title: Mouse_Vehicle_IP_04

city: Dallas

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd

institute: The University of Texas at Dallas

data_processing:
RNA-seq read files (fastq files) were processed and analyzed following the methodology described in GSE155676.     genes were excluded from the analysis, and the TPMs for non-mitochondrial coding genes were re-normalized to sum to 1 million.
Quality assessment was conducted using FastQC (Babraham Bioinformatics).
Reads were trimmed based on Phred scores and per-base sequence content.
The trimmed reads were then aligned to the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1.
Relative abundances in Transcripts Per Million (TPM) for each gene in every sample were quantified using StringTie v1.3.5.Non-coding and mitochondrial genes were excluded from the analysis, and the TPMs for non-mitochondrial coding genes were re-normalized to sum to 1 million.
Assembly: The trimmed reads were then aligned to the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1.
Supplementary files format and content: Quantile normalization on all coding genes was calculated at 30th percentile for IN fraction and  15th percentile for IP fraction. Differential gene expression analysis was performed by calculating the log2-fold change (based on median TPM values), strictly standardized mean difference (SSMD), and the Bhattacharya coefficient. This modified coefficient ranges from 0, indicating completely identical distributions, to +1 or -1, indicating entirely non-overlapping distributions, with the sign determined by the log-fold change value.
Supplementary files format and content: Tpm matrix file for all the non coding genes is provided

source_name: Dorsal Root Ganglion

extract_protocol:
Translating ribosome affinity purification was done as previously described by Tavares-Ferreira et.al. (33). Nav1.8-TRAP female mice (4 mice per condition) were euthanized by cervical dislocation and decapitation under isoflurane anesthesia, and their dorsal root ganglia (DRGs) were rapidly dissected in ice-cold dissection buffer (1× HBSS (Invitrogen, 14065006), 2.5 mM HEPES-NaOH [pH 7.4], 35 mM glucose, 5 mM MgCl2, 100 μg/ml cycloheximide, 0.2 mg/ml emetine). The DRGs were then transferred to ice-cold Precellys tissue homogenizing CKMix tubes containing lysis buffer (20 mM HEPES, 12 mM MgCl2, 150 mM KCl, 0.5 mM
dithiothreitol (DTT), 100 μg/ml cycloheximide, 20 μg/ml emetine, 80 U/ml SUPERase•IN (Promega) Samples were homogenized using a Precellys® Minilys Tissue Homogenizer at 10-second intervals for a total of 80 seconds in a cold room (4°C). The lysate was then centrifuged at 2000 × g for 5 minutes to obtain the post nuclear fraction. Following this, 1% NP-40 and 30 mM 1,2-dihexanoyl-sn-glycero-3-phosphocholine were added, and the samples were centrifuged at 15,000 × g for 10 minutes to produce the post mitochondrial fraction. A 200 μl sample of this fraction was set aside for INPUT (bulk RNA-sequencing), while the remaining lysate was incubated with protein G-coated Dynabeads (Invitrogen) bound to 50 μg anti-GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8, Memorial Sloan Kettering Centre) for 3 hours at 4°C with end-over-end mixing. The beads were washed with high salt buffer (20 mM HEPES, 5 mM MgCl2, 350 mM KCl, 1% NP-40, 0.5 mM DTT, and 100 μg/ml cycloheximide), and RNA was extracted using the Direct-zol kit (Zymo Research) following the manufacturer's instructions. RNA yield was quantified using a Qubit (Invitrogen), and RNA quality was assessed using a Fragment Analyzer (Advanced Analytical Technologies).
Libraries were prepared according to the manufacturer's instructions using the Total RNA Gold library preparation kit (with ribosomal RNA depletion) and sequenced on the NextSeq 2000 platform with 75-bp single-end reads.

treatment_protocol: Paclitaxel (Sigma Aldrich, Y0000698) was dissolved in a 1:1 solvent mixture of Kolliphor EL (Sigma-Aldrich) and ethanol . Female Nav1.8-TRAP mice were administered paclitaxel diluted in sterile Dulbecco’s phosphate buffered saline (DPBS; Thermo Scientific) or vehicle solvent intraperitoneally at a dosage of 4 mg/kg every other day, resulting in a cumulative dosage of 16 mg/kg.

value: Dorsal Root Ganglion

value: Neuronal Enchriment

value: Vehicle


title: old_CHD, scRNAseq of 4 samples

status: Public on Aug 06 2024

type: SRA

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNAseq libraries were sequenced on the NovaSeq X platform, targeting 25,000 read pairs per cell. Reads were aligned to the reference genome GRCh38, and the gene expression matrix was generated using Cell Ranger 7.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: gene expression matrix

molecule: total RNA

organism: Homo sapiens

source_name: untreated PBMC

extract_protocol:
The PBMCs were thawed and fluorescence-activated cell sorting (FACS) was performed to isolate live CD3+TCRαβ-TCRγδ+ cells and live CD3+TCRαβ+TCRγδ- cells.
These sorted T cells were then used to generate single-cell RNA sequencing (scRNAseq) libraries with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (for infants) and v2 (for 5-11-year-old children), following the manufacturer’s protocol (10x Genomics).

tag: disease condition

value: Congenital heart disease

tag: age

tag: sampling time

value: After cardiac surgery, 5-12-year-old

tag: treatment

value: untreated

tag: tissue

value: PBMC


title: Mouse_Vehicle_IP_03

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: cell type

tag: genotype


title: HDF1_Lamin_S301D

type: RNA

city: Epalinges

first: Soumitra

last: Ghosh

state: Choose State/Province

address: Chemin des Boveresses 155

department: Biochemistry

country: Switzerland

institute: University of Lausanne, Switzerland

description: HDFs expressing Wildtype lamin A/C

hyb_protocol: Libraries were hybridized to the human Clariom™ D arrays (Thermo Fisher Scientific).

scan_protocol: Standard Affymetrix protocol

data_processing: Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) was used for data processing and analysis.

label: biotin

source_name: Human Skin derived fibroblasts

label_protocol: The GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Cat. No. 902280) was used to prepare samples and to facilitate hybridization to the human Clariom™ D arrays (Thermo Fisher Scientific).

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA extraction and purification was carried out using the Direct-zol RNA Miniprep Kit (Zymo Research)
The quality of RNA samples was assessed, ensuring a purity of OD260/OD280 ≥ 1.8 and RIN ≥ 8. Global transcriptomic analysis was conducted at the Institute of Genetics and Genomics of Geneva (iGE3) using Clariom™ D GeneChip assays.

treatment_protocol: HDF cells were transduced with either Phospho Ser 301 mimetic mutant (S301D) and WT lamin A/C expressing lentiviruses and selected with puromycin. 6 Days post-transduction, cells were harvested, total RNA was isolated.

value: HDF

value: Wildtype lamin A/C


title: MGH227_scATAC

city: Boston

first: Jingyi

last: Wu

state: MA

address: 360 Longwood Ave

department: Department of Cancer Biology

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
CellRanger ATAC (version 1.1.0) was used for alignment, deduplication, and generating the single cell matrix, using GRCh38 as a reference.
processed data files format and content: filter_peak_matrix
processed data files format and content: single_cell_metadata
Assembly: hg38

molecule: genomic DNA

source_name: primary tissue

extract_protocol:
Nuclei were spun down and resuspended in 100 ul of lysis buffer for 4 min on ice. Nuclei were washed with 200-400 ul wash buffer and counted with trypan blue staining, then resuspended with sufficient nuclei buffer to achieve a concentration of 2000 nuclei/ul.
To perform tagmentation, 5 ul of nuclei suspension was added to 7 ul of ATAC buffer (10X Genomics) and 3 ul of Tn5 and incubated at 37°C for 1 h. Nuclei capture and library prep was then performed according to the 10X Genomics scATAC-seq protocol.

value: primary tissue

value: no


title: MCF10AT1_input_2

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Formaldehyde crosslinking, DNA purification (PCI) and Illumina library preparation

data_processing:
Reads were mapped to the hg38 genome with Bowtie2 v2.4.1.
Mapped reads were used to call LaminB1 peaks (LADs) using 10 runs of Enriched Domain Detector with auto-estimation of GapPenalty and BinSize parameters, and mean GapPenalty and BinSize outputs from these runs were used for a final EDD run.
Assembly: hg38

source_name: Mammary tissue

growth_protocol: MCF10A, MCF10AT1, and MCF10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% horse serum (MCF10A and MCF10Ca1a) or 2.5% horse serum (MCF10AT1), 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin. MCF10A cells were obtained from the American Type Culture Collection (CRL-10317). MCF10AT1 and MCF10Ca1a cells were obtained from the Barbara Ann Karmanos Cancer Institute (Detroit, Michigan).

extract_protocol:
For ChIP, cells were cross-linked for 10 min with 1% formaldehyde, sonicated in a Diagenode Bioruptor to produce chromatin fragments of ~200 base-pairs; lysates were clarified by sedimentation and Lamin B1-DNA complexes were isolated from supernatants by ChIP using antibodies against lamin B1, washed and DNA was eluted for library preparation. For input samples, cells were crossed, sonicated and lysaates clarified as above, and DNA was purified.
Diagenode Microplex library prepareation kit v2. TruSeq LT indexes, non-pooled samples.

treatment_protocol: All three cell types were cultured under proliferating conditions in media described above.

value: Mammary tissue

tag: cell line

value: MCF10AT cell line

value: Mammary epithelium; derivative of MCF10A

value: Human, female

value: Culrured, adherent, transformed, pre-malignant

tag: antibody


title: old_Ctrl, scRNAseq of 4 samples

description: 10x Genomics

value: Non-Congenital Heart Disease


title: MCF10A_LA_rep3

description: Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation

value: MCF10A cell line

value: Mammary epithelium; xenograft derivative of MCF10A

value: Cultured, adherent, nontransformed

value: Anti-lamin B1, Abcam, ab16048


title: Aldh2-/-, replicate 1, RNAseq

city: Manhasset

first: Lopa

last: Mishra

state: NY

address: 350 Community Drive

institute: The Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: hg38 for human samples; mm10 for mice samples
Supplementary files format and content: tab-delimited text files include fpkm values for each sample from mice; TPM values for each sample from human MASH model

source_name: liver

extract_protocol:
For RNA-seq, RNA was extracted from liver tissues and the MASH model cells using the RNeasy Plus Mini kit. RNA quality and concentration were assessed using the Thermo Scientific Nanodrop spectrophotometer before RNA sequencing.
About 1 μg of RNA was used to generate barcoded sequencing libraries. Novogene Corporation performed library preparation.

value: liver cells

value: liver


title: SAM24395476 COLO 201 shATF6.2, Day 4, rep3

city: South San Francisco

first: Matt

last: Grimmer

state: CA

address: 455 E Grand Ave.

department: Oncology Bioinformatics

institute: Genentech

description: COLO 201 shATF6.2 Day 4 rep3

data_processing:
Raw sequencing outputs for all samples were mapped to the UCSC human genome (GRCh38/hg38) using GSNAP software (RRID:SCR_005483)38 allowing a maximum of two mismatches per 50-base sequence (parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1–pairmax-rna=200000–clip-overlap). Gene expression counts were obtained by quantifying the number of reads uniquely mapping to each gene exonic locus. Lowly expressed genes were removed from all samples using a high-pass filter for genes with at least 15 counts in at least 10% of samples (4 of 33). Read counts were scaled by library size, quantile normalized and precision weights were calculated using the voom function of the limma R package (RRID:SCR_010943)41 to yield Log2 counts per million (LogCPM) values of sufficiently covered genes.
Assembly: hg38
Supplementary files format and content: tab-delimited .txt; combined Log2(CPM) for all samples

source_name: Colon

growth_protocol: Using either flat bottom 96 well plate (3595, Corning) or ultra-low attachment 96 well plate (7007, Corning), specified cell line was seeded at upper-left most well (A1) at initial high density of 2x105 cell/well. Cell suspension was serially diluted 1:2 vertically downward (A1 -> A8). Following, all cell bearing wells in column (A) were serially horizontally diluted 1:2 (A -> I). All wells were then evenly loaded to be at 50 μl and then treated with or without Dox (1μg/ml) at 50 μl to create a 100 μl culture at 0.5 μg/ml Dox treatment.

extract_protocol:
For bulk RNA sequencing (RNAseq), RNA from 1×106 cell was first extracted with RNeasy Plus kit (Qiagen), per manufacturer’s protocol. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
RNA-seq libraries were prepared with the TruSeq RNA Sample Preparation kit (Illumina, CA).
The libraries were sequenced on Illumina HiSeq 2500 sequencers to obtain on average 44 million 50-bp, stranded, single-end reads per sample.

treatment_protocol: All cell bearing wells in column (A) were serially horizontally diluted 1:2 (A -> I). All wells were then evenly loaded to be at 50 μl and then treated with or without Dox (1μg/ml) at 50 μl to create a 100 μl culture at 0.5 μg/ml Dox treatment. Colo201 shNTC, shATF6.1, shATF6.2 and CCK81 shNTC, shATF6 were harvested in biologic triplicates at 0, 2 and 4 days after treatment with Doxycycline (Dox, 0.5 μg/ml).

value: Colon

value: COLO 201 shATF6.2

value: Adenocarcinoma

value: Doxycline Day 4


title: MCF10A_input_2


title: MCF10AT1_LA_rep3


title: wild type, replicate 4, RNAseq


title: Aldh2-/-, replicate 2, RNAseq


title: SAM24395475 COLO 201 shATF6.2, Day 4, rep2

description: COLO 201 shATF6.2 Day 4 rep2


title: wild type, replicate 5, RNAseq


title: MCF10CA1_LA_rep2

value: MCF10AC1 cell line

value: Culrured, adherent, transformed, malignant


title: MCF10CA1_LA_rep1

value: Mammary tissue


title: MGH230_scATAC

value: primary tissue

value: no


title: SAM24395473 COLO 201 shATF6.2, Day 2, rep3

description: COLO 201 shATF6.2 Day 2 rep3

value: Doxycline Day 2


title: SAM24395474 COLO 201 shATF6.2, Day 4, rep1

description: COLO 201 shATF6.2 Day 4 rep1


title: Mouse_Vehicle_IP_02

value: Dorsal Root Ganglion

value: Neuronal Enchriment

value: Vehicle


title: MCF10CA1_input_1

value: Mammary epithelium; derivative of MCF10A

value: Human, female


title: Mouse_Paclitaxel_IP_04

value: Paclitaxel


title: wild type, replicate 2, RNAseq

value: liver cells

value: liver


title: MCF10AT1_LA_rep2

value: MCF10AT cell line

value: Culrured, adherent, transformed, pre-malignant

value: Anti-lamin B1, Abcam, ab16048


title: wild type, replicate 1, RNAseq


title: In-vitro Eff- 2

city: NEW HAVEN

first: Will

last: Krause

state: CT

address: 20 Winchester Ave., Unit one, Unit, Unit one

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

description:
Replicate for in-vitro seq Eff-
MACNOAC1

data_processing:
With trimmomatic version=0.39, Clontech adapters were trimmed
leading and trailing low quality bases were removed, and reads below the 36 bases long were dropped
Assembly: GRCm39
Supplementary files format and content: Tab delimited .txt files have alligned read counts in a matrix for all samples, either in-vivo or in-vitro

molecule: polyA RNA

source_name: Bone marrow derived macrophage

growth_protocol: Cells were differentiated from Bone marrow monocytes with GM-CSF for 7 days.

extract_protocol:
RNA was isolated with the Rneasy Mini Kit (qiagen).
YCGA RNA seq library prep (https://medicine.yale.edu/genetics/research/ycga/?locationId=2370)

treatment_protocol: Cells were treated with apoptotic fibroblasts for 12 hrs. Mice were wounded, wounds collected after 3 days. Mice were also treated with tamoxifen for 6 days.

value: Bone marrow derived macrophage

value: Wild Type

value: Apoptotic fibroblast


title: Mouse_Paclitaxel_IP_02


title: MCF10AT1_LA_rep1

value: Mammary tissue


title: MCF10AT1_input_1

value: Mammary epithelium


title: SAM24395471 COLO 201 shATF6.2, Day 2, rep1

description: COLO 201 shATF6.2 Day 2 rep1

value: Colon

value: COLO 201 shATF6.2

value: Adenocarcinoma

value: Doxycline Day 2


title: SAM24395468 COLO 201 shATF6.2, Day 0, rep1

description: COLO 201 shATF6.2 Day 0 rep1

value: Control Day 0


title: SAM24395469 COLO 201 shATF6.2, Day 0, rep2

description: COLO 201 shATF6.2 Day 0 rep2


title: MCF10A_LA_rep1

value: MCF10A cell line

value: Human, female

value: Cultured, adherent, nontransformed


title: SAM24395467 COLO 201 shATF6.1, Day 4, rep3

description: COLO 201 shATF6.1 Day 4 rep3

value: COLO 201 shATF6.1

value: Doxycline Day 4


title: Mouse_Vehicle_INPUT_03

value: Dorsal Root Ganglion

value: Neuronal Enchriment

value: Vehicle


title: MCF10A_input_1


title: In-vitro Eff- 1

description:
Replicate for in-vitro seq Eff-
MACNOACS

value: Bone marrow derived macrophage

value: Wild Type


title: Mouse_Paclitaxel_IP_01

value: Paclitaxel


title: In-vitro Eff+ 2

description:
Replicate for in-vitro seq Eff+
MACNACS1

value: Apoptotic fibroblast


title: Mouse_Vehicle_INPUT_04


title: MCF10A_LA_rep2

value: Mammary tissue

value: Mammary epithelium

value: Anti-lamin B1, Abcam, ab16048


title: SAM24395466 COLO 201 shATF6.1, Day 4, rep2

description: COLO 201 shATF6.1 Day 4 rep2

value: Colon

value: Adenocarcinoma


title: In-vitro Eff+ 1

description:
Replicate for in-vitro seq Eff+
MACANDAC


title: Mouse_Vehicle_IP_01


title: Mouse_Vehicle_INPUT_02


title: wild type, replicate 3, RNAseq

value: liver cells

value: liver


title: SAM24395472 COLO 201 shATF6.2, Day 2, rep2

description: COLO 201 shATF6.2 Day 2 rep2

value: COLO 201 shATF6.2

value: Doxycline Day 2


title: In-vivo Eff- 3

description:
Replicate for in-vivo seq Eff-
Effneg.3

source_name: Skin

value: Skin

value: Macrophage

value: LysMCreER/mTmG


title: SAM24395470 COLO 201 shATF6.2, Day 0, rep3

description: COLO 201 shATF6.2 Day 0 rep3

value: Control Day 0


title: Mouse_Paclitaxel_IP_03

value: Dorsal Root Ganglion

value: Neuronal Enchriment


title: SAM24395465 COLO 201 shATF6.1, Day 4, rep1

description: COLO 201 shATF6.1 Day 4 rep1

value: COLO 201 shATF6.1

value: Doxycline Day 4


title: scRNA_cMN7_Isl1_E11-5

first: Elizabeth

middle: C

last: Engle

address: 3 Blackfan Circle

institute: Boston Childrens Hospital

data_processing:
HiSeq 4000 software (Illumina) used for basecalling
bcl outputs from HiSeq 4000 were processed using 10x Cell Ranger RNA mkfastq pipeline (https://www.10xgenomics.com/support/software/cell-ranger/) for demultiplexing and fastq file generation
Transcript counts were tabulated using the Cell Ranger count function using default parameters
Tab separated values files and matrix files were processed and analysed using Seurat v4 (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: CN7 e10.5 GFP-positive and negative

extract_protocol:
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
10x Genomics Chromium Next GEM Single Cell 3' GEM-Library construction

value: CN7 e10.5 GFP-positive and negative

value: WILDTYPE


title: Mouse_Vehicle_INPUT_01

value: Vehicle


title: scRNA_cMN7_Isl1_E10-5_Neg

source_name: CN7 e10.5 GFP-negative

value: CN7 e10.5 GFP-negative


title: In-vivo Eff- 2

description:
Replicate for in-vivo seq Eff-
Effneg.2


title: In-vivo Eff- 1

description:
Replicate for in-vivo seq Eff-
Effneg.1


title: SAM24395464 COLO 201 shATF6.1, Day 2, rep3

description: COLO 201 shATF6.1 Day 2 rep3

value: Colon

value: Adenocarcinoma


title: Mouse_Paclitaxel_INPUT_03

value: Paclitaxel


title: Mouse_Paclitaxel_INPUT_04


title: In-vivo Eff+ 3

description:
Replicate for in-vivo seq Eff+
Effpos.3


title: scRNA_cMN6_Hb9_E11-5

source_name: CN6 e11.5 GFP-positive and negative

value: CN6 e11.5 GFP-positive and negative


title: SAM24395461 COLO 201 shATF6.1, Day 0, rep3

description: COLO 201 shATF6.1 Day 0 rep3


title: scRNA_cMN6_Hb9_E10-5

source_name: CN6 e10.5 GFP-positive and negative

value: CN6 e10.5 GFP-positive and negative


title: In-vivo Eff+ 2

description:
Replicate for in-vivo seq Eff+
Effpos.2

value: Skin


title: In-vivo Eff+ 1

description:
Replicate for in-vivo seq Eff+
Effpos.1

value: Macrophage


title: Mouse_Paclitaxel_INPUT_02


title: scRNA_cMN3_4_Isl1_E11-5B

source_name: CN3/4 e11.5 GFP-positive and negative

value: CN3/4 e11.5 GFP-positive and negative


title: SAM24395462 COLO 201 shATF6.1, Day 2, rep1

description: COLO 201 shATF6.1 Day 2 rep1

value: Doxycline Day 2


title: SAM24395460 COLO 201 shATF6.1, Day 0, rep2

description: COLO 201 shATF6.1 Day 0 rep2

value: Control Day 0


title: CN7_e11.5_R2

description: scCUT&Tag using antibody H3K27Ac (ab177178)

data_processing:
NextSeq 500 software (Illumina) used for basecalling
bcl outputs from NextSeq 500 were processed using 10x Cell Ranger ATAC mkfastq pipeline (https://www.10xgenomics.com/support/software/cell-ranger/) for demultiplexing and fastq file generation
CUT&Tag fragment counts were tabulated using the Cell Ranger count function using default parameters
.bam and/or fragment files were processed for peak calling using R ArchR package (https://github.com/GreenleafLab/ArchR)
Calculation of activity by contact (ABC) enhancer scores (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction)
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bigwig track format to visualise histone modification profiles along the genome
Library strategy: scCUT&Tag

source_name: CN7 e11.5 GFP-positive-R2

extract_protocol:
GFP positive cells FACS purified from e10.5 or e11.5 cells
“Single Cell CUT and Tag on 10X genomics platform” protocol from www.protocol.io and 10x Genomics Chromium Next GEM Single Cell ATAC Kit

value: CN7 e11.5 GFP-positive-R2


title: Sptbn1+/-, snRNAseq

description:
A894
10x Genomics

data_processing:
snRNA-seq: The demutiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0.
snRNA-seq: The preprocessing, QC, normalizing, clustering, and visulization were made using the Seurat v4.
Assembly: mm10
Supplementary files format and content: snRNA-seq: H5, with molecule, feature and matrix files for each sample
RNA-seq: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
RNA-seq: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Supplementary files format and content: RNA-seq: tab-delimited text file includes TPM values for each sample

extract_protocol:
snRNA-seq: Nuclei were isolated by lysing frozen mouse livers with a pestle and cold lysing buffer (10mM Tris-Cl, PH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.4 U/ul RNase Inhibitor, 1mM DTT) for 4 min on ice. The lysate was filtered over a 40um filter, centrifuged at 500xg at 4 deg and resuspended in 1X PBS with 1% BSA & 0.4 U/ul RNase Inhibitor.
snRNA-seq: Nuclei were labeled with 7-AAD (Sigma) and sorted on a BD FACS Aria to purify nuclei from the remaining debris. Sorted nuclei were counted and loaded onto a Chip G and 10X Genomics Chromium Controller to generate GEMs following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’v3.1 with Dual Indexing). Libraries were quantitated and fragment sizes determined using a High Sensitivity DNA Chip and Bioanalyzer (Agilent).
RNA-seq: RNA was extracted from liver tissues using the RNeasy Plus Mini kit. RNA quality and concentration were assessed using the Thermo Scientific Nanodrop spectrophotometer before RNA sequencing.
RAN-seq: About 1 μg of RNA was used to generate barcoded sequencing libraries. Novogene Corporation performed library preparation.

value: liver cells

value: liver

tag: strain

value: 12 months


title: SAM24395459 COLO 201 shATF6.1, Day 0, rep1

description: COLO 201 shATF6.1 Day 0 rep1

value: COLO 201 shATF6.1


title: scRNA_cMN3_4_Isl1_E11-5A

value: WILDTYPE


title: Mouse_Paclitaxel_INPUT_01

value: Dorsal Root Ganglion

value: Neuronal Enchriment


title: scRNA_cMN3_4_Isl1_E10-5C

source_name: CN3/4 e10.5 GFP-positive and negative

value: CN3/4 e10.5 GFP-positive and negative


title: CN7_e11.5_R1

source_name: CN7 e11.5 GFP-positive-R1

value: CN7 e11.5 GFP-positive-R1


title: WT, snRNAseq

description:
A757
10x Genomics

value: WT


title: SAM24395458 COLO 201 shNTC, Day 4, rep3

description: COLO 201 shNTC Day 4 rep3

value: Colon

value: COLO 201 shNTC

value: Adenocarcinoma

value: shNTC

value: Doxycline Day 4


title: SAM24395463 COLO 201 shATF6.1, Day 2, rep2

description: COLO 201 shATF6.1 Day 2 rep2

value: Doxycline Day 2


title: Aldh2-/-Sptbn1+/-, snRNAseq

description:
A625
10x Genomics


title: scRNA_cMN7_Isl1_E10-5_GFP_Pos

source_name: CN7 e10.5 GFP-positive

value: CN7 e10.5 GFP-positive


title: scRNA_cMN3_4_Isl1_E10-5B


title: SAM24395457 COLO 201 shNTC, Day 4, rep2

description: COLO 201 shNTC Day 4 rep2


title: CN7_e10.5_R1

source_name: CN7 e10.5 GFP-positive-R1

value: CN7 e10.5 GFP-positive-R1


title: scRNA_cMN3_4_Isl1_E10-5A


title: Aldh2-/-, snRNAseq

description:
A624
10x Genomics

value: liver cells

value: liver


title: SAM24395456 COLO 201 shNTC, Day 4, rep1

description: COLO 201 shNTC Day 4 rep1


title: CN6_e11.5_R2

source_name: CN6 e11.5 GFP-positive-R2

value: CN6 e11.5 GFP-positive-R2


title: SAM24395455 CCK-81 shATF6, Day 4, rep3

description: CCK-81 shATF6 Day 4 rep3

value: CCK-81 shATF6


title: CN34_e11.5_R2

source_name: CN3/4 e11.5 GFP-positive-R2

value: CN3/4 e11.5 GFP-positive-R2

value: WILDTYPE


title: Usf2-/- MEF, Glucose starvation media, rep1

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
USF2_KO_GS_1
readcounts_GS.txt

data_processing:
Reads were mapped to GRCm38 by STAR (v2.7.10b).
Read counts were generated by featureCounts (v2.0.3).
The differential gene expression analysis was performed using Bioconductor package DESeq2 (v1.38.3).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files, read counts from featureCounts

source_name: MEF

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen)
The illumina RNA libraries for RNA-seq were prepared by TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. The DNBseq RNA library construction method and sequencing process are carried out according to the following steps: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: MEF

value: Mouse Embryonic Fibroblasts

value: Usf2 KO

value: Glucose starvation


title: Usf2-/- MEF, Glucose starvation media, rep2

description:
USF2_KO_GS_2
readcounts_GS.txt


title: midbrain, C1-C4flxflx;CRE_rep1

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Capture Micro-C data was mapped to the mm10 genome using BWA (0.7.17) (Li and Durbin, 2009). BAM files were then processed to pairs format, filtered, sorted, selected for pairs that included both ends of an interaction within the captured region, and deduplicated using pairtools (1.0.2 ) (Open2C et al., 2023). Technical replicates resulting from sequencing of the same sample more than once were merged prior to duplicate removal. Replicates where libraries were obtained from different cells were merged post duplicate removal. Cool and balanced mcool files were generated using cooler (0.8.11) (Abdennur and Mirny, 2020). Visualization of contact data as heatmaps was done using higlass (Kerpedjiev et al., 2018) at resgen.io. For generation of viewpoint tracks, pairtools select was used to identify pairs where one mate is located within the viewpoint of interest. A custom genome containing the floxed C1-C4 rescue cassette instead of the C1-C4 boundary was generated using reform (https://github.com/gencorefacility/reform) to create a modified fasta mm10 genome file and GTF file. These files were then used instead of mm10.fa for alignment of midbrain samples..
Assembly: mm10
Supplementary files format and content: mcool files. Interaction frequency at Fgf3/4/15 locus

source_name: midbrain

growth_protocol: Mouse embryonic stem cells lines were derived and genotyped as previously described in (Chakraborty et al., 2023). For assays with cells in the Epiblast-like state, cells were grown in serum-free using  Neurobasal medium (Thermo Fisher, 21103049), DMEM/F12 Nutrient mixture (Thermo Fisher, 21103049), 1% penicillin¬—streptomycin (Thermo Fisher, #15140163), 2 mM Glutamax (Thermo Fisher, #35050079), β-mercaptoethanol supplemented with N2 (Thermo Fisher, #17502001), B-27 (Thermo Fisher, #17504001), MEK/ERK pathway inhibitor (PD0325901, Reprocell, #04-0006-02), GSK3 signaling inhibitor (CHIR99021, Reprocell, #04-0004-02) and leukemia inhibition factor (LIF, Sigma, #ESG1107). Before differentiation, ES cells were grown on mouse embryonic fibroblasts and serum containing media: Knockout Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher, #10829018) with 15% FBS (VWR, #97068-091), 2 mM Glutamax (Thermo Fisher, #35050079), 0.1 mM β-mercaptoethanol, 0.1 mM MEM non-essential amino acids (Thermo Fisher, #11140050), 1 mM sodium pyruvate (Thermo Fisher, #11360070), 1% penicillin¬—streptomycin (Thermo Fisher, #15140163) and Recombinant mouse LIF (Sigma, #ESG1107). Differentiation into the primitive endoderm-like state (XEN cells) was done as previously described (Niakan et al., 2013). Briefly, ES cell lines were first grown on mouse embryonic fibroblasts, enzymatically passaged with 0.05% trypsin and feeder depleted for 45 mins. Cells were washed twice with standard XEN media: advanced RPMI (Thermo Fisher, #12633012) with 15% FBS (VWR, #97068-091), 1% penicillin¬—streptomycin (Thermo Fisher, #15140163) and 0.1 mM β-mercaptoethanol to remove residual LIF. Cells were counted, 96000 cells were plated in gelatinized 6-well plates and grown overnight in standard XEN media. After 24 hours, media was replaced with standard XEN media supplemented with 0.01M retinoic acid dissolved in DMSO, 10ng/ml activin, 24ng/ml recombinant FGF2 and 1g/ml heparin. Cells were grown in presence of supplements for 2-3 days depending on morphology and confluency and media was replenished every 24 hours. Cells were passaged and grown for 7-10 days until XEN like colonies with stellate and refractile morphologies emerged. XEN like colonies were scraped and picked with a pipette under the microscope and plated in gelatinized plates to enrich its population and cultured for an additional 2 weeks until cell morphology was homogenous.

extract_protocol:
To stop fixations, Glycine was added at final concentration of 0.13M and incubated for 5 minutes at RT and 15 minutes on ice. Cells were then washed once in cold PBS, centrifuged at 2500g 4oC for 5 mins (these centrifugation conditions were used for all washes following fixation) and pellets frozen at -80oC. Thawed cell pellets were then lysed (10mM Tris-HCL pH8, 50mM NaCl, 5mM MgCl2, 1mMCaCl2, NP-40 and Roche Complete EDTA-free Sigma #11836170001) and digested with Micrococcal nuclease (LS004798, Worthington Biochem). MNase was titrated with 1 million cells at 3U, 5U and 10U for 20 min at 37 °C in 100μl. Then, the micrococcal nuclease reaction was carried out with 5 million cells per replicate, and the micrococcal nuclease step was scaled up to 500 μL with the optimal concentration of micrococcal nuclease determined with titration experiment. Phosphorylation of DNA ends was done for 30 minutes at 37 °C using T4 Polynucleotide Kinase (NEB M0201), 3’ exonuclease activity of Klenow polymerase (NEB M0210) was done also at 37 °C for 30 minutes with. Biotin incorporation with dATP and dCTP (Jena Biosciences NU-835-BIO14-L and NU-809-BIOX-L) was done at 25 °C for 90 minutes. T4-mediated proximity ligation was always done overnight with T4 ligase (NEB M0202M). Proteinase K (NEB P8107S) incubation was also performed overnight at 65 °C. After phenol/chloroform/iso-amyl alcohol extraction, the sample was split into two equal aliquots and was purified on two Zymo DNA clean and concentrator kit columns, eluted with 25 μL (preheated to 70 °C) elution buffer then pooled. Samples were loaded onto 3% TBE NuSieve GTG agarose gel in 4 separate wells. After excision of fragments containing dinucleosomes from each lane (>220bp,<400bp), samples were purified using a Zymo Gel DNA Recovery kit to extract DNA. DNA fragments were not polished prior to streptavidin binding. For biotin purification, 50 μL of Streptavidin C1 beads (Thermo 65002) were used per sample. Libraries were prepared using the KAPA Biosystems HyperPrep kit (Roche KK8502) and Illumina primers. After running a small-scale PCR to determine the optimal number of cycles for the required yield, 4 50μL PCR reactions were set up for each sample as instructed by manufacturers. 200 μL was transferred to a new tube and incubated with 0.9x SPRI beads. Samples were sequenced by 50 bp pair- end sequencing with a NovaSeq 6000 with an SP100 kit by the NICHD Molecular Genomics Core. Region capture of Micro-C samples was done as described previously (Goel et al., 2023) and as recommended by the Twist Bioscience’s Standard Hybridization Target Enrichment Protocol with a few modifications. Specifically, to increase stringency, all washes steps were done at 70 °C instead of 48 °C and room temperature. The regions covered by probes can be found in TableS1. While biotinylated probes used in cells were of 120bp, the probes used in embryonic material were of 80bp.
Library-prep with material on the beads was done using the Hyper Prep kit (Roche KK8502). For Capture Hi-C capture reactions, 1ug of Hi-C library per sample were hybridized with 120 nucleotide biotinylated RNA probes using the SureSelect kit from Agilent and PCR amplification using the polymerase from the Kapa Hyper Prep Kit. Following washes, material was amplified by PCR using the Kapa polymerase from the the Hyper Prep kit (Roche KK8502). Material from different samples was then combined and 1µg of pooled libraries was recaptured.
Paired end 50

treatment_protocol: Micro-C Libraries used for Capture were generated as previously described (Brown et al., 2023,(Brown et al., 2023; Slobodyanyuk et al., 2022) with a few modifications. Briefly, for mouse ES cell lines, 1 million cells per sample were trypsinized, washed in growth media and fixed for 35 minutes at room temperature while rotating in 1mg/ml DSG (D2650) in 1 ml of PBS. 1% formaldehyde (Thermo 28908) was then added and samples fixed for 10 more minutes. CHiC was processed separately for the two independent lines of each genotype that had been established from two independent blastocysts. E11.5 midbrains were dissected in chilled artificial cerebrospinal fluid (ACSF: 87 mM NaCl, 26 mM NaHCO3, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2, 10 mM glucose, 75 mM sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Cells were then incubated with 0.1% Pronase in PBS for 15 minutes (Sigma 10165921001) at room temperature and fixed as described above

value: midbrain

value: Brain

value: Pronase


title: midbrain, C1-C4flxflx;CRE_rep2


title: midbrain, C1-C4flxflx;CRE_rep3


title: CN6_e11.5_R1

source_name: CN6 e11.5 GFP-positive-R1

value: CN6 e11.5 GFP-positive-R1


title: SAM24395453 CCK-81 shATF6, Day 4, rep1

description: CCK-81 shATF6 Day 4 rep1

source_name: Colon

value: Colon

value: Adenocarcinoma

value: Doxycline Day 4


title: Usf2-/- MEF, Normal media, rep2

description:
USF2_KO_CTL_2
readcounts_GS.txt

value: Normal


title: CN34_e11.5_R1

source_name: CN3/4 e11.5 GFP-positive-R!

value: CN3/4 e11.5 GFP-positive-R!


title: midbrain, C1-C4flxflx_rep3


title: BW_hom_e10.5_R2

library_source: genomic single cell

data_processing:
NextSeq 500 software (Illumina) used for basecalling
bcl outputs from NextSeq 500 were processed using 10x Cell Ranger ATAC mkfastq pipeline (https://www.10xgenomics.com/support/software/cell-ranger/) for demultiplexing and fastq file generation
ATAC fragment counts were tabulated using the Cell Ranger count function using default parameters
.bam and/or fragment files were processed for peak calling and differential accessibility analysis using R ArchR package (https://github.com/GreenleafLab/ArchR)
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bw bigwig track format to visualise accessibility profiles along the genome

extract_protocol:
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
10x Genomics scATAC

value: CN7 e10.5 GFP-positive

value: cRE2 BW/BW


title: Usf2-/- MEF, Normal media, rep1

description:
USF2_KO_CTL_1
readcounts_GS.txt


title: midbrain, C1-C4flxflx_rep2


title: SAM24395452 CCK-81 shATF6, Day 2, rep3

description: CCK-81 shATF6 Day 2 rep3

value: CCK-81 shATF6

value: Doxycline Day 2


title: WT MEF, Glucose starvation media, rep2

description:
USF2_WT_GS_2
readcounts_GS.txt

value: MEF

value: Usf2 WT


title: BW_hom_e10.5_R1


title: SAM24395451 CCK-81 shATF6, Day 2, rep2

description: CCK-81 shATF6 Day 2 rep2


title: CN7_e10.5_R2

source_name: CN7 e10.5 GFP-positive-R2

value: CN7 e10.5 GFP-positive-R2

value: WILDTYPE


title: SAM24395450 CCK-81 shATF6, Day 2, rep1

description: CCK-81 shATF6 Day 2 rep1


title: WT MEF, Glucose starvation media, rep1

description:
USF2_WT_GS_1
readcounts_GS.txt

value: Mouse Embryonic Fibroblasts

value: Glucose starvation


title: blastocyst, RCMC_ES_C5-C6d_rep2

source_name: blastocyst

value: blastocyst

value: blastocyst derived ES cells

value: ES


title: CGQ_het_e10.5_R2

value: cRE2 WT/CGQ


title: SAM24395449 CCK-81 shATF6, Day 0, rep3

description: CCK-81 shATF6 Day 0 rep3

value: Colon

value: Adenocarcinoma

value: Control Day 0


title: SAM24395454 CCK-81 shATF6, Day 4, rep2

description: CCK-81 shATF6 Day 4 rep2

value: Doxycline Day 4


title: CGQ_het_e10.5_R1

value: CN7 e10.5 GFP-positive


title: blastocyst, RCMC_ES_C5-C6d_rep1


title: SAM24395448 CCK-81 shATF6, Day 0, rep2

description: CCK-81 shATF6 Day 0 rep2

value: CCK-81 shATF6


title: CGQ_hom_e10.5_R2

value: cRE2 CGQ/CGQ


title: blastocyst, RCMC_ES_WT_rep2

value: wt


title: Input, Glucose starvation, rep2

data_processing:
Seqeuncing adapters were removed with NGmerge (v0.2)
Reads were mapped to GRCm38 by Bowtie2 (v2.5.1).
Peaks were called using Macs2 (v2.2.7.1).
bigWig files were generated using bamCoverage (v3.5.1)
Assembly: GRCm38
Supplementary files format and content: bigWig format / narrowPeak format

extract_protocol:
Crosslinked DNA was fragmented with sonication and IP with H3K27Ac and USF2 antibody.
The illumina libraries for ChIP-seq were prepared by TruSeq DNA Sample prep Kit according to the manufacturer’s protocol.

tag: chip antibody

value: Input

value: MEF

value: WT


title: CGQ_hom_e10.5_R1


title: blastocyst, RCMC_ES_WT_rep1


title: SAM24395447 CCK-81 shATF6, Day 0, rep1

description: CCK-81 shATF6 Day 0 rep1


title: SAM24395446 CCK-81 shNTC, Day 4, rep3

description: CCK-81 shNTC Day 4 rep3

value: CCK-81 shNTC

value: shNTC


title: Midbrain, C1-C4flxflx;CRE_rep3

description:
MT_Fgf3vp_200bpbins_mean_merge_filtered.bedGraph
MT_Fgf4vp_200bpbins_mean_merge_filtered.bedGraph
MT_Fgf15vp_200bpbins_mean_merge_filtered.bedGraph

data_processing:
Promoter capture data was mapped to the mm10 genome using BWA (0.7.17) (Li and Durbin, 2009). BAM files were then processed to pairs format, filtered, sorted, selected for pairs that included both ends of an interaction within the captured region, and deduplicated using pairtools (1.0.2 ) (Open2C et al., 2023). Technical replicates resulting from sequencing of the same sample more than once were merged prior to duplicate removal. Replicates where libraries were obtained from different cells were merged post duplicate removal. For generation of viewpoint tracks, pairtools select was used to identify pairs where one mate is located within the viewpoint of interest. A custom genome containing the floxed C1-C4 rescue cassette instead of the C1-C4 boundary was generated using reform (https://github.com/gencorefacility/reform) to create a modified fasta mm10 genome file and GTF file. These files were then used instead of mm10.fa for alignment of midbrain samples..
Assembly: mm10
Supplementary files format and content: bed files. Interaction frequency at Fgf3/4/15 locus using each probes against each promoter
Library strategy: Micro-C

extract_protocol:
To stop fixations, Glycine was added at final concentration of 0.13M and incubated for 5 minutes at RT and 15 minutes on ice. Cells were then washed once in cold PBS, centrifuged at 2500g 4oC for 5 mins (these centrifugation conditions were used for all washes following fixation) and pellets frozen at -80oC. Thawed cell pellets were then lysed (10mM Tris-HCL pH8, 50mM NaCl, 5mM MgCl2, 1mMCaCl2, NP-40 and Roche Complete EDTA-free Sigma #11836170001) and digested with Micrococcal nuclease (LS004798, Worthington Biochem). MNase was titrated with 1 million cells at 3U, 5U and 10U for 20 min at 37 °C in 100μl. Then, the micrococcal nuclease reaction was carried out with 5 million cells per replicate, and the micrococcal nuclease step was scaled up to 500 μL with the optimal concentration of micrococcal nuclease determined with titration experiment. Phosphorylation of DNA ends was done for 30 minutes at 37 °C using T4 Polynucleotide Kinase (NEB M0201), 3’ exonuclease activity of Klenow polymerase (NEB M0210) was done also at 37 °C for 30 minutes with. Biotin incorporation with dATP and dCTP (Jena Biosciences NU-835-BIO14-L and NU-809-BIOX-L) was done at 25 °C for 90 minutes. T4-mediated proximity ligation was always done overnight with T4 ligase (NEB M0202M). Proteinase K (NEB P8107S) incubation was also performed overnight at 65 °C. After phenol/chloroform/iso-amyl alcohol extraction, the sample was split into two equal aliquots and was purified on two Zymo DNA clean and concentrator kit columns, eluted with 25 μL (preheated to 70 °C) elution buffer then pooled. Samples were loaded onto 3% TBE NuSieve GTG agarose gel in 4 separate wells. After excision of fragments containing dinucleosomes from each lane (>220bp,<400bp), samples were purified using a Zymo Gel DNA Recovery kit to extract DNA. DNA fragments were not polished prior to streptavidin binding. For biotin purification, 50 μL of Streptavidin C1 beads (Thermo 65002) were used per sample. Libraries were prepared using the KAPA Biosystems HyperPrep kit (Roche KK8502) and Illumina primers. After running a small-scale PCR to determine the optimal number of cycles for the required yield, 4 50μL PCR reactions were set up for each sample as instructed by manufacturers. 200 μL was transferred to a new tube and incubated with 0.9x SPRI beads. Samples were sequenced by 50 bp pair- end sequencing with a NovaSeq 6000 with an SP100 kit by the NICHD Molecular Genomics Core. Region capture of Micro-C samples was done as described previously (Goel et al., 2023) and as recommended by the Twist Bioscience’s Standard Hybridization Target Enrichment Protocol with a few modifications. Specifically, to increase stringency, all washes steps were done at 70 °C instead of 48 °C and room temperature. The regions covered by probes can be found in TableS1. While biotinylated probes used in cells were of 120bp, the probes used in embryonic material were of 80bp.
Library-prep with material on the beads was done using the Hyper Prep kit (Roche KK8502). For promoter Capture Hi-C, 1µg of Hi-C library per sample was hybridized with 120bp biotinylated oligos using the SeqCap EZ kits (Roche). Following washes, material was amplified by PCR using the Kapa polymerase from the Hyper Prep kit (Roche KK8502). Material from different samples was then combined and 1µg of pooled libraries was recaptured. Probes used for these assays can be found in Table S1.
Paired end 50

treatment_protocol: Micro-C Libraries used for Capture were generated as previously described (Brown et al., 2023,(Brown et al., 2023; Slobodyanyuk et al., 2022) with a few modifications. Mouse embryonic E11.5 or E12.5  midbrains were dissected in chilled artificial cerebrospinal fluid (ACSF: 87 mM NaCl, 26 mM NaHCO3, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2, 10 mM glucose, 75 mM sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Cells were then incubated with 0.1% Pronase in PBS for 15 minutes (Sigma 10165921001) at room temperature, counted and fixed for 35 mins at room temperature while rotating in 1mg/ml DSG (D2650) in 1 ml of PBS. 1% formaldehyde (Thermo 28908) was then added, and samples fixed for 10 more minutes.

value: midbrain

value: Brain

value: Pronase


title: Input, Glucose starvation, rep1

value: Mouse Embryonic Fibroblasts

value: Glucose starvation


title: midbrain, C1-C4flxflx_rep1


title: Input, Normal, rep2

value: Normal


title: SAM24395445 CCK-81 shNTC, Day 4, rep2

description: CCK-81 shNTC Day 4 rep2

value: Colon

value: Adenocarcinoma


title: SMNneg_e11.5_R1

source_name: SMN e11.5 GFP-negative

value: SMN e11.5 GFP-negative

value: WILDTYPE


title: Midbrain, C1-C4flxflx;CRE_rep2


title: Input, Normal, rep1


title: WT MEF, Normal media, rep1

description:
USF2_WT_CTL_1
readcounts_GS.txt

value: Usf2 WT


title: Midbrain, C1-C4flxflx;CRE_rep1


title: SAM24395444 CCK-81 shNTC, Day 4, rep1

description: CCK-81 shNTC Day 4 rep1

value: Doxycline Day 4


title: CN12neg_e10.5_R1

source_name: CN12 e10.5 GFP-negative

value: CN12 e10.5 GFP-negative


title: WT MEF, Normal media, rep2

description:
USF2_WT_CTL_2
readcounts_GS.txt

value: MEF


title: USF2 ChIP-seq, Glucose starvation, rep2

value: WT


title: SMNneg_e10.5_R1

source_name: SMN e10.5 GFP-negative

value: SMN e10.5 GFP-negative


title: CN7neg_e11.5_R1

source_name: CN7 e11.5 GFP-negative

value: CN7 e11.5 GFP-negative


title: CN12neg_e11.5_R1

source_name: CN12 e11.5 GFP-negative

value: CN12 e11.5 GFP-negative


title: HeLa cells, knockout, rep3

city: Shanghai

first: Haiping

last: Zhao

address: 131 DongAn Road

country: China

institute: Fudan University

description:
TSSC4_gene_counts.xls
TSSC4_gene_fpkm.xls
TSSC4_differentially expressed genes.xls
TSSC4_alternative splicing events.xls

data_processing:
The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent, USA).
Paired-end clean reads were aligned to the hg38 reference genome using HISAT2 (v2.0.5).
Differential expression analysis of the two conditions was performed using the edgeR R package (3.22.5).
rMATS (4.1.0) software was used to analyze the alternative splicing events.
Assembly: hg38
Supplementary files format and content: Excel  file includes raw counts for each Sample
Supplementary files format and content: Excel  file includes differentially expressed gene
Supplementary files format and content: Excel  file includes alternative splicing events

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and 100 U/mL of penicillin and 100 μg/mL of streptomycin, and the cells were cultured in a humidified incubator at 37°C in the presence of 5% CO2

extract_protocol:
TRIzol reagent (Invitrogen) was used for total RNA extraction according to the manufacturer’s instructions
RNA-seq library was loaded on an Illumina NovaSeq 6000 instrument for sequencing using a 2×150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries

value: HeLa

value: cervical cancer cell

value: TSSC4 knockout

value: puromycine selection


title: HeLa cells, knockout, rep2


title: Midbrain, C1-C4flxflx_rep3

description:
WT_Fgf3vp_200bpbins_mean_merge_filtered.bedGraph
WT_Fgf4vp_200bpbins_mean_merge_filtered.bedGraph
WT_Fgf15vp_200bpbins_mean_merge_filtered.bedGraph

value: midbrain

value: Brain

value: Pronase


title: USF2 ChIP-seq, Glucose starvation, rep1

value: Mouse Embryonic Fibroblasts

value: Glucose starvation


title: USF2 ChIP-seq, Normal, rep2

value: Normal


title: USF2 ChIP-seq, Normal, rep1


title: CN7neg_e10.5_R1T

source_name: CN7 e10.5 GFP-negative

value: CN7 e10.5 GFP-negative

value: WILDTYPE


title: HeLa cells, WT, rep3


title: Midbrain, C1-C4flxflx_rep1


title: CN7neg_e10.5_R1


title: Midbrain, C1-C4flxflx_rep2


title: ES cells_IgG_wt_rep2

data_processing:
Capture Hi-C data was mapped to the mm10 genome using BWA (0.7.17) (Li and Durbin, 2009). BAM files were then processed to pairs format, filtered, sorted, selected for pairs that included both ends of an interaction within the captured region, and deduplicated using pairtools (1.0.2 ) (Open2C et al., 2023). Technical replicates resulting from sequencing of the same sample more than once were merged prior to duplicate removal. Replicates where libraries were obtained from different cells were merged post duplicate removal. Cool and balanced mcool files were generated using cooler (0.8.11) (Abdennur and Mirny, 2020). Visualization of contact data as heatmaps was done using higlass (Kerpedjiev et al., 2018) at resgen.io. For generation of viewpoint tracks, pairtools select was used to identify pairs where one mate is located within the viewpoint of interest. A custom genome containing the floxed C1-C4 rescue cassette instead of the C1-C4 boundary was generated using reform (https://github.com/gencorefacility/reform) to create a modified fasta mm10 genome file and GTF file. These files were then used instead of mm10.fa for alignment of midbrain samples..
Assembly: mm10
Supplementary files format and content: bigwig, genomic enrichment
Library strategy: Cut&Run

growth_protocol: Mouse embryonic stem cells lines were derived and genotyped as previously described in (Chakraborty et al., 2023). Cells were grown in serum-free 2i media constituted of  Neurobasal medium (Thermo Fisher, 21103049), DMEM/F12 Nutrient mixture (Thermo Fisher, 21103049), 1% penicillin¬—streptomycin (Thermo Fisher, #15140163), 2 mM Glutamax (Thermo Fisher, #35050079), β-mercaptoethanol supplemented with N2 (Thermo Fisher, #17502001), B-27 (Thermo Fisher, #17504001), MEK/ERK pathway inhibitor (PD0325901, Reprocell, #04-0006-02), GSK3 signaling inhibitor (CHIR99021, Reprocell, #04-0004-02) and leukemia inhibition factor (LIF, Sigma, #ESG1107).

extract_protocol:
Pellets were resuspended in BioMag Plus Concanavalin A beads (Bangs Laboratories), equilibrated in Binding Buffer with 20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2 and1 mM MnCl2. Cell pellets were resuspended in Wash Buffer, mixed with a slurry of equilibrated Concavalin A coated magnetic beads, and rotated for 10 mins at room temperature. For each sample, 10 µl bead slurry was used and were placed on a magnetic separator to discard the supernatant. Beads were again resuspended in Wash Buffer containing 2 mM EDTA, 0.1% bovine serum albumin, 0.05% Digitonin, and 1:50 dilution of primary antibody against H3K27Ac (Abcam, ab4729). This was incubated on a nutating platform for 2 hours at room temperature. After incubation, beads were washed twice in Digitonin Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche Complete Protease Inhibitor no EDTA, 0.05% Digitonin and 0.1% bovine serum albumin), then incubated with lab prepared pA-MNase (600 µg/ml, 1:200) in Digitonin Buffer for 1 hour at 4 °C. After incubation, beads were washed twice, resuspended in 150 µl of Digitonin Buffer, and equilibrated to 0°C before adding 2mM CaCl2 and incubated at 0°C for 1 hour. After incubation, 150 µl of 2X Stop Buffer containing 200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/ml RNase A and 40 µg/ml glycogen was added. Beads were incubated for 30 mins at 37°C and then spun at 16,000 g for 5 mins at 4°C. Supernatant was transferred, mixed with 3 µl 10% SDS and 1.8U Proteinase K (NEB #P8107S) and incubated overnight at 55°C, shaking at 900 rpm. After incubation, 300 µl of 25:24:1 Phenol/Chloroform/ Isoamyl Alcohol was added, solutions were vortexed, and transferred to Maxtrack phase-lock tubes (Qiagen #129046). Tubes were centrifuged at 16,000 g for 3 mins at room temperature. 300 µl of Chloroform was added, solutions were mixed by inversion, and centrifuged at 16,000 g for 3 mins at room temperature. Aqueous layers were transferred to new tubes and DNA was isolated by ethanol precipitation and resuspended in 10 mM Tris-HCl pH 8.0 (Thermo Fisher #15568025).
Cut&Run libraries were prepared following the SMARTer ThruPlex TAKARA Library Prep kit with small modifications. For each sample, 10 µl of double stranded DNA, 2 µl of Template Preparation D Buffer and 1 µl of Template Preparation D Enzyme were combined, and End Repair and A-tailing was performed in a thermocycler with a heated lid at 22°C, for 25 mins and 55°C for 20 mins. 1 µl each of Library Synthesis D Buffer and Library Synthesis D Enzyme were subsequently added, and library synthesis was performed at 22 °C for 40 mins. Immediately after, 25 µl of Library Amplification D Buffer, 1 µl of Library Amplification D Enzyme, 4 µl of nuclease-free water and 5 µl of unique Illumina-compatible indexed primer were added to each sample. Library amplification was performed using the following cycling conditions: For denaturation - 72°C for 3 mins, 85°C for 2 mins and 98°C for 2 mins, addition of unique indexes - 4 cycles of 98°C for 20 secs, 67°C for 20 secs and 72°C for 10 secs, library amplification - 14 cycles of 98°C for 20 secs and 72°C for 10 secs. Post-PCR clean-up was performed on amplified libraries with SPRI beads using 0.6X left/1x right double size selection, washed twice gently in 80% ethanol and eluted in 10–12 µl 10 mM Tris pH 8.0.
Paired end 50

treatment_protocol: ES cells were detached from culture plates using Accutase (Sigma), counted and 200,000 cells per clone were spun at 600g for 3 mins at room temperature. Supernatant was discarded and cells were resuspended in Wash Buffer with 20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine and 1x Protease inhibitor cocktail at 600g for 3 mins at room temperature.

value: blastocyst

value: blastocyst derived ES cells

value: ES

value: wt


title: Usf2 KO MEF, H3K27Ac ChIP-seq

value: MEF

value: Usf2 KO


title: CN6neg_e11.5_R1

source_name: CN6 e11.5 GFP-negative

value: CN6 e11.5 GFP-negative


title: HeLa cells, WT, rep2

value: HeLa

value: cervical cancer cell

value: WT


title: ES cells_IgG_wt_rep1


title: Usf2 WT MEF, H3K27Ac ChIP-seq

value: Usf2 WT


title: HeLa cells, WT, rep1

value: puromycine selection


title: ES cells_h3k27ac_c5-c6d_rep2


title: CN6neg_e10.5_R1

source_name: CN6 e10.5 GFP-negative

value: CN6 e10.5 GFP-negative


title: Usf2 KO MEF, Input

value: Input

value: Mouse Embryonic Fibroblasts


title: CN34neg_e11.5_R1

source_name: CN3/4 e11.5 GFP-negative

value: CN3/4 e11.5 GFP-negative


title: 50nM siSptbn1, replicate 3, RNAseq

description:
P2B6
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt

source_name: liver

value: coculture human liver cells:hepatocyte, Kupffer cell, stellate cell

value: liver

value: 50nM siSptbn1

tag: time


title: 50nM siSptbn1, replicate 2, RNAseq

description:
P2B5
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt


title: ES cells_h3k27ac_c5-c6d_rep1

value: blastocyst

value: blastocyst derived ES cells

value: ES


title: Usf2 WT MEF, Input

source_name: MEF

value: MEF

value: Normal


title: CN34neg_e10.5_R1

source_name: CN3/4 e10.5 GFP-negative

value: CN3/4 e10.5 GFP-negative

value: WILDTYPE


title: HeLa cells, knockout, rep1

value: HeLa

value: cervical cancer cell

value: TSSC4 knockout


title: ES cells_h3k27ac_c7-c10d_rep2


title: Usf2 KO MEF, rep2

data_processing:
Seqeuncing adapters were removed with NGmerge (v0.2)
Reads were mapped to GRCm38 by Bowtie2 (v2.5.1).
The chromatin-accessible peaks were called using Macs2 (v2.2.7.1).
bigWig files were generated using bamCoverage (v3.5.1)
Assembly: GRCm38
Supplementary files format and content: bigWig format

extract_protocol:
Cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the Tn5 transposase
The illumina libraries for ATAC-seq were prepared by Illumina Tagment DNA TDE1 Enzyme and Buffer Kits according to the manufacturer’s protocol.

value: Usf2 KO


title: ES cells_h3k27ac_c7-c10d_rep1


title: 50nM siSptbn1, replicate 1, RNAseq

description:
P2B4
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt


title: SMN_e11.5_R2

source_name: SMN e11.5 GFP-positive

value: SMN e11.5 GFP-positive


title: 25nM siSptbn1, replicate 2, RNAseq

description:
P2B2
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt

value: 25nM siSptbn1


title: SMN_e11.5_R1


title: ES cells_h3k27ac_wt_rep2

value: wt


title: Usf2 WT MEF, rep2

value: Mouse Embryonic Fibroblasts

value: Usf2 WT


title: 25nM siSptbn1, replicate 3, RNAseq

description:
P2B3
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt

value: coculture human liver cells:hepatocyte, Kupffer cell, stellate cell

value: liver


title: SMN_e10.5_R2

source_name: SMN e10.5 GFP-positive

value: SMN e10.5 GFP-positive


title: ES cells_h3k27ac_wt_rep1

value: blastocyst

value: blastocyst derived ES cells

value: ES


title: SMN_e10.5_R1


title: 25nM siSptbn1, replicate 1, RNAseq

description:
P2B1
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt


title: siCtrl, replicate 3, RNAseq

description:
P2A3
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt

value: siControl


title: Positively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 3

first: Ian

middle: L

last: Morgan

state: MD

address: 50 Center Dr.

institute: National Heart Lung and Blood Institute

library_source: other

data_processing:
Trimmomatic to trim adapters from reads
BWA-MEM to align the reads to the reference sequence
SAMtools to index the reads
Pysam to extract reads, count enzyme-cleaved DNA ends, and normalize counts by spikein reads
Assembly: pBR322_plus_spikes.fa
Supplementary files format and content: TXT file with number and location of enzyme-cleaved DNA ends from forward and reverse reads
Library strategy: SHAN-seq

molecule: other

organism: Cloning vector pBR322

source_name: Synthetic plasmid

growth_protocol: Supercoiled pBR322 DNA was treated with no enzyme, E. coli gyrase, or E. coli topo IV.

extract_protocol:
Qiagen PCR Clean-up Kit
NEBNext Ultra II PCR-free Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1)

value: Not applicable

tag: supercoiling

value: pos

value: Calcium


title: CN12_e11.5_R2

source_name: CN12 e11.5 GFP-positive

value: CN12 e11.5 GFP-positive

value: WILDTYPE


title: siCtrl, replicate 2, RNAseq

description:
P2A2
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt


title: Positively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 2


title: C1-C4flxflx;CRE_rep6

data_processing:
Capture Hi-C data was mapped to the mm10 genome using BWA (0.7.17) (Li and Durbin, 2009). BAM files were then processed to pairs format, filtered, sorted, selected for pairs that included both ends of an interaction within the captured region, and deduplicated using pairtools (1.0.2 ) (Open2C et al., 2023). Technical replicates resulting from sequencing of the same sample more than once were merged prior to duplicate removal. Replicates where libraries were obtained from different cells were merged post duplicate removal. Cool and balanced mcool files were generated using cooler (0.8.11) (Abdennur and Mirny, 2020). Visualization of contact data as heatmaps was done using higlass (Kerpedjiev et al., 2018) at resgen.io. For generation of viewpoint tracks, pairtools select was used to identify pairs where one mate is located within the viewpoint of interest. A custom genome containing the floxed C1-C4 rescue cassette instead of the C1-C4 boundary was generated using reform (https://github.com/gencorefacility/reform) to create a modified fasta mm10 genome file and GTF file. These files were then used instead of mm10.fa for alignment of midbrain samples..
Assembly: mm10
Supplementary files format and content: mcool files. Interaction frequency at Fgf3/4/15 locus

source_name: E11.5 midbrain

extract_protocol:
To stop fixations, Glycine was added at final concentration of 0.13M and incubated for 5 minutes at RT and 15 minutes on ice. Cells were then washed once in cold PBS, centrifuged at 2500g 4oC for 5 mins (these centrifugation conditions were used for all washes following fixation) and pellets frozen at -80oC. Thawed cell pellets were then lysed (10mM Tris-HCL pH8, 10mM NaCl, 0.2% Igepal CA-630, Roche Complete EDTA-free Sigma #11836170001) and digested with 600U of DpnII (NEB).Biotin fill-in was done by incubating cells with a mixture of dCTP, dTTP, dGTP, Klenow polymerase (NEB M0210L) and 37.5µl Biotin-14-dATP (Thermo 19524016) for 4h at RT while shaking at 900rpm for 10 seconds every 5 minutes. Ligation was done overnight at 160C using T4 ligase (NEB cat #M0202M). Sonication was done using Covaris onetube-10 AFA strips using the following parameters for a 300bp fragment size (Duration: 10secs, repeat for 12 times, total time 120 secs, peak power-20W, duty factor 40%, CPB-50).Sonicated material was then size selected using SPRI beads with the following ratios: 0.55X and 0.75X. Hi-C material was then bound to 150µl Streptavidin C1 beads (Thermo 65002), washed and recovered following manufacturers recommendations. Bead-bound DNA was resuspended in 50µl 10mM Tris HCl.
Library-prep with material on the beads was done using the Hyper Prep kit (Roche KK8502). For Capture Hi-C capture reactions, 1ug of Hi-C library per sample were hybridized with 120 nucleotide biotinylated RNA probes using the SureSelect kit from Agilent and PCR amplification using the polymerase from the Kapa Hyper Prep Kit. Following washes, material was amplified by PCR using the Kapa polymerase from the the Hyper Prep kit (Roche KK8502). Material from different samples was then combined and 1µg of pooled libraries was recaptured.

treatment_protocol: Hi-C Libraries used for Capture were generated as previously described (Chakraborty et al., 2023) with a few modifications. Briefly, for mouse ES cell lines, 1 million cells per sample were trypsinized, washed in growth media and fixed for 35 minutes at room temperature while rotating in 1mg/ml DSG (D2650) in 1 ml of PBS. 1% formaldehyde (Thermo 28908) was then added and samples fixed for 10 more minutes. CHiC was processed separately for the two independent lines of each genotype that had been established from two independent blastocysts. E11.5 midbrains were dissected in chilled artificial cerebrospinal fluid (ACSF: 87 mM NaCl, 26 mM NaHCO3, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2, 10 mM glucose, 75 mM sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Cells were then incubated with 0.1% Pronase in PBS for 15 minutes (Sigma 10165921001) at room temperature and fixed as described above.

value: E11.5 midbrain

value: Brain

value: Pronase


title: siCtrl, replicate 1, RNAseq

description:
P2A1
TPM_values_siCtrl_vs_25nM_siSptbn1_vs_50nM_siSptbn1_96h.txt


title: C1-C4flxflx;CRE_rep5


title: Positively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 1


title: Positively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 3

value: 10 uM cip


title: CN12_e11.5_R1


title: CN7_e11.5_R2


title: HDF2_shAR_pSer301 ChIP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: skin

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. To determine chromatin binding of pSer301 and wild-type lamin A/C together with histone markers, chromatin was prepared using the Chromatin EasyShear Kit - Low SDS (Diagenode, Cat# C01020013) and sonicated using an E220 focused ultrasonicator (Covaris). The ChIP reaction was performed using the iDeal ChIP-seq kit (Diagenode, Cat# C01010055). Samples were pre-cleared using the beads provided in the kit and incubated overnight at 4°C with 5 µg of commercially available antibodies against lamin A/C (Abcam, #ab108595), phospho-Ser301 lamin A/C (Affinity, #AF7177), H3K27Ac (Abcam, #ab4729). Antibody-chromatin complexes were pulled down using protein A-coated magnetic beads. Elution was performed according to the manufacturer's instruction and chromatin was quantified using the Qubit Fluorometric Quantification Kit (Thermo Scientific).
For library preparation, 10 ng of DNA was utilized with the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: HDF cells were infected with either control(shCtrl) or AR silencing shRNAs (shAR), post selection ChIP experiments were performed as following.

value: skin

value: Human dermal fibroblasts

value: Phospho-Lamin A/C (Ser301) Antibody, Affinity; Cat# AF7177

value: With AR silencing


title: C1-C4flxflx;CRE_rep4


title: HDF2_shAR_LaminA/C ChIP

value: Lamin A antibody + Lamin C antibody [EPR4100], Abcam; Cat# ab108595


title: Positively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 2


title: C1-C4flxflx;CRE_rep3


title: CN12_e10.5_R1

source_name: CN12 e10.5 GFP-positive

value: CN12 e10.5 GFP-positive


title: C1-C4flxflx;CRE_rep2


title: Positively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 1


title: HDF2_shAR_H3K27Ac ChIP

value: Histone H3 (acetyl K27) antibody - ChIP Grade, Abcam; Cat# ab4729


title: Usf2 WT MEF, rep1

value: MEF

value: Mouse Embryonic Fibroblasts

value: Usf2 WT


title: CN7_e10.5_R3

source_name: CN7 e10.5 GFP-positive

value: CN7 e10.5 GFP-positive


title: C1-C4flxflx;CRE_rep7


title: CN7_e11.5_R1

source_name: CN7 e11.5 GFP-positive

value: CN7 e11.5 GFP-positive


title: CN7_e10.5_R2

value: WILDTYPE


title: HDF2_shAR_Input

value: Without AR silencing


title: C1-C4flxflx;CRE_rep1

value: E11.5 midbrain

value: Brain


title: HDF2_shCtrl_pSer301 ChIP


title: Positively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 3

value: Not applicable

value: pos

value: Calcium


title: CN7_e10.5_R1T


title: C1-C4flxflx_rep4

source_name: E12.5 midbrain

value: E12.5 midbrain

value: Pronase


title: Positively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 2


title: C1-C4flxflx_rep3


title: HDF2_shCtrl_LaminA/C ChIP

value: skin

value: Human dermal fibroblasts

value: Lamin A antibody + Lamin C antibody [EPR4100], Abcam; Cat# ab108595

value: With AR silencing


title: C1-C4flxflx_rep5


title: CN7_e10.5_R1


title: Positively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 3

value: 10 uM cip


title: HDF2_shCtrl_H3K27Ac ChIP

value: Histone H3 (acetyl K27) antibody - ChIP Grade, Abcam; Cat# ab4729


title: Positively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 1


title: Usf2 KO MEF, rep1

value: MEF

value: Mouse Embryonic Fibroblasts

value: Usf2 KO


title: HDF2_shCtrl_Input

value: Without AR silencing


title: Positively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 2


title: C1-C4flxflx_rep1

value: E11.5 midbrain


title: CN6_e11.5_R2

source_name: CN6 e11.5 GFP-positive

value: CN6 e11.5 GFP-positive

value: WILDTYPE


title: CN6_e11.5_R1


title: Positively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 1

value: Not applicable

value: pos


title: CN6_e10.5_R2

source_name: CN6 e10.5 GFP-positive

value: CN6 e10.5 GFP-positive


title: xen_c5-c6d_rep3

source_name: E3.5 blastocyst

value: E3.5 blastocyst

value: ES differentiated into Xen

value: Xen

value: Activin, Retinoic acid, FGF2, Heparin


title: Positively supercoiled pBR322 DNA not treated by any cutting enzyme replicate 3

value: No enzyme


title: HDF1_shAR_LaminA/C ChIP

value: skin

value: Human dermal fibroblasts

value: Lamin A antibody + Lamin C antibody [EPR4100], Abcam; Cat# ab108595

value: With AR silencing


title: CN6_e10.5_R1


title: Positively supercoiled pBR322 DNA not treated by any cutting enzyme replicate 2


title: HDF1_shAR_H3K27Ac ChIP

value: Histone H3 (acetyl K27) antibody - ChIP Grade, Abcam; Cat# ab4729


title: CN34_e11.5_R2

source_name: CN3/4 e11.5 GFP-positive

value: CN3/4 e11.5 GFP-positive


title: xen_c5-c6d_rep1


title: Positively supercoiled pBR322 DNA not treated by any cutting enzyme replicate 1


title: xen_wt_rep5

value: wt


title: CN34_e11.5_R1


title: HDF1_shAR_Input


title: C1-C4flxflx_rep2

value: E11.5 midbrain

value: Brain

value: Pronase


title: xen_wt_rep4


title: HDF1_shAR_pSer301 ChIP

value: Phospho-Lamin A/C (Ser301) Antibody, Affinity; Cat# AF7177


title: HDF1_shCtrl_H3K27Ac ChIP


title: CN34_e10.5_R1

source_name: CN3/4 e10.5 GFP-positive

value: CN3/4 e10.5 GFP-positive

value: WILDTYPE


title: xen_wt_rep2

value: E3.5 blastocyst

value: ES differentiated into Xen


title: xen_wt_rep1

value: Xen

value: Activin, Retinoic acid, FGF2, Heparin


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 3

value: Not applicable

value: neg

value: Calcium


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 1


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with calcium replicate 2


title: CN34_e10.5_R2


title: CN347SMN_e11.5_R2_ATAC

data_processing:
Basecalling on a NextSeq 500 for Multiome ATAC and Gene Expression libraries separately, using a custom sequencing recipe for ATAC provided by Illumina.
For Gex and ATAC outputs, demultiplexing and fastq file generation were performed using  10x Cell Ranger Arc (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/) mkfastq pipeline
10x Cell Ranger Arc countpipeline was used for data filtering and alignment
Tab separated values files, matrix files, and .bam/ fragment files were processed for peak calling, cluster annotation and peak to gene analysis were performed using R ArchR package (https://github.com/GreenleafLab/ArchR) and Seurat v4 (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bigwig track format to visualise accessibility profiles along the genome and tab separated values files and matrix files
Library strategy: scMultiome

source_name: CN3/4, CN7, CN12, SMN e11.5 GFP-positive

extract_protocol:
GFP positive cells FACS purified from e11.5 cells
10x Genomics scMultiome chemistry


title: xen_wt_rep3


title: HDF1_shCtrl_Input

value: skin

value: Human dermal fibroblasts

value: Without AR silencing


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 3

value: 10 uM cip


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 2


title: HDF1_shCtrl_LaminA/C ChIP

value: Lamin A antibody + Lamin C antibody [EPR4100], Abcam; Cat# ab108595

value: With AR silencing


title: CN347SMN_e11.5_R1_GEX

value: CN3/4, CN7, CN12, SMN e11.5 GFP-positive


title: xen_c5-c6d_rep2


title: es_c7-c10d_rep3

value: blastocyst derived ES cells

value: ES


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with calcium replicate 1


title: HDF1_shCtrl_pSer301 ChIP

value: Phospho-Lamin A/C (Ser301) Antibody, Affinity; Cat# AF7177


title: CN347SMN_e11.5_R1_ATAC

value: WILDTYPE


title: Visium, Human MI (V11)

city: La Jolla

first: Kevin

middle: Robert

last: King

address: 9500 Gilman Dr.

department: Medicine

institute: UCSD

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v6.1.1  or Space Ranger v1.3.1
Further processing was done with Seurat v4.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using SCTransform v2 from Seurat R package version 4.3
Assembly: refdata-gex-mm10-2020-A; refdata-gex-GRC38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
Sections obtained from mice were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomics kit for Fresh/Frozen samples (10x Genomics). Samples were immediately snap-frozen in OCT using isopentane that was cooled in a liquid nitrogen bath. For cryosectioning, samples were equilibrated to −22 °C. 10 μm thick short axis sections were cut from the blocks onto Visium slides (10X Genomics) and processed according to the manufacturer’s protocol. Tissue permeabilization time was optimized at 30 minutes for infarcted mouse hearts. Hematoxylin and eosin (H&E) images generated during the Visium protocol were captured at 20x magnification on Nikon Eclipse Ti2-E widefield microscope and exported as tiled tiffs for analysis. Libraries were sequenced on the Illumina NovaSeq platform, and resulting data were processed using SpaceRanger (v.1.2.2, 10X Genomics)
Single-nucleus RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (10X Genomics). Spatial transcriptomics assays were barcoded based on tissue-covered capture spot and library preparation was performed with 10X Genomics using dual-end indices. Paired end sequencing was performed on an Illumina Novaseq instrument. Low-level analysis, including demultiplexing, mapping to a reference transcriptome (mm10-2020-A or GRCh38-2020-A), and eliminating redundant UMIs, was performed with Cell Ranger 6.1.1 pipeline for 10X samples.

value: Cardiac

value: 45-year-old male

value: STEMI,LAD occlusion


title: CN347SMN_e11.5_R2_GEX


title: Delta-TRRAP_ChIPseq_H2AZac_Rep2

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Delta-TRRAP EP400, H2AZac, rep2

data_processing:
ChIP-Seq read alignment with Bowtie2 (version 2.4.5) with the following options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Bowtie2 .sam output converted to .bam with samtools2 (version 1.15.1)
.bam files sorted and indexed with samtools2 (version 1.15.1)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.1) with the following options: --normalizeUsing RPKM --extendReads --ignoreDuplicates
Irreproducible Discovery Rate (IDR) analysis: macs2 (version 2.2.7.1) peak calling with a liberal p-value cutoff (-p 1e-3); peaks sorted by pValue before running IDR (version 2.0.3) with the following options: --input-file-type narrowPeak --rank p.value
Differential peak calling with MACS2 bdgdiff analysis: macs2 (version 2.2.7.1) peak calling with --nomodel and fixed fragment size (--extsize 191); effective sequencing depth obtained from macs2 output and used to run macs2 bdgdiff with the foolowing options: -l 250 -g 150
Peak coordinates merged and/or intersected with bedtools (version 2.30.0) or bedops (version 2.4.41)
ChIP-Seq heatmaps generated with deepTools (version 3.5.1) computeMatrix and plotHeatmap tools
Assembly: hg38
Supplementary files format and content: bdgdiff .bed files: contain coordinates of unchanged (common), depleted (cond 1) or enriched (cond2) ChIP-seq peaks in EPC1 mutants (HSA-6mut or Delta-TRRAP) compared to WT EPC1. The last column in the file represent the log10 likelihood ratio to show how likely the observed signal in one or the other condition in a particular region is from that condition comparing to the other condition.The higher the value, the greater the difference. Only highly reproducible peaks (IDR score <=0.05) are included in the list (reproducible IDR and bdgdiff peaks intersected with bedops --element-of 25%)
Supplementary files format and content: *.bw files: coverage files generated with deepTools

growth_protocol: RPMI medium 1640 1x, 5% Newborn Calf Serum (Thermo Fisher Scientific 16010159), 1% GlutaMAX

extract_protocol:
Chromatin was isolated from crosslinked nuclei through lysis and sonication, and histone-DNA complexes were pulled-down with antibodies.
KAPA Hyper Prep kit (Roche, 07962363001) according to manufacturer's instructions

treatment_protocol: 500 nM dTAGV-1 for 24h before processing for ChIP

value: Lymphoblast

value: endogenous EP400-dTAG + exogenous Delta-TRRAP EP400

value: H2A.Zac (Diagenode C15410173)


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 3

value: Not applicable

value: neg

value: Calcium


title: SMN_e11.5_R2

data_processing:
Basecalling Illumina NextSeq 500
bcl outputs were converted to fastq using bcl2fastq conversion software (Illumina)
Bulk ATAC sequencing data was processed  by running the .fastq files through the Encode ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) using default parameters.
To analyze peaks for each bulk sample, Irreproducible Discovery Rate (IDR) optimal peaks were used , generated between pseudoreplicates or biological replicates when appropriate.
After generating peaksets for each bulk sample, a bulk master peakset was created by concatenating all the individual peaksets and merging with bedtools merge. We further generated bulk peaksets specific to each sample using bedtools subtract, allowing for ≤ 50% overlap between peaks.
Assembly: mm10
Supplementary files format and content: .bam binary file containing aligned fragments
Supplementary files format and content: .bw bigwig track format to visualise accessibility profiles along the genome

source_name: SMN e11.5 GFP-positive

extract_protocol:
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
Standard Illumina chemistry

value: SMN e11.5 GFP-positive


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 2


title: es_c7-c10d_rep1

value: E3.5 blastocyst


title: Delta-TRRAP_ChIPseq_input_Rep2

description: Delta-TRRAP EP400, input, rep2


title: Negatively supercoiled pBR322 DNA cleaved by topo IV with cip replicate 1


title: Delta-TRRAP_ChIPseq_H2AZ_Rep2

description: Delta-TRRAP EP400, H2AZ, rep2

value: H2A.Z (Abcam ab4174)


title: SMN_e11.5_R1


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 3

value: 10 uM cip


title: es_c5-c6d_rep3

value: blastocyst derived ES cells


title: SMN_e10.5_R2

source_name: SMN e10.5 GFP-positive

value: SMN e10.5 GFP-positive


title: es_c5-c6d_rep4

value: ES


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 2

source_name: Synthetic plasmid


title: SMN_e10.5_R1

value: WILDTYPE


title: CN7neg_e11.5_R2

source_name: CN7 e11.5 GFP-negative

value: CN7 e11.5 GFP-negative


title: es_c5-c6d_rep1


title: WT_ChIPseq_H2AZ_Rep2

description: WT EP400, H2AZ, rep2

value: endogenous EP400-dTAG + exogenous WT EP400


title: Negatively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 1


title: WT_ChIPseq_input_Rep2

description: WT EP400, input, rep2


title: Negatively supercoiled pBR322 DNA not treated by any cutting enzyme replicate 2

value: No enzyme


title: es_c7-c10d_rep2


title: es_wt_rep7

value: wt


title: Delta-TRRAP_ChIPseq_H2AZ_Rep1

description: Delta-TRRAP EP400, H2AZ, rep1

value: Lymphoblast

value: endogenous EP400-dTAG + exogenous Delta-TRRAP EP400


title: Delta-TRRAP_ChIPseq_H2AZac_Rep1

description: Delta-TRRAP EP400, H2AZac, rep1

value: H2A.Zac (Diagenode C15410173)


title: CN7neg_e11.5_R1


title: CN7_e11.5_R1

value: CN7 e11.5 GFP-positive


title: Delta-TRRAP_ChIPseq_input_Rep1

description: Delta-TRRAP EP400, input, rep1


title: es_wt_rep6


title: WT_ChIPseq_H2AZac_Rep2

description: WT EP400, H2AZac, rep2


title: es_wt_rep5


title: Negatively supercoiled pBR322 DNA not treated by any cutting enzyme replicate 1

value: Not applicable

value: neg


title: Usf2 KO MEF, Amino acid starvation media, rep2

description:
KO_AAS_2
readcounts_AAS.txt

source_name: MEF

value: MEF

value: Mouse Embryonic Fibroblasts

value: Usf2 KO

value: Amino acid starvation


title: es_c5-c6d_rep2

value: E3.5 blastocyst

value: blastocyst derived ES cells


title: WT_ChIPseq_H2AZ_Rep1

description: WT EP400, H2AZ, rep1

value: H2A.Z (Abcam ab4174)


title: WT_ChIPseq_H2AZac_Rep1

description: WT EP400, H2AZac, rep1


title: CN7_e10.5_R2

value: CN7 e10.5 GFP-positive

value: WILDTYPE


title: es_wt_rep4

value: ES


title: Usf2 KO MEF, Normal media, rep2

description:
KO_CTL_2
readcounts_AAS.txt

value: Normal


title: Usf2 KO MEF, Amino acid starvation media, rep1

description:
KO_AAS_1
readcounts_AAS.txt


title: WT_ChIPseq_input_Rep1

description: WT EP400, input, rep1

value: Lymphoblast

value: endogenous EP400-dTAG + exogenous WT EP400


title: CN3_e11.5

source_name: CN3 e11.5 GFP-positive

value: CN3 e11.5 GFP-positive


title: es_wt_rep1

value: wt


title: CN7_e11.5_R2

value: CN7 e11.5 GFP-positive


title: CN7_e10.5_R1


title: 7835-b-total

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: counts_per_sample_acute_total_brain_041223.csv

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline. The analyzed DeSeq2 results were uploaded on the web-based application called iPathway Guide and significantly upregulated and downregulated genes and pathways were identified. The log2fold change threshold was >0.6 and the p-value threshold was <0.05 was applied.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: brain

growth_protocol: Endothelial RNA isolation was performed with modified established TRAP assay protocols(7, 11). Protocol buffer solutions are listed in Supplemental Table. Mice were euthanized with an overdose of pentobarbital. The chest cavity was opened immediately after confirmation of the absence of a paw reflex, and mice were subjected to an intracardiac perfusion with ice-cold HBSS containing 100 μg/ml CHX for 2 minutes at a rate of 5 ml/min. Brains were immediately removed and placed in plates containing 1 ml of dissection buffer and minced with razor blades pre-rinsed with RNAse Away solution. Approximately 100 mg of minced tissue was moved to RNAse-free tubes and lysed using RNAse-free disposable pestles. Samples were then centrifuged at 4 °C, 2000x g for 10 minutes. The supernatant was removed to a new tube and then 1/9 volume of 10% Igepal and 1/9 volume of 300 mM DHPC were added. Tubes were mixed by inversion several times and incubated for 5 minutes on ice. Then, samples were centrifuged at 4 °C 20,000x g for 10 minutes. 50 μl of the supernatant was transferred to a new tube for processing total RNA and the rest was transferred to another new tube for ribosome pulldown for endothelial-specific RNA. For total RNA, 500 μl of Trizol were added to each tube and RNA extraction was conducted with 100 μl of Chloroform. Then supernatant was moved to RNeasy Micro spin columns and an equal volume of 70% EtOH (approx. 350μl) was added to purify RNA by following the manufacturer’s instructions. For the TRAP RNA, supernatants were incubated with prewashed Dynabeads on a nutating rocker for 15 minutes at RT to remove non-specific binding to the beads, and magnets were used for separation. The supernatant was then incubated with Dynabeads bound to anti-EGFP antibodies on a nutating rocker for 45 minutes at 4 °C. Followed by the washes with RNA buffer, the beads reached RT and then incubated for an extra 5 minutes in RLT buffer containing β-mercaptoethano

extract_protocol:
RNA was then purified using RNeasy Micro spin columns following the manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: Acute systemic inflammation was induced by a single IP injection of 250μg LPS dissolved in 200μl of sterile saline solution. Control mice were injected with 200μl of sterile saline solution

value: brain

value: total cells

value: saline


title: es_wt_rep2


title: Visium, Ruptured MI, biol rep4 (V30)

value: Cardiac

value: WT

value: MI surgery


title: Usf2 KO MEF, Normal media, rep1

description:
KO_CTL_1
readcounts_AAS.txt

value: MEF

value: Mouse Embryonic Fibroblasts

value: Usf2 KO


title: es_wt_rep3

value: E3.5 blastocyst

value: blastocyst derived ES cells


title: MCF10AT1, rep2

first: Roberto

last: Rossini

address: Blindernveien 31

data_processing:
nf-core/hic v2.0.0
Samples were processed using a modified version of nf-core/hic v2.0.0 (see manuscript for more details).
TADs were called using HiCExplorer v3.7.2.
Subcompartments were called using a modified version of dcHiC d4eb244.
TAD cliques were identified using robomics/call_tad_cliques v0.3.1.
Chrom3D simulations were performed using a patched version of Chrom3D v1.0.2.
CNVs were detected using HiNT v2.2.8.
Assembly: hg38
Supplementary files format and content:
TSV containing the list of valid pairwise interactions
CRAM with the alignments produced by nf-core/hic
HIC contact matrix
MCOOL contact matrix
TSV with TADs called at 500kbp resolution
TSV with TADs called at 100kbp resolution
TSV with TADs called at 50kbp resolution
TSV with TADs called at 20kbp resolution
TSV with TADs called at 10kbp resolution
TSV with TADs called at 500kbp resolution (merged replicates)
TSV with TADs called at 100kbp resolution (merged replicates)
TSV with TADs called at 50kbp resolution (merged replicates)
TSV with TADs called at 20kbp resolution (merged replicates)
TSV with TADs called at 10kbp resolution (merged replicates)
TSV with insulation scores at 500kbp
TSV with insulation scores at 100kbp
TSV with insulation scores at 50kbp
TSV with insulation scores at 20kbp
TSV with insulation scores at 10kbp
TSV with insulation scores at 500kbp (merged replicates)
TSV with insulation scores at 100kbp (merged replicates)
TSV with insulation scores at 50kbp (merged replicates)
TSV with insulation scores at 20kbp (merged replicates)
TSV with insulation scores at 10kbp (merged replicates)
HIC contact matrix (merged replicates)
MCOOL contact matrix (merged replicates)
TSV with the mapping report produced by nf-core/hic
BEDGRAPH with the compartment PCA computed at 10kbp
BEDGRAPH with the compartment PCA computed at 20kbp
BEDGRAPH with the compartment PCA computed at 50kbp
BEDGRAPH with the compartment PCA computed at 100kbp
BEDGRAPH with the compartment PCA computed at 200kbp
BEDGRAPH with the compartment PCA computed at 500kbp
BEDGRAPH with the subcompartments computed at 10kbp
BEDGRAPH with the subcompartments computed at 20kbp
BEDGRAPH with the subcompartments computed at 50kbp
BEDGRAPH with the subcompartments computed at 100kbp
BEDGRAPH with the subcompartments computed at 200kbp
BEDGRAPH with the subcompartments computed at 500kbp
TAR file with the IGV report generated by dcHiC at 10kbp
TAR file with the IGV report generated by dcHiC at 20kbp
TAR file with the IGV report generated by dcHiC at 50kbp
TAR file with the IGV report generated by dcHiC at 100kbp
TAR file with the IGV report generated by dcHiC at 200kbp
TAR file with the IGV report generated by dcHiC at 500kbp
BED file with the list of TADs used to compute TAD cliques
TSV with the list of TAD cliques
TAR file containing Chrom3D models
TAR file containing the CNVs called using HiNT

source_name: mammary gland

growth_protocol: MCF10A, MCF10AT1, and MCF10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% horse serum (MCF10A and MCF10Ca1a) or 2.5% horse serum (MCF10AT1), 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin

extract_protocol: HiC Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics, USA) according to manufacturer instructions. For each cell line (10A, T1, C1) 1 million cells were used per HiC reaction. Cells were fixed with 1.2% formaldehyde for 12 min. All subsequent steps were carried out according to the Arima protocol. Resulting libraries were amplified with 5 PCR cycles and sequenced on an Illumina NovaSeq 6000 instrument in paired-end run with 2 x101 bp.

value: mammary gland

value: epithelial cell

tag: disease

value: breast cancer


title: MCF10Ca1a, rep2


title: 7832-b-total


title: MCF10AT1, rep1


title: Usf2 WT MEF, Amino acid starvation media, rep2

description:
WT_AAS_2
readcounts_AAS.txt

data_processing:
Reads were mapped to GRCm38 by STAR (v2.7.10b).
Read counts were generated by featureCounts (v2.0.3).
The differential gene expression analysis was performed using Bioconductor package DESeq2 (v1.38.3).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files, read counts from featureCounts

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen)
The illumina RNA libraries for RNA-seq were prepared by TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol. The DNBseq RNA library construction method and sequencing process are carried out according to the following steps: 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Usf2 WT

value: Amino acid starvation


title: MCF10Ca1a, rep1


title: 7822-b-total

value: wt


title: MCF10A, rep2


title: 7834-b-total

value: brain

value: LPS


title: NCI-H1299,input

city: Zhengzhou

first: Cai

last: Zhang

address: 1#, Jianshedong Road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Basecalling were performed using bcl2fastq v2.17 For Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score >30 with Trimmomatic v0.36,  discarding reads left with adaptor and <20 bp.
ChIP-seq reads were aligned to UCSC hg38 genome using Bowtie2 v2.4.4. Only uniquely mapping reads with at most two mismatches were retained.
To creat ChIP-Seq coverage plots, the locations of the mapped ChIP-Seq reads were extended to 150bp to represent sequenced fragments (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.2.7 with the significance cut-off p-value <0.01.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of NDA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: RPMI-1640, 10% fetal bovine serum, 2mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.Cells were cultured in a humidiﬁed 5% CO2 incubator at 37℃.

extract_protocol:
NCI-H1299 cells were cross-linked with 1% formaldehyde (vol/vol) for 10 min at room temperature. After quenching and cell lysis,chromatin was sonicated using a E220 focused-ultrasonicator (Covaris), and immunoprecipitated with anti-H3K18la (PTM Bio, #PTM-1427RM) at 4 °C. The DNAs were extracted by phenol-chloroform method.
The high-throughput DNA sequencing library was prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech). Library products of 200-500 bp in length were enriched, quantified and sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: Human non-small cell lung cancer


title: Usf2 WT MEF, Amino acid starvation media, rep1

description:
WT_AAS_1
readcounts_AAS.txt


title: Visium, anti-Ifnar-ab Day 3 MI (V34)

value: Cardiac

value: MI surgery + antibody treatment


title: SARS-CoV-2-MTDB-deg

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequence reads were aligned to the Wuhan-hu1 genome using minimap2 with parameters “-ax splice -N32 -un -k13”. Bigwig files were generated by Deeptools bamCoverage using parameters "--binSize 50 --normalizeUsing None"
Genome_build: wuhan-hu1

organism: Severe acute respiratory syndrome coronavirus 2

source_name: MTDB-deg

growth_protocol: Vero CCL-81 cells at 80% confluency were incubated with SARS-CoV-2 inoculum for 1 h at 37 ºC. After incubation, the inoculum was removed and DMEM medium supplemented with 2.5% FCS was added for 24 h, or until samples were harvested

extract_protocol: 500 ng of SARS-CoV-2 RNA was incubated with or without 100 µM of MTDB-deg in 1x HEPES buffer for 2 h at 37 ºC with mild agitation. The samples were then prepared for sequencing following the manufacturer’s protocol for Direct RNA Sequencing (SQK-RNA002, ONT). The prepared libraries were loaded on FLO-MIN106D flow cells (ONT) and sequenced on a MinION Mk1C device (ONT).

value: MTDB-deg


title: Usf2 WT MEF, Normal media, rep2

description:
WT_CTL_2
readcounts_AAS.txt

value: MEF

value: Normal


title: Visium, Sting-/- Day 3 MI (V32)

value: Sting-/-

value: MI surgery


title: Visium, Ruptured MI, biol rep3 (V29)

value: WT


title: CN3_e10.5

source_name: CN3 e10.5 GFP-positive

value: CN3 e10.5 GFP-positive

value: WILDTYPE


title: 7443-b-total

value: total cells


title: Usf2 WT MEF, Normal media, rep1

description:
WT_CTL_1
readcounts_AAS.txt

value: Mouse Embryonic Fibroblasts

value: Usf2 WT


title: 7816-b-total

value: wt


title: SARS-CoV-2-Control

source_name: Control

value: Control


title: Visium, Cgas-/- Day 3 MI (V35)

value: Cgas-/-


title: PXPS_C2

city: Toronto

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Quality of reads assessed by FastQC tool
The reads were aligned to the mouse reference genome GRCm38.p6 using Star aligner
RNA-Seq reads were counted using HtSeq and differential expression was analysed by DEseq2
Assembly: Gencode (Version M25 / GRCm38.p6)
Supplementary files format and content: count matrix (.txt file)

organism: Mus

source_name: Tumour

extract_protocol:
The total RNA was extracted with RNeasy kit (Qiagen, 74004) as per manufacturers instructions
RNA converted into cDNA library using TruSeq Stranded Total RNA kit (Illumina) using manufacturers instructions.

value: Tumour


title: Visium, Ruptured MI, biol rep1 rep2 (V16)

value: Cardiac


title: SARS-CoV-2-TDB-deg

source_name: TDB-deg

value: TDB-deg


title: NCI-H1299,H3K18la,ChIP rep2

value: Human non-small cell lung cancer

value: H3K18la(PTM BIO, #PTM-1427RM)


title: NCI-H1299,H3K18la,ChIP rep1


title: PXPS_C1