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 Shen Available
ATAC-seqENCODEYin Shen Available
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 B1mEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSCell line availableNuclear laminaLamin B1mTagRFP-T
ImagingAICSCell line availableDual-nuclear lamina/ERLaminB1/Sec61BmEGFP/mTagRFPt
ImagingAICSImaging data availableNucleolus - DFCFBLmEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSImaging data available Nucleolus - GCNPM1mEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSImaging data available Nuclear poreNUP153mEGFP
ImagingAICSImaging data available HistonesH2B (HIST1H2BJ)mEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSCell line availableParaspecklesFUSmEGFP
ImagingAICSImaging data available Cohesin complexSMC1AmEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSCell line availableTranscription factorSOX-2mEGFP
ImagingAICSCell line availableDual-nucleolarFBL/NPM1mEGFP/mTagRFPt
ImagingAICSCell line availableTriple-nucleolarFBL/NPM1/UBTFmEGFP/mTagRFPt/Halo
ImagingAICSImaging data availableTelomeresTERF2mEGFPAlso see, Nuclear Project Dataset 2
ImagingAICSImaging data available SpecklesSONmEGFPAlso see, Nuclear Project Dataset 1
ImagingAICSClonal QC - pausedHeterochromatinCBX1mEGFP
ImagingAICSClonal QC - pausedTranscription factorOCT-4mEGFP
ImagingAICSCell line availableCTCF-binding sitesCTCFmEGFPdata coming 2022
ImagingAICSImaging data availableDNA replication fociPCNAmEGFPAlso see, Nuclear Project Dataset 4
ImagingAICSImaging data availableRNA polymerase IIRPB1mEGFPAlso see, Nuclear Project Dataset 3
ImagingAICSCell line availablePolycomb repressive complex 2EZH2mEGFPdata coming 2022

Data on allencell.org and Quilt

  • 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.
  • Our Nuclear Project dataset 1 contains 3D images of a nuclear structure, plasma membrane (CellMask Deep Red), DNA (NucBlue),along with label-free predicted structures. The dataset includes: SON-mEGFP (with predicted LMNB1 + predicted FBL + predicted NPM1), Lamin B1-mEGFP (with predicted FBL), NPM1-mEGFP (with predicted FBL), FBL-mEGFP, H2B-mEGFP (with predicted FBL + predicted NPM1), and SMC1A-mEGFP (with predicted FBL + predicted NPM1) The data is available on Quilt. Note that the Nuclear Project dataset 1 was updated on Dec. 17, 2020 to include new imaging data and label-free predictions
  • Our Nuclear Project datasets 2, 3 and 4 contain 3D images of a nuclear structure, plasma membrane (CellMask Deep Red), DNA (NucViolet),along with label-free predicted structures. The data is available on Quilt. The datasets are as follows:

Reference Data Sets

  Shared Analysis Products

Analysis TitleFileFormatGenerated FromDescriptionProvider
Noble Lab analyses - submitted 2020-05-06
Embeddings of WTC-11 snHi-C based on contact decay profile4DNFIGLS3JZNzip4DNESF829JOW, 4DNESJQ4RXY5Embeddings 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 scHiCluster4DNFI488OK8Hzip4DNESF829JOW, 4DNESJQ4RXY5Embeddings 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 HiCRep4DNFIHM5K63Hzip4DNESF829JOW, 4DNESJQ4RXY5Embeddings 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 profile4DNFIHA69V3Yzip4DNES5R3NDIU, 4DNESHQOY22TEmbeddings 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 scHiCluster4DNFIKTK5Z1Uzip4DNES5R3NDIU, 4DNESHQOY22TEmbeddings 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 HiCRep4DNFIPX8D8DXzip4DNES5R3NDIU, 4DNESHQOY22TEmbeddings 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 seurat4DNFIS9Z64DXzipE-MTAB-6687Embeddings 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 VAE4DNFI7WJOKPRcsv--Embeddings (512 dimensions trained with Variational autoencoders by Allen Institute).William Noble, UW