddings of scRNAseq for E-MTAB-6687; GRCh37; includes top 30 principal components (batch corrected) and cell cycle assignment by Seurat; pprocessed May 06, 2020. William Noble, UW
Embeddings of WTC-11 imaging trained from VAE 4DNFI7WJOKPR csv -- Embeddings (512 dimensions trained with Variational autoencoders by Allen Institute). William Noble, UW