title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: Control R1


title: H7_Normoxia_Primed_Batch1

status: Public on Mar 07 2024

type: RNA

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

hyb_protocol: Cyanine 3-labeled cRNAs were hybridized onto Agilent Whole Human Genome kit 4 x 44K slides (Catalog number G4112F, Agilent Technologies) containing 44,397 oligonucleotide probes in 2X Hi-RPM Hybridization buffer (Catalog number 5188-5242, Agilent Technologies) at 65°C for 17 hours at 10 r.p.m. as recommended.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: Sample amplification and labeling were carried out using the Low Input Quick Amp labeling Kit (Catalog number 5190-2305, Agilent Technologies, Santa Clara, CA). Briefly, total RNAs (200 ng) were reverse transcribed into cDNAs using T7 primer mix in 5X First Strand Buffer, 0.1 M DTT, 10 mM dNTP Mix, and Affinity Script RNase Block Mix. The cDNAs were used to synthesize Cy3-labeled cRNAs in a reaction containing nuclease-free water, 5X Transcription Buffer, 0.1 M DTT, NTP Mix, T7 RNA polymerase blend, and Cyanine 3-CTP. The RNeasy Mini Kit (QIAGEN) was used to purify the linearly amplified cRNA samples. Cyanine 3-labeled cRNAs were measured using the NanoDrop Spectrophotometer.

growth_protocol: Three NIH registered human embryonic stem cell (hESC) lines, H1 (WA01, registration number 0043), H7 (WA07, registration number 0061), and H9 (WA09, registration number 0062), were used in this study. All three hESC lines were obtained from WiCell Research Institute (Madison, WI) and previously extensively characterized in our NIH Stem Cell Unit (Chen et al., 2014a; Chen et al., 2012; Mallon et al., 2013). More detailed information regarding these hESC lines is available at the website of the NIH Stem Cell Unit (stemcells.nih.gov/research/).

extract_protocol: RNA was extracted by using the basic Trizol protocol (Invitrogen Inc., Carlsbad, CA) with slight modifications. Briefly, hESCs per sample were dissolved in 1 mL of the Trizol solution and stored in - 80°C freezer prior to use. HESC lysates were further subjected to chloroform extraction and isopropanol precipitations. A DNA-Free kit (Applied Biosystems/Ambion, Austin, TX) was used to remove genomic DNA contamination. The quality of RNAs was agarose gel verified. RNA concentration was determined by using the ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies Wilmington, DE).

treatment_protocol: The human primed hESC lines H1, H7, and H9 (at passages 55, 57, and 56, respectively) were used to generate naïve-like hESCs. After 3-day induction or selection of primed hESCs in RSeT medium, the cell colonies (in each well) were dissociated as a single-cell suspension by TrypLE™ Express (ThermoFisher Scientific, REF number 12604-013) and passaged on mouse embryonic fibroblast (MEF) feeder in a 1:6 split ratio. The cells were grown in a humidified incubator with 5% CO2, 3% O2 (hypoxia), and 20% O2 (normoxia). The ROCK inhibitor Y-27632 (10 µM) was added to enhance single-cell plating efficiency for the initial 3 passages. The RSeT naïve-like hESCs were fully characterized at passages 4 and 10 in this study. Two batches (Batch1 and Batch2) of primed hESCs (at passages 55, 56, and 57) were used as controls for comparison.

tag: line

tag: growth condition

value: Normoxia

tag: state

value: Primed

tag: passage

tag: batch


title: Caco2 185+5.7kb del2.1kb #314 viewpoint int1 Rep. 2

type: SRA

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 4C-seq library with the CFTR intron 1 region as the viewpoint

library_source: genomic

data_processing:
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: Aligned 4C-seq of each sample of at a single viewpoint in bigWig format

molecule: genomic DNA

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925).
All libraries were constructed with Illumina sequencing adapters as per PMID: 31351925.
4C-seq

tag: cell line

tag: cell type

value: human colorectal adenocarcnioma cell line

tag: genotype


title: H1_Hypoxic_Primed_Batch1

value: Hypoxic


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA R1

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) reads.
Assembly: hg38

source_name: colorectal carcinoma cell line

growth_protocol: HCT116 + Rad21-mAID-mClover cells were cultured in glutamax McCoy's 5A Modified Medium supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were treated with DMSO and 500uM IAA for 1 hour before fixation. G1 cells were isolated by FACS.

tag: tissue

value: colorectal carcinoma cell line


title: Caco2 185+5.7kb del2.1kb #314 viewpoint int1 Rep. 1


title: intestinal organoids, DMSO_2

city: Basel

first: Clara

last: Baader

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

library_source: transcriptomic

data_processing:
Sequenced reads were aligned using the qAlign tool
Raw counts were optained using the qCount tool (QuasR package, version 1.32.0)
Count table was filtered to only keep genes which had at least 1 cpm in at least 3 samples
Differential gene expression was calculated edgeR (Bioconductor, version 3.34.0)
Assembly: BSgenome.Mmusculus.UCSC.mm10
Supplementary files format and content: Raw counts expression matrix .txt file

organism: Mus musculus

source_name: small intestine

extract_protocol:
Organoids were digested to single cells and RNA extracted using RNeasy RNA purification Kit.
200ng of total RNA was used as input for the Illumina Stranded mRNA Prep

treatment_protocol: Organoids were treated for 24h with 5uM of NIBR-LTSi or corresponding amounts of DMSO

value: small intestine

value: organoid

tag: treatment

value: control


title: H9_Normoxia_RSeT_Passage4

value: Naive-like


title: H7_Normoxia_RSeT_Passage4


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 and Ethanol for 1 hour before fixation. G1 cells were isolated by FACS.


title: C_BT_mCD45

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data analysis was executed utilizing the Cell Ranger Software Suite (10x Genomics). The binary base call (BCL) files extracted from the sequencer were employed as inputs for the Cell Ranger pipeline to produce the digital expression matrix for each sample. Subsequently, the matrix, along with the features and barcodes, was imported into R using the read10X() and CreateSeuratObject functions to construct the count matrix and Seurat objects for further downstream analysis.
Assembly: hg38
Supplementary files format and content: Cell-gene matrix, barcodes and genes

source_name: Immune cells

extract_protocol:
Bone marrow cells (the tumor site) harvested from experimental animals at Day 28 were subjected to FACS sorting for isolating mouse immune cells (mouse CD45+; Sample_01: blank mice, Sample_02: vehicle treated, Sample_03: BCAR-T treated, Sample_04: Allo15BCAR-NKT treated). Cells isolated from 10 experimental mice were combined for each group.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Bone marrow

tag: time point

value: Immune cells


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA + ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 and 500uM IAA for 1 hour before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #314 viewpoint prom Rep. 2

description: 4C-seq library with the CFTR promoter region as the viewpoint


title: Caco2 185+5.7kb del2.1kb #314 viewpoint prom Rep. 1


title: pbmc

city: Wuhan

first: Pingping

last: Han

state: Hubei

address: Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
Sus scrofa genome Sscrofa 11.1 and annotation GTF (v11.1.97) from Ensemble were used to build the reference genome index (Yates et al., 2020). The annotation GTF file was modified to include both gene symbol (if available) and Ensembl ID as a gene reference (e.g. GZMA_ENSSSCG00000016903) using custom Perl scripts. Processed paired end reads were aligned and gene expression count matrices generated using the CellRanger (v6.0.2; 10X Genomics) with default parameters.(cellranger_barcodes.tsv.gz,cellranger_features.tsv.gz,cellranger_matrix.mtx.gz)
Low-quality cells (with < 500 detected genes and < 1,000 unique molecular identifiers (UMIs) per cell, and mitochondrial gene content per cell > 10%) were excluded. To further refine the dataset, the Scrublet python package (v0.2.3) was employed to identify and remove doublet cells. A preset doublet formation rate of 0.06 was used for samples generated in this study. The cells with doublet probability score > 0.25 were removed. The filtered data were stored in CellRanger format.(Doublet_removal_barcodes.tsv.gz,Doublet_removal_features.tsv.gz,Doublet_removal_matrix.mtx.gz)
Assembly: Sscrofa 11.1
Supplementary files format and content: Tab-separated raw values files and matrix files
Supplementary files format and content: Tab-separated double-cell-removed value files and matrix files

organism: Sus scrofa domesticus

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples (2 mL) were collected into EDTA anticoagulant tube and gently inverted 2-3 times to ensure thorough mixing. Subsequently, the mixed blood samples were transferred to 15 mL centrifuge tube and treated with 6 mL of red blood cell lysis solution for 15 min, followed by centrifugation at 1600 rpm for 10 min at 4℃ to collect cell pellets. The cell pellets were then re-suspended in cold phosphate-buffered saline (PBS), passed through a 100 μm cell strainer, and incubated with 3 μL CD3ε antibody (clone BB23-8E6-8C8, BD Pharmingen) for 30 min at 4℃ in the dark, followed by FACS to obtain living CD3+ PBMCs. The cell viability assay using trypan blue staining. After cell counting, the samples from the three healthy pigs were mixed in equal volumes to obtain 9×105 cells. The mixed cells were used for constructing 10× genomics sequencing library and subsequent sequencing by Genergy Biotechnology (Shanghai, China)
RNA libraries were prepared with Chromium Single cell 3'Reagent v2 Kits according to the manufacturer's protocol.

value: Peripheral blood

value: Peripheral blood mononuclear cells

value: healthy


title: intestinal organoids, NIBR_LTSi_1

value: NIBR-LTSi


title: Caco2 185+5.7kb del2.1kb #314 viewpoint -20.9kb Rep. 2

description: 4C-seq library with the CFTR -20.9kb region as the viewpoint


title: 2_month

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: knee joint synovium

extract_protocol:
We harvested synovial and fat pad cells as described above from control (2-month-old), 1-week DMM (DMM at 2 months of age and tissue harvest at 1 week later), and 2-month DMM (DMM at 2 months of age and tissue harvest at 2 months later) mice. Briefly, after euthanasia, mouse knee joints were harvested and washed with ice-cold PBS. The joint capsule was opened by reversing the quadricep to dissect synovial and fat pad tissues out under the microscopy. Tissues from 5-10 mice were combined and digested by 0.25% trypsin-EDTA for 30 min first, followed by another 300 U/mL type I collagenase digestion for 30 min. Cells from the second digestion were resuspended into FACS buffer containing 25 mM HEPES (Thermofisher scientific) and 2% FBS in PBS and sorted for live cells using Influx B (BD Biosciences, San Jose, CA).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: knee joint synovium

value: synovium cell

value: wt


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: Control R3

treatment_protocol: Cells were treated with DMSO and Ethanol for 1 hour before fixation. G1 cells were isolated by FACS.


title: intestinal organoids, DMSO_3


title: 1_week

description: 10x Genomics


title: SHARPIN patient post-treatment (sample 6)

city: Cologne

first: Hirotsugu

last: Oda

state: NRW

address: Joseph-Stelzmann-Str. 26

department: CECAD

country: Germany

institute: University of Cologne

data_processing:
Sequenced reads were mapped against the human reference genome (GRCh38) using HISAT2. Mapped reads were quantified using HTSeq.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
Whole blood was collected from patients and controls in PAX tubes and RNA was extracted using PAXgene Blood RNA Kit (Qiagen).
Total RNA with high quality (RIN > 8) was used for cDNA library preparation using the NEBNext Ultra II Directional RNA library preparation kit with NEBNext Poly(A) mRNA magnetic isolation module and NEBNext Globin and rRNA Depletion kit (E7765, E7490 and E7755, New England Biolab).

value: Whole blood

value: SHARPIN deficiency

value: Anti-TNF


title: SHARPIN patient post-treatment (sample 5)


title: Control

description: 10x Genomics


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA R3

value: colorectal carcinoma cell line


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: ICRF-193 R3


title: Caco2 185+5.7kb del2.1kb #314 viewpoint -20.9kb Rep. 1

value: human colorectal adenocarcnioma cell line


title: PE4H_4

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

description:
mouse with humanized homozygous APOE4 allele crossed with heterozygous P301S tau transgenic line PS19
PE4H_4

data_processing:
Bioinfomatics analysis was performed by LC Sciences
Cutadapt and in-house perl scripts to remove reads with adaptor contamination and low quality bases.
HISAT2 was used to map reads to the genome.
StringTie and ballgown was used to estimate expression levels of all transcripts and genes
Differential expression analysis was performed with DESeq2 and edgeR
GO and KEGG enrichment analysis was performed with in-house perl-scripts (LC Sciences)
Assembly: GRCm38.p5/v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: forebrain

extract_protocol:
RNA was extracted from frozen, pulverized forebrains using TRIzol reagent (Invitrogen) followed by an RNeasy mini column (Qiagen) with an on-column DNase treatment.
RNA sequencing libraries were constructed using Illumina's TruSeq-stranded mRNA sample preparation protocol by LC Sciences.

value: forebrain


title: H1_Normoxia_Primed_Batch1

value: Normoxia

value: Primed


title: H7_Hypoxic_Primed_Batch1

value: Hypoxic


title: H1_Normoxia_RSeT_Passage4

value: Naive-like


title: intestinal organoids, NIBR_LTSi_2

value: small intestine

value: organoid


title: intestinal organoids, DMSO_1

value: control


title: SHARPIN patient post-treatment (sample 3)


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA + ICRF-193 R3


title: PE4H_3

description:
mouse with humanized homozygous APOE4 allele crossed with heterozygous P301S tau transgenic line PS19
PE4H_3


title: Caco2 185+5.7kb del2.1kb #314 viewpoint -80.1kb Rep. 1

description: 4C-seq library with the CFTR -80.1kb region as the viewpoint


title: PE4H_2

description:
mouse with humanized homozygous APOE4 allele crossed with heterozygous P301S tau transgenic line PS19
PE4H_2


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: Control R1

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38

treatment_protocol: Cells were treated with DMSO and Ethanol for 2 hours before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #78 viewpoint +48.9kb Rep. 2

description: 4C-seq library with the CFTR +48.9kb region as the viewpoint


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA R1

treatment_protocol: Cells were treated with DMSO and 500uM IAA for 2 hours before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #78 viewpoint int1 Rep. 2


title: Caco2 185+5.7kb del2.1kb #78 viewpoint +48.9kb Rep. 1


title: PE4H_1

description:
mouse with humanized homozygous APOE4 allele crossed with heterozygous P301S tau transgenic line PS19
PE4H_1


title: Control 3

value: Wild type

value: No


title: Control 4


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 and Ethanol for 2 hours before fixation. G1 cells were isolated by FACS.


title: PE3H_4

description:
mouse with humanized homozygous APOE3 allele crossed with heterozygous P301S tau transgenic line PS19
PE3H_4


title: Caco2 185+5.7kb del2.1kb #78 viewpoint int1 Rep. 1


title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Async untreated R1

source_name: uterine/cervical adenocarcinoma cell line

growth_protocol: HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Untreated control cells.

value: HeLa-S3 (CCL-2.2)


title: SHARPIN patient post-treatment (sample 4)


title: PE3H_2

description:
mouse with humanized homozygous APOE3 allele crossed with heterozygous P301S tau transgenic line PS19
PE3H_2


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA + ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 and 500uM IAA for 2 hours before fixation. G1 cells were isolated by FACS.


title: PE3H_3

description:
mouse with humanized homozygous APOE3 allele crossed with heterozygous P301S tau transgenic line PS19
PE3H_3


title: Caco2 185+5.7kb del2.1kb #78 viewpoint prom Rep. 2


title: Control 2


title: Control 1


title: SHARPIN patient pre-treatment (sample 2)


title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: DMSO R1

treatment_protocol: Cells were treated with DMSO for 4 hours before fixation.

value: uterine/cervical adenocarcinoma cell line


title: Caco2 185+5.7kb del2.1kb #78 viewpoint prom Rep. 1


title: PE3H_1

description:
mouse with humanized homozygous APOE3 allele crossed with heterozygousP301S tau transgenic line PS19
PE3H_1


title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R1

treatment_protocol: Cells were treated with 5uM Camptothecin for 4 hours before fixation.


title: Caco2 185+5.7kb del2.1kb #78 viewpoint -20.9kb Rep. 2


title: SHARPIN patient pre-treatment (sample 1)

value: Whole blood


title: PE2H_3

description:
mouse with humanized homozygous APOE2 allele crossed with heterozygous P301S tau transgenic line PS19
PE2H_3


title: PE2H_2

description:
mouse with humanized homozygous APOE2 allele crossed with heterozygous P301S tau transgenic line PS19
PE2H_2


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: t0 Mitotic R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole.


title: Caco2 185+5.7kb del2.1kb #78 viewpoint -80.1kb Rep. 2


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: Async untreated R2


title: HEK293T, clone 30 ∆ZFP143 3h, Micro-C, rep. 2

city: Cambridge

first: Domenic

last: Narducci

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Assembly: hg38
*library strategy: Micro-C
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. These filtered reads were subsequently converted to .cool format using cooler (v0.9.1) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Assembly: mm39;hg38
Supplementary files format and content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions

growth_protocol: mESCs were cultured under 5% CO2 at 37°C under feeder-free conditions. The mESCs were grown in medium consisting of KnockOut DMEM (ThermoFisher #10829-018) supplemented with 15% FBS, 1000 U/mL LIF (homemade), 1 mM MEM Non-Essential Amino Acid Solution (ThermoFisher #11140050), 2 mM GlutaMAX supplement (ThermoFisher #35050061), 100 μg/mL Penicillin-Streptomycin (ThermoFisher #15140122), 0.1 mM 2-mercaptoethanol (ThermoFisher #31350010), 10 μM MEK inhibitor (Tocris #PD0325901), and 3 μM GSK inhibitor (Sigma-Aldrich #SML1046) on plates pre-coated with sterile 0.1% gelatin (Sigma-Aldrich, G1890). The mESCs were passaged every 2 days by dissociation with TrypLE Express Enzyme (ThermoFisher #12605028), and half the medium was replaced daily.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-10 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

treatment_protocol: For depletion of ZFP143 in the clone A and clone B cell lines, the cells were incubated in media containing 100 μM 5-Ph-IAA (MedChemExpress #HY-134653) and 300 nM HaloPROTAC3 (Promega # GA3110), and for depletion of CTCF in the same lines the, the cells were incubated in media containing 100 nM dTAG-13 (Tocris # 6605) for 3 hours. For the depletion of ZFP143 in the clone D cell line, the cells were incubated in media containing 100 nM dTAG-13, and for the depletion of ZNF143 in the clone 30 HEK293T cell line, the cells were incubated in media containing 500 μM IAA for 3 hours.

value: Clone 30, Homozygous ZNF143-AID1

value: 500uM IAA

tag: time

value: 3 hours


title: PE2H_1

description:
mouse with humanized homozygous APOE2 allele crossed with heterozygous P301S tau transgenic line PS19
PE2H_1


title: CUMC5979_Ispinesib treated

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Microwell-based scRNA-seq, fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix

data_processing:
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample. For samples had been sequenced on both Illumina NextSeq 500 and NovaSeq 6000, we combined the addresses from the NextSeq 500 and the corrected addresses from the NovaSeq 6000.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected. Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded. Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding to beads associated with cells in our microwell system using the emptyDrops algorithm from Lun et al, Genome Biology, 2019.
We removed CBs that satisfied any of the following criteria 1) fractional alignment to the mitochondrial genome greater than 1.96 standard deviations above the mean, 2) ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons greater than 1.96 standard deviations above the mean, 3) average number of reads per molecule or average number of molecules per gene >2.5 standard deviations above the mean for a given sample, 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4..
Assembly: Genome_build: GRCh38
Supplementary files format and content: Gene expression count matrix files are tab-delimited text files that contain the gene expression level of each individual cell. The file header contains cell-barcodes and cell malignant annotations. The first two columns being the gene IDs and gene symbols.

source_name: acute slice culture of glioma resection

growth_protocol: Tumor specimens were collected immediately after surgical removal and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. Preparation of ex vivo tissue slices was modified from methods described previously by Zhao et al, Genome Medicine, 2021. Briefly, the collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2. Then, the medium was replaced with pre-warmed medium containing drugs with 1.8 nM Ispenesib or corresponding volume of vehicle (DMSO). Slices were then cultured with the treatment medium in a humidified incubator at 37℃ and 5% CO2 for 18 hrs before being collected for dissociation.

extract_protocol:
Collected tissue samples or tissue slices were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
Microwell 3' scRNA-seq were performed as described in Yuan et al. Sci Rep (2016). Briefly, individual single cell was compartmentalized with a barcoded-mRNA-capture-bead (MACOSKO-2011-10, ChemGenes) and lysed in microwell-based platform, mRNA were captured and reverse transcribed on the bead, and cDNA-beads were pooled for PCR amplification and illumina Nextera library construction for each sample.

value: acute slice culture of glioma resection

tag: age

tag: gender

value: Male

tag: location

value: right temporal

tag: diagnosis

value: Glioblastoma, WHO Grade IV

value: 1.8 nM Ispenesib for 18 hrs


title: CUMC5966_Ispinesib treated

value: Female

value: left parieto-occipital


title: HEK293T, clone 30 ∆ZFP143 3h, Micro-C, rep. 1


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 0-6hrs DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t0hr. Cells were fixed at t6hr.


title: HEK293T, clone 30 untreated, Micro-C, rep. 2


title: E4H_3

description:
mouse with humanized homozygous APOE4 allele
E4H_3

value: forebrain


title: HEK293T, clone 30 untreated, Micro-C, rep. 1


title: Caco2 viewpoint +48.9kb Rep. 2

value: human colorectal adenocarcnioma cell line

value: WT


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 0-6hrs Camp R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 5uM Camptothecin was added at t0hr. Cells were fixed at t6hr.


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 2-8hrs DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr. Cells were fixed at t8hr.


title: Caco2 viewpoint int1 Rep. 2

description: 4C-seq library with the CFTR intron 1 region as the viewpoint


title: Caco2 185+5.7kb del2.1kb #314 viewpoint -80.1kb Rep. 2


title: AlloBCAR-NKT, scTCR-seq

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The raw sequencing data were processed and mapped to the human TCR reference genome (hg38) using the Cell Ranger VDJ software. The frequencies of the α or β chain recombination were plotted to identify the unique TCR repertoires in each cell population.
Assembly: hg38
Supplementary files format and content: Sample_matrix.mtx.gz, a part of the filtered feature-barcode matrix which contains only detected cell-associated barcodes
Supplementary files format and content: Sample_features.tsv.gz, a part of the filtered feature-barcode matrix which contains only detected cell-associated barcodes
Supplementary files format and content: Sample_barcodes.tsv.gz, a part of the filtered feature-barcode matrix which contains only detected cell-associated barcodes
Library strategy: scTCR-seq

source_name: NKT cell

extract_protocol:
scTCR-seq was utilized to study the TCR sequencing of Allo/15BCAR-NKT cells. Five different cell types were delivered to the UCLA TCGB Core for library construction and scTCR-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: AlloBCAR-NKT

value: In vitro culture


title: E4H_1

description:
mouse with humanized homozygous APOE4 allele
E4H_1


title: E3H_2

description:
mouse with humanized homozygous APOE3 allele
E3H_2


title: PBMC-NKT, scTCR-seq

description: 10x Genomics

value: PBMC-NKT


title: E4H_2

description:
mouse with humanized homozygous APOE4 allele
E4H_2


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: t0 Mitotic R2

value: HeLa-S3 (CCL-2.2)

value: uterine/cervical adenocarcinoma cell line


title: Caco2 185+5.7kb del2.1kb #78 viewpoint -20.9kb Rep. 1

description: 4C-seq library with the CFTR -20.9kb region as the viewpoint


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: t2 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. Cells were fixed at t2hr.


title: Caco2 viewpoint -20.9kb Rep. 2


title: ASCT1 after second shot [P3-T3]

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v6.0.0) and the GRCh38 genome annotation
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression) and contig tables (VDJ)
Library strategy: TCR-seq

source_name: blood

extract_protocol:
Peripheral mononuclear blood cells (PBMCs) were isolated from heparinized whole blood by density gradient centrifugation and frozen at -80 °C until further analysis.
After thawing of PBMCs, we continued to treat samples individually, using one 10x lane per sample. Samples were converted to barcoded scRNA-seq libraries using a Chromium Next GEM Single Cell V(D)J Reagent Kit (10x Genomics, Pleasanton, CA, USA) according to manufacturer’s instructions. 5’ Library Kit was used to prepare single-cell RNA libraries according to the manufacturer’s protocol. Full-length TCR/BCR V(D)J segments were enriched from amplified cDNA from 5′ libraries via PCR amplification using a Chromium Single-Cell V(D)J Enrichment Kit according to the manufacturer’s protocol (10x Genomics).

value: blood

tag: donor

tag: timepoint

value: after second shot


title: Allo15BCAR-NKT, scTCR-seq

description: 10x Genomics

tag: growth condition


title: Caco2 viewpoint +48.9kb Rep. 1


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 0-6hrs DMSO R2


title: Caco2 viewpoint int1 Rep. 1


title: Caco2 viewpoint prom Rep. 2

description: 4C-seq library with the CFTR promoter region as the viewpoint


title: ASCT1 after first shot [P3-T2]

value: after first shot


title: Caco2 viewpoint -20.9kb Rep. 1


title: Caco2 185+5.7kb del2.1kb #78 viewpoint -80.1kb Rep. 1

description: 4C-seq library with the CFTR -80.1kb region as the viewpoint


title: E2H_2

description:
mouse with humanized homozygous APOE2 allele
E2H_2


title: E3H_1

description:
mouse with humanized homozygous APOE3 allele
E3H_1


title: Caco2 viewpoint prom Rep. 1


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: t2 R2


title: E2H_3

description:
mouse with humanized homozygous APOE2 allele
E2H_3


title: E2H_1

description:
mouse with humanized homozygous APOE2 allele
E2H_1


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 0-6hrs Camp R2


title: AlloNKT, scTCR-seq

description: 10x Genomics

value: AlloNKT


title: PE2H_4

description:
mouse with humanized homozygous APOE2 allele crossed with heterozygous P301S tau transgenic line PS19
PE2H_4


title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R2


title: PBMC-Tc, scTCR-seq

description: 10x Genomics

source_name: T cell

value: PBMC-Tc


title: Caco2 viewpoint -80.1kb Rep. 1


title: Caco2 viewpoint -80.1kb Rep. 2


title: DpnII Hi-C on HeLa S3 MR DMSO or Camp treatment: 2-8hrs DMSO R2


title: ASCT3 after second shot [P2-T3]


title: ASCT1 pre-vaccination [P3-T1]

value: pre-vaccination


title: inguinal white adipose tissue, Cebpa_iWAT

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

data_processing:
Sequencing reads were demultiplexed, trimmed, and aligned using pipe4C pipeline.
The generated SAM files were converted to BAM files, indexed, and sorted with Samtool (v1.11).
4C-seq data analysis was performed using the pipe4C and r3Cseq package.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text and wig files

source_name: Inguinal

growth_protocol: 3T3-L1 cells were grown in DMEM supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Invitrogen) at 37℃ in 5% CO2. Adipocyte differentiation of  3T3-L1 cells was performed according to a standard adipogenic MDI cocktail (MDI: IBMX, dexamethasone, and insulin).After reaching confluence, the medium was changed, and the cells were incubated for 48 h. To induce differentiation, the cells were incubated for 48 h in DMEM supplemented with MDI cocktail (2 μg/mL of dexamethasone, 0.5 mM IBMX, and 10 μg/mL of insulin) and 10% FBS. Then, the medium was changed with DMEM containing 10 µg/mL insulin and 10% FBS every two days until the cells exhibited an adipocyte phenotype at day 7 post induction.

extract_protocol:
For cultured cells, 1 × 107 cells were cross-linked with fresh 2% formaldehyde for 10 min at room temperature. For adipose tissue, 1g frozen adipose tissue were crushed into powder using a mortar and pestle pre-chilled in liquid nitrogen, and the powder was suspended in PBS and fixed with fresh 2% formaldehyde for 30 min at RT. Crosslinking was quenched with glycine to a final concentration of 0.13 M. Crosslinked cells were lysed for 15 min on ice in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, and 0.2% NP-40 supplemented with protease inhibitor. Nuclei were isolated by centrifugation and by removing the supernatant. The cross-linked chromatin was digested using primary restriction enzyme DpnII (New England Biolabs) and religated by T4 DNA ligase (New England Biolabs) with rotation overnight at 16℃. After reversal of crosslinking and RNA removal, DNA was extracted by phenol/chloroform and purified by ethanol precipitation. Re-ligated DNA was digested using secondary restriction enzyme NlaIII (New England Biolabs) and religated by T4 DNA ligase (New England Biolabs) overnight at 16℃. DNA was extracted by phenol/chloroform and purified using a QIAquick PCR Cleanup kit.
The DNA product served as the template for 4C-PCR. 4C PCR was performed with a total amount of input of 3.2 μg and separated into 16 reactions. Two-step PCR strategy was used to construct 4C-seq sequencing library. PCR products were pooled. The PCR products were then run on 2% agarose gels. Smears from 200 to 800 bp were excised on the gel, and unwanted PCR product bands were removed. The DNA was purified using Qiagen PCR cleanup kit and eluted in 10 mM Tris-HCl (pH 7.5). 4C-seq libraries were sequenced using the Illumina NovaSeq 6000 platform (Illumina).

tag: strain

value: Inguinal

tag: developmental stage

value: 8 weeks old


title: DpnII Hi-C on HeLa S3 MR DMSO or Etop added at t0: t0 Mitotic R1


title: ASCT3 after first shot [P2-T2]


title: mRNA-Seq 3T3-L1, Cebpa-mRNA-Seq 3T3-L1, rep2

source_name: Mouse embryo

value: Preadipocytes

value: Mouse embryo


title: DpnII Hi-C on HeLa S3 MR DMSO or Etop added at t0: t6 DMSO R1


title: DpnII Hi-C on HeLa S3 MR DMSO or Etop added at t0: t6 500nM Etop R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 500nM Etoposide was added at t0hr. Cells were fixed at t6hr.


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint prom Rep. 1

value: human bronchial epithelial cell line


title: mRNA-Seq 3T3-L1-AD, Cebpa-mRNA-Seq 3T3-L1-AD, rep2

value: Adipocytes

value: Adipogenic induced differentiation day 7


title: mRNA-Seq 3T3-L1, Cebpa-mRNA-Seq 3T3-L1, rep1


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint -20.9kb Rep. 1


title: mRNA-Seq 3T3-L1-AD, Cebpa-mRNA-Seq 3T3-L1-AD, rep1


title: ASCT2 after second shot [P1-T3]


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint -20.9kb Rep. 2


title: ASCT3 pre-vaccination [P2-T1]


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint -80.1kb Rep. 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: t0 Mitotic R1


title: input_elf7, rep2

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

data_processing:
Raw reads were trimmed using cutadapt v4.4 with parameters -q 15,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 20
Clean reads were aligned to the TAIR10 genome using bowtie2 v2.5.1 with default parameters
Duplicates were marked with sambamba v1.0. Alignments were filtered using samtools (v1.17) view with options -q 5 -F 4 -F 1024
BigWig files were obtained using bedtools (v2.31.0) genomecov and UCSC bedGraphToBigWig. Bigwigs were scaled to their normalization factors using wiggletools (v1.2.11) scale
For FLAG-ELF7, GFP-VIP3 and Pol II ChIPs, samples were scaled by sequencing depth (CPM). H2Bub samples were normalized by the amount of Drosophila reads in the IP and the input as in Nassrallah et al. 2018
Peaks were called using macs2 v2.2.7.1 with options --keep-duplicates all --nomodel --extsize 200 --broad --broad-cutoff 0.05 -gs 119144248
Assembly: TAIR10
Supplementary files format and content: Raw bigwigs
Supplementary files format and content: broadPeaks

organism:
Arabidopsis thaliana
Drosophila melanogaster

source_name: whole seedlings

extract_protocol:
H2B and H2Bub ChIP-Rx were conducted in parallel using the same two biological replicates of 7-day-old WT and elf7-3 seedlings grown under standard conditions. For each biological replicate, two immunoprecipitations (IP) were performed using an anti-H2Bub antibody (MM-0029-P, Medimabs) and one using an anti-H2B (ab1790, abcam). 100 µg of Arabidopsis chromatin mixed with 3 µg of Drosophila chromatin was used for each IP. DNA eluted from the two technical replicates of H2Bub IP was pooled before library preparation. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). Flag-ELF7 and GFP-VIP3 ChIP-seq was performed using 7-day-old seedlings and an anti-Flag M2 antibody (F1804, Sigma). We used double in vitro crosslinking using 1.5 mM ethylene glycol bis (succinimidyl succinate) for 20 min and then with 1% formaldehyde for 10 min at room temperature. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). ChIP-seq for RNAPII was done using the anti-NRPB1 antibody (active motif, Clone: 4H8) using similar growth conditions and protocol than for H2Bub profiling without Drosophila cells spike-in. Library preparation and sequencing were carried out by the Epigenomics platform at IPS2 (Paris, France).
Libraries were prepared using commercial kits as follows: GFP-VIP3, H2B and H2Bub with NEBNext® Ultra DNA Library Prep for Illumina® kit, PolII with NEBNext® Ultra II DNA Library Prep for Illumina® kit, and Flag-ELF7 with Ovation Ultralow System V2.

value: whole seedlings

value: 7-day-old seedlings


title: ASCT2 after first shot [P1-T2]


title: DpnII Hi-C on HeLa S3 MR DMSO or Etop added at t0: t6 1uM Etop R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 1uM Etoposide was added at t0hr. Cells were fixed at t6hr.

value: HeLa-S3 (CCL-2.2)


title: J1, Input, RA, 48 h

city: Clayton

first: Michael

last: Uckelmann

state: Victoria

address: 23 Innovation Walk

department: Biochemistry

country: Australia

institute: Monash University

description: J1 mES cells

data_processing:
reads were quality-trimmed and adapeters were removed with Trimgalore using paired-end mode and default settings
Reads were aligned to the mouse mm10 reference genome using bowtie2 with options --very-sensitive
PCR duplicates were removed using Picard
read pairs were fixed with Samtools fixmate
BigWigs were generated using bamCoverage with CPM normalisation
Supplementary files format and content: bigWig
Supplementary files format and content: bed files containing peak information

growth_protocol: DMEM, 20 % FBS, 1x non-essential amino acids (Gibco #11140-050), 1x Glutamax (Gibco #35050-061),  PenStrep 100 u/ml (Thermo Fischer), 0.5 x EmbryoMax 2-Mercaptoethanol (Merck Millipore #ES-007-E), 2.5 ug/ml Plasmocin (Invivogen), 1000 U/ml ESGRO Leukemia Inhibitory Factor (LIF) (Merck Millipore)

extract_protocol:
Samples were crosslinked with 1% Formaldehyde for 10 minutes and then sonicated using the Bioruptor, 30 cycels of 30 seconds on and 30 seconds off, total sonication time of 15 minutes
Libraries were constructed using NEBnext ultra II library prep kit

treatment_protocol: 1 uM of retinoic acid for 48 hours, media was refreshed after 24 hours

value: mouse embryonic stem cells

value: wildtype

tag: chip antibody

value: none (input)

value: 1 uM retinoic acid fo r48 hours


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: t2 R1

tag: cell line

value: uterine/cervical adenocarcinoma cell line


title: J1, H3K27me3, RA, 48 h

description: J1 mES cells

tag: cell type


title: input_elf7, rep1

tag: genotype


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint -80.1kb Rep. 1


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint prom Rep. 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr. Cells were fixed at t4hr.

tag: tissue


title: J1, CBX8, RA 48 h,

description: J1 mES cells

tag: treatment


title: input_WT, rep2

value: wild type


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr. Cells were fixed at t4hr.


title: 16HBE14o- -18.5kb del7.1kb #84 viewpoint prom Rep. 2


title: J1, CBX8 knockout, RA, biol rep 2

description: biological replicate 2

data_processing:
reads were quality-trimmed and adapeters were removed with Trimgalore using paired-end mode and default settings
Reads were aligned to the mouse mm10 reference genome using bowtie2 in "very-sensitive" mode
mitochondrial reads were removed using a pythion script from https://github.com/harvardinformatics/ATAC-seq, PCR duplicates were removed using Picard
read pairs were fixed with Samtools fixmate
BigWig files were calculated using BamCoverage with CPM normalisation
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: broadPeak file conataing peak location

source_name: J1 mES cells

extract_protocol: according to ATAC-seq kit from Diagenode (Diagenode cat nr. C01080002).

treatment_protocol: 48 hours of either 1 uM retinoic acid (RA) or an equivalent volume of DMSO

value: J1 mES cells

value: CBX8 knockout

value: RA


title: input_WT, rep1


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 DMSO R1


title: J1, CBX8 knockout, RA, biol rep 1

description: biological replicate 1


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint -20.9kb Rep. 2

data_processing:
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: Aligned 4C-seq of each sample of at a single viewpoint in bigWig format

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925).
All libraries were constructed with Illumina sequencing adapters as per PMID: 31351925.
4C-seq


title: J1, CBX8 knockout, DMSO, biol rep 2

description: biological replicate 2

value: DMSO


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint -20.9kb Rep. 1


title: H2B_elf7, rep1

value: anti-H2B (ab1790, abcam)


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: t0 Mitotic R2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr. Cells were fixed at t8hr.


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint -80.1kb Rep. 2

value: human bronchial epithelial cell line


title: J1, CBX8 knockout, DMSO, biol rep 1

description: biological replicate 1


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint prom Rep. 1


title: H2B_WT, rep2


title: 16HBE14o- -18.5kb del7.1kb #76 viewpoint -80.1kb Rep. 1


title: H2B_WT, rep1


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: t2 R2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 DMSO R2


title: H2Bub_elf7, rep2

value: anti-H2Bub (MM-0029-P, Medimabs)


title: J1, WT, RA, biol rep 2

description: biological replicate 2

value: WT


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint prom Rep. 2


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint prom Rep. 1


title: H2Bub_elf7, rep1

value: whole seedlings


title: J1, WT, DMSO, biol rep 2

description: biological replicate 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 DMSO R2


title: H2B_elf7, rep2

value: 7-day-old seedlings


title: J1, WT, RA, biol rep 1

description: biological replicate 1


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint -20.9kb Rep. 2


title: WT_Ctrl_4

city: Shanghai

first: Wei

last: Gu

state: Shanghai

address: 51 Rijing Road

department: Beigene Institute

institute: Beigene

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Assembly: GRCm38
Supplementary files format and content: Normalized gene counts table and RPKM table

source_name: Intestine epithelium

extract_protocol:
Qiagen Mini RNA extract kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina, following manufacturer's protocol.
Library construction performed by Novogene.co.  Non-directional eukaryotic mRNA library

treatment_protocol: Epithilal tissues were collected by EDTA method 30 days after Tamoxifen injection.

tag: genotyping

value: Wild Type

tag: intestine part

value: Colon


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint -20.9kb Rep. 1


title: H2Bub_WT, rep2


title: H2Bub_WT, rep1


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 ICRF-193 R2

value: HeLa-S3 (CCL-2.2)


title: WT_Ctrl_3


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t0 Mitotic R1


title: ASCT2 pre-vaccination [P1-T1]

value: blood

value: pre-vaccination


title: MTA2_KO_5

value: Mta2 Knock out


title: J1, WT, DMSO, biol rep 1

description: biological replicate 1

value: mouse embryonic stem cells


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint -80.1kb Rep. 2


title: 16HBE14o- -18.5kb del7.1kb #18 viewpoint -80.1kb Rep. 1


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t4 DMSO R1

value: uterine/cervical adenocarcinoma cell line


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 ICRF-193 R2


title: 16HBE14o- -16kb del3.7kb #247 viewpoint prom Rep. 2


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t4 Merb R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 200uM Merbarone was added at t2hr. Cells were fixed at t4hr.


title: WT_Ctrl_2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t0 Mitotic R1

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) reads.
Assembly: hg38


title: C_BT_MM

description: 10x Genomics

data_processing:
Data analysis was executed utilizing the Cell Ranger Software Suite (10x Genomics). The binary base call (BCL) files extracted from the sequencer were employed as inputs for the Cell Ranger pipeline to produce the digital expression matrix for each sample. Subsequently, the matrix, along with the features and barcodes, was imported into R using the read10X() and CreateSeuratObject functions to construct the count matrix and Seurat objects for further downstream analysis.
Assembly: hg38
Supplementary files format and content: Cell-gene matrix, barcodes and genes

source_name: Bone marrow

extract_protocol:
Bone marrow cells (the tumor site) harvested from experimental animals at Day 28 were subjected to FACS sorting for isolating MM-FG cells (GFP+; Sample_02: vehicle treated, Sample_03: BCAR-T treated, and Sample_04: Allo15BCAR-NKT treated). Cells isolated from 10 experimental mice were combined for each group. Preinfusion sampling of in vitro cultured  MM-FG tumor cells (Sample_01) were also also sorted and subjected to scRNA-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

tag: time

value: Tumor cells

value: Bone marrow


title: C_ctrl_MM

description: 10x Genomics


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and was readded at t4hr and t6hr. Cells were fixed at t8hr.


title: WT_Ctrl_1


title: 16HBE14o- -16kb del3.7kb #247 viewpoint prom Rep. 1


title: 16HBE14o- -16kb del3.7kb #247 viewpoint -20.9kb Rep. 2


title: A_MM

description: 10x Genomics

source_name: In vitro

value: In vitro


title: MTA2_KO_3


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and was readded at t4hr and t6hr. Cells were fixed at t8hr.


title: D_BI15

description: 10x Genomics

extract_protocol:
Bone marrow cells (the tumor site) harvested from experimental animals at Day 28 were subjected to FACS sorting for isolating Allo/15BCAR-NKT cells (hCD45+6B11+hTCRαβ+; Sample_05: AlloBCAR-NKT, Sample_08: Allo15BCAR-NKT), BCAR-T cells (hCD45+6B11-hTCRαβ+; Sample_02). Cells isolated from 10 experimental mice were combined for each group. Preinfusion sampling of therapeutical cells (Sample_04: AlloBCAR-NKT, Sample_07: Allo15BCAR-NKT, Sample_01: BCAR-T), and restimulation sampling (one week in vitro stimulation after bone marrow cell collection) of therapeutical cells (Sample_06: AlloBCAR-NKT, Sample_09: Allo15BCAR-NKT, Sample_03: BCAR-T) were also sorted and subjected to scRNA-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: T cells


title: 16HBE14o- -16kb del3.7kb #247 viewpoint -80.1kb Rep. 2

value: human bronchial epithelial cell line


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t0 Mitotic R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole.


title: C_BI15_MM

description: 10x Genomics


title: E3H_3

description:
mouse with humanized homozygous APOE3 allele
E3H_3

value: forebrain


title: 16HBE14o- -16kb del3.7kb #247 viewpoint -20.9kb Rep. 1


title: C_BI15_BM

description: 10x Genomics


title: A_BI15

description: 10x Genomics


title: MTA2_KO_1


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4.5 Txn Inhib R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 200uM DRB and 25uM Triptolide were added at t0. Cells were fixed at t4.5hr.


title: Mouse_colonoid_Ctbp2_KO2

data_processing:
Adapter and low quality bases trimming (Q<20) using Trim Galore! with default parameters
Paired end alignment using STAR with defaut parameters
Generation of counts relative to genes using featureCounts with defaut paramets (unstranded mode)
Generation of normalized read counts and differential expression genes with normal shrinkage mode by DEseq2 package in Rstudio
Assembly: GRCm38
Supplementary files format and content: Normalized gene counts table  (Raw data of sample Satb2_KO1 (A1) and Satb2_KO2 (A3) were processed from GSE167283 )

source_name: 3D cultured mouse colonic organoids

growth_protocol: Mouse colonic organoids were cultured at P2. Lentivirus, contain control, Satb2, Mta2, Chd4, Gatad2a, Smarca5, Smarca4, Smarcd2 and Ctbp2 sgRNA along with Cas9, infected organoids and selected with puromycin.

treatment_protocol: Mouse organoid were differentiated for 4 days. Materigel was removed by Cell recovery solution, pellet organoids were resuspended in RLT lysis buffer (Qigen Kit)

value: Ctbp2 sgRNA

value: Colonic Organoid


title: MTA2_KO_4


title: 16HBE14o- -16kb del3.7kb #169 viewpoint prom Rep. 2


title: D_BI

description: 10x Genomics


title: 16HBE14o- -16kb del3.7kb #247 viewpoint -80.1kb Rep. 1


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4 ICRF-193 R1


title: Mouse_colonoid_Ctbp2_KO1


title: 16HBE14o- -16kb del3.7kb #169 viewpoint prom Rep. 1


title: C_BI_BM

description: 10x Genomics


title: Mouse_colonoid_Smarca5_KO2

value: Smarca5 sgRNA


title: 16HBE14o- -16kb del3.7kb #169 viewpoint -20.9kb Rep. 2


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4.5 Txn Inhib ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 200uM DRB and 25uM Triptolide were added at t0, 30uM ICRF-193 was added at t2.5hr. Cells were fixed at t4.5hr.


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO added at t0. Cells were fixed at t4hr.


title: MTA2_KO_2


title: Mouse_colonoid_Smarca5_KO1


title: A_BI

description: 10x Genomics


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t0 Mitotic R2


title: D_BT

description: 10x Genomics


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4 DMSO R2


title: 16HBE14o- -16kb del3.7kb #169 viewpoint -80.1kb Rep. 2


title: C_BT_BM

description: 10x Genomics


title: 16HBE14o- -16kb del3.7kb #169 viewpoint -80.1kb Rep. 1


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4.5 Txn Inhib R2


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4 ICRF-193 R2


title: A_BT

description: 10x Genomics


title: WK5_BI15

description: 10x Genomics

source_name: In vitro culture

extract_protocol:
scRNA-seq was utilized to study the genome-wide transcriptome profiling of Allo/15BCAR-NKT cells during their in vitro differentiation from gene-engineered HSCs. CB CD34+ HSCs of the same donor were engineered with either Lenti/iNKT-BCAR or Lenti/iNKT-BCAR-IL15 virus, followed by differentiating into AlloBCAR-NKT or Allo15BCAR-NKT cell product, respectively, in the Ex Vivo HSC-Derived CAR-NKT Cell Culture. At day 7, 14, 21, 28 and 42, cell cultures were collected and immediately delivered to the UCLA TCGB Core for library construction and scRNA-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: In vitro culture


title: DpnII Hi-C on HeLa S3 MR Txn and Topo II inhib: t4.5 Txn Inhib ICRF-193 R2


title: 16HBE14o- -16kb del3.7kb #46 viewpoint prom Rep. 1


title: Mouse_colonoid_Smarcd2_KO1

value: Smarcd2 sgRNA


title: Mouse_colonoid_Smarcd2_KO2


title: Mouse_colonoid_Smarca4_KO2

value: Smarca4 sgRNA


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t0 Mitotic R2

value: HeLa-S3 (CCL-2.2)


title: WK4_BI15

description: 10x Genomics


title: Mouse_colonoid_Gatad2a_KO2

value: Gatad2a sgRNA


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 DMSO R2


title: 16HBE14o- -16kb del3.7kb #169 viewpoint -20.9kb Rep. 1


title: WK3_BI15

description: 10x Genomics


title: 16HBE14o- -16kb del3.7kb #46 viewpoint prom Rep. 2


title: Mouse_colonoid_Gatad2a_KO1


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 ICRF-193 R2


title: 16HBE14o- -16kb del3.7kb #46 viewpoint -20.9kb Rep. 1


title: 16HBE14o- -16kb del3.7kb #46 viewpoint -80.1kb Rep. 2


title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: DMSO R2

treatment_protocol: Cells were treated with DMSO for 4 hours before fixation.


title: WK2_BI15

description: 10x Genomics


title: Mouse_colonoid_Smarca4_KO1


title: WK1_BI15

description: 10x Genomics


title: 16HBE14o- -16kb del3.7kb #46 viewpoint -80.1kb Rep. 1


title: Mouse_colonoid_Chd4_KO1

value: Chd4 sgRNA


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t0 Mitotic R3


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 DMSO R3


title: 16HBE14o- viewpoint prom Rep. 2

value: WT


title: WK5_BI

description: 10x Genomics

value: BCAR-T


title: Mouse_colonoid_Mta2_KO1

value: Mta2 sgRNA


title: 16HBE14o- -16kb del3.7kb #46 viewpoint -20.9kb Rep. 2


title: WK4_BI

description: 10x Genomics


title: WK3_BI

description: 10x Genomics


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2 with reaadding: t8 ICRF-193 R3

value: uterine/cervical adenocarcinoma cell line


title: Mouse_colonoid_Mta2_KO2


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: unsorted DMSO R1

treatment_protocol: Cells were treated with DMSO for 2 hours before fixation.


title: 16HBE14o- viewpoint prom Rep. 1


title: Mouse_colonoid_Ctrl_2

value: Ctrl sgRNA


title: 16HBE14o- viewpoint -20.9kb Rep. 2


title: Mouse_colonoid_Chd4_KO2


title: Mouse_colonoid_Ctrl_1


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: G1 sort DMSO R1

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were treated with DMSO for 2 hours before fixation. G1 cells were isolated by FACS.


title: WK1_BI

description: 10x Genomics


title: 16HBE14o- viewpoint -20.9kb Rep. 1


title: 16HBE14o- viewpoint -80.1kb Rep. 2


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: G1 sort ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 for 2 hours before fixation. G1 cells were isolated by FACS.


title: CAR19TIF-2mon-scRNA-seq

city: Beijing

first: Gang

last: Jin

address: Zhongguancun North street

department: Institute for Immunology

institute: Tsinghua University

data_processing:
The ultimate constructed and purified library with the target recovery of ~ 6,000 single cells was sequenced on Illumina Hiseq.
Cell Ranger toolkit (v2.0.0) was used for 10X Genomics scRNA-seq data alignment and quantification.
Bowtie2 was used to get the alignment results.
The generated data files including aligned and filtered reads, barcodes and unique molecular identifiers were processed by Seurat (v3.1.1) for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed file in tsv and mtx file format

source_name: CD8+Thy1.1+ CAR19TIF

extract_protocol:
Two months after transfer, CD8+Thy1.1+ CAR19TIF cells from recipient mice were sorted by flow cytometry
the isolated sample was directly processed for scRNA-seq library preparation by using Chromium Single Cell 3' Library& Gel Bead Kit v2 (10X Genomics) according to manufacturer’s protocol.

value: CD8+Thy1.1+ CAR19TIF


title: Allo15BCAR-NKT Donor 3

first: Shuo

state: CA

address: 630 Charles E Young Dr S

institute: UCLA

data_processing:
The raw bisulfite sequencing reads were trimmed by cutadapt to remove sequencing adapters.
The trimmed reads were then aligned to hg19 reference genome by Bismark.
Then duplicated reads from PCR amplification were identified and removed by Bismark.
The deduplicated reads were then sorted and indexed using samtools.
The methylation level was calculated at every CpG site by Bismark.
Assembly: hg19
Supplementary files format and content: *.bed: Methylation level (beta value) at CpG sites in the bed format.

growth_protocol: The therapeutic cells were generated from an Ex Vivo HSC-derived NKT cell culture.

extract_protocol:
Genomic DNA from samples was isolated with QIAGEN DNeasy Blood & Tissue kit following the corresponding manufacturer’s protocols.
The isolated genomic DNA was sonicated by Covaris system. Size selection by Ampure XP beads (Beckman-Coulter) was performed to enrich DNA fragments of around 250 bp in average sizes before library construction. In brief, 0.7 volume beads were added to the fragmented genomic DNA. After incubation, the supernatant was transferred to a new tube and an additional 1.3 volume beads were added (“0.5×–2× bead size selection”). After washing two times with 80% ethanol, genomic DNA was eluted with 40 ul EB buffer. Subsequently, 200ng genomic DNA was used for DNA library preparation with NEBNext Ultra II DNA library prep Kit (Cat#E7645). DNA library preparation has the following steps: DNA fragments end prep, adaptor ligation, size selection or purification of Adaptor-ligated DNA with Ampure XP beads, bisulfite conversion by Epitect Fast DNA Bisulfite Kits (QIAGEN, Cat#59826), PCR enrichment of Adaptor-ligated DNA, and purification of PCR product with 0.9x Ampure XP beads. The average size of resulting DNA fragments was around 480bp, validated by Tapestation. The libraries were then subjected to sequencing on Illumina NovaSeq sequencer with 2x150bp configuration (Azenta).

treatment_protocol: The therapeutic cells were engineered with BCMA-targeting CAR.


title: 16HBE14o- viewpoint -80.1kb Rep. 1

first: Ann

address: 2109 Adelbert Rd

institute: Case Western Reserve University

value: human bronchial epithelial cell line


title: Allo15BCAR-NKT Donor 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 DMSO R3

first: Job

address: 368 Plantation Street

institute: University of Massachusetts Medical School/HHMI

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t4hr.


title: ARP-1 LILRB1-KD rep8

city: houston

first: Miao

last: Xian

state: TX

address: 6560 Fannin St.

institute: houston methodist hospital

data_processing:
data filtering: fastp 0.20.0
read alignment: kallisto 0.46.2
gene abundance: DESeq2
Assembly: human genome genecode release 34
Supplementary files format and content: FPM

source_name: bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

tag: disease state

value: multiple myeloma


title: Allo15BCAR-NKT Donor 1


title: ARP-1 LILRB1-KD rep7


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t4 DMSO R1

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t4hr. G1 cells were isolated by FACS.


title: ARP-1 LILRB1-KD rep6


title: WK2_BI

first: Lili

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

description: 10x Genomics


title: AlloBCAR-NKT Donor 3

source_name: BCAR-iNKT

value: BCAR-iNKT


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t4 ICRF-193 R1

source_name: uterine/cervical adenocarcinoma cell line

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t4hr. G1 cells were isolated by FACS.


title: AlloBCAR-NKT Donor 1


title: ARP-1 LILRB1-KD rep4


title: BCAR-T Donor 3

source_name: BCAR-T


title: ARP-1 LILRB1-KD rep3


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t8 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.


title: BCAR-T Donor 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 DMSO R3

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t8hr.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t8 ICRF-193 R3

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t8hr.


title: ARP-1 LILRB1-KD rep2


title: BCAR-T Donor 1


title: ARP-1 LILRB1-KD rep1


title: ARP-1 LILRB1-KD rep5


title: AlloBCAR-NKT Donor 2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 2-7hr DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t7hr. G1 cells were isolated by FACS.


title: DU145-L597R

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38(Ensembl GRCh38.104)
Supplementary files format and content: fpkm(txt)

source_name: prostate

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: prostate

value: prostate cancer cells


title: ARP-1 CTR-KD rep8

value: CTR-KD


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 2-7hr ICRF-193 R1

city: Worcester

last: Dekker

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t7hr. G1 cells were isolated by FACS.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: unsorted t4 ICRF-193 R3

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t4hr.


title: ARP-1 CTR-KD rep6


title: DU145-P-Enter


title: MDA468_RSL3_b

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: count matrix for ferroptosis inducers - MDA468 and HCC70.csv

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome (hg38) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution.

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: Treatment was performed in low cell density (~50% confluency). Treatment with single reagents (JQ1, BTZ, erastin, RSL3) was done in the indicated concentrations and time points. Treatment with the JQ1 + BTZ combinations was done by diluting the components in growth medium, followed by 2-3 minutes of vortexing. The combination was added immediatly to the cells. DMSO concentrations were equalized in all treatments.

value: triple negative breast cancer line

tag: concentration

value: 4 hr


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t8 ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.

value: HeLa-S3 (CCL-2.2)


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t3hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t3hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.


title: ARP-1 CTR-KD rep5


title: DU145-WT


title: MDA468_RSL3_a


title: MDA468_Erastin_b

value: Erastin

value: 1 μM

value: 9 hr


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr ICRF-193 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t4hr, and cells were fixed at t9hr. G1 cells were isolated by FACS.


title: ARP-1 CTR-KD rep7


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t4hr, and cells were fixed at t9hr. G1 cells were isolated by FACS.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t4 DMSO R2


title: ARP-1 CTR-KD rep2


title: MDA468_DMSO_b

value: WT

value: DMSO


title: ARP-1 CTR-KD rep3


title: ARP-1 CTR-KD rep4


title: ARP-1 CTR-KD rep1


title: MDA468_DMSO_a


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t8 DMSO R2

value: uterine/cervical adenocarcinoma cell line


title: MDA468_Erastin_a


title: WT_FLAG, rep2

organism: Arabidopsis thaliana

value: whole seedlings

value: 7-day-old seedlings

value: wild type

value: anti-FLAG M2 (F1804, Sigma)


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t4 ICRF-193 R2


title: MDA468_24h_JB6_b

description: count matrix for combinations - MDA468 24h.csv

value: JQ1 + BTZ

value: 24 hr


title: WT_FLAG, rep1


title: MDA468_24h_JB6_a


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: unsorted ICRF-193 R1

treatment_protocol: Cells were treated with 30uM ICRF-193 for 2 hours before fixation.


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: unsorted DMSO R2

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler file (.mcool) containing high quality (Mapq>30) reads. Not read normalized.
Assembly: hg38

treatment_protocol: Cells were treated with DMSO for 2 hours before fixation.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at t2: G1 sort t8 ICRF-193 R2


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: G1 sort DMSO R2

treatment_protocol: Cells were treated with DMSO for 2 hours before fixation. G1 cells were isolated by FACS.


title: MDA468_24h_JB3_a


title: ELF7_FLAG, rep1

value: FLAG-ELF7 elf7-3


title: MDA468_24h_JB3_b


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: unsorted ICRF-193 R2


title: ELF7_FLAG, rep2


title: CUMC5944_Ispinesib treated

description:
Microwell-based scRNA-seq, fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
Sample was sequenced on both Illumina NextSeq 500 and NovaSeq 6000 instruments

data_processing:
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample. For samples had been sequenced on both Illumina NextSeq 500 and NovaSeq 6000, we combined the addresses from the NextSeq 500 and the corrected addresses from the NovaSeq 6000.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected. Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded. Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding to beads associated with cells in our microwell system using the emptyDrops algorithm from Lun et al, Genome Biology, 2019.
We removed CBs that satisfied any of the following criteria 1) fractional alignment to the mitochondrial genome greater than 1.96 standard deviations above the mean, 2) ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons greater than 1.96 standard deviations above the mean, 3) average number of reads per molecule or average number of molecules per gene >2.5 standard deviations above the mean for a given sample, 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4..
Assembly: Genome_build: GRCh38
Supplementary files format and content: Gene expression count matrix files are tab-delimited text files that contain the gene expression level of each individual cell. The file header contains cell-barcodes and cell malignant annotations. The first two columns being the gene IDs and gene symbols.

source_name: acute slice culture of glioma resection

extract_protocol:
Collected tissue samples or tissue slices were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
Microwell 3' scRNA-seq were performed as described in Yuan et al. Sci Rep (2016). Briefly, individual single cell was compartmentalized with a barcoded-mRNA-capture-bead (MACOSKO-2011-10, ChemGenes) and lysed in microwell-based platform, mRNA were captured and reverse transcribed on the bead, and cDNA-beads were pooled for PCR amplification and illumina Nextera library construction for each sample.

value: acute slice culture of glioma resection

tag: age

tag: gender

value: Male

tag: location

value: left frontal

tag: diagnosis

value: Glioblastoma, WHO Grade IV

value: 1.8 nM Ispenesib for 18 hrs


title: MDA468_24h_JB2_b

value: triple negative breast cancer line


title: DpnII Hi-C on HeLa S3 async unsorted or G1 sorted with DMSO or ICRF-193: G1 sort ICRF-193 R2

treatment_protocol: Cells were treated with 30uM ICRF-193 for 2 hours before fixation. G1 cells were isolated by FACS.

value: HeLa-S3 (CCL-2.2)


title: MDA468_24h_JB2_a

value: WT


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 2-7hr DMSO R2


title: CUMC5886_Ispinesib treated

value: Female

value: splenial extension into left parietal


title: SingleCells_GD4_HD5_HD6

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
FASTQ files obtained from sequencing were provided to the BD Rhapsody WTA Analysis Pipeline Targeted Multiplex Rhapsody Pipeline v1.0 with default settings
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. Putative cells information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices were read into R (4.2) separately and converted to Seurat objects using the Seurat R package (4.1.1)
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: neutrophils

extract_protocol:
Total CD66b+ neutrophils from the LDN and NDN fractions of peripheral blood from G-CSF-treated donors, and the NDN fraction of peripheral blood or the LDN fraction of BM from healthy donors (HDs) as controls, were isolated by magnetic bead selection with fluorescence-conjugated anti-CD66b mAbs and processed with BD Rhapsody Single-Cell Analysis System for scRNA-seq.
cDNA Libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit and BD Single-Cell Multiplexing kit (BD Biosciences) following the manufacturer's protocol

value: neutrophils


title: SingleCells_GD5_GD6_HD7


title: MDA468_24h_J_b


title: MDA468_24h_J_a


title: HCI-005_Vehicle_2

type: genomic

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

institute: Garvan Institute of Medical Research

description: human breast cancer patient derived xenografts

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing:
All arrays were processed and normalised using the Sesame pipeline (Zhou et al. 2018) with functions inferInfiniumIChannel(), dyeBiasNL(), pOOBAH() and noob() with default arguments.
Normalised beta values from sesame::getBetas().
Unmethylated and methylated signal intensities are taken from the “UR” and “UG” columns respectively from the sample SigDF object

label: Cy5 and Cy3

source_name: Breast tumour PDX

label_protocol: Standard Illumina Protocol

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. MCF7 and TAMR cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol: For the LNCaP, PrEC, TAMR and MCF7 cells and PDX samples genomic DNA was isolated using the QIAamp DNA Mini kit (Qiagen). For the prostate tumour samples fresh-frozen tissue cores (10x5mm) were retrieved, and matched H&E slides reviewed by a specialist pathologist to identify areas of tumour. Regions of high tumour content were microdissected from the core and DNA extracted using the Qiagen AllPrep kit (Qiagen).

treatment_protocol: For the breast cancer PDX model mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC) and treated until ethical end-point. For the TAMR cell experiments cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35.

value: Breast cancer PDX model HCI-005

value: Vehicle


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 2-7hr ICRF-193 R2

value: uterine/cervical adenocarcinoma cell line


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr DMSO R2


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr ICRF-193 R2


title: Gar15-13_Decitabine_2

value: Breast cancer PDX model Gar15-13

value: Decitabine


title: SingleCells_BM1_HD3_HD4


title: Gar15-13_Vehicle_4


title: Gar15-13_Vehicle_3


title: SingleCells_BM2_GD3


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr DMSO R2


title: HCI-005_Decitabine_3


title: HCI-005_Decitabine_1


title: Gar15-13_Decitabine_1


title: SYN_11452

description: prostate tumour

source_name: Prostate tumour

value: Prostate tumour


title: MDA468_24h_B6_b

value: BTZ

value: 6 nM

value: 24 hr


title: SingleCells_HD2_GD2


title: HCI-005_Vehicle_1


title: MDA468_24h_DMSO_a

value: DMSO


title: MDA468_24h_B6_a


title: SingleCells_HD1_GD1


title: Stromal cell Durvalumab treated replicate 3

city: Silver Spring

first: Carole

last: Sourbier

address: 10903 New Hampshire Ave

department: CBER

institute: FDA

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed for quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Homo sapiens sequence/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Stromal cells

extract_protocol:
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.

value: Fibroblast

value: Durvalumab