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

Assay	Source	Lab	Status	Structure	Gene/Protein	FP	Notes
DNAse-Hi-C	4D Nucleome	Murry	Released				Four cardiomyocyte differentiation time points
Repli-seq	4D Nucleome	Gilbert	Released
Hi-C	4D Nucleome	Dekker	Released
Micro-C	4D Nucleome	Dekker	Released
Single cell Hi-C	4D Nucleome	Shendure	Released
Single cell Hi-C	4D Nucleome	Ren	Released
PLAC-seq	4D Nucleome	Ren	Partially released				H3K4me3, CTCF, H3K27Ac, (PolII)
ChIA-PET	4D Nucleome	Ruan	Released				CTCF, PolII
RNA-seq	ENCODE	Yin Shen	Available
ATAC-seq	ENCODE	Yin Shen	Available
pcHi-C	Song et. al	Yin Shen	Available
ATAC-seq	Song et. al	Yin Shen	Available
RNA-seq	Song et. al	Yin Shen	Available
CUT&RUN	Song et. al	Yin Shen	Available
Phasing	Song et. al	Yin Shen	Available				hg19 only
scRNA-seq	Friedman et.al	Joseph Powell and Nathan Palpant	Available
scRNA-seq	Friedman et.al	Joseph Powell and Nathan Palpant	Available
Imaging	AICS		Imaging data available	Nuclear lamina	Lamin B1	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Cell line available	Nuclear lamina	Lamin B1	mTagRFP-T
Imaging	AICS		Cell line available	Dual-nuclear lamina/ER	LaminB1/Sec61B	mEGFP/mTagRFPt
Imaging	AICS		Imaging data available	Nucleolus - DFC	FBL	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Imaging data available	Nucleolus - GC	NPM1	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Imaging data available	Nuclear pore	NUP153	mEGFP	Also see Average Morphed Cell Dataset 1
Imaging	AICS		Imaging data available	Histones	H2B (HIST1H2BJ)	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Cell line available	Paraspeckles	FUS	mEGFP
Imaging	AICS		Imaging data available	Cohesin complex	SMC1A	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Cell line available	Transcription factor	SOX-2	mEGFP
Imaging	AICS		Cell line available	Dual-nucleolar	FBL/NPM1	mEGFP/mTagRFPt
Imaging	AICS		Cell line available	Triple-nucleolar	FBL/NPM1/UBTF	mEGFP/mTagRFPt/Halo
Imaging	AICS		Imaging data available	Telomeres	TERF2	mEGFP	Also see, Nuclear Project Dataset 2 and Average Morphed Cell Dataset 1
Imaging	AICS		Imaging data available	Speckles	SON	mEGFP	Also see, Nuclear Project Dataset 1 and Average Morphed Cell Dataset 1
Imaging	AICS		Clonal QC - paused	Heterochromatin	CBX1	mEGFP
Imaging	AICS		Clonal QC - paused	Transcription factor	OCT-4	mEGFP
Imaging	AICS		Cell line available	CTCF-binding sites	CTCF	mEGFP	data coming 2023
Imaging	AICS		Imaging data available	DNA replication foci	PCNA	mEGFP	Also see, Nuclear Project Dataset 4 and Average Morphed Cell Dataset 1
Imaging	AICS		Imaging data available	RNA polymerase II	RPB1	mEGFP	Also see, Nuclear Project Dataset 3 and Average Morphed Cell Dataset 1
Imaging	AICS		Cell line available	Polycomb repressive complex 2	EZH2	mEGFP	data coming 2023

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:
- Nuclear Project dataset 2 mEGFP-tagged TRF2 (with predicted FBL + predicted NPM1) Released Aug. 27, 2021
- Nuclear Project dataset 3 mEGFP-tagged RPB1 (with predicted FBL + predicted NPM1) Released Dec. 22, 2021
- Nuclear Project dataset 4 mEGFP-tagged PCNA (with predicted FBL + predicted NPM1) Released July 29, 2022
Our Average Morphed Cell Dataset 1 contains 3D average morphed cells for 11 different nuclear structures. These average morphed cells are 3D image stacks that represent the relative likelihood of a structure being at a given location in the cell and nucleus. These average morphed cell likelihood maps were generated by applying a standardized framework for analysis of integrated intracellular organization to thousands of real 3D microscopy images of 11 different nuclear structures in human induced pluripotent stem cells. (paper: Viana et al, 2023; GitHub repo: cvapipe_analysis). Importantly, these average morphed cells can also be combined together to give an integrated view of nuclear organization on average and as a function of different cell and nuclear sizes and shapes.

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

Reference Data Sets

Song et. al. (Yin Shen lab) have recently generated pcHi-C, ATAC-seq, RNA-seq, and CUT&RUN for three neural differentiation states derived from WTC-11 cells. The data can be accessed in GEO. The data set also includes phased genome reference for WTC-11 against the hg19 genome reference.
Two single cell RNA-seq data sets from Friedman et. al. (Powell and Palpant lab) (E-MTAB-6268, E-MTAB-6687) are available on Array Express.

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