title: PEDV_DMSO_cell

city: Hubei

first: Dehua

last: Luo

address: shizishan 1st

institute: HZAU

data_processing:
Data cleaning: fastp, v0.23.4, with the parameters: -z 4 -q 20 -u 30 -f 10;
Sequence alignment: rf-map module with the following parameters: -ctn -cmn 0 -cqo -cq5 20 -b2;
SHAPE-MaP data analysis was performed using RNA Framework v2.6.9 (https://github.com/dincarnato/RNAFramework):
Identification and visualization of SHAPE reactivity: rf-norm module with the following parameters: -sm 3 -nm 3 -rb AC -n 500 -mm 1;
Secondary structure prediction: rf-fold module with the following parameters: -fw 3000 -fo 300 -wt 200 -pw 1000 -po 250 -dp -sh -nlp -md 600
Assembly: PEDV AJ1102(F12) (GenBank accession: MK584552.1)
Supplementary files format and content: The REACT file displays the chemical reactivity of each nucleotide in the genome for different sets of PEDV data
Supplementary files format and content: The CT file displays the entire genome structure of PEDV

organism: Porcine epidemic diarrhea virus

source_name: Renal

extract_protocol:
At 12 h post-infection, infected cells were washed 3 times with 10 ml cold PBS and then resuspended in PBS containing NAI at a final concentration of 100 mM. Another sample was added with an equal amount of DMSO as a control. Samples were then incubated at room temperature with continuous shaking for 15 minutes, after which the reaction was terminated by the addition of DTT at a final concentration of 0.5 M. The supernatant was then removed and the cells were lysed by adding 6 ml of Trizol. Extract the RNA by adding 1.2 ml of chloroform:isoamyl alcohol (24:1).
Sequencing libraries were generated using a VAHTS® Universal V8 RNA-seq Library Prep Kit For MGI (Vazyme #NRM605), according to manufacturer’s protocol. Libraries concentration were measured using a Qubit dsDNA HS Assay Kit (ThermoFisher, Cat. No. Q32851). 1 μl of the final library product was taken and the library quality was analysed using the Agilent DNA1000 Kit (Agilent, Cat. No. 5067-1504).

value: Renal

value: Vero E6


title: PBMCs, ADT, Day 7, CAR147

status: Public on Aug 12 2024

type: SRA

city: New York

first: Isabella

last: Grabski

state: NY

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

library_source: transcriptomic

data_processing:
Cellranger v5.0.0 for CITE-seq data, and Cellranger v6.1.2 for TCR data
Assembly: hg38
Supplementary files format and content: Gene expression, TCR sequences, and antibody abundance

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Cryopreserved infusion product bag washings and peripheral blood mononuclear cells (PBMCs) were thawed in warmed RPMI with 10% fetal bovine serum. Cells were washed in 100ul cell staining buffer (biolegend) and resuspended in the Cite-Seq antibody cocktail for 30 minutes at 4 degrees Celcius according to manufacturer instructions. Following incubation, cells were washed three times in cell staining buffer and finally resuspended in 0.04% bovine serum albumin in PBS at a concentration of 1000 cells per microliter. 10,000 cells were loaded into the Chromium Next GEM Chip for each sample.
CITE-seq and scTCR-seq: Cryopreserved infusion products and PBMCs were thawed, stained with CITE-seq antibodies according to established protocols, and resuspended in 0.04% ultra pure bovine serum albumin (ThermoFisher) in PBS at 1000cells/μl before loading on a 10x Genomics Chromium instrument according to manufacturer instructions. scRNA-seq libraries were processed using the Chromium single cell 5’ library and GelBeadkitv2 with coupled scTCR-seq library generation (ChromiumsinglecellV(D)J enrichment kit [humanTcell](10xGenomics)), and sequenced (IlluminaNovaSeqS4platform). Amplified cDNA libraries and final sequencing libraries were assessed for quality control with a Bioanalyzer High Sensitivity DNA Kit (Agilent).

tag: tissue

value: PBMCs

tag: time point

value: Day 7


title: KP1_IFN-Beta

city: Madrid

first: Laura

last: Serrano-Ron

state: Madrid

address: Calle Emilio Ortuño 35 1B

department: Bioinformatics Unit

country: Spain

institute: CNIO

description: normalizedcounts_genes_IFNB_vs_empty.tsv

data_processing:
FASTQ files obtained from the RNA sequencing were processed using the cluster_RNAseq pipeline (https://github.com/cniobu/cluster_rnaseq).
Samples were subjected to quality control using FastQC (version 0.11.9) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Subsequently, polyA tails and adapters were removed using BBDuk (BBMap version 38.90-3) (https://sourceforge.net/projects/bbmap/).
The resulting reads were aligned to the mouse reference genome (GRCm39) using STAR (version 2.7.10b)
genomic feature counts were obtained using htseq-count (version 0.12.4) and differential expression analysis was performed with DESeq2 (version 1.30.1)
Assembly: Mouse reference genome (GRCm39)
Supplementary files format and content: tab-separated values files include normalized counts for each sample. Two separated files are provided, each one including the samples concerning each comparison (IFN-beta expressing cells vs non-expressing cells or constitutively active STING expressing cells vs non-expressing cells).

molecule: polyA RNA

organism: Mus musculus

source_name: KP1 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin

growth_protocol: DMEM + 10% of tetracycline-free FBS

extract_protocol:
Total RNA from established cells lines was isolated using the RNeasy Mini Kit (Qiagen 74104) following manufacturer’s recommendations. DNA digestion with RNase-Free DNase (Qiagen, 70254) was performed during isolation.
Sequencing libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, 015)

treatment_protocol: 1 μg/ml doxycycline for 48 hours with daily replenishment of the media

tag: cell line

tag: cell type

value: lung adenocarcinoma cell line

tag: genotype

tag: treatment

value: 1 ug/ml doxycycline for 48 h


title: control, Hoxa5 ab, ChIP

city: Cleveland

first: Polyxeni

last: Philippidou

state: OH

address: 2210 Circle Dr.

department: Neuroscience

institute: Case Western Reserve University

library_source: genomic

data_processing:
75-nucleotide sequence reads were mapped to the mm10 genome using Bowtie2 (v2.3.5.1) with flag “--local”.
Reads were then sorted and indexed with samtools (v1.10) and filtered for blacklist regions defined by ENCODE.
MACS2 was used to call narrowpeak with a flag “--nomodel --ext 220” against the input control. Macs2 peaks were further filtered using the adj P cutoff of e-7 and the signal value > 5.
Assembly: mm10
Supplementary files format and content: bigwig, bed(except for input)

molecule: genomic DNA

source_name: cervical spinal cord

extract_protocol:
e12.5 cervical spinal cords from multiple embryos were microdissected in ice cold PBS and combined for Chromatin immunoprecipation.
Hoxa5, Pbx1, and input libraries were prepared by Active Motif and 75-nucleotide sequence reads were generated by Illumina sequencing (NextSeq 500)

value: cervical spinal cord

value: Wt

tag: chip antibody


title: PBMCs, TCR, Day 7, CAR147


title: KP1_empty

description:
normalizedcounts_genes_IFNB_vs_empty.tsv
normalizedcounts_genes_STING_vs_emtpy.tsv

source_name: KP1 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, TCR, Day 7, CAR128


title: PEDV_SHAPE_cell_rep1

country: China

description:
PEDV_cell_rep1.react.xml.gz
PEDV_cell.whole.ct.gz


title: PBMCs, RNA, Day 7, CAR147


title: KL3_IFN-Beta

source_name: KL3 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, TCR, Baseline, CAR147

value: Baseline


title: CRISPR_12hpf_repeat2

city: Qingdao

first: WEI

last: WANG

state: Shandong

address: 23 Hongkong east road haier building G zone

institute: Ocean University of China

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was mapped to the reference genome using 10X Genomics’ Cell Ranger (Version 3.0.1) pipeline to generate UMI count matrix for the downstream analysis
Assembly: 20 SBC barcodes including the flanking sequences were added as pseudogenes to the Ciona robusta reference genome (http://ghost.zool.kyoto-u.ac.jp/download_ht.html).
Supplementary files format and content: Raw sequencing data was mapped to the reference genome using 10X Genomics' Cell Ranger (version 3.0.1) and three files including barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz were generated by Cell Ranger for downstream analysis.

organism: Ciona robusta

source_name: Ciona Robusta Embryo

extract_protocol:
FACS purified cell was loaded onto 10X Chromium chip for GEM generation
Expression Library was prepared according to the 10X Chromium Single Cell 3' Reagent Kits protocol

value: Ciona Robusta Embryo

value: FACS purified cardiac progenitors

value: cardio-pharyngeal progenitors


title: BLA, p56_1

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: 10x Genomics

data_processing:
We used cellranger (version 7.0.1) to extract fastq files and align the reads to the mouse genome (10x genomics reference build MM10 2020 A)
Assembly: mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix files

molecule: nuclear RNA

source_name: brain, amygdala tissue

extract_protocol:
Mice were deeply anesthetized by i.p. injections of 200 mg/kg Ketamine and 40 mg/kg Xylazine, and perfused with 10 mL ice-cold Sucrose-HEPES Cutting Buffer containing (in mM) 110 NaCl, 2.5 KCl, 10 HEPES, 7.5 MgCl2, and 25 glucose, 75 sucrose (~350 mOsm/kg), pH=7.4 2.All the solutions/reagents were kept on ice in the following procedures unless otherwise specified. The brain was extracted and cut (300 μm) on a vibratome (Leica VT1000S, Germany) in cutting buffer, and the slices were transferred into a  Dissociation Buffer  containing (in mM): 82 Na2SO4, 30 K2SO4, 10 HEPES, 10 glucose and 5 MgCl2, pH=7.4 2.BLA was microdissected under a microscope (Olympus SZX10) covering the anterior (Bregma −0.59) and posterior (Bregma −3.0) for adult BLA and the anterior (Bregma −0.8) and posterior (Bregma −2.8) for juvenile BLA. The protocol for single nucleus isolation was optimized from previous studies (Matson KJE, et al. Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing. J Vis Exp (2018).
Nanoliterscale Gel Beads-in-emulsion (GEMs) generation, barcoding, cDNA amplification, and library preparation were done using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s protocol.

value: brain, amygdala tissue

tag: Sex

value: male

value: neuronal cell types


title: KL3_empty

source_name: KL3 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, ADT, Baseline, CAR147


title: KL2_STINGV154M

description: normalizedcounts_genes_STING_vs_emtpy.tsv

source_name: KL2 cell line transduced with STING(V154M) tetracycline inducible vector, 48 hours post-doxycyclin


title: CRISPR_12hpf_repeat1


title: TVC514-Trajectory


title: PBMCs, RNA, Baseline, CAR147


title: PBMCs, RNA, Day 14, CAR147

value: Day 14


title: KL2_IFN-Beta

source_name: KL2 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin


title: Prdm1-KO_K3

city: Tianjin

first: Youwei

last: Wang

state: --- Select One ---

address: 92 Weijin Road

department: Medical College

institute: Tianjin University

data_processing:
Standard methods were used to analyze the RNA-seq data, including aligning the reads to the genome by HISAT2 (v2.1.0), and gene expression values (Counts) were calculated using RSEM (v1.3.1)
Assembly: mm10
Supplementary files format and content: Excel Spreadsheet file includes raw counts for each Sample

source_name: spleen

extract_protocol:
Total RNA from FACS sorted splenic NK cells of Prdm1+/+ and Prdm1ΔNcr1 mice was extracted by TRIzol reagent (Invitrogen), then reverse transcribed into cDNA for library construction.
Library construction was prepared using Illumina mRNA Library kit following manufacturer's protocol

value: spleen

value: NK cells

value: Prdm1 kncokout

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr6 mice


title: PEDV_SHAPE_cell_rep2

description:
PEDV_cell_rep2.react.xml.gz
PEDV_cell.whole.ct.gz

value: Renal

value: Vero E6


title: KL2_empty

source_name: KL2 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin

value: lung adenocarcinoma cell line

value: 1 ug/ml doxycycline for 48 h


title: KRAS mutant AT2 cells run 2

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina).
Quality control of the scRNAseq data was performed (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The samples were mapped against the reference genome obtained from Gencode (version GRCm38) using STAR and quantified using featureCounts
The sequencing data was filtered at the sample level regarding sequencing depth, library size, number of expressed genes, mitochondrial genes proportion, spike-in controls and cell cycle stage
Cells with loglibrary sizes with more than 3 median absolute deviations (MADs) below the median loglibrary size were removed. Next, cells where the log-transformed number of expressed genes was 3 MADs below the median were also discarded. Both spike-ins and mitochondrial content 5 were used to exclude damaged cells. In this case, cells with a mitochondrial/spike-in content higher than 3 MADs were excluded. Sequencing data was filtered also at the gene level, considering only genes expressed at least in one cell and with an average expression higher than 5 counts per cell. Next, data was normalized and the top 50 most expressed genes.
Assembly: Reference genome obtained from Gencode (version GRCm38)
Supplementary files format and content: Tab-separated values file including raw counts for all samples

source_name: Alveolar type 2 cell

extract_protocol:
Four weeks postinfection with Ad5-CMV-Cre mice with the genotype KRAS(+/LSLG12V):ROSA26(LSLeYFP/LSLeYFP) and their KRAS wild type littermates were anesthetized and lungs were perfused. Dispase I was instilled into the lungs through tracheal intubation. 1% certified low melt agarose was also instilled. Lungs were introduced in HBSS and incubated at room temperature for 45 min. After this time, lungs were minced, incubated for 4 min in DMEM containing 0.1 mg/ml DNase I and 25mM Hepes, and passed through 100 µm and 40 µm cell strainers. After removing red blood cells with the ACK Lysing Buffer cells were stained for subsequent Fluorescence-activated Cell Sorting (FACS). Non-endothelial cells (CD31—) and non-leukocytes cells (CD45—), epithelial cells (EpCAM-PEmed) and positive for MHC-II (I-A/I-E)-PE-Cy7 were considered AT2 cells.
Single cell lysis, reverse transcription and preamplification were performed overnight on the C1™ system. The following day, samples were harvested and libraries for single-cell mRNA next generation sequencing were prepared using the Illumina Nextera XT DNA Library preparation kit according to Fluidigm’s instructions.

value: Alveolar type 2 cell


title: PBMCs, ADT, Day 14, CAR122

value: PBMCs


title: Prdm1-KO_K2

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr5 mice


title: Differentiation DMSO 0%

type: RNA

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: MC3T3-E1 cells were cultured in osteogenic medium with DMSO 0% at 37°C for 3 days.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin, and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite was used.

label: biotin

source_name: Mouse MC3T3-E1 preosteoblast cells

label_protocol: Five hundred nanograms (ng) of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: Mouse MC3T3-E1 preosteoblast cells were cultured in MEM α medium supplemented with 10% fetal bovine serum (FBS) at 37°C in humidified air with 5% CO2.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: For dimethyl sulfoxide (DMSO) treatment, the cells were cultured in osteogenic medium (MEM α medium supplemented with 10% FBS, 150 μM ascorbic acid 2-phosphate, and 10 mM beta-glycerophosphate) with or without 0.6% DMSO at 37°C for 3 days. For control experiments, cells were cultured in MEM α medium supplemented with 10% FBS at 37°C for 3 days. The mineralization level detected by alizarin red S staining was significantly increased in the cells treated with 0.6% DMSO.

tag: strain

tag: age

value: new bone

value: calvaria

tag: life span

value: infinite

tag: morphology

value: fibroblast-like


title: MC3T3-E1 Control

description: MC3T3-E1 cells were cultured in normal medium at 37°C for 3 days.


title: KRAS mutant AT2 cells run 1


title: Differentiation DMSO 0.6%

description: MC3T3-E1 cells were cultured in osteogenic medium with DMSO 0.6% at 37°C for 3 days.


title: Control day 6

description: MC3T3-E1 cells were cultured in normal medium at 37°C for 6 days.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

treatment_protocol: For cell differentiation, the cells were cultured in osteogenic medium (MEM α medium supplemented with 10% FBS, 150 μM ascorbic acid 2-phosphate and 10 mM beta-glycerophosphate) at 37°C for 3 or 6 days. For control experiments, cells were cultured in MEM α medium supplemented with 10% FBS at 37°C for 3 or 6 days. The mineralization level detected by alizarin red S staining was significantly increased in the cells in osteogenic medium for 6 days.

value: newborn


title: Differentiation day 6

description: MC3T3-E1 cells were cultured in osteogenic medium at 37°C for 6 days.


title: KL1_STINGV154M

source_name: KL1 cell line transduced with STING(V154M) tetracycline inducible vector, 48 hours post-doxycyclin


title: Control day 3


title: KRAS wild type AT2 cells run 2


title: Prdm1-KO_K1

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr4 mice


title: PBMCs, RNA, Day 14, CAR122

value: Day 14


title: PBMCs, TCR, Day 14, CAR122


title: PBMCs, ADT, Day 7, CAR122

value: Day 7


title: PBMCs, TCR, Day 7, CAR122


title: KRAS wild type AT2 cells run 1


title: Prdm1-WT_C2

value: spleen

value: NK cells

value: control

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr2 mice


title: thoracic, control, rep3

description:
rRNA-depleted
AV_061218_12

data_processing:
75 bp raw reads were analyzed by FASTQC (v0.11.9)  for quality control.
aligned to mm39 genome assembly via STAR (v2.7.5b) aligner.
features were quantitated using featureCounts(v2.0.1).
Assembly: mm39
Supplementary files format and content: tab-delimited txt file contains raw counts for each sample

source_name: thoracic

extract_protocol:
RNA was extracted using the PicoPure RNA isolation system.
rRNA depleted libraries were prepared from 10 to 20 ng of total RNA using the KAPA stranded RNA-seq kit with Riboerase (KAPA, #KK8483) and amplified by 15 cycles of PCR.

value: thoracic

value: Motor neuron

value: No treatment


title: KL1_empty

source_name: KL1 cell line transduced with empty tetracycline inducible vector, 48 hours post-doxycyclin

value: lung adenocarcinoma cell line

value: 1 ug/ml doxycycline for 48 h


title: Prdm1-WT_C3

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr3 mice


title: Normal lung 4

data_processing:
quality of RNAseq reads was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
RNAseq reads were mapped onto the reference genome mouse GRCm38/mm10 using STAR (v2.4.0j)
The abundance of each gene was quantified and evaluated using the RSEM statistical method.
Assembly: Reference genome mouse GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Adjacent normal alveolar regions

extract_protocol:
Small adenomas and adjacent normal alveolar regions were harvested by Laser Capture Microdissection. For RNA extraction, the PicoPure™ RNA Isolation Kit (Applied Biosystems, KIT0204) was used following manufacturer’s recommendations.
Sequencing libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen, 015)

value: Adjacent normal alveolar regions

value: No recombination. As wild-type mice


title: Prdm1-WT_C1

value: Splenic NKp46+ cells were FACS sorted from Prdm1+/+ or Prdm1ΔNcr1 mice


title: PBMCs, ADT, Baseline, CAR122

source_name: PBMCs

value: PBMCs

value: Baseline


title: thoracic, control, rep2

description:
rRNA-depleted
AV_061218_10


title: Normal lung 2


title: Normal lung 3


title: cervical, control, rep2

description:
rRNA-depleted
AV_061218_9

source_name: cervical

value: cervical


title: Differentiation day 3

description: MC3T3-E1 cells were cultured in osteogenic medium at 37°C for 3 days.

value: newborn

value: calvaria

value: infinite

value: fibroblast-like


title: Normal lung 1


title: Infusion product, ADT, CAR122

source_name: Infusion product

value: Infusion product


title: thoracic, control, rep1

description:
rRNA-depleted
AV_061218_6

value: thoracic

value: control


title: KL1_IFN-Beta

source_name: KL1 cell line transduced with IFN-Beta tetracycline inducible vector, 48 hours post-doxycyclin


title: PBMCs, RNA, Baseline, CAR122


title: KL adenoma 4

source_name: lung adenoma

value: lung adenoma


title: Infusion product, TCR, CAR122


title: cervical, control, rep1

description:
rRNA-depleted
AV_061218_5

value: Motor neuron

value: No treatment


title: KL adenoma 3


title: cervical, control, rep3

description:
rRNA-depleted
AV_061218_11


title: MouseE13_Rep2_50um pixel-size device

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

data_processing:
*library strategy: Spatial Transcriptomics
To decode sequencing data, the FASTQ file Read 2 underwent processing, involving the extraction of unique molecular identifiers (UMIs) and spatial Barcode A and Barcode B. The Read 1 containing cDNA sequences was trimmed using Cutadapt V3.4 and then aligned to either the mouse GRCm38-mm10 or human GRCh38 reference genome using STAR V2.7.7a. Utilizing ST_Pipeline V1.7.6, spatial barcode sequences were demultiplexed based on the predefined coordinates of the microfluidic channels and ENSEMBL IDs were converted to gene names, generating the gene-by-pixel expression matrix for downstream analysis. Matrix entries corresponding to pixel positions devoid of tissues were excluded.
Assembly: GRCm38-mm10 or human GRCh38
Supplementary files format and content: Integrated Seurat .rds object

source_name: Embryo

extract_protocol:
The spatially barcoded tissue was enclosed with a clean polydimethylsiloxane (PDMS) reservoir and securely clamped using acrylic chips. A 2X lysis buffer was prepared in advance, consisting of 20 mM Tris-HCl pH 8.0, 400 mM NaCl, 100 mM EDTA, and 4.4% SDS. For tissue digestion, 70 µL of the lysis mix (30 µL 1X DPBS, 30 µL 2X lysis buffer, 10 µL 20 µg/µL Proteinase K solution) was loaded into the PDMS reservoir, sealed with parafilm, and incubated in a humidified box at 55°C for 2 hours. After the reaction, the parafilm was removed, and all the liquid containing cDNA was collected into a 1.5mL DNA low-bind tube.
PCR amplification was executed to directly ligate sequencing primers, using a 100 µL system consisting of 50 µL 2X KAPA HiFi HotStart ReadyMix, ~42 µL solution from the rRNA removal step, 4 µL 10 µM P5 Primer, and 4 µL 10 µM P7 Primer. The resulting library underwent purification using SPRIselect beads at a 0.8X ratio, quality control checked using TapeStation, and was then sequenced on an Illumina NovaSeq 6000 Sequencing System with a paired-end 150bp read length.

value: Embryo

tag: disease

value: Normal

value: Patho-DBiT Protocol


title: Infusion product, RNA, CAR122


title: PBMCs, ADT, Day 14, CAR116

value: Day 14


title: PBMCs, RNA, Day 7, CAR122

value: PBMCs

value: Day 7


title: CIN 612 2

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

data_processing:
FastQC (v0.11.8) was used to check the quality of raw and trimmed reads. Trimmomatic (v0.38) was used to cut adapters and trim low-quality bases with a default setting.
STAR Aligner version 2.7.1a was used to align the reads.
Picard tools (version 2.20.4) was applied to mark duplicates of mapping
The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version1.6.0)/Htseq was used to count mapped reads for genomic features such as genes, exons, promoters, gene bodies, genomic bins and chromosomal locations. De-Seq2 (version 1.14.1) was used to do the differential analysis. The Gene Ontology analysis was done using ClusterProfiler package in R.
Assembly: Hg38
Supplementary files format and content: The DeSeq2 files are in Microsoft excel comma separated value format. Raw counts for HFK 1 and 2 are in txt format.

source_name: Cervix

growth_protocol: HFK and CIN 612 cells were maintained in E-media containing 10% FBS DMEM

extract_protocol:
RNA was extracted using an Rneasy mini plus kit (Qiagen).
RNA seq-PolyA technique was applied by Admera Biosciences. Briefly, PolyA+RNA was captured and then fragmented and primed for cDNA synthesis. Following cDNA synthesis, 3' ends were adenylated and 5' ends repaired. DNA sequencing adapters were ligated and the ligated fragments were PCR amplified.

value: Cervix

value: CIN 612

value: Keratinocytes

value: HPV positive


title: KL adenoma 2


title: MouseBrain_50um pixel-size device

source_name: Brain

value: Brain


title: KL adenoma 1


title: HiC_Th1_Ets1Het

city: Philadelphia

first: Golnaz

last: Vahedi

state: PA

address: 421 Curie Blvd

department: Department of Genetics

institute: University of Pennsylvania

data_processing:
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. In NOD mice, the BEDPE was shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910).
Assembly: GRCm38
Supplementary files format and content: hic file obtained from Juicer tools.

source_name: Thymus

extract_protocol:
Hi-C libraries were generated on 1×106 cells using with Arima-HiC+ kit (Arima Genomics) following manufacturer's recommendations.
Library was prepared using Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

treatment_protocol: Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco).  For Th1 polarization, 0.2x106 naïve CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C.

value: Thymus


title: HiC_Th1_WT_for_Ets1Het_mice


title: Prdm1-KO

description: 10x Genomics

data_processing:
The “Seurat” R package (v4.2.0) was used for data analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
FACS-sorted liver CD45+ cells with more than 80% cell viability were used for library preparation. Each sample contained cells from three Prdm1+/+ or Prdm1ΔNcr1 mice.
Library was performed  according to manufacturer’s instructions. Briefly, Gel Bead-in-Emulsions (GEMs) were generated using the 10X Genomics Chromium system, which combinates Master Mix, Single Cell 3’ v3.1 Gel Beads, and Partitioning Oil with single cells. GEMs were mixed with cell lysate and reverse transcription reagent to produce full-length cDNA. After incubation, the GEMs were broken, and recovered cDNA were amplified via PCR. Fragmentation, End repair, A-tailing, and Adaptor Ligation were performed to obtain final libraries, which contain P5 and P7 sequences. The 3’ library was sequenced on Novaseq 6000 with approximately 50k read pairs/cell sequencing depth.

value: Liver

value: CD45+ cells

value: 6-8 weeks old


title: CIN 612 1


title: HFK 2

source_name: Foreskin

value: Foreskin

value: HFKs


title: Mouse_Lymphnode_20um pixel-size device

source_name: Lymph node

value: Lymph node


title: PBMCs, TCR, Day 14, CAR116


title: KP adenoma 5

value: lung adenoma


title: Prdm1-WT

description: 10x Genomics


title: KP adenoma 4


title: MouseE13_Rep1_50um pixel-size device

value: Embryo

value: Normal

value: Patho-DBiT Protocol


title: PBMCs, RNA, Day 14, CAR116

value: PBMCs

value: Day 14


title: knockout 477

city: Boston

first: Translational

last: Bioinformatics

state: MA

address: 72 East Concord Street

institute: Clinical and Translational Science Institute

data_processing:
Base calls were converted to FASTQ using the illumina package bcl2fastq and removal of adapters and low-quality reads was performed using fastp (version 0.21.0).
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.23.10).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 6 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 6 matrix of variance-stabilizing-transformed (VST) expression values

source_name: intestinal epithelium

growth_protocol: Mice were individually housed in metabolic cages located within ambient temperature (22 °C) and light-controlled (12h light/dark cycle) environmental enclosures. Mice were housed on pine chip bedding, without nestlets, and provided ad libitum access to food and acidified water.  Mice were monitored daily for body weight, glucose levels and temperature for 20 days until placement in metabolic cages at day 21.

extract_protocol:
Mice were euthanized by CO2 asphyxiation followed by cardiac puncture in accordance with humane animal use guidelines. Tissues were rapidly collected and flash frozen in liquid nitrogen before storage at -80C unless collected for staining. IECs were collected by first sectioning isolated small intestine into duodenum, jejunum, and ileum. Each section was flushed with cold PBS and the intestine was opened longitudinally with luminal side facing up. IECs were physically separated from the lamina propria using a clean glass slide, immediately placed in a microcentrifuge tube and flash frozen.  Total RNA from IECs was isolated using the RNeasy mini Mini kit (Qiagen).
Paired-end libraries were synthesized using a TruSeq RNA Sample Preparation kit (Illumina).

treatment_protocol: NCoR1loxP/loxP SMRTloxP/loxP female mice were crossed with male NCoR1loxP/loxP SMRTloxP/loxP mice expressing tamoxifen-inducible Cre under the control of the villin 1 promoter (B6.Cg-Tg(Vil1-cre/ERT2)23Syr/J) to generate control mice and NCoR1/SMRT IEC double knockout (I-DKO) mice. At age 8-9 weeks, mice underwent i.p. tamoxifen injection at a dose of 15 mg/100 g body weight for five days.

value: intestinal epithelium


title: PBMCs, ADT, Day 7, CAR116

value: Day 7


title: PBMCs, TCR, Day 7, CAR116


title: KP adenoma 2


title: knockout 423


title: HFK 1

value: Keratinocytes


title: PBMCs, RNA, Day 7, CAR116


title: CIN 612 DRIP 2

data_processing:
Admera Biosciences (NJ) performed most of the bioinformatic analyses from our DRIP-sequencing experiments. Their bioinformatics methods are as follows: An in-house bioinformatics pipeline was used to analyze DRIP-Seq data. First, FastQC (v0.11.8) was used to check the quality of raw and trimmed reads.
Trimmomatic (v0.38) was used to cut adapters and trim low-quality bases with a default setting.
BWA (v0.7.10-r789) was used to map the trimmed reads to the reference genome* using the Burrows-Wheeler Alignment algorithm (BWA-MEM).
Mapped reads that have low-quality MAPQ score (MAPQ < 10), not-properly-paired, or duplicated (assessed with Picard tools (v 2.20.4)) were removed. BAM was used to generate BW format (normalized by RPKM) for visualization.
MACS (v2.2.4) was chosen to call peaks. If there was no replicate, the R package MAnorm (v2.2.6) was used for sample comparison. On the other hand, if there were replicates, their called peaks were merged and the DiffBind package (v2.14.0) was then used for differential analysis. Peak annotation and combined density profiles were performed by the ChIPseeker package (v1.22.1) and deepTools, respectively.
Assembly: Hg38
Supplementary files format and content: The bigwig files remain in BW format

extract_protocol:
1 × 107 cells were harvested and collected in Southern lysis buffer before being treated with RNase A (5 ng/mL) and Proteinase K (7.5 ng/mL) at 37 °C overnight. DNA was purified from these samples using phenol-chloroform extractions, and 25 to 50 mg of DNA was used for each sample. DNA was sheared using a Bioruptor (Diagenode) on high power, 30 s on/90 s off cycles for 20 min or digested using 1U of mung bean nuclease for 1 h at 37 °C. Input DNA was removed before loading the samples into preblocked magnetic beads in IP buffer containing 2 mg of the RNA:DNA hybrid antibody. Immunoprecipitations were allowed to incubate overnight at 4 °C while rotating. The next day, samples were washed 8 times with RIPA buffer for 5 min while rotating. One wash in TE buffer was performed before samples were eluted for 10 min at 65 °C in 10% sodium dodecyl sulfate (SDS), 10 mM Tris pH 7.4, 50 mM ethylenediaminetetraacetic acid (EDTA). DNA was purified from these elutions using a PCR purification kit (Qiagen) and stored at −20 °C.
Samples were stored at -80° C until being shipped to Admera Biosciences (NJ), who performed the sequencing experiments. Briefly, the library was prepared using a KAPA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s recommendation. Input DNA was end-repaired and 3’-dA tailed. Adapter was then ligated to the DNA, and the ligated product was PCR amplified and cleaned up using the SPRIselect Reagent (Beckman Coulter). Quality control was then performed for the final library, followed by sequencing.

value: Cervix

value: CIN 612

value: S9.6 (Millipore, MABE1095)

value: HPV positive


title: knockout 476


title: KP adenoma 3


title: HFK H3K9me3 2

data_processing:
FastQC (v0.11.8) was used to check the quality of raw and trimmed reads. Trimmomatic (v0.38) was used to cut adapters and trim low-quality bases with a default setting. BWA (v0.7.10-r789) was used to map the trimmed reads to the reference genome* using the Burrows-Wheeler Alignment algorithm (BWA-MEM). Mapped reads that have low-quality MAPQ score (MAPQ < 10), not-properly-paired, or duplicated (assessed with Picard tools (v 2.20.4)) were removed. BAM was used to generate BW format (normalized by RPKM) for visualization. MACS (v2.2.4) was chosen to call peaks.
Agreement between biological replicates was assessed using multiBAMSummary (Galaxy Version 3.5.4+galaxy0), and then plotting principal component analyses using plotPCA (Galaxy Version 3.5.4+galaxy0) and plotting Pearson coefficients as a heatmap using plotCorrelation (Galaxy Version 3.5.4+galaxy0) (Supp Fig 8). From the BAM files, BAM Compare (Galaxy Version 3.5.4+galaxy0) was used to normalize log2 IP to input ratios for both biological replicates of H3K36me3, H3K9me3, and gH2AX ChIPs from HFK and CIN 612 cells.  ComputeMatrix was used to prepare files for visualization via plotProfile and plotHeatmap. CHIPseeker (Galaxy Version 1.28.3+galaxy0) was used on the BED files generated by Admera Biosciences or NUseq to determine the genomic distribution of each modified histone. MACS (v2.2.4) was used to call peaks. HOMER (Galaxy Version 4.11+galaxy0) was used to annotate where peaks occurred relative to their genomic location (intron, exon, etc.) and the corresponding gene name.
Assembly: Hg38
Supplementary files format and content: bigWig

extract_protocol:
1 × 107 cells were harvested and collected in Southern lysis buffer before being treated with RNase A (5 ng/mL) and Proteinase K (7.5 ng/mL) at 37 °C overnight. DNA was purified from these samples using phenol-chloroform extractions, and 25 to 50 mg of DNA was used for each sample. DNA was sheared using a Bioruptor (Diagenode) on high power, 30 s on/90 s off cycles for 20 min. Input DNA was removed before loading the samples into preblocked magnetic beads in IP buffer containing 2 ug of the H3K36me3 antibody. Immunoprecipitations were allowed to incubate overnight at 4 °C while rotating. The next day, samples were washed 8 times with RIPA buffer for 5 min while rotating. One wash in TE buffer was performed before samples were eluted for 10 min at 65 °C in 10% sodium dodecyl sulfate (SDS), 10 mM Tris pH 7.4, 50 mM ethylenediaminetetraacetic acid (EDTA). DNA was purified from these elutions using a PCR purification kit (Qiagen) and stored at −20 °C.
Samples were stored at -80° C until being shipped to Admera Biosciences (NJ) or Northwestern sequencing core (NU seq), who performed the sequencing experiments. Briefly, the library was prepared using a KAPA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s recommendation. Input DNA was end-repaired and 3’-dA tailed. Adapter was then ligated to the DNA, and the ligated product was PCR amplified and cleaned up using the SPRIselect Reagent (Beckman Coulter). Quality control was then performed for the final library, followed by sequencing.

value: Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade (ab8898)


title: control 486


title: KP adenoma 1


title: control 483


title: CIN 612 DRIP 1


title: K adenoma 4


title: control 482


title: K adenoma 5


title: HFK DRIP 2

value: Foreskin


title: CIN 612 Input


title: Bulk ATAC, macrophages  8 weeks post curing, sample 4

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_8wPC_4_bulk_ATAC

data_processing:
Raw data scRNAseq and Multiome  files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Bulk ATAC-seq data was aligned to the mouse genome using Bowtie2
Assembly: mm10
Supplementary files format and content: Compressed .tar.gz files containing raw UMI counts in Cellranger output format, details for the ADT antibodies, ATAC Bigwig (.bw) files, and comma-delimited text files including metadata per cell

extract_protocol: All methods listed in Musrati et al. Infection history imprints prolonged changes to the Kupffer Cell epigenome, transcriptome and function.

value: Liver

value: Flt3-Cre Rosa26-Yfp

value: infected with Trypanosoma brucei brucei and treated with melarsoprol

tag: library type

value: ATAC


title: SStim day 10 CD8+ T cells, pool2_lane3, ADT

city: South San Francisco

first: Jia

last: Lu

state: CA

address: 201 Haskins Way, Suite 101

institute: Lyell Immunopharma

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool2-lane3_barcodes.tsv.gz
Pool2-lane3_features.tsv.gz
Pool2-lane3_matrix.mtx.gz

library_source: other

data_processing:
10X Genomics Cell Ranger software (v6.1.2) was used to process reads from each sequencing lane with GRCh38 as reference genome. The Cell Ranger outputs were further processed using Seurat package in R. In brief, Seurat objects of the same pool were combined, and cells were filtered using thresholds for quality control metrics. CD8+ T cells were selected by gating on CD8 and CD4 protein expression measured by CITE-Seq, and CD8+ T cells from the two pools were combined for clustering analysis and UMAP generation using RNA expression without protein expression. In clustering analysis, cells from different donors were integrated together to account for donor heterogeneity.
Assembly: hg38
Supplementary files format and content: Cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each lane
Supplementary files format and content: RDS file, Seurat object containing clustering results and cell-level annotation
Library strategy: CITE-Seq

molecule: protein

source_name: Live CD45+CD8+EGFR+ CAR-T cells; Live CD45+CD4+EGFR+ CAR-T cells

extract_protocol:
Samples were collected and cryopreserved at the end of the third stimulation (Day 10) for transcriptomic analyses. Cryopreserved samples were thawed, and cells were aliquoted for flow staining, followed by Fc receptor blocking using Human TruStain FcX™ blocking reagent (BioLegend) for 10 minutes at 4 °C. Cells were then stained with a mix of fixable viability dye eFluor™ 506; fluorochrome-conjugated antibodies specific for human CD45, CD8, CD4, EGFR; DNA-conjugated Total-Seq C antibodies against cell surface protein markers, and unique DNA-barcoded Hashtag antibodies for 30 minutes at 4 °C. Live CD45+EGFR+CD8+ T cells and LiveCD45+EGFR+CD4+ T cells were flow sorted into PBS containing 2% BSA, using the BD FACSAria™ Fusion cell sorter (BD Biosciences).
Sorted cells from samples barcoded with unique hashtag antibodies were pooled together and then counted using the Cellometer K2 Fluorescent Cell Counter (Nexcelom). Approximately 5 x 10^4 pooled cells were loaded into each lane of the Chromium Next GEM Chip K using a Chromium Next GEM Single Cell 5′ Reagent Kit v2 (10x Genomics). After single-cell capture and lysis, cDNA was generated, and DNA conjugated to antibodies bound to cell surface proteins was amplified over 13 cycles according to the manufacturer’s protocol (10x Genomics). The amplified cDNA from polyadenylated mRNA and the amplified DNA from cell surface protein antibody barcodes were separated by size selection for generating independent barcoded 5′ Gene Expression (GEX) libraries and Antibody derived tag (ADT) libraries, respectively. The GEX and ADT libraries prepared from multiple channels of the Chromium Next GEM Chip K were quantified, pooled, and sequenced together using the NovaSeq 6000 system (Illumina).

value: ADT


title: K adenoma 3

value: lung adenoma


title: HFK DRIP 1

value: HFKs


title: SStim day 10 CD8+ T cells, pool2_lane3, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool2-lane3_barcodes.tsv.gz
Pool2-lane3_features.tsv.gz
Pool2-lane3_matrix.mtx.gz

value: Live CD45+CD8+EGFR+ CAR-T cells; Live CD45+CD4+EGFR+ CAR-T cells

value: GEX


title: K adenoma 2


title: SStim day 10 CD8+ T cells, pool2_lane2, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool2-lane2_barcodes.tsv.gz
Pool2-lane2_features.tsv.gz
Pool2-lane2_matrix.mtx.gz


title: K562_G4_mutant_clone1_HiCAR_4

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description:
K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01.bed
K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz
K562_G4_mutant_clone_1_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi

data_processing:
reads were aligned to hg38(human) /mm10(mouse) reference genome using bwa mem with flags -SP5M
Pairtools pipeline was used to generate pairs and bam files and identify unique valid interactions
FitHiChIPwas used with CovBias for normalization, and q value thresholds of q<0.01
Assembly: hg38, mm10
Supplementary files format and content: Bed, WashU.bed,BigWigs

molecule: other

growth_protocol: K562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. GM12878 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. E14 mESC cells were cultured in serum/LIF medium, containing 10% fetal bovine serum and 1,000 U/mL LIF.

extract_protocol: HiCAR was performed with 100,000 K562 cells, crosslinked with 1% formaldehyde.ViCAR was performed on beads using 15 µL MyOneT1 beads per sample. For 4 samples, 60 µL MyOneT1 beads were washed 3x with 500 µL PBS pH6.8 and resuspended in 60 µL PBS pH 6.8 with 0.01% Tween-20. 30 µL biotin-Conjugated con A solution (2.3mg/ml, Sigma Aldrich C2272) were added to the bead suspension, and binding performed at room temperature (RT) for 30mins with rotation (400rpm). After 30 min, supernatant was removed on a magnet, and beads were washed once with 60 µL PBS pH 6.8 with 0.01% Tween-20, and twice with 1mL binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2). After the last wash, beads were resuspended in 60µL binding buffer. 200,000-500,000 cells per sample were fixed in 1 mL 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 10 min at RT with rotation. Formaldehyde was quenched by addition of Glycine to a final concentration of 0.2M, and samples were incubated at RT for 10min. Cells were spun for 4 min at 1300xg at 4°C, supernatant was removed, cells resuspended in 1 mL PBS, and then pelleted again by spinning at 4 min at 1300xg at 4°C. To prepare nuclei, cells were resuspended in 1 mL NE1 buffer (20 mM HEPES pH7.5, 10 mM KCl, 0.5 mM spermidine (S0266-5G), 0.1% Triton X-100, 20% glycerol, plus 1 Roche Complete Protease Inhibitor EDTA-Free tablet), and incubated on ice for 10 min. Nuclei were pelleted by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and cells were washed in 1 mL PBS. Nuclei were pelleted again by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and nuclei were resuspended in 150 µL wash buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine, plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 15µL conA-MyOneT1 beads (prepared above) were added, and samples incubated for 10 min at RT, with rotation at 800rpm. Beads were immobilized on a magnet, supernatant removed, and samples washed twice in 100 µL antibody buffer (2 mM EDTA, 1% BSA (Sigma-Aldrich A8577), 0.05% digitonin (EMD Milipore 300410), 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). After the second wash, beads were resuspended in 100 µL antibody buffer, and blocked for 1 h, at RT with rotation at 800rpm. After 1 h, primary antibodies were added. For the following antibodies, 2 µL antibody were added to 100 µL sample: anti- anti-H3K27me3 (Cell Signalling 9733), H3K4me3 (Abcam ab8580), anti-H3K4me1 (Thermo 710795). For BG4, 4 µL 1.3 µM antibody prepared in-house1 were added to 100 µL sample. Primary antibody incubation was performed at 4°C overnight, with rotation at 600 rpm. The next day, supernatant was removed on a magnet, and beads washed twice with 100 µL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). For BG4 samples, 4 µL anti-FLAG antibody (Cell Signaling 2368) in 100 µL dig-wash buffer was added to beads with incubation for 1h at RT, shaking at 800 rpm. BG4 samples were then washed 3x in 100 µL dig-wash buffer. Next, for all samples, 1 µL anti-Rabbit IgG antibody in 100 µL dig-wash buffer was added (Antibodies-Online ABIN101961), and samples were rotated at 800rpm at RT for 1h. pA-Tn5 was prepared in-house and loaded with ME-rev and BfaI-truseqR1-pmeI-nextera. Samples were washed 3x in dig-wash buffer, resuspended in 50 µL of a 1:250 dilution of pA-Tn5 in dig-300 buffer (0.01% digitonin, 20 mM HEPES pH7.5, 300 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). Tagmentation was performed for 1 h at 37°C, shaking at 800rpm. Nuclei were washed twice in 200 µL TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA) on a magnet, then washed twice in 300 µL 0.075% BSA in PBS. Beads were resuspended in nuclei in 50µL solution containing 32.5 µL nuclease-free water, 5 µL 10x NEBuffer r3.1(NEB B6003S) and 12.5µL 2% SDS and incubated at 62°C for 10 min without rotation. 139 µL solution containing 100 µL nuclease-free water, 14 µL 10x NEBuffer3.1, 25 µL 10% Triton X-100 and incubated 37°C for 15 min, shaking at 800 rpm. Supernatant was removed on a magnet and resuspended in 300 µL 1.1X NEBuffer r3.1. Next, supernatant was removed on a magnet and resuspended in 101 µL solution containing: 90 µL 1.1X NEBuffer r3.1, 10µL CviQI (NEB, R0639L), 1µL splint oligo. Samples were incubated for 3h at 25°C, with rotation at 800 rpm. After 3h, 374 µL solution containing 283.6µL nuclease-free water, 40µL 10% Triton X-100, 2.4 µL 20 mg/mL BSA (NEB B9000S), 48 µL 10X T4 ligation Buffer was added. 6 µL T4 DNA ligase were then added, samples were mixed by pipetting, and in situ ligation was performed overnight at 16°C with interval shaking. The next day, beads were captured on a magnet and supernatant was removed. Beads were resuspended in 100µL solution containing 0.5mg/mL Proteinase K, 0.5% SDS and 10mM Tris-HCl buffer pH 8.0. Samples were mix by vortexing and incubated for 1 hr at 55 ºC, then for 2 h at 68 ºC, shaking at 800rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013): sample and beads were added to 500 µL binding buffer, transferred to a spin column, washed twice following manufacturer’s instructions, and DNA was eluted in 20 µL elution buffer.

value: lymphoblast cells


title: SStim day 10 CD8+ T cells, pool2_lane1, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool2-lane1_barcodes.tsv.gz
Pool2-lane1_features.tsv.gz
Pool2-lane1_matrix.mtx.gz


title: Bulk ATAC, macrophages  8 weeks post curing, sample 2

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_8wPC_2_bulk_ATAC


title: K adenoma 1


title: GM12878_H3K27ac_ViCAR_3

description:
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05.bed
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz
GM12878_H3K27ac_ViCAR.05_01kb.interactions_FitHiC_Q0.05_WashU.bed.gz.tbi


title: Bulk ATAC, macrophages  8 weeks post curing, sample 1

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_8wPC_1_bulk_ATAC


title: Bulk ATAC, macrophages  2 weeks post curing, sample 3

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_2wPC_3_bulk_ATAC


title: SStim day 10 CD8+ T cells, pool1_lane5, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool1-lane5_barcodes.tsv.gz
Pool1-lane5_features.tsv.gz
Pool1-lane5_matrix.mtx.gz


title: C2C12 cells, Sorafenib, rep 3

city: Hannover

first: Bushra

last: Khan

state: Lower Saxony

address: Carl-Neuberg-Straße 1

department: Institute of Molecular and Cell Physiology

institute: Hannover Medical School

description:
N4609
6: N4609_quant sf

data_processing:
BCL to FASTQ conversion: BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing and quality control: Raw data processing was conducted by use of nfcore/rnaseq (version 3.9) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The genome reference and annotation data were taken from GENCODE.org (Mus musculus; GRCm38.p6).
Normalization and differential expression analysis: Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: GENCODE.org (Mus musculus; GRCm38.p6)
Supplementary files format and content: The processed data file contains the results of one DESeq2 analyses we have performed (two-group comparison, one-factor design). This file comprises the normalized expression values for each sample (first control condition ‘DMSO’, followed by experimental condition ‘Sorafenib’) that were used in the respective DESeq2 analysis as well as the results of the statistical test (right-most columns). Significant differentially expressed genes (DEGs) can be identified based on their adjusted p-values (last column). The file is currently sorted according to adjusted p-values in ascending order. The first couple of columns contain information to the respective genes.

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated using the High Pure RNA Isolation kit (#11828665001, Roche, Switzerland) with minor modifications to the manufacturer’s protocol. Briefly, the cells were collected using trypsin, followed by centrifugation at 900 rpm for 4 min. The cell pellet obtained post trypsinization was homogenized in 200 µL DPBS, followed by lysis in 400 µL lysis/binding buffer. The tube was briefly vortexed for 15 s, and the contents were transferred to the collection tube containing the high pure filter tube. The tube was centrifuged at 10000 g for 30 s. The flowthrough containing the digested proteins and other cellular components was discarded. DNase I (diluted 1:10 in DNase incubation buffer) was added to the filter tube and incubated for 15 min at RT to allow digestion of residual DNA. To the same filter tube, 500 µL wash buffer I was added and centrifuged at 10000 g for 30 s. The flowthrough containing the digested DNA fragments was discarded, and the filter tube was washed with 500 µL wash buffer II at 10000 g for 30 s. The wash was repeated with 200 µL wash buffer II at 13000 g for 2 min. Once the flowthrough was discarded, the empty tube was spun down at 13000 g for 1 min to get rid of residual buffer. The filter tube was transferred to a sterile 1.5 mL tube and 50 µL elution buffer was added. Post centrifugation at 18000 g for 1 min, the eluate containing the RNA was collected and stored at -80°C.
500ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 7 cycles of final pcr. One additional purification step was introduced at the end of the standard procedure, using 1.2x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).

value: skeletal muscle

value: Sorafenib


title: HFK gH2AX 2

value: Keratinocytes

value: Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb #80312


title: Bulk ATAC, macrophages  2 weeks post curing, sample 2

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_2wPC_2_bulk_ATAC


title: SStim day 10 CD8+ T cells, pool2_lane4, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool2-lane4_barcodes.tsv.gz
Pool2-lane4_features.tsv.gz
Pool2-lane4_matrix.mtx.gz


title: K562_G4_mutant_clone1_HiCAR_1


title: Bulk ATAC, macrophages  8 weeks post curing, sample 3

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_8wPC_3_bulk_ATAC


title: C2C12 cells, DMSO, rep 3

description:
N4608
3: N4608_quant sf

value: DMSO


title: SStim day 10 CD8+ T cells, pool2_lane2, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool2-lane2_barcodes.tsv.gz
Pool2-lane2_features.tsv.gz
Pool2-lane2_matrix.mtx.gz


title: SStim day 10 CD8+ T cells, pool1_lane5, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool1-lane5_barcodes.tsv.gz
Pool1-lane5_features.tsv.gz
Pool1-lane5_matrix.mtx.gz


title: HFK Input


title: C2C12 cells, DMSO, rep 2

description:
N4606
2: N4606_quant sf


title: K562_G4_mutant_clone1_HiCAR_2


title: SStim day 10 CD8+ T cells, pool2_lane4, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool2-lane4_barcodes.tsv.gz
Pool2-lane4_features.tsv.gz
Pool2-lane4_matrix.mtx.gz


title: K562_G4_mutant_clone2_HiCAR_4

description:
K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01.bed
K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz
K562_G4_mutant_clone_2_.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi


title: K562_G4_mutant_clone1_HiCAR_3


title: C2C12 cells, Sorafenib, rep 2

description:
N4607
5: N4607_quant sf


title: C2C12 cells, Sorafenib, rep 1

description:
N4605
4: N4605_quant sf


title: SStim day 10 CD8+ T cells, pool2_lane1, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool2-lane1_barcodes.tsv.gz
Pool2-lane1_features.tsv.gz
Pool2-lane1_matrix.mtx.gz


title: SStim day 10 CD8+ T cells, pool1_lane4, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool1-lane4_barcodes.tsv.gz
Pool1-lane4_features.tsv.gz
Pool1-lane4_matrix.mtx.gz


title: Bulk ATAC, macrophages  2 weeks post curing, sample 1

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_2wPC_1_bulk_ATAC


title: SStim day 10 CD8+ T cells, pool1_lane3, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool1-lane3_barcodes.tsv.gz
Pool1-lane3_features.tsv.gz
Pool1-lane3_matrix.mtx.gz


title: K562_G4_mutant_clone2_HiCAR_3


title: Mut1, motor neurons, Hoxa5-deficient

data_processing:
ATAC-seq data were processed using the standardized uniform Encyclopedia of DNA Elements (ENCODE) pipeline from the ENCODE consortium. Briefly, FastQC (v0.11.9) was used to check the pre-alignment read quality.
FASTQ files from ATAC-seq reads were mapped to UCSC mm10 with Bowtie2 (v2.3.4.3).
All unmapped reads, non-uniquely mapped reads, PCR duplicates and ChrM reads were removed using Samtools (v1.9).
Peaks were called using MACS2 (v2.2.4) with parameters “--nomodel --shift 37 --ext 73 --pval 1e-2 -B --SPMR --call-summits”
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Choline Acetyltransferase (ChAT)::GFP transgenic reporter line was used to sort GFP-positive motor neurons at e12.5 from both control and Hoxa5-deficient littermates.
The cell pellet was resuspended in transposition reaction mix (12.5 μl TD-Buffer, 1.25 μl Tn5, 11.25 μl water) and Nextera DNA Library Prep Kit was used for library preparation (Illumina, Cat# 15028212)

value: cervical

value: Motor neuron

value: Mut


title: Mut2, motor neurons, Hoxa5-deficient


title: C2C12 cells, DMSO, rep 1

description:
N4604
1: N4604_quant sf


title: K562_G4_mutant_clone2_HiCAR_1


title: Bulk ATAC, Control macrophages, sample 3

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_control_3_bulk_ATAC

value: Liver

value: Flt3-Cre Rosa26-Yfp

value: treated with melarsoprol (2 weeks post treatment)


title: K562_G4_mutant_clone2_HiCAR_2


title: Bulk ATAC, Control macrophages, sample 1

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_control_1_bulk_ATAC

value: ATAC


title: SStim day 10 CD8+ T cells, pool1_lane3, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool1-lane3_barcodes.tsv.gz
Pool1-lane3_features.tsv.gz
Pool1-lane3_matrix.mtx.gz


title: Bulk ATAC, Control macrophages, sample 2

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_control_2_bulk_ATAC


title: K562_WT_HiCAR_2

description:
K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01.bed
K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz
K562_WT_HiCAR.10_01kb.interactions_FitHiC_Q0.01_WashU.bed.gz.tbi

value: WT


title: SStim day 10 CD8+ T cells, pool1_lane4, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool1-lane4_barcodes.tsv.gz
Pool1-lane4_features.tsv.gz
Pool1-lane4_matrix.mtx.gz


title: K562_WT_HiCAR_4


title: K562_WT_HiCAR_3


title: Wt1, motor neurons, control

value: Control


title: Wt2,  motor neurons, control


title: nasal mucosa,digested,37℃,rep1

city: Nanjing

first: Wenqian

address: No.1 Weigang, Xuanwu District

institute: Nanjing Agricultural University

description: 10x Genomics

data_processing:
Raw sequencing data were processed by using 10X Genomics Cell Ranger software (version 3.1.0, USA)
The sequence reads were aligned to the porcine reference genome Sscrofa 11.1.
Assembly: porcine reference genome Sscrofa 11.1
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Sus scrofa

source_name: Nasal mucosa

extract_protocol:
Nasal mucosae were dissected from 5-day-old Large White piglets, then were cut into small pieces, which were digested with collagenase Type IV and hyaluronidase for 30 min at 37°C. The released nasal cells were filtered through 70μm cell strainer centrifuged and re-suspended in PBS. Suspended cells activity was determined by trypan blue staining and adjusting the live cells concentration to 1000 to 2000 cells per microliter.
The cells were captured with a 10× Genomics Chromium Single Cell Instrument after binding to barcoded gel beads. The raw scRNA-seq dataset were obtained after reverse transcription and RNA sequencing. These processes were completed by Gene Denovo (Guangzhou, China).

value: Nasal mucosa

value: Suprabasal cells, basal cells, fibroblast, goblet cells, serous cell, endothelial, ciliated cells, club cells, T cells, macrophage, duct cells, NK cells, dendritic cells, neutrophil, B cells, ionocyte, smooth muscle, erythroid


title: SStim day 10 CD8+ T cells, pool1_lane2, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool1-lane2_barcodes.tsv.gz
Pool1-lane2_features.tsv.gz
Pool1-lane2_matrix.mtx.gz

value: Live CD45+CD8+EGFR+ CAR-T cells; Live CD45+CD4+EGFR+ CAR-T cells

value: GEX


title: Multiome, 8 weeks post curing liver nuclei, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
liver_8wPC_cDNA

value: infected with Trypanosoma brucei brucei and treated with melarsoprol

value: mRNA


title: SStim day 10 CD8+ T cells, pool1_lane2, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool1-lane2_barcodes.tsv.gz
Pool1-lane2_features.tsv.gz
Pool1-lane2_matrix.mtx.gz

value: ADT


title: Multiome, 8 weeks post curing liver nuclei, ATAC

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
liver_8wPC_ATAC

library_source: genomic single cell


title: SStim day 10 CD8+ T cells, pool1_lane1, ADT

description:
ADT library: read 1 file contains cell barcode and UMI; read 2 file contains Antibody Derived Tag reads and Hashtag Antibody Derived Tag reads.
Pool1-lane1_barcodes.tsv.gz
Pool1-lane1_features.tsv.gz
Pool1-lane1_matrix.mtx.gz


title: Bulk ATAC, Control macrophages, sample 4

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_control_4_bulk_ATAC


title: K562_WT_HiCAR_1

value: lymphoblast cells


title: nasal mucosa,digested,30min,rep1

description: 10x Genomics


title: Multiome, Control liver nuclei, ATAC

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
liver_control_ATAC

value: treated with melarsoprol (8 weeks post treatment)


title: CIN 612 H3K9me3 2

value: Cervix

value: CIN 612

value: Keratinocytes

value: Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade (ab8898)

value: HPV positive


title: SStim day 10 CD8+ T cells, pool1_lane1, GEX

description:
GEX library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
Pool1-lane1_barcodes.tsv.gz
Pool1-lane1_features.tsv.gz
Pool1-lane1_matrix.mtx.gz


title: WT_K562_BG4_ViCAR_rep2

data_processing:
reads were aligned to hg38 reference genome using bwa mem with flags -SP5M
Pairtools pipeline was used to generate pairs and bam files and identify unique valid interactions
FitHiChIPwas used with CovBias for normalization, and q value thresholds of q<0.05 and q<0.01
Assembly: hg38
Supplementary files format and content: Bed, WashU.bed, BigWigs

growth_protocol: K-562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2

extract_protocol:
ViCAR was performed on beads using 15 µL MyOneT1 beads per sample. For 4 samples, 60 µL MyOneT1 beads were washed 3x with 500 µL PBS pH6.8 and resuspended in 60 µL PBS pH 6.8 with 0.01% Tween-20. 30 µL biotin-Conjugated con A solution (2.3mg/ml, Sigma Aldrich C2272) were added to the bead suspension, and binding performed at room temperature (RT) for 30mins with rotation (400rpm). After 30 min, supernatant was removed on a magnet, and beads were washed once with 60 µL PBS pH 6.8 with 0.01% Tween-20, and twice with 1mL binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2 and 1mM MnCl2). After the last wash, beads were resuspended in 60µL binding buffer. 200,000-500,000 cells per sample were fixed in 1 mL 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 10 min at RT with rotation. Formaldehyde was quenched by addition of Glycine to a final concentration of 0.2M, and samples were incubated at RT for 10min. Cells were spun for 4 min at 1300xg at 4°C, supernatant was removed, cells resuspended in 1 mL PBS, and then pelleted again by spinning at 4 min at 1300xg at 4°C. To prepare nuclei, cells were resuspended in 1 mL NE1 buffer (20 mM HEPES pH7.5, 10 mM KCl, 0.5 mM spermidine (S0266-5G), 0.1% Triton X-100, 20% glycerol, plus 1 Roche Complete Protease Inhibitor EDTA-Free tablet), and incubated on ice for 10 min. Nuclei were pelleted by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and cells were washed in 1 mL PBS. Nuclei were pelleted again by spinning for 4 min at 1300xg at 4°C, supernatant was removed, and nuclei were resuspended in 150 µL wash buffer (20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine, plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). 15µL conA-MyOneT1 beads (prepared above) were added, and samples incubated for 10 min at RT, with rotation at 800rpm. Beads were immobilized on a magnet, supernatant removed, and samples washed twice in 100 µL antibody buffer (2 mM EDTA, 1% BSA (Sigma-Aldrich A8577), 0.05% digitonin (EMD Milipore 300410), 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). After the second wash, beads were resuspended in 100 µL antibody buffer, and blocked for 1 h, at RT with rotation at 800rpm. After 1 h, primary antibodies were added. For the following antibodies, 2 µL antibody were added to 100 µL sample: anti- anti-H3K27me3 (Cell Signalling 9733), H3K4me3 (Abcam ab8580), anti-H3K4me1 (Thermo 710795). For BG4, 4 µL 1.3 µM antibody prepared in-house1 were added to 100 µL sample. Primary antibody incubation was performed at 4°C overnight, with rotation at 600 rpm. The next day, supernatant was removed on a magnet, and beads washed twice with 100 µL dig-wash buffer (0.05% digitonin, 20 mM HEPES pH7.5, 150 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). For BG4 samples, 4 µL anti-FLAG antibody (Cell Signaling 2368) in 100 µL dig-wash buffer was added to beads with incubation for 1h at RT, shaking at 800 rpm. BG4 samples were then washed 3x in 100 µL dig-wash buffer. Next, for all samples, 1 µL anti-Rabbit IgG antibody in 100 µL dig-wash buffer was added (Antibodies-Online ABIN101961), and samples were rotated at 800rpm at RT for 1h. pA-Tn5 was prepared in-house and loaded with ME-rev and BfaI-truseqR1-pmeI-nextera. Samples were washed 3x in dig-wash buffer, resuspended in 50 µL of a 1:250 dilution of pA-Tn5 in dig-300 buffer (0.01% digitonin, 20 mM HEPES pH7.5, 300 mM KCl, 0.5 mM spermidine plus 1 Roche Complete Protease Inhibitor EDTA-free tablet). Tagmentation was performed for 1 h at 37°C, shaking at 800rpm. Nuclei were washed twice in 200 µL TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA) on a magnet, then washed twice in 300 µL 0.075% BSA in PBS. Beads were resuspended in nuclei in 50µL solution containing 32.5 µL nuclease-free water, 5 µL 10x NEBuffer r3.1(NEB B6003S) and 12.5µL 2% SDS and incubated at 62°C for 10 min without rotation. 139 µL solution containing 100 µL nuclease-free water, 14 µL 10x NEBuffer3.1, 25 µL 10% Triton X-100 and incubated 37°C for 15 min, shaking at 800 rpm. Supernatant was removed on a magnet and resuspended in 300 µL 1.1X NEBuffer r3.1. Next, supernatant was removed on a magnet and resuspended in 101 µL solution containing: 90 µL 1.1X NEBuffer r3.1, 10µL CviQI (NEB, R0639L), 1µL splint oligo. Samples were incubated for 3h at 25°C, with rotation at 800 rpm. After 3h, 374 µL solution containing 283.6µL nuclease-free water, 40µL 10% Triton X-100, 2.4 µL 20 mg/mL BSA (NEB B9000S), 48 µL 10X T4 ligation Buffer was added. 6 µL T4 DNA ligase were then added, samples were mixed by pipetting, and in situ ligation was performed overnight at 16°C with interval shaking. The next day, beads were captured on a magnet and supernatant was removed. Beads were resuspended in 100µL solution containing 0.5mg/mL Proteinase K, 0.5% SDS and 10mM Tris-HCl buffer pH 8.0. Samples were mix by vortexing and incubated for 1 hr at 55 ºC, then for 2 h at 68 ºC, shaking at 800rpm. DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013): sample and beads were added to 500 µL binding buffer, transferred to a spin column, washed twice following manufacturer’s instructions, and DNA was eluted in 20 µL elution buffer.
To fill-in: 31 µL solution containing 20.5 µL nuclease-free water, 5 µL 10x rCutSmart buffer (B6004S), 4 µL 10 mM dNTP, 1.5 µL T4 DNA polymerase (NEB M0203L) were added to the DNA, and samples were incubated at RT for 30 min, followed by 20 min at 75°C. To digest DNA, 1 µL NlaIII was added and samples were incubated at 37°C for 1 h. DNA was purified using 0.9X AMPure XP beads, eluting DNA in 80 µL 10 mM Tris-HCl (pH8.0). For circularization, DNA was diluted to 2 ng/µL in 938 µL nuclease-free water, then 50 µL 10x T4 ligation buffer and 6 µL T4 DNA ligase (NEB M0203L) were added. Samples were incubated at RT for 2 h. After ligation, DNA was purified using DNA Clean & Concentrator-5 (Zymo D4013), by combining 1 mL sample with 2 mL binding buffer, transferring 750 µL of the mix to the spin column 4 times, spinning between each transfer, washing following manufacturer’s instructions, and eluting in 20 µL. 2.3 µL 10x rCutSmart buffer and 1.8 µL PmeI (NEB R0560L) added to the DNA, and digestion performed at 37°C for 1 h. PCR reactions contained: 21 µL DNA, 2 µL i7 primer, 2 µL i5 primer and 25 µL NEBNext High-Fidelity 2X PCR Master Mix (M0541S), and the following PCR programme performed: step 1 72°C 4 min, step 2 98°C 30 s, step 3 98°C 10 s, step 4 59°C 30s, step 5 72°C 45s, step 6 72°C 5min, repeating steps 3-5 for a total of 12 cycles. PCR reactions were cleaned up using 1.3X AMPure XP beads, and libraries size-selected using 0.4X followed by 1.4X AMPure XP beads. Libraries were sequenced in paired end mode using the NextSeq 500 (36 bp paired-end) or NextSeq 2000 (60 bp paired-end) with 3 dark cycles for the first 3 bp of Read 1.


title: Multiome, Control liver nuclei, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
liver_control_cDNA

value: Liver

value: Flt3-Cre Rosa26-Yfp


title: CIN 612 H3K9me3 1


title: CIN 612 Input 2 (control for H3K9me3 ChIP)


title: Citeseq, 8 weeks post curing macrophages, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
MF_8wPC_ADT

data_processing:
Raw data scRNAseq and Multiome  files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Bulk ATAC-seq data was aligned to the mouse genome using Bowtie2
Assembly: mm10
Supplementary files format and content: Compressed .tar.gz files containing raw UMI counts in Cellranger output format, details for the ADT antibodies, ATAC Bigwig (.bw) files, and comma-delimited text files including metadata per cell
Library strategy: Cite-seq


title: SStim day 10 CD8+ T cells, StimR, donor3

data_processing:
Trim_galore (v0.6.5) was used for adaptor trimming and STAR (v2.7.2c) was used for alignment to the human GRCh38 reference genome. Gene expression quantification was performed by RSEM (v1.3.1) with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes transcript lengths, counts, TPM and FPKM for each sample (RSEM output)

source_name: Live CD45+EGFR+CD8+ CAR-T cells

extract_protocol:
Samples were collected and cryopreserved at the end of the third stimulation (Day 10) for transcriptomic analyses. Cryopreserved samples were thawed and cells were aliquoted for flow staining, followed by Fc receptor blocking using Human TruStain FcX™ blocking reagent (BioLegend) for 10 minutes at 4 °C, prior to staining with a cocktail of fluorochrome-conjugated antibodies specific for human CD45, CD8, CD4, EGFR and fixable viability dye eFluor™ 506 for 30 minutes at 4 °C. Approximately 3 x 104 live CD45+EGFR+CD8+ T cells were flow sorted into 100 μL of Lysis Binding Mix (Thermo Fisher Scientific) using the BD FACSAria™ Fusion cell sorter (BD Biosciences) and stored at −80 °C until processing. Total RNA was extracted from sorted CD45+EGFR+CD8+ T cells using the MagMAX™ mirVana™ Total RNA Isolation kit (Thermo Fisher Scientific) and stored at −80 °C.
Libraries for mRNA sequencing were prepared with 5 ng of total RNA for cDNA generation using the SMART-Seq v4 Ultra Low Input RNA kit (Takara) following the manufacturer’s protocol. Next,150 pg of cDNA was used to prepare barcoded libraries using the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s protocol. Barcoded libraries from multiple samples were then pooled in an equimolar ratio, purified, and sequenced together using the NovaSeq 6000 system (Illumina)

value: Live CD45+EGFR+CD8+ CAR-T cells

value: CAR-T cells produced using StimR


title: Citeseq, 8 weeks post curing macrophages, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
MF_8wPC_cDNA


title: WT_K562_BG4_ViCAR_rep1

value: WT


title: SStim day 10 CD8+ T cells, benchmark reagent, donor3

value: CAR-T cells produced using benchmark reagent


title: SStim day 10 CD8+ T cells, benchmark reagent, donor2


title: K562_BG4_ViCAR_rep4_reseq2


title: HFK Input 1 (control for H3K9me3 ChIP)

value: Foreskin

value: HFKs


title: K562_BG4_ViCAR_rep3_reseq


title: K562_BG4_ViCAR_rep4


title: K562_BG4_ViCAR_rep4_reseq


title: Citeseq, 2 weeks post curing macrophages, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
MF_2wPC_cDNA

value: infected with Trypanosoma brucei brucei and treated with melarsoprol

value: mRNA


title: SStim day 10 CD8+ T cells, StimR, donor2


title: SStim day 10 CD8+ T cells, benchmark reagent, donor1


title: SStim day 10 CD8+ T cells, StimR, donor1


title: CIN 612 gH2AX 2

value: Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb #80312


title: Citeseq, Infected macrophages, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
MF_infected_cDNA

value: infected with Trypanosoma brucei brucei, 28 days post infection


title: K562_BG4_ViCAR_rep3

value: lymphoblast cells


title: Kute4, T35, D60, Inflammatory soup, replicate 2

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description:
T35_IS_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv

data_processing:
Reads were pseudo-aligned with kallisto version 0.50.1 to the human genome: Homo Sapiens GCRh38, kallisto index version 13. An average of 32M reads were sequenced per sample, of which an average of 28M reads were successfully aligned. See Supplementary Table 1 for alignment statistics for each sample.
Genes were considered to be expressed in our dataset if their Transcripts Per Million (TPM) value was equal to 1 or more in all samples of a given group.
Assembly: Homo Sapiens GCRh38
Supplementary files format and content: Supplementary_Table_1_Alignment_Stats alignment statitics for all samples
Supplementary files format and content: Supplementary_Table_2_TPM xlsx file containing TPM values for all samples, as well as differential expression tables for the different groups
Supplementary files format and content: genecounts_iSN_timepoints.csv  comma-separated value file including raw gene counts for timepoint experiment samples
Supplementary files format and content: genecounts_iSN_IS.csv  comma-separated value file including raw gene counts for inflammatory soup experiment samples

source_name: HPSI0714i-kute_4 (Kute4)

growth_protocol: Experiments were conducted with two iPSC lines derived from one healthy male and one healthy female human donor: HPSI0714i-kute_4 (Kute4), female origin, obtained via the Human Induced Pluripotent Stem Cell (HIPSCI) Initiative at King’s College London and UKBi013-A-GCamP6f (UKB), male origin. iPSCs were maintained on 6-well plates coated with vitronectin (StemCell Technologies, catalogue #100-0763) in Stemflex media (ThermoFisher, #A3349401) until 80% confluence. Cells were gently dissociated from wells using Versene (ThermoFisher, #15040066) for 4 mins at 37°C. Prior to differentiation, iPSCs were seeded on 6-well plates coated with Geltrex (ThermoFisher, #A1413302) and allowed to expand in Stemflex media to 60% confluence. At this point (day 1), the medium was changed to mouse embryonic fibroblast conditioned medium (MEF, Bio-Techne, #AR005) supplemented with 10ng/mL human recombinant FGF-2 (Miltenyi, #130-093-839). 24 hours later (day (D)0), differentiation was initiated according to the Chambers protocol [7]. Briefly, from D0-D3, KSR media (Knockout DMEM (ThermoFisher, #10829018), 15% knockout serum replacement (ThermoFisher, #10828010), 1% Glutamax (ThermoFisher, #35050038), 1% non-essential amino acids (ThermoFisher, #11140035), 100uM beta-mercaptoethanol (ThermoFisher, #31350010), 1% antibiotic/antimycotic (ThermoFisher, #15240096) was added and changed daily. From D0-D1, 10µM SB431542 (Bio-techne, #1614-10) and 100nM LDN 193189 (Bio-techne, #6053-10) (SMAD inhibitors) were added to media. From D2-D3, in addition to SMAD inhibitors, 3µM CHIR99021 (Bio-techne, catalogue #4423-10), 10µM SU5402 (Merck, #SML0443), 10µM DAPT (Bio-techne, #2634-10) were also added to media. From D4-D5, media composition was changed to 75% KSR media + 25% N2 media (Neurobasal medium (ThermoFisher, #21103049), 2% B27 supplement (ThermoFisher, #17504044), 1% N2 supplement (ThermoFisher, #17502048), 1% Glutamax, 1% antibiotic/antimycotic) with all 5 inhibitors included. From D6-7, media composition was changed to 50% KSR + 50% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. From D8-9, media composition was changed to 25% KSR + 75% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. On D10, media composition was changed to 100% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. On D11, immature neurons were dissociated from wells using TrypLE (ThermoFisher, #12604013) for 7 mins at 37°C. Neurons were replated to Geltrex-coated 13mm glass coverslips at a density of 75,000 cells/well. Neurons were matured and maintained in N2 media containing 25ng/mL human b-NGF (Peprotech, #450-01), 25ng/mL human NT3 (Peprotech, #450-03), 25ng/mL human GDNF (Peprotech, #450-10), 25ng/mL human BDNF (Peprotech, #450-02). From D11-D14, media also contained 10mM ROCKi (Enzo, #ALX-270-333-M005) and 3µM CHIR99021. Media was changed twice a week. To remove proliferating, non-neuronal cells, 1-2µM Cytosine beta-D-arabinofuranoside (AraC, SLS, #C1768-100MG) was added every other media change until non-neuronal cells were removed.    For sequencing, neurons were matured to different timepoints (30-70 days).

extract_protocol:
For each group, two coverslips from a 24-well plate of neurons were combined into 350 µL RLT buffer from the RNeasy Micro Plus kit (Qiagen, #74134), supplemented with 1% beta-mercaptoethanol (PanReac AppliChem, #A1108.0100). The samples were stored at -80 °C degrees, until batch-controlled RNA extraction, library preparation and sequencing. RNA was purified using the RNeasy Micro Plus kit (Qiagen, #74134) following manufacturer’s instructions. We quantified the RNA amount using a Qubit high sensitivity RNA assay (Invitrogen, #Q32851) and checked its quality using a Tapestation 4150 system (Agilent). All samples had a RIN value of more than 9.9.
Samples were processed at once within the same library preparation and multiplexed into the same Illumina sequencing lane (150bp, paired-end reads) by the service provider Novogene Sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Two batch-controlled sequencing experiments were conducted, comparing iSNs at three different timepoints (day 29-30, day 50-53, day 69-70) and comparing day 60 neurons treated with modified-Inflammatory soup (control media with 100 ng/ml NGF (Peprotech, #450-01-100), 100 ng/ml TNF (Peprotech, #300-01A-100), 1 μM histamine (Sigma-Aldrich, #H7250), 1 μM bradykinin (Sigma-Aldrich, #B3259), 1 μM serotonin (Sigma-Aldrich, #H9523), 1 μM prostaglandin E2 (Bio-techne, #2296)) versus control media (N2 media without growth factors) for 24 hours.

value: HPSI0714i-kute_4 (Kute4)

value: iPSC

tag: differentation batch

value: Inflammatory soup


title: Citeseq, Control macrophages, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
MF_control_ADT

value: treated with melarsoprol (8 weeks post treatment)

value: ADT


title: K562_BG4_ViCAR_rep2_reseq2


title: Kute4, T35, D60, Inflammatory soup, replicate 1

description:
T35_IS_1
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv


title: CIN 612 gH2AX 1

value: Cervix

value: CIN 612

value: Keratinocytes

value: HPV positive


title: HFK H3K9me3 1

value: Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade (ab8898)


title: Citeseq, Control macrophages, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
MF_control_cDNA

value: Liver

value: Flt3-Cre Rosa26-Yfp


title: CIN 612 Input 1 (control for H3K9me3 ChIP)


title: Citeseq, 2 weeks post curing macrophages, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
MF_2wPC_ADT

value: infected with Trypanosoma brucei brucei and treated with melarsoprol


title: K562_BG4_ViCAR_rep2

value: WT


title: CIN 612 Input 2 (control for gH2AX ChIP)


title: UKB, T9, D60, Inflammatory soup , replicate 2

description:
T9_IS_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv

source_name: UKBi013-A-GCamP6f (UKB)

value: UKBi013-A-GCamP6f (UKB)


title: K562_BG4_ViCAR_rep2_reseq


title: CIN 612 Input 1 (control for gH2AX ChIP)


title: HFK gH2AX 1

value: Foreskin

value: HFKs

value: Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb #80312


title: Citeseq, Infected macrophages, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
MF_infected_ADT

value: infected with Trypanosoma brucei brucei, 28 days post infection


title: LPD rep6

city: Zhongshan

first: Yilie

last: Liao

state: China

address: Tsuihang New District

institute: Zhongshan Institute for Drug Discovery

description:
LP5_8
Liver from mice fed with 5% protein chow diet for 3 weeks

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).
Raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle.
Clean reads were separately aligned to reference genome with orientation mode using TopHat software.
Differential gene expression was determined by DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes differential expression analysis results by DESeq2

growth_protocol: B6.Cg-Lepob/J (ob/ob) mice, 8-week-old, 12/12h light on/off, ad libum fed

extract_protocol:
Livers were dissected and snap-frozen in liquid nitrogen. Total RNA were extracted with TRIzol reagent, and genomic DNA was removed using DNase I (TaKara).
RNA library was prepared for sequencing using TruSeqTM RNA sample preparation kit from Illumina (San Diego, CA).

treatment_protocol: Mice were subjected to chow diet containing either standard (25% kcal) or low (5% kcal) dietary protein content for 3 weeks (n=6 for each group).

value: B6.Cg-Lepob/J (ob/ob)

value: Lep-/-


title: LPD rep5

description:
LP5_6
Liver from mice fed with 5% protein chow diet for 3 weeks


title: UKB, T9, D60, Inflammatory soup , replicate 1

description:
T9_IS_1
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv

value: iPSC

value: Inflammatory soup


title: K562_BG4_ViCAR_rep1_reseq2

value: lymphoblast cells


title: K562_BG4_ViCAR_rep1_reseq


title: LPD rep4

description:
LP4_5
Liver from mice fed with 5% protein chow diet for 3 weeks


title: HFK Input 1 (control for gH2AX ChIP)

value: Keratinocytes


title: Kute4, T35, D60, Control, replicate 1

description:
T35_N2_1
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv

value: HPSI0714i-kute_4 (Kute4)

value: Control


title: K562_BG4_ViCAR_rep1


title: UKB, T9, D60, Control, replicate 2

description:
T9_N2_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv


title: LPD rep2

description:
LP4_3
Liver from mice fed with 5% protein chow diet for 3 weeks

value: Liver


title: HPEpiC, Untreated, Biol rep5, Tube4

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School

data_processing:
Libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option.
Adapter sequences were then trimmed using trimmomatic v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35
Trimmed reads were aligned to the Homo sapiens GRCh38 using STAR v.2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v.1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
The combined transcript model annotation file was constructed using Ensembl hg38 and FANTOM5 hg38 as previously described (PMID: 35841888) and used as annotation to prepare STAR indexes and for FeatureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Count values for each sample

source_name: HPEpiC

growth_protocol: Human pulmonary alveolar epithelial cells (HPEpiC) were seeded at a density of 1.5e4 cells per well in 96-well CellCarrier plates (PerkinElmer) or 3e5 cells per well in 6 well tissue culture plates (Corning) and cultured in AEpiCM (ScienCell Research Laboratories).

extract_protocol:
Total RNA was isolated using RNeasy columns (Qiagen). 1.0 ug of total RNA with RQS > 9 was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: The cells were cultured for 24 hours prior to being treated with: Human IL11 (UniProtKB:P20809, GenScript), human TGFβ1 (PHP143B, Bio-Rad)

value: HPEpiC

value: pulmonary alveolar epithelial cells

value: Untreated


title: UKB, T9, D60, Control, replicate 1

description:
T9_N2_1
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv

value: UKBi013-A-GCamP6f (UKB)


title: HPEpiC, IL11-treated, Biol rep4, Tube4


title: LPD rep1

description:
LP4_1
Liver from mice fed with 25% protein chow diet for 3 weeks


title: SPD rep6

description:
SP2_10
Liver from mice fed with 25% protein chow diet for 3 weeks


title: Kute4, T34, D70

description:
T34_D70_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

value: Day 70


title: SPD rep5

description:
SP2_8
Liver from mice fed with 25% protein chow diet for 3 weeks


title: HPEpiC, TGFβ1-treated, Biol rep4, Tube4


title: Kute4, T35, D60, Control, replicate 2

description:
T35_N2_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_IS.csv


title: HPEpiC, Untreated, Biol rep4, Tube4


title: HPEpiC, IL11-treated, Biol rep3, Tube3


title: SPD rep4

description:
SP1_5
Liver from mice fed with 25% protein chow diet for 3 weeks


title: SPD rep3

description:
SP1_4
Liver from mice fed with 25% protein chow diet for 3 weeks


title: UKB, T8, D70

description:
T8_D70_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv


title: SPD rep2

description:
SP1_3
Liver from mice fed with 25% protein chow diet for 3 weeks


title: Kute4, T35, D50

description:
T35_D52_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

value: Day 50


title: HPEpiC, TGFβ1-treated, Biol rep3, Tube3


title: HPEpiC, IL11-treated, Biol rep2, Tube2


title: Kute4, T34, D50

description:
T34_D50_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv


title: HPEpiC, Untreated, Biol rep3, Tube3


title: LPD rep3

description:
LP4_4
Liver from mice fed with 5% protein chow diet for 3 weeks


title: UKB, T9, D50

description:
T9_D50_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv


title: HPEpiC, TGFβ1-treated, Biol rep2, Tube2


title: Lung,WT,blm

description:
female, BD mouse sample tag 1
male, BD mouse sample tag 3
WTblmCre1_SampleTag01_mm_RSEC_MolsPerCell_MEX.zip
WTblmCre2_SampleTag03_mm_RSEC_MolsPerCell_MEX.zip
processed_seurat_annotated.rds
processed_seurat_AT_annotated.rds

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option. FASTQ files were demultiplexed using the unique sample-tags, trimmed, mapped and annotated using the BD Rhapsody™ Sequence Analysis Pipeline (Revision 2.0) on the Seven Bridges Genomics platform (accessed on June 2023).
Low-quality read pairs were removed based on read length, average base quality score, and highest single-base frequency. Filtered reads were aligned to the Mus musculus genome (GRCm39 assembly) using STAR v2.7.4a embedded in the pipeline and annotated using the mouse GENCODE release M31 GTF.
Reads with identical cell labels, identical unique molecular identifier (UMI) sequences, and identical genes were collapsed into a single raw molecule, followed by removing artefacts using recursive substitution error correction (RSEC) developed by BD Biosciences.
Assembly: mm39
Supplementary files format and content: matrix files and Seurat files

source_name: Lung

extract_protocol:
Lungs were perfused with cold sterile saline through the right ventricle. The lungs were then intratracheally inflated with 1.5 ml of Dispase 50 U/ml (Corning) followed by installation of 0.5 ml of 1% low melting agarose (BioRad) via the trachea. The lungs were excised and incubated on an orbital shaker for 45 min at room temperature. Each lobe was then minced into small pieces in DMEM (GIBCO) supplemented with 10% FBS (GIBCO) and 0.33 U/ml DNase I (Roche) and placed on the orbital shaker for an additional 10 minutes. The cells were then filtered through a 100 µm cell strainer and centrifuged at 400 g for 5 min at 4°C. The cell pellet was resuspended in ACK-buffer (GIBCO), incubated for 2 min on ice and then filtered through a 40 µm cell strainer. The cells were centrifuged at 400 g for 5 min at 4°C and resuspended in DPBS (GIBCO) supplemented with 5% FBS, and then stained with the following antibodies: EpCAM-BV785 (BioLegend #118245), CD45-APC (BioLegend, 103112), CD31-APC/Cy7 (BioLegend, 102534), I-A/I-E - AlexaFluor488 (MHC-II) (BioLegend, 107616) and 4’, 6-diamidino-2-phenylindole (DAPI) (Life Technologies, 62248) was used to eliminate dead cells. The cells were then sorted on the BD FACS Aria III system (BD Bioscience).
Single cell capturing was performed using the BD Rhapsody™ Express Single-Cell Analysis System (BD Biosciences). Libraries were generated using BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit according to the manufacturer’s protocols.

treatment_protocol: Mice at 10-14 weeks of age were anesthetized by isoflurane inhalation and subsequently administered a single dose of bleomycin (Sigma-Aldrich) oropharyngeally at 0.75 U/kg body weight (for IL11EGFP reporter mice) or 1.5 U/kg body weight (for all other mouse strains) in a volume of saline not exceeding 50 µl per mouse. Uninjured control mice received equal volumes of saline oropharyngeally. Mice were sacrificed at indicated time points post-bleomycin administration and lungs were collected for downstream analysis. Therapeutic doses of monoclonal anti-IL11 (X203, Aldevron) or IgG control antibodies were injected intraperitoneally at 20 mg/kg starting from day 4 and subsequently on day 7 and day 10 post-bleomycin administration.

value: Lung

value: WT

value: bleomycin


title: UKB, T8, D50

description:
T8_D53_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv