title: Wildtype male mouse 7

first: Joseph

last: Dougherty

address: 4370 Duncan Ave

department: Genetics

description:
Library name: WT_M_7
ScaleBio Single Cell RNA Sequencing Kit

data_processing:
Base calls were converted to fastq format and demultiplexed by Index1 barcode by GTAC@MGI for each sample. We combined and gzipped the files into one R1 and R2 file and used a perl script to create the combined  I1 file. Fastq files were demultiplexed, combined, and processed using ScaleBio's nextflow pipeline (nf v.23.04.4, ScaleBio Seq Suite: RNA Workflow v1.5-beta2; https://github.com/ScaleBio/ScaleRna/tree/v1.5.0-beta2). Filtered count matrices were imported using Seurat v4.3.0 to create Seurat objects for downstream analyses.
Quality control removed multiplets (DoubletFinder v2.0.3) and filtered for nuclei with >800 UMIs, 300-7000 genes, and <1% mitochondrial reads. The final dataset contained 138,033 nuclei (median: 2530 UMIs, 1447 genes per nucleus). Count matrices were log-normalized (scaling factor: 10,000), and top 3,000 variable genes were identified using VST. PCA was performed on these features (100 PCs calculated, top 50 used). Dimensionality reduction used UMAP. Clustering was performed using Louvain algorithm (resolution 0.01-2.4), with optimal resolution (2.0) determined by clustree v0.5.0.
Cluster markers were identified using FindAllMarkers (logfc.threshold=0.5, min.pct=0.25) and visualized via heatmaps. Filtered raw count data was converted to h5ad format with  Ensembl IDs using org.Mm.eg.db v.3.16.0 and analyzed using MapMyCells (RRID: SCR_024672) to align the nuclei with the 10X Whole Mouse Brain (CCN20230722) reference. For orthogonal annotation, nuclei were also projected onto HypoMap using mapscvi v.0.02 (https://github.com/lsteuernagel/mapscvi). Mapping results–class and subclass annotations and bootstrapping probabilities from MapMyCells and projected labels and prediction probability from HypoMap–were integrated into the Seurat object metadata. Based on annotations, glial cells comprised only 10,577 nuclei (8.2%) of the dataset.
A neuronal-only subset was created for further analysis, (124,601 nuclei; median: 2660 UMIs, 1498 genes) and underwent reprocessing as described above. Re-clustering with 50 PCs at resolution 1.8 yielded 75 initial clusters.  Marker genes were identified using FindAllMarkers as above. To refine our clustering, we performed hierarchical clustering and manually compared annotation results across MapMyCells, HypoMap, and FindAllMarkers marker genes. We merged 8 cluster pairs based on shared marker profiles and removed 2 glial clusters, resulting in 65 final neuronal clusters. Clusters were annotated following Allen Brain Institute taxonomy (Miller et al, eLife, 2020): predicted location, marker genes (or "Mixed" when nonspecific), and neurotransmitter type (Glut/Gaba).
Assembly: mm10
Supplementary files format and content: MYTsocop-deep_S1_I1_001.fastq.gz, combined index file for all samples
Supplementary files format and content: MYTsocop-deep_S1_R1_001.fastq.gz, combined R1 file for all samples
Supplementary files format and content: MYTsocop-deep_S1_R2_001.fastq.gz, combined R2 file for all samples
Supplementary files format and content: ScaleBio Seq Suite: RNA Workflow output: SAMPLE_ID_matrix.mtx.gz
Supplementary files format and content: ScaleBio Seq Suite: RNA Workflow output: SAMPLE_ID_features.tsv.gz
Supplementary files format and content: ScaleBio Seq Suite: RNA Workflow output: SAMPLE_ID_barcodes.tsv.gz
Supplementary files format and content: Processed, filtered, and cell-type annotated seurat object: combined_neuronal_seurat.rds

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Mice were anesthetized and brains were quickly extracted, meninges removed, and the hypothalamus was dissected using 3D printed molds to allow for precise extraction of tuberal hypothalamus from A/P -0.5 mm to -2.6 mm, M/L -1.5mm and 1.5mm and DV of 4-6mm. Dissected hypothalamus were flash frozen in liquid nitrogen, and stored at -80°C. Molds will be made available on Tinkercad.
Nuclei were isolated from flash frozen tissue. Samples were processed in 9 batches of 4, counterbalanced for sex and genotype. Brain tissues were Dounce homogenized in ice-cold homogenization buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 mM DTT, 1X complete EDTA-free Protease Inhibitor (Roche 4693132001), and 0.2U/ul RNasin Inhibitor (Promega N2515)) with a 2 ml KIMBLE KONTES Dounce Tissue Grinder (DWK 885300-002) with 15 strokes with the “A” large clear ance and 15 strokes of the “B” small clearance pestle. The homogenate was transferred to a 15 ml LoBind Eppendorf centrifuge tube (Eppendorf 0030122208). Walls of the homogenizer tubes were washed with 1 ml of ice-cold homogenization buffer and combined with the homogenate. Nuclei were pelleted by centrifugation in a swinging bucket rotor (Eppendorf S-4-104) at 500 × g for 5 mins at 4 °C. Pellets were resuspended in ice-cold 1 ml homogenization buffer. Density gradient centrifugation was performed to purify the nuclei from debris and myelin from tissue dissociation. An ice-cold 50% iodixanol-PBS working solution was prepared by diluting the stock solution of 60% w/v Optiprep (Sigma-Aldrich D1556) with DPBS (ThermoFisher 14190136). A 35% (w/v) iodixanol solution was then made by diluting the 50% iodixanol with DPBS. To make the 25% Iodixanol layer, 1 ml ice-cold 50% iodixanol was added to 1 ml of the resuspended pellets from the first centrifugation. This was carefully layered on top of 2 ml 35% iodixanol in a clear polycarbonate tube (Beckman Coulter 355672) and centrifuged at 10,000 × g for 30 min at 4 °C in a S0410 swinging bucket rotor (Beckman Coulter 364660) with no braking using an Allegra 64R (Beckman Coulter 367586). After centrifugation, myelin and debris at the top of the 25% iodixanol layer were aspirated and discarded. Up to 2 mL of purified nuclei from the interface of the 25% and 35% iodixanol layers were collected using a low retention P1000 pipette and transferred to a clean 15 ml LoBind Eppendorf centrifuge tube. The volume was brought up to 6 ml with nuclei wash and resuspension buffer (1% bovine serum albumin (Sigma A1595), 0.2 U/uL RNase Inhibitor (Promega N2515), in calcium- and magnesium-free DPBS) and pelleted by centrifuging at 500 × g for 5 min at 4 °C. Supernatant was carefully removed and discarded, while the pellet was washed with nuclei wash buffer and centrifuged at 500 × g for 5 min at 4 °C to ensure removal of carryover iodixanol. The pellet was then resuspended in 1x ice-cold DPBS, filtered through a 40 μm Flowmi cell strainer, and manually counted using a hemocytometer with propidium iodide. 200 k–1.7 M nuclei were used as input for the ScaleBio Sample Fixation Kit (Scale Biosciences 2020001) according to the manufacturer’s low sample input protocol. After fixation, the nuclei were manually counted once more and checked for quality using a microscope with a 60× objective. The nuclei were then stored at −80 °C until all samples had been collected and fixed.
Libraries were prepared from cohort 1 (10 male WT, 10 male Hets, 10 female WTs, 6 female Hets). Frozen fixed nuclei were thawed on ice and counted twice via hemocytometer. Using the ScaleBio Single Cell RNA Sequencing Kit v1.0 (Scale Biosciences 2020008), all 36 samples were prepared in one batch. Nuclei were loaded at 10,000 per well (2-3 wells/sample) to add RT barcodes as sample identifiers. Pooled nuclei were distributed across the 384-well plate for Ligation Barcode addition, then pooled again with 1600 nuclei per well for second strand synthesis. After tagmentation and indexing PCR, libraries were pooled (5μl each), cleaned with 0.8X SPRIselect beads (Beckman Coulter B23317), and fragment size/concentration quantified using High Sensitivity D5000 Screentape (Agilent) and NEBNext Library Quant Kit (New England Biolabs E7630S). Sequencing was performed on a Novaseq X Plus (Illumina; shared 25B flowcell) to a target depth of 20,000 reads per nucleus.

value: Brain

tag: age (days)

value: male

tag: strain

tag: brain region

value: tuberal hypothalamus and thalamus


title: Wildtype male mouse 9

status: Public on Mar 11 2025

type: SRA

city: St. Louis

state: MO

country: USA

institute: Washington University in St. Louis

description:
Library name: WT_M_9
ScaleBio Single Cell RNA Sequencing Kit

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue

tag: Sex

tag: genotype

value: WT


title: Wildtype male mouse 6

description:
Library name: WT_M_6
ScaleBio Single Cell RNA Sequencing Kit


title: HDL069-Col-CD8-TEM

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: mRNA

library_source: transcriptomic

data_processing:
For scRNA-seq, we aligned the reads corresponding to each sample index to the GRCh38 genome / GENCODE v.24 transcriptome annotation with STAR v2.5.0 (23104886) after removing 3’ poly(A) tails from read 2 (anything >7 A’s) and discarding any resulting fragments < 25 nts in length.
We then constructed an address for each read with a unique, strand-specific, exonic alignment comprised of the cell-identifying barcode, unique molecular identifier (UMI) barcode, and gene identifier.
Next, we applied the algorithm described by Griffiths et al. to correct of index swapping between clusters on the Illumina flow cell (29991676). Finally, we collapsed PCR duplicates using UMIs and corrected errors in both the cell-identifying and UMI barcodes to generate an initial molecular count matrix.
To identify cell barcodes associated with cells, we used the EmptyDrops algorithm (Lun et al., Genome Biol, 2019) and then further filtered the resulting count matrix to remove cells above of the 95% confidence interval for the fraction of molecules aligned to the mitochondrial genome (possible dead cells), the fraction of molecules aligned to introns (possible nuclei), and the number of molecules per gene (filters red blood cells and other artifacts). We also pre-emptively removed cells with sufficiently low coverage that they would interfere with unsupervised clustering. To identify highly variable genes for clustering, we use the drop-out curve method previously described (Levitin et al., Mol Sys Bio, 2019), removing all cells in which fewer than three highly variable genes were detected.
For bulk RNA-seq, adapter-trimmed paired-end reads were aligned to the GRCh38 reference genome with ENSEMBL transcriptome annotation using the STAR aligner v.2.5.2b. Read quantification was performed using the featureCounts program in the Subread v.1.5.2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: InfantAdult_Tcells.scrnaseq.cts.txt: For scRNA-seq, the processed data are in a single, tab-delimited text file that contains the gene expression counts for each individual cell.
Supplementary_files_format_and_content: *.counts.txt: For each bulk RNA-seq sample, there is a tab-delimited text file containing the output of featureCounts.

molecule: total RNA

organism: Homo sapiens

source_name: Colon

extract_protocol:
For single-cell RNA-seq, RNA was extracted and poly(A) mRNA was converted into barcoded cDNA using the 10x Genomics Chromium platform. For bulk RNA-seq, RNA was extracted using the Qiagen RNeasy Micro Kit.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell Gene Expression 3' v2 chemistry for donors D363, D370, Adult Donor A, Adult Donor B, HDL049, HDL055, D381 and the 10x Genomics Single Cell Gene Expression 3' v3 chemistry for donors D457, D471, HDL082. For bulk RNA-seq, library preparation was done using the SMART-Seq® ultra-low input RNA kit (Takara bio).

treatment_protocol: For both bulk and single-cell RNA-seq, cells were dissociated from each tissue. Organ donor samples (whole lungs, intestinal blocks, spleen, blood) in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 24-36 hours of procurement. Single cell suspensions were obtained from spleen, lung, intestine, and lymph node samples using mechanical and enzymatic digestion as previously described (Thome et al., Nature Med, 2016; Sathaliyawala et al., Immunity, 2013; Granot et al, Immunity, 2017). Lymph nodes were isolated by dissection from the mesentery of intestinal blocks and the tracheobronchial tree of the lung. Isolated lymph nodes and spleen samples were placed in complete media (IMDM (Gibco, ref #12440-053) +1% PSQ (100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, GeminiBio, cat #c400-110) + 10% FBS (GeminiBio, cat #100-106)) and mechanically disrupted with scissors and double filtered through 100μm strainers. Suspensions were washed with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS) followed by red blood cell lysis (ACK lysing buffer, Gibco, ref A10492-01), then resuspended in complete media. Lung parenchyma were separated from the large airways (trachea) using scissors then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNase 0.1mg/mL (Millipore Sigma cat# DN25-5G) on a shaker at 37⁰ for 30 minutes. Intestinal tissue was washed with sterile PBS to remove luminal contents, chopped into pieces using scissors, then placed into digestion media on a shaker at 37⁰ degrees for 30 minutes. Following incubation, lung and intestinal samples were strained and washed with wash buffer. Samples were centrifuged with resultant cell pellet diluted for mononuclear cells isolation by density gradient centrifugation (Lymphocyte Separation Medium, Corning, cat #25-072-CI) followed by resuspension in complete media. Peripheral blood mononuclear cells were isolated from blood samples by density centrifugation. For bulk RNA-seq, CD4 and CD8 TEM cells were isolated by FACS. For scRNA-seq, pan T cells were isolated by negative selection using the EasySep Human T cell Enrichment Kit (STEMCELL Technologies) and dead cells were removed using a column-based Dead Cell Removal Kit (Miltenyi). T cells were rested overnight at 37C for 16 hours in complete medium or activated with Human CD3/CD28 T cell Activator (STEMCELL) 16 37C for 16 hours prior to scRNA-seq.

value: Colon

tag: cell type

value: T cells

tag: age (years)

value: Male

tag: stimulation

tag: donor id

tag: cell isolation

value: CD8 Effector Memory T cells by FACS

tag: assay type

value: bulk RNA-seq


title: HDL069-Ile-CD8-TEM

description: mRNA

source_name: Ileum

value: Ileum


title: HDL047-Lg-CD8-TEM

description: mRNA

source_name: Lung

value: Lung


title: H1,NCP,HP1bSUV,3,1rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

description:
Library name: H1_NCP_HP1bSUV_3_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent

library_source: genomic

data_processing:
Bowtie2 alignment
Coverage and read counts were computed using custom python scripts
Nucleosome peak calling using custom python scripts
Condensabilities for each genomic bins and each nucleosomes were computed
Assembly: hg38 (Human), mm10 (Mouse)
Supplementary files format and content: Condensability scores for 10kb, 1kb genomic bins and individual nucleosome resolution
Library strategy: Condense-seq

molecule: genomic DNA

extract_protocol:
DNA library were prepared using NEBNext Ultra II kit
Condense-seq

treatment_protocol: Native nuclesomes were purified from cells using HAP (hydroxy apartite purification) protocol and genomic DNA were purified by phenol chloroform extraction

tag: cell line

tag: treatment


title: HDL047-Ile-CD8-TEM

description: mRNA


title: HDL073-Ile-CD8-TEM

description: mRNA


title: Wildtype male mouse 8

description:
Library name: WT_M_8
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,HP1bSUV,2,1rep

description:
Library name: H1_NCP_HP1bSUV_2_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: HDL047-Col-CD8-TEM

description: mRNA


title: HDL046-Lg-CD8-TEM

description: mRNA

value: Female


title: H1,NCP,HP1bSUV,1,1rep

description:
Library name: H1_NCP_HP1bSUV_1_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: Wildtype male mouse 4

description:
Library name: WT_M_4
ScaleBio Single Cell RNA Sequencing Kit


title: HDL071-Jej-CD8-TEM

description: mRNA

source_name: Jejunum

value: Jejunum


title: HDL047-Jej-CD8-TEM

description: mRNA


title: Wildtype male mouse 5

description:
Library name: WT_M_5
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,HP1bSUV,0,1rep

description:
Library name: H1_NCP_HP1bSUV_0_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: HDL042-Lg-CD8-TEM

description: mRNA


title: H1,NCP,HP1a,5,1rep

description:
Library name: H1_NCP_HP1a_5_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: HDL042-Ile-CD8-TEM

description: mRNA


title: HDL042-Jej-CD8-TEM

description: mRNA


title: HDL069-Jej-CD8-TEM

description: mRNA


title: HDL040-Jej-CD8-TEM

description: mRNA


title: HDL040-Lg-CD8-TEM

description: mRNA


title: Wildtype male mouse 3

description:
Library name: WT_M_3
ScaleBio Single Cell RNA Sequencing Kit


title: Wildtype male mouse 2

description:
Library name: WT_M_2
ScaleBio Single Cell RNA Sequencing Kit


title: Wildtype male mouse 10

description:
Library name: WT_M_10
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,HP1a,4,1rep

description:
Library name: H1_NCP_HP1a_4_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: HDL040-Ile-CD8-TEM

description: mRNA


title: Wildtype male mouse 1

description:
Library name: WT_M_1
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,HP1a,3,1rep

description:
Library name: H1_NCP_HP1a_3_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: HDL090-Ile-CD4-TEM

description: mRNA

value: CD4 Effector Memory T cells by FACS


title: H1,NCP,HP1a,2,1rep

description:
Library name: H1_NCP_HP1a_2_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: HDL081-Lg-CD4-TEM

description: mRNA


title: Wildtype female mouse 9

description:
Library name: WT_F_9
ScaleBio Single Cell RNA Sequencing Kit

value: female


title: H1,NCP,HP1a,1,1rep

description:
Library name: H1_NCP_HP1a_1_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: Wildtype female mouse 8

description:
Library name: WT_F_8
ScaleBio Single Cell RNA Sequencing Kit


title: HDL081-Jej-CD4-TEM

description: mRNA


title: HDL081-Ile-CD4-TEM

description: mRNA


title: HDL081-Col-CD4-TEM

description: mRNA


title: H1,NCP,HP1a,0,1rep

description:
Library name: H1_NCP_HP1a_0_1rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: HDL078-Lg-CD4-TEM

description: mRNA


title: Wildtype female mouse 6

description:
Library name: WT_F_6
ScaleBio Single Cell RNA Sequencing Kit


title: HDL078-Jej-CD4-TEM

description: mRNA


title: H1,NCP,Ca,5,1rep

description:
Library name: H1_NCP_Ca_5_1rep
Native nucleosome sample, Calcium used as condensing agent


title: HDL078-Col-CD4-TEM

description: mRNA


title: Wildtype female mouse 5

description:
Library name: WT_F_5
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,Ca,0,1rep

description:
Library name: H1_NCP_Ca_0_1rep
Native nucleosome sample, Calcium used as condensing agent


title: HDL074-Jej-CD4-TEM

description: mRNA


title: Wildtype female mouse 4

description:
Library name: WT_F_4
ScaleBio Single Cell RNA Sequencing Kit


title: HDL078-Ile-CD4-TEM

description: mRNA


title: HDL074-Lg-CD4-TEM

description: mRNA


title: HDL074-Ile-CD4-TEM

description: mRNA


title: Wildtype female mouse 3

description:
Library name: WT_F_3
ScaleBio Single Cell RNA Sequencing Kit


title: HDL090-Jej-CD4-TEM

description: mRNA


title: HDL074-Col-CD4-TEM

description: mRNA


title: HDL090-Col-CD4-TEM

description: mRNA


title: H1,NCP,PEG,0,1rep

description:
Library name: H1_NCP_PEG_0_1rep
Native nucleosome sample, PEG 8000 used as condensing agent


title: HDL073-Lg-CD4-TEM

description: mRNA


title: Wildtype female mouse 2

description:
Library name: WT_F_2
ScaleBio Single Cell RNA Sequencing Kit


title: Wildtype female mouse 7

description:
Library name: WT_F_7
ScaleBio Single Cell RNA Sequencing Kit


title: HDL073-Jej-CD4-TEM

description: mRNA


title: Human brain endothelial cells infected with E. coli RS218- replicate 3

city: Gainesville

first: Subhashinie

last: Kariyawasam

state: Florida

address: 1945 SW 16th Ave

department: Comparative, Diagnostic, and Population Medicine

institute: University of Florida

description: Library name: BR3

data_processing:
Raw sequencing reads generated from the NovaSeq X Series platform were analyzed using the CLC Genomics Workbench V 25.0.0 (Qiagen, Redwood City, CA, USA). The quality of the raw reads was assessed, and adapter sequences and low-quality bases (Phred score < 30) were trimmed.  High-quality reads were subsequently mapped to the E. coli RS218 reference genome assembly ASM81734v1 (RefSeq assembly GCF_000817345.1). Gene expression was calculated using the RPKM (reads per kilobase of exon model per million mapped reads), and applying the equation RPKM = number of gene reads/(mapped reads (millions) × gene length (kb). False discovery rate (FDR) was applied to identify statistically significant alterations in gene expression. To identify differential gene expression (DGE) in two groups (treated vs. control), TMM Normalization (Trimmed Mean of M values) described for Whole-Transcriptome RNA-seq Technology was applied.
Assembly: E. coli RS218 reference genome assembly ASM81734v1 (RefSeq assembly GCF_000817345.1)
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: csv files

organism: Escherichia coli

source_name: Whole cell

growth_protocol: The E. coli RS218 strain suspension (OD600 0.2) was incubated separately in CSF, serum, and colonic fluid at 37°C with shaking (200 rpm) for 6 hours. Culture in LB broth under same conditions served as control. For HBEC infection, human cerebral microvascular endothelial cell line ((HBEC-5i) purchased from ATCC® CRL-3245™  and E. coli RS218 were added to the HBEC monolayers at a multiplicity of infection (MOI) of 100:1. The co-culture was incubated at 37°C in a 5% CO₂ atmosphere for 6 hours.

extract_protocol:
Total RNA was extracted using the RiboPure RNA Purification Kit (Invitrogen, Wal-tham, MA, USA) and was further processed for rRNA depletion to enrich for bacterial mRNA using the MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen, Waltham, MA, USA).
RNA libraries were prepared using the TruSeq® Stranded mRNA Library Kit (Illumina Inc., San Diego, CA, USA). Enriched mRNA was fragmented and primed for synthesis of first-strand and second-strand complementary DNA (cDNA). The resulting double-stranded cDNA fragments were adenylated at the 3' ends, ligated to multiple index adapters (TruSeq RNA Combinatorial Dual Indexes; Illumina Inc., San Diego, CA, USA), and enriched through PCR amplification.

value: Whole cell

value: Neonatal Meningitis E. coli

value: Infection in 6 hrs


title: Human brain endothelial cells infected with E. coli RS218- replicate 2

description: Library name: BR2


title: Wildtype female mouse 10

description:
Library name: WT_F_10
ScaleBio Single Cell RNA Sequencing Kit

value: Brain


title: H1,NCP,CoH,0,1rep

description:
Library name: H1_NCP_CoH_0_1rep
Native nucleosome sample, Cobalt Hexammine used as condensing agent


title: Wildtype female mouse 1

description:
Library name: WT_F_1
ScaleBio Single Cell RNA Sequencing Kit

value: tuberal hypothalamus and thalamus


title: HDL073-Ile-CD4-TEM

description: mRNA


title: Human brain endothelial cells infected with E. coli RS218- replicate 1

description: Library name: BR1

value: WT


title: H1,NCP,PEG,6,1rep

description:
Library name: H1_NCP_PEG_6_1rep
Native nucleosome sample, PEG 8000 used as condensing agent


title: H1,NCP,spd,6,1rep

description:
Library name: H1_NCP_spd_6_1rep
Native nucleosome sample, Spermidine used as condensing agent


title: HDL073-Col-CD4-TEM

description: mRNA

value: Colon


title: E. coli RS218 in Cerebrospinal Fluid-replicate 3

description: Library name: CSF3

value: Incubation in 6 hrs


title: HDL071-Lg-CD4-TEM

description: mRNA

value: T cells

value: Male


title: H1,NCP,spd,0,1rep

description:
Library name: H1_NCP_spd_0_1rep
Native nucleosome sample, Spermidine used as condensing agent


title: Myt1l heterozygous male mouse 8

description:
Library name: Het_M_8
ScaleBio Single Cell RNA Sequencing Kit

value: male

value: Het


title: Myt1l heterozygous male mouse 9

description:
Library name: Het_M_9
ScaleBio Single Cell RNA Sequencing Kit


title: E. coli RS218 in Cerebrospinal Fluid-replicate 2

description: Library name: CSF2


title: H1,NCP,CoH,5,1rep

description:
Library name: H1_NCP_CoH_5_1rep
Native nucleosome sample, Cobalt Hexammine used as condensing agent


title: H1,NCP,sp,9,1rep

description:
Library name: H1_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent


title: Myt1l heterozygous male mouse 7

description:
Library name: Het_M_7
ScaleBio Single Cell RNA Sequencing Kit


title: HDL071-Ile-CD4-TEM

description: mRNA

value: Ileum

value: bulk RNA-seq


title: E. coli RS218 in Colonic Fluid-replicate 3

description: Library name: CF3


title: Myt1l heterozygous male mouse 6

description:
Library name: Het_M_6
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,sp,8,1rep

description:
Library name: H1_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,7,1rep

description:
Library name: H1_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent


title: E. coli RS218 in Colonic Fluid-replicate 2

description: Library name: CF2


title: Myt1l heterozygous male mouse 5

description:
Library name: Het_M_5
ScaleBio Single Cell RNA Sequencing Kit


title: H1,NCP,sp,6,1rep

description:
Library name: H1_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent


title: HDL069-Lg-CD4-TEM

description: mRNA

value: Lung


title: H1,NCP,sp,5,1rep

description:
Library name: H1_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: E. coli RS218 in Colonic Fluid-replicate 1

description: Library name: CF1


title: Myt1l heterozygous male mouse 4

description:
Library name: Het_M_4
ScaleBio Single Cell RNA Sequencing Kit


title: Myt1l heterozygous male mouse 3

description:
Library name: Het_M_3
ScaleBio Single Cell RNA Sequencing Kit


title: HDL069-Jej-CD4-TEM

description: mRNA

value: Jejunum

value: CD4 Effector Memory T cells by FACS


title: E. coli RS218 in Serum-replicate 3

description: Library name: S3

value: Whole cell


title: E. coli RS218 in Serum-replicate 2

description: Library name: S2

value: Neonatal Meningitis E. coli


title: HDL069-Ile-CD4-TEM

description: mRNA


title: H1,NCP,sp,4,1rep

description:
Library name: H1_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: Myt1l heterozygous male mouse 2

description:
Library name: Het_M_2
ScaleBio Single Cell RNA Sequencing Kit


title: HDL069-Col-CD4-TEM

description: mRNA


title: H1,NCP,sp,3,1rep

description:
Library name: H1_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: E. coli RS218 in Cerebrospinal Fluid-replicate 1

description: Library name: CSF1


title: Myt1l heterozygous male mouse 10

description:
Library name: Het_M_10
ScaleBio Single Cell RNA Sequencing Kit


title: HDL047-Lg-CD4-TEM

description: mRNA


title: H1,NCP,sp,2,1rep

description:
Library name: H1_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent


title: E. coli RS218 in Serum-replicate 1

description: Library name: S1


title: E. coli RS218 in LB broth-replicate 3

description: Library name: L3


title: HDL071-Jej-CD4-TEM

description: mRNA


title: H1,NCP,sp,1,1rep

description:
Library name: H1_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent


title: HDL047-Jej-CD4-TEM

description: mRNA


title: H1,NCP,sp,0,1rep

description:
Library name: H1_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: Myt1l heterozygous female mouse 6

description:
Library name: Het_F_6
ScaleBio Single Cell RNA Sequencing Kit

value: female


title: HDL071-Col-CD4-TEM

description: mRNA


title: HDL047-Ile-CD4-TEM

description: mRNA


title: E. coli RS218 in LB broth-replicate 1

description: Library name: L1


title: Myt1l heterozygous female mouse 5

description:
Library name: Het_F_5
ScaleBio Single Cell RNA Sequencing Kit

value: Brain


title: NPC_DF2-KO rep2

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

country: China

institute: Zhejiang University

description: the column NPC_DF2-KO rep2'

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQformat, which contains sequence information and corresponding sequencing quality information.
For the initial RNA-seq data, quality evaluation was performed using the FastQC tool (version 0.11.9). This step assessed the overall integrity of the RNA-seq fastq files and identified any potential issues.
The bulk RNA-seq libraries were processed with paired-end sequencing. This was followed by trimming the sequences using cutadapt (version 4.1).
The trimmed reads were aligned to the human genome (hg38) using STAR (version 2.7.10a), organized with samtools (version 1.6), and the read counts were quantified against Gencode (version 41) annotations with featureCounts (version 2.0.1).
Assembly: hg38
Supplementary files format and content: csv: matrix of gene counts of all samples

molecule: polyA RNA

source_name: hESC

extract_protocol:
Total RNA was extracted from hESCs with AG RNAex Pro Reagent (Accurate Biology, AG21101), adhering to the manufacturer’s protocol
Total RNA worked as input for the RNA sample preparation. Sequencing libraries were generated using NEBNext Ultra Libraries Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s protocol and index codes were added to attribute sequences to each sample. Sepecifically, poly-T oligo-attached magnetic beads were used to purified mRNA from total RNA. Fragmentation was applied with divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). M-MuLV Reverse Transcriptase (RNase H) and random hexamer primers were used to create first strand cDNA. RNase H and DNA Polymerase I were then used to synthesise second strand cDNA. The remaining overhangs were transformed into blunt ends by polymerase and exonuclease reactions. To become ready for hybridization, NEB Next Adaptors with hairpin loop structures were ligated after the 3' ends of DNA fragments had been adenylated. Purification of the library fragments was done using the AMPure XP system (Beverly, USA) to select cDNA fragments that were preferably 370–420 bp in length. Subsequently, 3 μL USER Enzyme (NEB, USA) was employed with adaptor-ligated, size-selected cDNA at 37°C for 15 min, and then 5 min at 95 °C before PCR. After that, Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primer were used to carry out PCR. Finally, the PCR products were purified using the AMPure XP system, and the Agilent 5400 system (Agilent USA) was used to evaluate the library quality and quantify the results using QPCR (1.5 nM). The qualified libraries were pooled and sequenced using PE150 technique on Illumina platforms in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and necessary data amount.

value: hESC

value: human embryonic stem cells


title: ZAR1_PAIso-seq2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Obtained hifi reads were segmented into single reads according to the concatenating primer, only the reads between successive barcodes were considered as confident reads. And the segmented reads were splitted into samples according to the barcodes, and the UMI sequences for each reads were extracted at the same time. Then the duplicated reads were removed according to the UMI sequence, and the clean reads were aligned to the mm10 genome (gencode, vM25) by using minimap2 (v2.24), and the information of poly(A) tails of mapped clean-reads was extracted and annotated according to the previous pipeline. The polyA length of each gene was calculated as the geometric average of all reads of the gene.
Assembly: mm10
Supplementary files format and content: pA_length.xlsx

source_name: oocytes

extract_protocol:
100 GV and MII stage oocytes harvested from WT and Zar1/2-/- mice and 100 MI stage oocytes harvested from WT mice were put into PAIso-seq2 library construction as published protocol. In brief, total RNA was extracted with TRIzol Reagent and Direct-zol RNA MicroPrep (Zymo Research, Cat. no. R2060), and the barcode containing adapter were ligated to the 3’-end of mRNA. Then the RNA were purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016).
After being purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016), the RNA were RT into cDNA by the UMI containing template-switching oligo (TSO) primer and the first PCR amplification were proceeded. Then the cDNA from rRNA will be removed by the CRISPR-Cas9 system and the second PCR amplification will be performed to get enough cDNA. Then the cDNA from each sample will be concatenated into long molecules by following the MAS-ISO-seq procedure. Finally, all the samples were mixed up according to the molar ratios of cDNA, and at least 500ng of cDNA was sent for SMRTbell library preparation and sequenced on PacBio Revio platform.

value: oocytes


title: HDL046-Lg-CD4-TEM

description: mRNA

value: Female


title: Myt1l heterozygous female mouse 2

description:
Library name: Het_F_2
ScaleBio Single Cell RNA Sequencing Kit

value: tuberal hypothalamus and thalamus


title: WT_NPC rep2

description: the column 'NPC_WT rep2'


title: Sarc_MicroC

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedgraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedgraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops
Supplementary files format and content: domains.bed includes genomic coordinates of identified chromatin domains
Library strategy: Micro-C

organism: Sphaeroforma arctica

source_name: Sphaeroforma arctica

growth_protocol: Sphaeroforma arctica culture was grown in Marine Broth (37.4 g/L) at 12 ºC. Salpingoeca rosetta culture was kept in artificial sea water with salinity 33 ppt supplemented with 4 % CGM3 and 4 % SWC at 23 ºC. Nematostella vectensis specimens were grown in 1/3 artificial sea water with salinity 14 ppt at 25 ºC. Cladtertia collaboinventa colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).

treatment_protocol: To synchronize cells in G1/early S phase, S. arctica cells were treated with 200 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours, S. rosetta culture was treated with 0.05 mM aphidicolin for 18 hours.

value: coenocytes

value: wild type

value: 200 mM hydroxyurea for 18 hours


title: HDL047-Col-CD4-TEM

description: mRNA

value: Colon

value: T cells

value: Male


title: HDL042-Lg-CD4-TEM

description: mRNA

value: Lung

value: bulk RNA-seq


title: Myt1l heterozygous female mouse 4

description:
Library name: Het_F_4
ScaleBio Single Cell RNA Sequencing Kit

value: Het


title: NPC_DF2-KO rep1

description: the column 'NPC_DF2-KO rep1'


title: Myt1l heterozygous female mouse 1

description:
Library name: Het_F_1
ScaleBio Single Cell RNA Sequencing Kit


title: HDL042-Ile-CD4-TEM

description: mRNA

value: Ileum

value: CD4 Effector Memory T cells by FACS


title: Myt1l heterozygous female mouse 3

description:
Library name: Het_F_3
ScaleBio Single Cell RNA Sequencing Kit

value: Brain

value: female


title: E. coli RS218 in LB broth-replicate 2

description: Library name: L2

value: Whole cell

value: Neonatal Meningitis E. coli

value: WT

value: Incubation in 6 hrs


title: human_gDNA_3_4_rep2

city: Cambridge

first: Jason

last: Buenrostro

state: MA

address: 7 Divinity Ave

institute: Harvard University

data_processing:
The sequencing data was processed the same way as SHARE-seq ATAC-seq data.
Assembly: hg38
Supplementary files format and content: File for Tn5 tagmentation fragments. Tab-delimited table with 5 columns: Chromosome, start coordinate, end coordinate, replicade index, count
Library strategy: Transposition into naked DNA

source_name: size-selected genomic DNA

extract_protocol:
Human genomic DNA was obtained from Promega (#G1521, female)
The genomic DNA was digested with the restriction enzyme SbfI-HF (New England Biolabs, R3642L). For each of two replicates, 25 μg of DNA was digested with 200 units SbfI-HF in a 500 μl reaction at 37 °C overnight. The digested DNA was run on a 1% agarose gel and fragments corresponding to 2-2.5 kb, 2.5-3 kb, 3-4 kb, and 4-5 kb were excised. All fragments from replicate 1 and the 3-4 kb fragment from replicate 2 were purified using the QIAquick gel extraction kit (Qiagen). The purified products were concentrated using the Zymo DNA clean & concentrator kit. Finally, tagmentation and library preparation were performed following the standard bulk ATAC protocol, using the same ratio of DNA mass to Tn5 when a lower amount of DNA was recovered after size selection.

value: size-selected genomic DNA


title: Tadh_ChIP_SMC1

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
peaks were called with MACS2.
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1; Ephydatia muelleri genome assembly Emue_v2; Trichoplax adhaerens genome assembly TadhH1_v1
Supplementary files format and content: BigWig

organism: Trichoplax adhaerens

source_name: Whole-organism

growth_protocol: Capsaspora owczarzaki strain ATCC30864 was maintained in axenic culture at 23 ºC in the ATCC medium 1034 (modified PYNFH medium). Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. For experiments we used adult lobate animals that were starved for 2 days.  Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.  Trichoplax adhaerens colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
Capsaspora owczarzaki cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392).  Mnemiopsis leidyi specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water by triturating every 2 min for a total of 10 min. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. Seven days post hatching sponges Ephydatia muelleri were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Next, animal tissues were dissociated into cells and double crosslinked with 1% formaldehyde and 3 mM DSG. Crosslinked cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate choanocytes. Trichoplax adhaerens specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation. The pool of chromatin was incubated for 14 - 16 hours at 4 ºC with 6 µL (3.4 µg) anti-H3K4me2 (Abcam, ab32356), 2.5 µL anti-H3K4me3 (Millipore, 07-473), 5 µL (5 µg) anti-SMC1 (ThermoFisher , A300-055A) or 2 µL (2 µg) anti-H3 (Abcam, ab1791).

treatment_protocol: To synchronize cells in G1/early S phase, C. owczarzaki cells were treated with 100 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours. Synchronised cells were scraped off the surface and pelleted at 2,200 g for 5 min at room temperature (RT).

value: Whole-organism

value: wild type

tag: chip antibody

value: SMC1, ThermoFisher  A300-055A


title: HPC-7, p30_constitutive, UT, R3

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute

description:
Library name: MC80
HPC7_constitutive_counts_table.txt

data_processing:
RNA-seq raw sequencing reads were aligned to the human or mouse reference genome (hg38 and mm39 assemblies respectively) with bowtie2 v2.4.4 with the “--very-sensitive” tag
Quantification of gene expression was performed with featureCounts from Subread v2.0.3 using uniquely mapping reads on NCBI RefSeq gene annotation for either human hg38 or mouse mm39.
The RNA-seq of KO-52 overexpressing CEBPA was normalized using ERCC RNA Spike-In controls (4456740, lifeTechnologies): 1µL of 1:100 dilution of spike-in mix 1 was added to 500ng of RNA.
Assembly: mm39, hg38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

growth_protocol:
HPC-7 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco 12440-053) supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco 15140-122), 1% L-glutamine (Gibco 25030-024), 50μM b-mercaptoethanol (Gibco 31350-010), and 50 ng/mL murine SCF (Miltenyi Biotec, 130-101-697).
KO52 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Dominique Dutscher, L0106-500) supplemented with 10% FBS, 1% penicillin/streptomycin and 2% L-glutamine.

extract_protocol:
RNA was isolated from 1-2 x 106 cells in 1mL of TRIzol Reagent (ABP Biosciences FP312) following the manufacturer’s instructions. For low starting cell number samples, RNA was extracted with Direct-zol RNA MicroPrep kit (Zymo R2060).
1) Oligo dT Selection to enrich the mRNA. 2) RNA fragment and reverse transcription (second-strand cDNA synthesis with dUTP instead of dTTP). 3) End repair, add A and adaptor ligation 4) PCR 5) Single strand separation and cyclization 6) DNA nanoball synthesis

treatment_protocol:
For TLR4 stimulation, cells were exposed to LPS (Escherichia coli O111:B4, Sigma L2630) at a final concentration of 100 ng/mL
For CEBPA transient expression in KO-52, 3x106 KO-52 cells were electroporated with 2µg of plasmid: p42-FLAG-GFP, p30-FLAG-GFP (Vector Builder) or the GFP empty plasmid with a Nucleofector 2b (Lonza) using program V-001. GFP+ cells were sorted 24h after transfection. 24h post-sorting, cells were treated with 100ng/mL LPS.
For constitutive expression of CEBPA in HPC-7, cells were transduced with pMSCV-p30-flag-IRES-GFP (VB240912-1465qes) and pMSCV-p42-flag-IRES-GFP (VB240912-1467fsn) plasmids from VectorBuilder


title: WT_NPC rep1

description: the column 'NPC_WT rep1'

value: hESC

value: human embryonic stem cells


title: Myt1l heterozygous male mouse 1

description:
Library name: Het_M_1
ScaleBio Single Cell RNA Sequencing Kit

value: male

value: tuberal hypothalamus and thalamus


title: Tadh_MicroC

data_processing:
*library strategy: Micro-C
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1; Ephydatia muelleri genome assembly Emue_v2; Trichoplax adhaerens genome assembly TadhH1_v1
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedGraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedGraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops

growth_protocol: Capsaspora owczarzaki strain ATCC30864 was maintained in axenic culture at 23 ºC in the ATCC medium 1034 (modified PYNFH medium). Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.  Trichoplax adhaerens colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
Capsaspora owczarzaki cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392).  Mnemiopsis leidyi specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water by triturating every 2 min for a total of 10 min. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. Seven days post hatching sponges Ephydatia muelleri were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Next, animal tissues were dissociated into cells and double crosslinked with 1% formaldehyde and 3 mM DSG. Crosslinked cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate choanocytes. Trichoplax adhaerens specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).


title: HDL042-Jej-CD4-TEM

description: mRNA

value: Jejunum

value: T cells

value: Female

value: bulk RNA-seq


title: Tadh_ChIP_H3K4me3

value: H3K4me3, Millipore, 07-473


title: HDL042-Col-CD4-TEM

description: mRNA

value: Colon

value: CD4 Effector Memory T cells by FACS


title: Tadh_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: HPC-7, p30_constitutive, UT, R1

description:
Library name: MC78
HPC7_constitutive_counts_table.txt


title: Tadh_ChIP_H3

value: H3, Abcam ab1791


title: human_gDNA_3_4_rep1

value: size-selected genomic DNA


title: HDL040-Lg-CD4-TEM

description: mRNA

value: Lung

value: Male


title: human_gDNA_25_3


title: HDL040-Jej-CD4-TEM

description: mRNA


title: HPC-7, p42_constitutive, UT, R3

description:
Library name: MC74
HPC7_constitutive_counts_table.txt


title: human_gDNA_4_5


title: Sarc_ChIP_H3K4me3

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
ATAC peaks were called with MACS2.
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: BigWig

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation.

value: wild type

value: 200 mM hydroxyurea for 18 hours


title: HDL040-Col-CD4-TEM

description: mRNA


title: human_gDNA_2_25


title: no_TF_control

data_processing:
The sequencing data was processed the same way as SHARE-seq ATAC-seq data.
Assembly: hg38
Supplementary files format and content: File for Tn5 tagmentation fragments. Tab-delimited table with 5 columns: Chromosome, start coordinate, end coordinate, replicade index, count.

source_name: BAC clone RP11-526L8

growth_protocol: BAC clone RP11-526L8 (BACPAC Resources) were cultured in LB for 14 hours.

extract_protocol:
The BAC DNA was extracted using ZR BAC DNA Miniprep Kit (Zymo, D4048) following manufacturer’s instructions. The purified DNA was quantified using Qibit (ThermoFisher).
50 ng of BAC DNA was incubated with recombinant c-MYC/MAX (Active Motif, 81087) or CEBPA (OriGene, TP760685), tagmentation buffer (20mM Tris,10mM MgCl2, and 20% DMF), and water in a 40 μl volume at room temperature for 1 hour. Then, a master mix consisting of 0.15 μl pre-assembled Tn5 (seqWell, Tagify(TM)), 4.85 μl dilution buffer (50mM Tris, 100mM NaCl, 0.1mM EDTA, 1mM DTT, 0.1% NP-40, and 50% glycerol), and 5 μL Tagmentation buffer was added to the samples for tagmentation in 50 μl final volume (final TF concentration of 0 nM,  50 nM and 100 nM) for 30 minutes at 37°C. Tagmented DNA was purified using a Qiagen Minelute PCR clean up kit and subsequently amplified for 5 cycles by PCR. Samples were then pooled and sequenced on a Nova platform (Illumina).
Transposition into naked DNA.

value: BAC clone RP11-526L8

value: no TF control


title: Sarc_ChIP_H3K4me2


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_input_3

city: Houston

first: Eric

last: Van Nostrand

state: Tx

address: 1 Baylor Plaza

department: Biochemistry and Molecular Pharmacology

institute: Baylor College of Medicine

description: Library name: EV143_input

library_source: other

data_processing:
Standard processing of eCLIP data was performed as previously described (Blue SB, et al. Nature Protocols 2022), with mapping performed to a custom genome index that included both the VSV genome and either hg19 (for 293T experiments) or mm10 (for MEF experiments) as described below.
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> EV225_IP.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o EV225_IP.trim.gz   --report minimal   >>EV225_IP.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir  [mus_musculus_repbase_v2 or homo_sapiens_repbase_v2]   --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix EV225_IP.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn EV225_IP.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir [hg19+VSV or mm10+VSV] --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix EV225_IP.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn EV225_IP.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o EV225_IP.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index EV225_IP.genome.map.bam umi_tools dedup   --random-seed 1   --stdin EV225_IP.genome.map.bam   --method unique   --stdout EV225_IP.bam
Make bigwigs: samtools index EV225_IP.bam b2bw EV225_IP.bam  --cpus 1
Isolate VSV-mapped reads only: bigWigToWig EV225.pos.bw -chrom=chrVSV EV225.pos.bw.chrVSV.wig
wigToBigWig EV225.pos.bw.chrVSV.wig /path/to/hg19_and_vsv.chrom.sizes EV242.pos.bw.chrVSV.wig.bw
Assembly: hg19 (for 293T) or mm10 (for MEF) with the addition of VSV (using accession NC_001560.1 with GFP was inserted between G and L as described in PMID 10400792)
Supplementary files format and content: bw files contain read density (in bigwig format) for the VSV genome (positive or negative strand as indicated in filename). Bigwig files are not included for datasets with zero reads

molecule: other

growth_protocol: HEK293T cells were obtained from ATCC (catalog # CRL-3216) and grown in complete medium containing DMEM (Gibco, Carlsbad, CA), 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, Carlsbad, CA). For transient transfections, HEK293T cells were seeded the day prior to transfection in a 24-well plate (Genesee, El Cajon, CA) with 500 μL of complete media. Cells were transiently transfected with 500 ng of total DNA and 1.5 μL of TransIT-X2 (Mirus Bio, Madison, WI) following the manufacturer’s protocol.  For generation of inducible cell lines, sequences for mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 separated by a P2A site were cloned into the Flp-In vector pcDNA5/FRT/TO. Flp-In T-REx HEK293 cells (Invitrogen) maintained in 5 μg/mL of blasticidin were transfected at 70% confluency with mCherry or IFIT constructs and the vector containing the Flp recombinase pOG44 in a 1:10 molar ratio using TransIT-X2 (Mirus Bio). After one day, cells were transferred to new dishes, and on the following day, hygromycin (100 μg/mL) was added to cells. Following selection, cells were maintained in 5 μg/mL of blasticidin and 100 μg/mL of hygromycin. For induction of mCherry or IFIT proteins, cells were treated with 500 ng/mL of doxycycline for 24 h.   MEFs from Ifit2-/- and ΔIfit3a/b mice were prepared from day 13.5-14.5 embryos according to published protocols. Isolated MEFs were maintained in DMEM supplemented with 10% heat-inactivated, fetal bovine serum (FBS) (Cytiva), 100 U/mL penicillin-streptomycin (Invitrogen), non-essential amino acids (Cellgro), and Glutamax (Gibco). Passage 0 (P0 MEFs were frozen or split 1:4 when approximately 80% confluent (around 3 days). To generate transformed MEFs, 5x106 P1 primary MEFs were transfected with 10 μg of a plasmid (SV2) encoding the SV40 T antigen under control of a CMV promoter, using FuGene reagent (Promega) (3:1 μL FuGene to μg DNA ratio). Upon achieving confluence, MEF cultures were split 1:10. This process was repeated for approximately ten passages, at which time the transformed MEFs were frozen or used for experiments.

extract_protocol:
eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million 293T or MEF cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of IFIT-bound RNA with antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.

treatment_protocol: Flp-In T-REx HEK293 cells expressing mCherry, IFIT2, IFIT3, or IFIT2 and IFIT3 in 10 cm culture dishes were induced with doxycycline for 24 h. Cells were then infected with VSV at an MOI of 3.0, and dishes were crosslinked using a UV cross-linker (254 nm; CL-1000 from UVP/Analytik Jena) at 400 mJ/cm2. Downstream sample processing and eCLIP were performed as previously described, using antibodies against FLAG (M2 / F1804, Sigma) and HA (HA.11 / 901502, Biolegend) for 293T experiments, and IFIT2 (PA3-845, ThermoFisher) and IFIT3 (ABF1048, Millipore) for MEF experiments. Most experiments were performed in biological duplicate, excepting the uninfected 293T samples (which were single replicates).

value: IFIT2:FLAG+IFIT3:HA o/e

value: uninfected


title: MYC_MAX_50nM

value: c-MYC/MAX 50nM


title: Sarc_ChIP_H3K4me1

value: H3K4me1, Cell Signaling, 5326S


title: HPC-7, p30_constitutive, UT, R2

description:
Library name: MC79
HPC7_constitutive_counts_table.txt


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_IP_3

description: Library name: EV143_IP


title: HPC-7, p42_constitutive, UT, R1

description:
Library name: MC72
HPC7_constitutive_counts_table.txt


title: Sarc_ChIP_input


title: HPC-7, p42, CEBPa, ChIP

description: Library name: p42

data_processing:
ChIP-seq reads were pre-processed with TrimGalore v0.6.6 for quality and adapter trimming.
Trimmed reads were aligned to mouse genome mm39 or human genome hg38 using Bowtie2 v. 2.4.4 with ‘--very-sensitive’ flag set and a minimum fragment length (-X flag) of 1000bp, all other parameters set to default.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis.
ChIP-seq peaks were identified by MACS2 v. 2.2.5 for individual replicates and pooled replicates for each condition, using input libraries as control. Peaks identified in each condition were merged with bedtools merge (v. 2.31.1) to generate a common peak set.
Reads from each sample were quantified over the common peak set using the regionCounts function from the csaw R package and differential binding analysis was performed with DESeq2
Assembly: mm39, hg38
Supplementary files format and content: bigWig files for each sample, generated with deeptools bamCoverage and normalized by counts per million mapped reads (CPM)
Supplementary files format and content: tab-delimited text files include narrowPeak files from MACS2 and merged peaks in bed format.

extract_protocol:
HPC-7 cells were cross-linked with 1% formaldehyde and lysed (1% Triton, 0.1% sodium deoxycholate, 0.1% SDS, 0.2M NaCl, 10mM Tris pH 7.5, 10mM EDTA and 1X protease inhibitor cocktail (Roche 11836170001)). Sonication was performed in the same buffer with 0.5% SDS in a Bioruptor (Diagenode) for 60 cycles (30s ON 30s OFF), vortexing every 20 minutes. Sodium butyrate 5mM was added to the buffers in the cells for the H3K27ac ChIP to inhibit deacetylases. For H3K4me1 ChIP-seq, DNA was digested in 50mM Tris pH 7.5, 4mM MgCl2 and 2mM CaCl2 with 10U micrococcal nuclease (Thermo Scientific EN0181) for 15 min at 22ºC. For ATF4 ChIP, KO-52 cells were pre-treated with 2µg/mL tunicamycin for 4h and additionally crosslinked with 1mM DSG (A35392, ThermoScientific) for 45 minutes. Lysates were sonicated for 30 min in lysis buffer (0.1% SDS). Lysates were incubated with 4µg of H3K27ac antibody (Abcam ab4729), 8µg of anti-ERa (sc-8002X), 3µg anti-H3K4me1 (Diagenode, C15410194), 22µL anti-CEBPA (8178, Cell Signaling) or 10 µL  anti-ATF4 (11815, Cell Signaling) overnight at 4ºC. Antibody-bound chromatin was pulled down with protein G Dynabeads (Invitrogen 10003D). Samples were washed, RNase-treated and reverse cross-linked by incubation at 65°C in 1% SDS, 0.1M NaHCO3 and proteinase K. DNA was purified using ChIP DNA Clean & Concentrator Kit (Zymo D5205).
Libraries were prepared using the NEBNext Ultra DNA Library Prep kit (E7645, New England Biolabs).

treatment_protocol:
For TLR4 stimulation, cells were exposed to LPS (Escherichia coli O111:B4, Sigma L2630) at a final concentration of 100 ng/mL
To induce ATF4 translation, cells were incubated with tunicamycin (Sigma, T7765) at 2µg/mL for KO-52 cells.

value: CEBPa (8178, Cell Signaling)


title: MYC_MAX_100nM

value: c-MYC/MAX 100nM


title: CEBPA_100nM

value: CEBPA 100nM


title: HPC-7, p30, CEBPa, ChIP

description: Library name: p30


title: KO52, p30, Tm, ATAC-seq, R2

description:
Library name: AT_MC36
KO52_p30_Tm_merged_peaks.narrowPeak

data_processing:
ATAC-seq reads were pre-processed with TrimGalore v0.6.6 for quality and adapter trimming.
Trimmed reads were aligned to human genome hg38 using Bowtie2 v. 2.4.4 with ‘--sensitive’ flag set and a minimum fragment length (-X flag) of 500bp, all other parameters set to default.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis.
Peaks were identified by MACS2 v. 2.2.5 for individual replicates and pooled replicates for each condition. Peaks identified in each condition were merged with bedtools merge (v. 2.31.1) to generate a common peak set.
Reads from each sample were quantified over the common peak set using bedtools multicov v. 2.30.0  and differential binding analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: bigWig files for each sample, generated with deeptools bamCoverage and normalized by counts per million mapped reads (CPM)
Supplementary files format and content: tab-delimited text files include narrowPeak files from MACS2 and merged peaks in bed format.

growth_protocol: KO52 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Dominique Dutscher, L0106-500) supplemented with 10% FBS, 1% penicillin/streptomycin and 2% L-glutamine.

extract_protocol:
Nuclei from 50,000 cells were extracted by lysis in 10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin. After a wash, samples were transposed using an in-house synthetized Tn5 and loaded with stantard illumina compatible adaptors, 30 min, 37 °C. DNA was purified by Zymo ChIP DNA Clean and Concentrator Kit.
Transposed fragments were amplified with NEBNext High-Fidelity PCR Master Mix (NEB M0541). Libraries were cleaned and size-selected using CleanNGS beads (CNGS-0050) and assessed by Tapestation and Qubit.

treatment_protocol: To induce ER stress, cells were incubated with tunicamycin (Sigma, T7765) at 2µg/mL. DMSO was used as control

value: Tm 8h


title: KO52, p30, Tm, ATAC-seq, R1

description:
Library name: AT_MC35
KO52_p30_Tm_merged_peaks.narrowPeak


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_IP_3

description: Library name: EV142_IP


title: HPC-7, p42, INPUT

description: Library name: INP_p42


title: 293T_IFIT3:HAoe_HA_input_3

description: Library name: EV141_input

value: IFIT3:HA o/e


title: HPC-7, p30, INPUT

description: Library name: INP_p30


title: Pericyte TBX4 KD-2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
HISAT 2 was used to align reads to the hg38 genome build
Reads were quantified to hg38 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: hg38
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)

extract_protocol:
RNEasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pericyte


title: Pericyte TBX4 KD-3


title: KO52, p30, DMSO, ATAC-seq, R2

description:
Library name: AT_MC34
KO52_p30_DMSO_merged_peaks.narrowPeak

value: DMSO


title: 293T_IFIT3:HAoe_HA_IP_3

description: Library name: EV141_IP


title: HPC-7, p42_constitutive, UT, R2

description:
Library name: MC73
HPC7_constitutive_counts_table.txt


title: TGF

city: Chikusa-ku

first: Hiro

last: Kohda

state: Nagoya

address: Furo-cho

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya Univ.

description: Library name: sample 3

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads filtering is as follows: 1. Remove reads with adapter contamination, 2. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%), and 3. Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.(Yan et al, 2011)
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Gene expression level is calculated by the number of mapped reads.
Assembly: mm39
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample

source_name: visceral adipoe tissue

extract_protocol:
RNA was harvested using RNeasy Plus Universal Mini Kit (Qiagen). About 0.6 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Adipose tissue–derived fibroblasts were prepared from the SVF of HFD-fed mice using a magnetic cell sorting system (AutoMACS; Miltenyi Biotec) as CD45-, CD31-, and Ter119-negative cells. Adipose tissue–derived fibroblasts were treated with recombinant human transforming growth factor-β1 (TGFß1) (3 ng/mL; BioLegend) or recombinant mouse Osm (3 ng/mL; BioLegend) for 24 h.

value: visceral adipoe tissue

value: Fibroblast

value: WT

value: reconbinant TGFβ1


title: 293T_IFIT2:FLAGoe_FLAG_input_3

description: Library name: EV140_input

value: IFIT2:FLAG o/e


title: Pericyte Control-3

value: Lung

value: Control


title: KO52, p30, DMSO, ATAC-seq, R1

description:
Library name: AT_MC33
KO52_p30_DMSO_merged_peaks.narrowPeak


title: Pericyte TBX4 KD-1


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_input_3

description: Library name: EV142_input

value: IFIT2:FLAG+IFIT3:HA o/e

value: uninfected


title: 293T_IFIT1:FLAGoe_FLAG_input_3

description: Library name: EV139_input

value: IFIT1:FLAG o/e


title: Pericyte Control-2


title: 293T_IFIT2:FLAGoe_FLAG_IP_3

description: Library name: EV140_IP


title: KO52, p42, DMSO, ATAC-seq, R2

description:
Library name: AT_MC30
KO52_p42_DMSO_merged_peaks.narrowPeak


title: Veh

description: Library name: sample 1


title: Obese

description: Paraffin embedded Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the Space Ranger software version 2.0.1 (10x Genomics) to generate FASTQ files
Alignment to the mouse reference genome mm10 and initial quality control steps were performed as per the software guidelines.
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned_fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene
Library strategy: Spatial Transcriptomics

extract_protocol:
Five-micrometer thick paraffin embedded sections of epididymal adipose tissue were prepared using a microtome
After permeabilization of the tissue sections with proteinase K, RNA in the tissue sections was transferred to the Visium slide with the spatial barcodes using CytAssist instrument (10x Genomics). The cDNA synthesis and library preparation were conducted according to the 10x Genomics instructions.

treatment_protocol: Male C57BL/6J mice were fed a standard diet or high-fat diet for 36 weeks.

value: high-fat diet, 36 weeks


title: Pericyte Control-1


title: KO52, p42, Tm, ATAC-seq, R1

description:
Library name: AT_MC31
KO52_p42_Tm_merged_peaks.narrowPeak


title: Lean

value: standard diet, 36 weeks


title: KO52, p42, DMSO, ATAC-seq, R1

description:
Library name: AT_MC29
KO52_p42_DMSO_merged_peaks.narrowPeak


title: FLF TBX4 KD-2

value: TBX4 KD


title: 293T_control_FLAG_input_3

description: Library name: EV138_input


title: FLF TBX4 KD-1


title: KO52, EV, Tm, ATAC-seq, R2

description:
Library name: AT_MC28
KO52_EV_Tm_merged_peaks.narrowPeak

value: Tm 8h


title: Mlei_MicroC

organism: Mnemiopsis leidyi

value: Whole-organism

value: wild type


title: 293T_control_FLAG_IP_3

description: Library name: EV138_IP


title: KO52, EV, Tm, ATAC-seq, R1

description:
Library name: AT_MC27
KO52_EV_Tm_merged_peaks.narrowPeak


title: FLF Control-2


title: Emue_ChIP_H3K4me2_rep2

organism: Ephydatia muelleri

source_name: Ephydatia muelleri

value: choanocytes

value: H3K4me2, Abcam ab32356


title: Osm

description: Library name: sample 2

value: visceral adipoe tissue

value: Fibroblast

value: reconbinant Onscostatin M


title: KO52, EV, DMSO, ATAC-seq, R2

description:
Library name: AT_MC26
KO52_EV_DMSO_merged_peaks.narrowPeak

value: DMSO


title: KO52, p42, Tm, ATAC-seq, R2

description:
Library name: AT_MC32
KO52_p42_Tm_merged_peaks.narrowPeak


title: 293T_control_HA_input_3

description: Library name: EV137_input

value: WT


title: FLF Control-1

value: Lung

value: Control


title: 293T_control_HA_IP_3

description: Library name: EV137_IP

value: uninfected


title: KO52, EV, DMSO, ATAC-seq, R1

description:
Library name: AT_MC25
KO52_EV_DMSO_merged_peaks.narrowPeak


title: Emue_ChIP_H3K4me1

value: H3K4me1, Cell Signaling, 5326S


title: hESC_DF2-ADAR_rep2

description: the column 'hESC_DF2-ADAR_rep2'

value: hESC

value: human embryonic stem cells


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_input_VSV_rep2

description: Library name: EV136_input

value: IFIT2:FLAG+IFIT3:HA o/e

value: VSV infected


title: Emue_ChIP_input


title: hESC_DF2-ADAR_rep1

description: the column 'hESC_DF2-ADAR_rep1'


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_IP_VSV_rep2

description: Library name: EV136_IP


title: KO52, p30, LPS, R2

description:
Library name: MC55
Ko52_counts_table_1.txt

value: LPS 2h


title: Emue_MARSseq

data_processing:
*library strategy: massively parallel RNA single-cell sequencing (MARS-seq)
R1 files (read 1) were mapped to Ephydatia muelleri genome using STAR with default parameters.
Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4).
The MetaCell R package was used to quantify normalized gene expression.
Assembly: Ephydatia muelleri genome assembly Emue_v2
Supplementary files format and content: Emue_choanocytes_sc_expression.tar.gz with Metacell normalization gene expression matrix in TSV format
Supplementary files format and content: Readme_MARSseq.xlsx with plate well coordinates and cell barcodes

source_name: choanocytes

growth_protocol: Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.

extract_protocol:
To collect cells for MARS-seq libraries, 7 days post hatching sponges were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Animal tissues were dissociated, choanocytes were FACS sorted into four 384-well MARS-seq plates.
The MARS-seq libraries were prepared as described in Sebé-Pedrós et al. 2018 (PMID: 29942020).

value: wild type


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_input_VSV_rep2

description: Library name: EV135_input


title: Emue_ChIP_H3K4me3_rep2

value: choanocytes

value: H3K4me3, Millipore, 07-473


title: KO52, p30, LPS, R1

description:
Library name: MC54
Ko52_counts_table_1.txt


title: Emue_ChIP_H3K4me3


title: ectoderm_DF2-KO_rep1

description: the column 'ectoderm_DF2-KO_rep1'


title: mesoderm_DF2-KO_rep2

description: the column 'mesoderm_DF2-KO_rep2'


title: KO52, p42, LPS, R3

description:
Library name: MC53
Ko52_counts_table_1.txt


title: 293T_IFIT3:HAoe_HA_input_VSV_rep2

description: Library name: EV134_input

value: IFIT3:HA o/e


title: Emue_ChIP_H3

value: H3, Abcam ab1791


title: Emue_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: KO52, p42, LPS, R2

description:
Library name: MC52
Ko52_counts_table_1.txt


title: mesoderm_DF2-KO_rep1

description: the column 'mesoderm_DF2-KO_rep1'


title: Emue_ATAC

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
Aligned reads were filtered with deeptools alignmentSieve  and shifted with -ATACshift, which corresponds to mate reads being shifted +4 bp and -5 bp for positive and negative strands, respectively. To generate nucleosome-position data tracks, nucleosome-free and nucleosome-bound regions were defined using the following length thresholds 0 – 120 bp and 150 – 240 bp, respectively.
ATAC peaks were called with MACS2.
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1
Supplementary files format and content: BigWig with ATAC-seq nucleosome-free read coverage

growth_protocol: Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. For experiments we used adult lobate animals that were starved for 2 days. Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.

extract_protocol:
Two M. leidyi adult specimens were dissociated using CMFSW with 0.25% α-Chymotrypsin (Sigma-Aldrich, C8946). To isolate nuclei, dissociated cells were transferred into cold hypotonic ATAC lysis buffer adjusted for marine animals (10 mM Tris-HCl (pH 7.5), 35 mM NaCl, 3 mM MgCl2, 0,1% Tween-20, 0.01% NP-40, 0.01% digitonin, 70 µM Pitstop (Abcam, AB1206875MG)). Cell lysis was stopped after 2 min by adding marine ATAC wash buffer (10 mM Tris-HCl (pH 7.5), 35 mM NaCl, 3 mM MgCl2, 0,1% Tween-20, 1% BSA).  To isolate choanocytes of E. muelleri, 7 days post hatching sponges were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). After 10 min incubation, sponges were washed twice with Strekal’s media, collected and dissociated for 15 min at 28 ºC using Protease XIV (Sigma-Aldrich, P5147). Cells were pelleted at 800 g for 5 min at RT and resuspended in Strekal’s media with 2 mM EDTA (pH 8.0). Further dissociation and trituration of sponge tissue continued for additional 15 min at RT. Cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted.
ATAC-seq libraries were prepared using Omni-ATAC protocol as described in Corces et al. 2017 (PMID: 28846090).


title: 293T_IFIT3:HAoe_HA_IP_VSV_rep2

description: Library name: EV134_IP


title: KO52, EV, LPS, R3

description:
Library name: MC50
Ko52_counts_table_1.txt


title: endoderm_DF2-KO_rep2

description: the column 'endoderm_DF2-KO_rep2'

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQformat, which contains sequence information and corresponding sequencing quality information.
For the initial RNA-seq data, quality evaluation was performed using the FastQC tool (version 0.11.9). This step assessed the overall integrity of the RNA-seq fastq files and identified any potential issues.
The bulk RNA-seq libraries were processed with paired-end sequencing. This was followed by trimming the sequences using cutadapt (version 4.1).
The trimmed reads were aligned to the human genome (hg38) using STAR (version 2.7.10a), organized with samtools (version 1.6), and the read counts were quantified against Gencode (version 41) annotations with featureCounts (version 2.0.1).
Assembly: hg38
Supplementary files format and content: csv: matrix of gene counts of all samples

extract_protocol:
Total RNA was extracted from hESCs with AG RNAex Pro Reagent (Accurate Biology, AG21101), adhering to the manufacturer’s protocol
Total RNA worked as input for the RNA sample preparation. Sequencing libraries were generated using NEBNext Ultra Libraries Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s protocol and index codes were added to attribute sequences to each sample. Sepecifically, poly-T oligo-attached magnetic beads were used to purified mRNA from total RNA. Fragmentation was applied with divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). M-MuLV Reverse Transcriptase (RNase H) and random hexamer primers were used to create first strand cDNA. RNase H and DNA Polymerase I were then used to synthesise second strand cDNA. The remaining overhangs were transformed into blunt ends by polymerase and exonuclease reactions. To become ready for hybridization, NEB Next Adaptors with hairpin loop structures were ligated after the 3' ends of DNA fragments had been adenylated. Purification of the library fragments was done using the AMPure XP system (Beverly, USA) to select cDNA fragments that were preferably 370–420 bp in length. Subsequently, 3 μL USER Enzyme (NEB, USA) was employed with adaptor-ligated, size-selected cDNA at 37°C for 15 min, and then 5 min at 95 °C before PCR. After that, Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primer were used to carry out PCR. Finally, the PCR products were purified using the AMPure XP system, and the Agilent 5400 system (Agilent USA) was used to evaluate the library quality and quantify the results using QPCR (1.5 nM). The qualified libraries were pooled and sequenced using PE150 technique on Illumina platforms in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and necessary data amount.


title: 293T_IFIT2:FLAGoe_FLAG_input_VSV_rep2

description: Library name: EV133_input

value: IFIT2:FLAG o/e


title: KO52, p30, LPS, R3

description:
Library name: MC56
Ko52_counts_table_1.txt


title: endoderm_DF2-KO_rep1

description: the column 'endoderm_DF2-KO_rep1'


title: 293T_IFIT1:FLAGoe_FLAG_IP_3

description: Library name: EV139_IP

value: IFIT1:FLAG o/e


title: 293T_IFIT2:FLAGoe_FLAG_IP_VSV_rep2

description: Library name: EV133_IP


title: ectoderm_DF2-KO_rep2

description: the column 'ectoderm_DF2-KO_rep2'


title: hESC_DF2-KO rep2

description: the column 'hESC_DF2-KO rep2'


title: KO52, EV, LPS, R2

description:
Library name: MC49
Ko52_counts_table_1.txt


title: 293T_IFIT1:FLAGoe_FLAG_input_VSV_rep2

description: Library name: EV132_input


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_IP_VSV_rep2

description: Library name: EV135_IP


title: KO52, EV, LPS, R1

description:
Library name: MC48
Ko52_counts_table_1.txt


title: hESC_DF2-KO rep1

description: the column 'hESC_DF2-KO rep1'


title: Yeast cell, tryptophan prototrophic, YPD+3-IAA 2 h, biological replicate 1

city: Ann Arbor

first: Yuxiang

last: Huang

state: MI

address: 2214 Stone Road

department: MCDB

institute: University of Michigan

description: Library name: 9282-YH-13

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: Reads were mapped using Bowtie2  (parameters: -f -v 3 -k 500 --best --strata) to the yeast transcriptome derived from yeast genome version S288C.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

extract_protocol:
RNA was harvested by Rneasy mini plus kt (Qiagen), 1 μg total RNA was used for generating polyA-riched molecules and constructed for sequencing.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: yeast cells


title: Yeast cell, tryptophan prototrophic, YPD+DMSO 2 h, biological replicate 3

description: Library name: 9282-YH-12


title: 293T_IFIT1:FLAGoe_FLAG_IP_VSV_rep2

description: Library name: EV132_IP


title: Yeast cell, tryptophan prototrophic, YPD+3-IAA 2 h, biological replicate 2

description: Library name: 9282-YH-14


title: 293T_control_FLAG_input_2

description: Library name: EV131_input

value: WT


title: KO52, p30, UT, R2

description:
Library name: MC46
Ko52_counts_table_1.txt


title: KO52, p42, LPS, R1

description:
Library name: MC51
Ko52_counts_table_1.txt


title: U937 BP3-mAID, 24h, mRNA, rep1

city: GuangZhou,GuangDong Province

first: Feng

state: China

institute: Guangzhou Laboratory

description:
BP3-mAID_24h_mRNA
U937_gene_dif.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by by cutadapt v. 4.1 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the human genome (hg38) with HISAT2 v.2.1.1 with “--rna-strandness RF” parameters, and supplying the GENCODE Release 39 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Read counts on genes were calculated by HTSeq v.2.0.2 against the GENCODE Release 39 gene annotation. Differentially expressed genes were calculated by DESeq2 with fold change > 1.5 and adjusted P-value < 0.05.
Assembly: hg38
Supplementary files format and content: Processed results from DESeq2.

growth_protocol: MOLM13 and U937 BP3-mAID cells were maintained in regular RPMI-1640 medium containing 10% FBS and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was isolated using the TRIzol reagent. mRNA was then purified from total RNA using VAHTS® mRNA Capture Beads.
Libraries for RNA-seq were constructed using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina following manufacturer’s protocol.

treatment_protocol: MOLM13 cells were transfected with shBP3-1, shBP3-2 or shNS lentiviruses to induse knockdown of IGF2BP3. U937 BP3-mAID cells were treated with 5-Ph-IAA or not for the indicated times to cause the degradation of IGF2BP3-mAID.

value: Human acute myeloid leukemia (AML) cells


title: U937 BP3-mAID, 24h, mRNA, rep2

description:
BP3-mAID_24h_mRNA
U937_gene_dif.xlsx


title: Yeast cell, tryptophan prototrophic, YPD+DMSO 2 h, biological replicate 1

description: Library name: 9282-YH-10


title: KO52, p30, UT, R1

description:
Library name: MC45
Ko52_counts_table_1.txt


title: 293T_control_FLAG_IP_2

description: Library name: EV131_IP


title: 293T_control_HA_input_2

description: Library name: EV130_input


title: U937 BP3-mAID, 6h, mRNA, rep2

description:
BP3-mAID_6h_mRNA
U937_gene_dif.xlsx


title: Yeast cell, tryptophan prototrophic, YPD+3-IAA 2 h, biological replicate 3

description: Library name: 9282-YH-15


title: U937 BP3-mAID, 6h, mRNA, rep1

description:
BP3-mAID_6h_mRNA
U937_gene_dif.xlsx


title: Yeast cell, tryptophan auxotrophic, YPD+Con.A 2 h, biological replicate 2

description: Library name: 9282-YH-8


title: 293T_control_HA_IP_VSV_rep2

description: Library name: EV130_IP


title: KO52, p42, UT, R2

description:
Library name: MC43
Ko52_counts_table_1.txt


title: U937 BP3-mAID, NT, mRNA, rep2

description:
BP3-mAID_NT_mRNA
U937_gene_dif.xlsx

value: NT


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_input_VSV_rep1

description: Library name: EV129_input


title: Yeast cell, tryptophan auxotrophic, YPD+Con.A 2 h, biological replicate 1

description: Library name: 9282-YH-7


title: KO52, p42, UT, R1

description:
Library name: MC42
Ko52_counts_table_1.txt


title: KO52, p30, UT, R3

description:
Library name: MC47
Ko52_counts_table_1.txt


title: U937 BP3-mAID, NT, mRNA, rep1

description:
BP3-mAID_NT_mRNA
U937_gene_dif.xlsx


title: KO52, EV, UT, R3

description:
Library name: MC41
Ko52_counts_table_1.txt


title: Yeast cell, tryptophan auxotrophic, YPD+3-IAA 2 h, biological replicate 3

description: Library name: 9282-YH-6


title: MOLM13, shBP3-1, total RNA, rep2

description:
MOLM13_shBP3-1_totalRNA
MOLM13_gene_dif.xlsx


title: 293T_IFIT2:FLAG+IFIT3:HAoe_FLAG_IP_VSV_rep1

description: Library name: EV129_IP


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_input_VSV_rep1

description: Library name: EV128_input


title: Yeast cell, tryptophan auxotrophic, YPD+3-IAA 2 h, biological replicate 2

description: Library name: 9282-YH-5


title: Yeast cell, tryptophan prototrophic, YPD+DMSO 2 h, biological replicate 2

description: Library name: 9282-YH-11


title: KO52, EV, UT, R2

description:
Library name: MC40
Ko52_counts_table_1.txt


title: Yeast cell, tryptophan auxotrophic, YPD+3-IAA 2 h, biological replicate 1

description: Library name: 9282-YH-4


title: MOLM13, shBP3-1, total RNA, rep1


title: 293T_IFIT2:FLAG+IFIT3:HAoe_HA_IP_VSV_rep1

description: Library name: EV128_IP


title: MOLM13, shBP3-2, total RNA, rep2

description:
MOLM13_shBP3-2_totalRNA
MOLM13_gene_dif.xlsx


title: KO52, EV, UT, R1

description:
Library name: MC39
Ko52_counts_table_1.txt


title: 293T_IFIT3:HAoe_HA_input_VSV_rep1

description: Library name: EV127_input


title: Yeast cell, tryptophan auxotrophic, YPD+Con.A 2 h, biological replicate 3

description: Library name: 9282-YH-9


title: Yeast cell, tryptophan auxotrophic, YPD+DMSO 2 h, biological replicate 3

description: Library name: 9282-YH-3


title: KO-52, Tm, INPUT

description: Library name: SC2_INP

value: Tm


title: 293T_IFIT3:HAoe_HA_IP_VSV_rep1

description: Library name: EV127_IP


title: KO52, p42, UT, R3

description:
Library name: MC44
Ko52_counts_table_1.txt


title: MOLM13, shNS, total RNA, rep2

description:
MOLM13_shNS_totalRNA
MOLM13_gene_dif.xlsx

value: shNS


title: Yeast cell, tryptophan auxotrophic, YPD+DMSO 2 h, biological replicate 2

description: Library name: 9282-YH-2


title: KO-52, Tm, ATF4, ChIP

description: Library name: SC4

value: ATF4 (11815, Cell Signaling)


title: Yeast cell, tryptophan auxotrophic, YPD+DMSO 2 h, biological replicate 1

description: Library name: 9282-YH-1


title: MOLM13, shNS, total RNA, rep1


title: 293T_IFIT2:FLAGoe_FLAG_input_VSV_rep1

description: Library name: EV126

value: VSV infected


title: 293T_IFIT2:FLAGoe_FLAG_IP_VSV_rep1

description: Library name: EV126_IP


title: HoiH23_MicroC

data_processing:
Raw reads were mapped to the reference genome using bwa mem (version: 0.7.17-r1188) with the -SP5M option.
The mapped reads were sorted and filtered with pairtools (version 0.3.0). Pairs that mapped within 2 bp distance from each other were considered duplicates and removed. We also discarded reads mapping within the distance of 200 bp, which eliminates self-ligated pairs and reads mapping to adjacent nucleosomes.
Unique valid pair reads from biological and technical replicates were pooled to obtain final chromatin interaction matrices. Contact matrices were normalized with cooler (version 0.8.11) using ICE balancing method.
Insulation profiles were calculated using cooltools insulation module. Chromatin loops were identified using SIP (version 1.6.1).
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: pairs.gz contains a tsv table with valid chromatin contact detected in Micro-C experiments.
Supplementary files format and content: mcool contains chromatin contact matrices at different resolutions
Supplementary files format and content: insulation_score.bedgraph is a BedGraph file with insulation score values
Supplementary files format and content: boundary_strength.bedgraph is a BedGraph file with boundary strength values
Supplementary files format and content: loops.txt includes genomic coordinates of detected chromatin loops
Supplementary files format and content: domains.bed includes genomic coordinates of identified chromatin domains
Library strategy: Micro-C

organism: Cladtertia collaboinventa

source_name: Cladtertia collaboinventa

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Micro-C libraries were prepared as previously described by Hsieh et al., 2020 (PMID: 32213323) and Krietenstein et al. 2020 (PMID: 32213324).

value: Whole-organism


title: 293T_IFIT1:FLAGoe_FLAG_input_VSV_rep1

description: Library name: EV125_input


title: MDA-MB-231 Pladienolide B treated replica 3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: hg38
Supplementary files format and content: deseq2_norm_with_annotations.txt: Gene expression values normalized by DESeq2 unsing FAST DB v2021_3 annotations

growth_protocol: MDA-MB-231 cells were grown in RPMI medium (Euroclone), supplemented with 10% fetal bovine serum, Sodium Pyruvate, HEPES, penicillin and streptomycin (GIBCO, Life Technologies) and glucose (Thermo Fisher)

extract_protocol:
total RNA was extracted and DNAse treated using the RNEasy mini kit (Qiagen) according to manufacturer’s instruction
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand).

treatment_protocol: 24hrs post-seeding MDA-MB-231 cells were treated with Pladienolide B (10nM, 6hrs), Indisulam (3.3µM, 12hrs) or DMSO, as control.

value: triple negative breast cancer cell line

value: Pladienolide B 10 nM

tag: time

value: 6 hrs


title: Sros_MicroC

organism: Salpingoeca rosetta

source_name: Salpingoeca rosetta

value: ATCC PRA-390

value: chain colonies and swimmers

value: wild type

value: 0.05 mM aphidicolin for 18 hours


title: Sros_ChIP_H3K4me3

value: H3K4me3, Millipore, 07-473


title: 4L_SMARCB1_ChIP

first: Elena

last: Grossi

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: 4L_SMARCB1_ChIP

data_processing:
Single-end reads were trimmed with Trimmomatic, paired reads with NGmerge.
Reads were aligned to GRCh38/hg38 using Bowtie2 with standard parameters and quality was assessed using fastQC.
samtools was used to generate bam files and filter out low quality, mitochondrial and duplicated reads.
bigwig files were generated from filtered bam files using deepTools bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: skin

growth_protocol: Melanoma cells were maintained in DMEM, 10% FBS and 1X penicillin-streptomycin. Primary normal human epithelial melanocytes (NHEM - batches SW5, SW11 and NHM1) were cultured in Melanocyte Growth Media 254, 1X HMGS, 0.2 mM CaCl2 and 10 ng/mL PMA.

extract_protocol:
For ChIP-seq: For histone modifications, 10-15M cells were crosslinked with 1% Formaldehyde; For chromatin remodelers and TFs, 10-40M cells were double cross-linked with 0.25 M disuccinimidyl glutarate (DSG), followed by 1% formaldehyde. Nuclei were isolated and lysed, and chromatin was fragmented by sonication. Extracts were incubated with specific antibodies O/N, followed by 2h incubation with magnetic Protein A+G beads. After extensive washes, DNA was eluted from the beads and reverse crosslinked. For ChIC: Chromatin Immuno Cleavage (ChIC or CUT&RUN) was performed using CUTANA ChIC/CUT&RUN kit following manufacturer’s protocol.
Libraries for ChIP-seq were prepared according to Carcamo et al., Cell Rep 39, 110637. 10.1016/j.celrep.2022.110637. Libraries for ChIC were prepared using NEBNext Ultra II DNA library kit, following manufacturer’s recommendations.

value: skin

value: melanoma

value: BRAFV600E subtype

value: metastatic

tag: batch

value: SMARCB1 - Thermo Fisher A301-087A


title: NHEM_H2AK119ub_ChIP

description: Library name: SW11_H2AK119ub_ChIP

source_name: neonatal foreskin

value: neonatal foreskin

value: NHEM

value: normal

value: H2AK119ub - Cell signaling #8240


title: 4L_H2AK119ub_ChIP

description: Library name: 4L_H2AK119ub_ChIP


title: 293T_IFIT1:FLAGoe_FLAG_IP_VSV_rep1

description: Library name: EV125_IP

value: IFIT1:FLAG o/e

value: VSV infected


title: 293T_control_FLAG_input_VSV_rep1

description: Library name: EV124_input

value: WT


title: Sros_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: Sros_ChIP_H3K4me1

value: H3K4me1, Cell Signaling, 5326S


title: MDA-MB-231 Pladienolide B treated replica 1

value: triple negative breast cancer cell line

value: Pladienolide B 10 nM

value: 6 hrs


title: MOLM13, shBP3-2, total RNA, rep1

value: Human acute myeloid leukemia (AML) cells