title: PTC para-cancerous tissue_rep3, sup

city: 福建省福州市

first: 瀛若

last: 林

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
B3

hyb_protocol: Cy3- and Cy5-labeled cRNAs were combined and hybridized to Arraystar Human mRNA & lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours.

scan_protocol: After washing, the slides were scanned using an Agilent Scanner G2505C.

data_processing: Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. GO and KEGG pathway enrichment analyses were conducted for differentially m6A-methylated mRNAs and lncRNAs. Quantile normalization and statistical analysis were performed using GeneSpring GX software (Agilent).

source_name: para-cancerous tissues of PTC patients without AITD

label_protocol: IP and Sup RNAs were amplified into cRNAs and labeled with Cy5 and Cy3, respectively, using the Arraystar Super RNA Labeling Kit.

growth_protocol: Isolated cancerous and para-cancerous tissue pairs were immediately frozen in liquid nitrogen for 40 minutes before storage in a -80°C freezer.

extract_protocol: Total RNA was extracted using PureLink™ RNA Mini Kit, followed by quality assessment with NanoDrop spectrophotometry and denaturing agarose gel electrophoresis.

treatment_protocol: No neoadjuvant therapy was administered prior to tissue collection.

value: PTC without AITD, 26 cases (3 men, 23 women), surgical resection, para-cancerous tissue pairs

tag: fraction

value: SUP RNA


title: M15_VEH_EX

status: Public on Feb 28 2025

type: genomic

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

country: USA

institute: University of Kentucky

hyb_protocol: DNA was amplified, fragmented and hybridized to the Infinium Mouse Methylation BeadChip using the standard protocol. Since conversion was a variable in the study, conversion conditions for each sample are available in their associated metadata.

scan_protocol: Arrays were imaged using the Illumina iScan with recommended Illumina settings

data_processing:
methylprep package v 1.7.1
Average Beta

molecule: genomic DNA

organism: Mus musculus

source_name: Gastrocnemius

label_protocol: standard protocol

growth_protocol: Sedentary or voluntary unweighted wheel running for ~20 months.

extract_protocol: Qiagen blood and tissue genomic DNA kit

treatment_protocol: Vehicle or Tamoxifen injections which results in satellite cells being replete and depleted, respectively, prior to the onset of the growth protocol

tag: tissue

value: Gastrocnemius

tag: cell type

value: Skeletal Muscle

tag: genotype

tag: treatment

value: VEH

value: EX


title: PTC para-cancerous tissue_rep2, sup

type: RNA

address: 福建省福州市台江区福建医科大学附属第一医院

country: China

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
B2

molecule: total RNA

organism: Homo sapiens


title: wildtype control/3d glut/3d kctd20 + glut 2

type: SRA

city: Los Angeles

first: Joshua

last: Berlind

address: 1425 San Pablo St

institute: University of Southern California

description:
Library name: 1B
10X Genomics
1A1Bbarcodes.tsv.gz
1A1Bmatrix.mtx.gz
1A1Bfeatures.tsv.gz

library_source: transcriptomic single cell

data_processing:
Data alignment and QC was conducted through the University of Southern California Center for Advanced Research Computing (CARC) using the Cell Ranger count Feature Barcode Analysis pipeline (10X Genomics) for concurrent UMI identification, reference genome (human hg38 genome) alignment, and HTO assignment. Samples were demultiplexed using the HTODemux pipeline in R version 4.0.158. Data was further processed using Seurat v4.0 to remove cells with < 200 detectable genes and > 50% mitochondrial rate118,119. We retrieved roughly 39,000 high quality cells with a depth of 20,000-25,000 reads/cell.
cell hash sequences for demultiplexing- glutamate: CAGGTTGTTGTCATT; glutamate + kctd20 aso: TATTTCCACCCGGTC
Assembly: hg38
Supplementary files format and content: tab separated values files and matrix files

source_name: neural

extract_protocol:
Organoids were dissociated for single-cell RNA sequencing as described with minor modifications117. In brief, organoids were incubated in Papain (Worthington LK003176) with DNase1 (Worthington LK003170) reconstituted per manufacturer instructions for 60 minutes at 37⁰C with gentle shaking at 27 rpm with regular pipetting. Single-cell suspension was added to Earle’s Balanced Salt Solution (EBSS) with Ovomucoid Inhibitor (Worthington LK003182) and DNase1, pelleted, resuspended in ice-cold Neurobasal-A (Invitrogen) with 0.2% bovine serum albumin (BSA), and filtered through 40 µM Flowmi tips (Sigma BAH136800040-50EA). Cell count and viability was determined by Trypan Blue staining using a hemocytometer. Cells were labeled with hashtag-oligonucleotide (HTO) antibodies (Biolegend TotalSeq-B, 405287, 405289, 405291) and libraries were prepared following manufacturer protocols (10X Genomics, CG000206 Rev D).
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding for Cell Surface Protein); PN-1000128, PN-1000079, PN-1000127, PN-1000213

value: neural

tag: cell line

value: organoid

value: neurons, glia

value: wildtype

value: mixed


title: Mtb, control, rep 1

city: New Delhi

first: Ranjan

middle: Kumar

last: Nanda

address: International Centre for Genetic Engineering and Technology, New Delhi-110067, India

department: Translational Health Group

country: India

institute: International Centre for Genetic Engineering and Technology (ICGEB), New Delhi component

library_source: transcriptomic

data_processing:
Adapter Contamination was removed using bbduk.sh (from BBmap toolkit v39.06) with options (ktrim=l k=23 mink=11 hdist=1 tpe tbo).
Hisat2 (v2.2.1) was used for the alignment of reads to the Mtb genome (Refseq Accession: NC_000962.3) which was subsequently sorted using Samtools (v1.13).
The sorted alignment files in BAM format were used as input for counting reads using featureCounts (v2.0.3).
Assembly: NC_000962.3
Supplementary files format and content: "raw_counts.tsv" file is in TSV format and contains raw read counts of all libraries.

organism: Mycobacterium tuberculosis

source_name: Bacteria

growth_protocol: Middlebrook 7H9 supplemented with OADC enrichment.

extract_protocol:
DFO (0.1 mg/ml) and control were harvested at day 5 post-addition of Deferoxamine by centrifuging the Mtb cultures at 3,500 g for 10 minutes at room temperature. The cell pellet was washed with Tris-EDTA to remove extra media and the pellet was suspended in Trizol reagent (1 ml). The samples were subjected to bead beating (4 cycles, 45 sec each) after adding zirconia beads (~200 μl, 0.1 mm) at 6.5 m/s speed with incubation of 30 sec on ice after each cycle. Chloroform (0.2 ml) was added to the samples and after briefly shaking the tubes, the samples were incubated on ice (for 5 min) and centrifuged at 13,400 g, 4ºC for 20 min. Upper aqueous layer was transferred to a fresh tube and RNA was precipitated by adding isopropyl alcohol (0.5 ml). The samples were then incubated at -80ºC for 20 min and subsequently centrifuged for 10 min at 13,400 g and 4ºC. The purified RNA pellet was washed with 75% ethanol and resuspended in nuclease-free water.
NEBNext Ultra RNA library prep kit

treatment_protocol: Deferoxamine was added at the concentration of 0.1 mg/mL in log-phase Mtb cultures.

tag: strain

value: Bacteria

value: Wildtype

value: Control


title: M10_TAM_SED

value: TAM

value: SED


title: GM12878, 1000U, Cell 9

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy for each sample. hic and mcool files included contact matrices for each sample.
Supplementary files format and content: .3dg files of single-cell 3D genome structures

source_name: blood

growth_protocol: GM12878 lymphoblastoid cells were grown in RPMI1640 medium (Gibco, Thermo Fisher Scientific, Cat. # 11875093) media supplemented with 15% FBS and 1% Pen/Strep. GM12878 were cultured at 37° C with 5% CO2 at recommended density.

extract_protocol:
1 million cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Single cells were amplified with the state-of-art transposase-based WGA (Multiplexed End Tagging Amplification), barcoded in 96-well plate, then pooled for library preparation.

value: blood

value: lymphoblastoid

value: WT

tag: mnase titration

value: 1000U MNase


title: MAPT V337M 3d kctd20 + glut

description:
Library name: 7A
10X Genomics

value: MAPT V337M

value: 3d glutamate + kctd20 aso


title: M3_VEH_EX

value: Gastrocnemius

value: Skeletal Muscle

value: VEH

value: EX


title: M6_TAM_SED


title: M2_TAM_SED


title: M32_TAM_SED


title: MAPT V337M 3d glut

description:
Library name: 6A
10X Genomics

value: neural

value: organoid

value: neurons, glia

value: 3d glutamate


title: GM12878, 1000U, Cell 7


title: isogenic control/3d glut/3d kctd20 + glut 2

description:
Library name: 2B
10X Genomics
2A2Bbarcodes.tsv.gz
2A2Bmatrix.mtx.gz
2A2Bfeatures.tsv.gz

value: MAPT V337V

value: mixed


title: MAPT V337M control

description:
Library name: 5A
10X Genomics

value: control


title: M28_VEH_SED

value: SED


title: GM12878, 1000U, Cell 6

value: blood

value: lymphoblastoid


title: PTC cancerous tissue_rep3, sup

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
A3

source_name: cancerous tissues of PTC patients without AITD

value: PTC without AITD, 26 cases (3 men, 23 women), surgical resection, cancerous tissue pairs

value: SUP RNA


title: PTC cancerous tissue_rep2, sup

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
A2


title: PTC para-cancerous tissue_rep3

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

value: PTC without AITD, 26 cases (3 men, 23 women), surgical resection, para-cancerous tissue pairs

value: IP RNA


title: PTC para-cancerous tissue_rep1, sup

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
B1


title: GM12878, 1000U, Cell 4

value: WT

value: 1000U MNase


title: GM12878, 1000U, Cell 8


title: M21_VEH_SED

value: Gastrocnemius

value: Skeletal Muscle

value: VEH


title: wildtype/isogenic/MAPT V337M 6d kctd20 +glut 1

description:
Library name: 4A
10X Genomics
4A4Bbarcodes.tsv.gz
4A4Bmatrix.mtx.gz
4A4Bfeatures.tsv.gz

value: neural

value: organoid

value: neurons, glia

value: 6d glutamate + kctd20 aso


title: PTC cancerous tissue_rep1, sup

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

description:
IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.
A1


title: M24_VEH_SED


title: isogenic control/3d glut/3d kctd20 + glut 1

description:
Library name: 2A
10X Genomics
2A2Bbarcodes.tsv.gz
2A2Bmatrix.mtx.gz
2A2Bfeatures.tsv.gz

value: MAPT V337V

value: mixed


title: M5_VEH_SED

value: SED


title: wildtype/isogenic/MAPT V337M 6d glut 1

description:
Library name: 3A
10X Genomics
3A3Bbarcodes.tsv.gz
3A3Bmatrix.mtx.gz
3A3Bfeatures.tsv.gz

value: 6d glutamate


title: M1_VEH_SED


title: PTC para-cancerous tissue_rep1

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院


title: GM12878, 1000U, Cell 3

value: blood

value: lymphoblastoid


title: wildtype control/3d glut/3d kctd20 + glut 1

description:
Library name: 1A
10X Genomics
1A1Bbarcodes.tsv.gz
1A1Bmatrix.mtx.gz
1A1Bfeatures.tsv.gz

value: wildtype


title: Foxj1CreERT2_spinalCord_P10107_2289_P10107_2432

status: Public on Feb 27 2025

city: Stockholm

first: Behzad

last: Yaghmaeian Salmani

state: Solna, Stockholm

address: Department of Cell and Molecular Biology (CMB) Karolinska Institute,, Biomedicum, Solnavägen 9, Solna, Stockholm, P.O. Box 285 SE-171 77 Stockholm, Sweden

department: CMB

country: Sweden

institute: Karolinska Institute

description: Library name: Foxj1CreERT2_spinalCord

data_processing:
the sequenced reads were aligned to the mouse genome (mm10) that was merged with the eGFP sequence using the Star v2.3.1o (Dobin et al., 2013) and filtered for uniquely mapping reads. The expression values were then calculated for each Ensembl ID (release 69) based on the kilobase gene model with million mappable reads using ‘rpkmforgenes’ (Ramsköld et al., 2009).
analysis and the visualizations were carried out through ‘Seurat’ R package v3 (Stuart et al., 2019)
Assembly: mouse mm10
Supplementary files format and content: ependymalData_rawCounts.tsv contains raw counts from RNA assay
Supplementary files format and content: ependymalData_normalizedCounts.tsv contains normalized counts from RNA assay

molecule: polyA RNA

source_name: adult mouse brain

extract_protocol:
Cells were sorted using BD FACS Aria III (BD Biosciences) and collected on 96-well PCR plates. The RNA was extracted and cDNA libraries prepared using standard SmartSeq2 protocol using Tn5 made in the lab (Picelli et al., 2013, 2014).
The RNA was extracted and cDNA libraries prepared using standard SmartSeq2 protocol using Tn5 made in the lab (Picelli et al., 2013, 2014).

value: adult mouse brain

value: FoxJ1CreERT2 R26TdT


title: Foxj1CreERT2_MB_P10107_1001_1480_P11266_1001_1192

description: Library name: Foxj1CreERT2_MB


title: GM12878, 1000U, Cell 2

value: WT

value: 1000U MNase


title: GM12878, 1000U, Cell 1


title: Nkx2.2Cre_P11266_1193_P11266_1624

description: Library name: Nkx2.2Cre

value: Nkx2-2Cre R26TrapC


title: Foxj1CreERT2_3rdVentricle_P10107_1481_P10107_1768

description: Library name: Foxj1CreERT2_3rdVentricle


title: Sed_liver_2

city: CHARLOTTESVILLE

first: Chengli

last: Shen

state: Virginia

address: 345 Crispell Dr.

institute: University of Virginia

description: Library name: L2

data_processing:
Fastq files were generated using Cell Ranger mkfastq (10x Genomics) and were analyzed with the 10x Genomics Cell Ranger software v7.0.0. Mapping of the FASTQ files was performed using the mm10 reference genome (GRCm38.91). We performed preliminary data analysis using CellRanger count/aggr and generated a file containing barcode tables, gene tables, and gene expression matrices.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files (in barcodes.tsv.gz: barcode-1 --- >Sed_liver_1, barcode-2  --->Sed_liver_2, barcode-3   ---> Ex_liver_1, barcode-4   ---> Ex_liver_2)

source_name: liver

extract_protocol:
Sed and PEx mice bearing MC38 tumors were sacrificed 3 weeks after tumor injection. The liver was harvested and processed into single-cell suspensions using liver dissociation kits and then passed through a 70 μm cell strainer. Differential centrifugation separated non-parenchymal cells (NPCs) from hepatocytes (50 g for 5 minutes, repeated twice). The supernatant was centrifuged again (300 g for 10 minutes) to obtain CD45+ immune cells were sorted using CD45+ beads from these single-cell suspensions, achieving a purity greater than 90%.
Following quality control checks for cell viability and concentration, samples were transferred to a pre-chilled 96-well plate, heat-sealed, and reverse transcription was carried out using a Veriti 96-well thermal cycler. Following reverse transcription, cDNA was extracted using Recovery Agent (10x) and purified with a Silane DynaBead clean-up as described in the user guide. The purified cDNA was then amplified for 12 cycles, diluted at a 4:1 ratio (elution buffer, Qiagen, to cDNA), and analyzed on a Bioanalyzer (Agilent Technologies) to measure cDNA concentration. cDNA libraries were prepared using the 10X Chromium Single Cell 3’ Library and Gel Bead Kit v3.1.

value: hepatic immune cells

value: liver

tag: age

tag: Sex

value: male


title: Ex_liver_1

description: Library name: L3


title: Sed_liver_1

description: Library name: L1


title: Foxj1CreERT2_LV_P10107_2001_P10107_2288

description: Library name: Foxj1CreERT2_LV


title: GM12878, 1000U, Cell 5


title: LCM_P70_5

description:
Library name: P7956_2691
merged_LCM.csv

data_processing:
For LCM samples, reads were aligned and mapped to reference transcriptome mm10 using STAR V 2.3
For in vitro samples, Salmon/1.6.0 was used to create an index on the transcriptome Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl.
DESeq2 package version 1.34.0 was used to analyze RNA-seq data, including differential gene expression
Assembly: mouse mm10 for STAR, Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl for Salmon
Supplementary files format and content: merged_LCM.csv contains normalized counts per sample
Supplementary files format and content: neurosphere_rawCounts.csv contains raw counts per sample

source_name: midbrain floor plate

extract_protocol:
RNA extraction was performed with Qiagens RNeasy micro RNA kit. 1ng of RNA was used for cDNA and amplified for 15 cycles.
cDNA libraries were made using the protocol Smart-seq2 for sensitive full-length transcriptome profiling in single cells. cDNA libraries were tagmented using home-made Tn5 enzyme and amplified for 11 cycles. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects and Nextera dual indexes (Illumina).

value: midbrain floor plate

value: Lmx1aCreERT2; R26TRAPC

tag: time


title: Ex_liver_2

description: Library name: L4


title: LCM_P70_6

description:
Library name: P7956_2692
merged_LCM.csv


title: PTC cancerous tissue_rep3

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

value: PTC without AITD, 26 cases (3 men, 23 women), surgical resection, cancerous tissue pairs

value: IP RNA


title: PTC cancerous tissue_rep1

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院


title: PTC para-cancerous tissue_rep2

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院

value: PTC without AITD, 26 cases (3 men, 23 women), surgical resection, para-cancerous tissue pairs


title: PTC cancerous tissue_rep2

address: 福建省福州市台江区福建医科大学附属第一医院

institute: 福建医科大学附属第一医院


title: LCM_P70_4

description:
Library name: P7956_2690
merged_LCM.csv


title: LCM_P70_2

description:
Library name: P7956_2688
merged_LCM.csv


title: LCM_P70_3

description:
Library name: P7956_2689
merged_LCM.csv


title: LCM_P70_1

description:
Library name: P7956_2687
merged_LCM.csv


title: LCM_E18_5

description:
Library name: P7956_2686
merged_LCM.csv


title: LCM_E18_4

description:
Library name: P7956_2685
merged_LCM.csv


title: LCM_E18_1

description:
Library name: P7956_2682
merged_LCM.csv


title: LCM_E13_5

description:
Library name: P7956_2681
merged_LCM.csv


title: LCM_E11_2

description:
Library name: P7956_2674
merged_LCM.csv


title: LCM_E11_3

description:
Library name: P7956_2675
merged_LCM.csv


title: LCM_E18_3

description:
Library name: P7956_2684
merged_LCM.csv


title: LCM_E11_1

description:
Library name: P7956_2673
merged_LCM.csv


title: LCM_E18_2

description:
Library name: P7956_2683
merged_LCM.csv


title: LCM_E11_4

description:
Library name: P7956_2676
merged_LCM.csv


title: LCM_E13_4

description:
Library name: P7956_2680
merged_LCM.csv


title: LCM_E13_2

description:
Library name: P7956_2678
merged_LCM.csv


title: LCM_E13_3

description:
Library name: P7956_2679
merged_LCM.csv


title: Aggressive B-cell lymphoma R31R

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Cytoscan HD arrays Cytoscan HD and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: LN

label_protocol: CytoScan™ Reagent Kit / 901808,t

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: type of sample

value: Aggressive B-cell lymphoma

tag: gender

value: frozen tissue


title: LCM_E13_1

description:
Library name: P7956_2677
merged_LCM.csv


title: Mouse DSMX47 4G

city: Cambridge

first: Muxin

last: Gu

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

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads for each library were mapped with TopHat version 2.0.13 against the mouse genome, build GRCm38.68, downloaded via the Ensembl BioMart data-mining tool. HiSeq libraries were aligned with the following options: --keep-fasta-order --no-sort-bam -r 100 -p 12 --library-type fr-firststrand --no-coverage-search --microexon-search --transcriptome-index = GRCm38.known, where GRCm38.known is a transcriptome index file in GTF format prepared beforehand in an initial single TopHat run without input reads. Differential expression analysis was carried out with these counts in the Bioconductor package DESeq2, version 1.6.3, with a BH independent filtering method with an FDR of 1%
Assembly: GRCm38
Supplementary files format and content: DESeq output

source_name: bone marrow

growth_protocol: Primary mouse cells were cultured in X-VIVO 20 medium (Lonza) supplemented with 5% serum (Stem Cell Technologies), IL3 (10 ng/ml; Peprotech), IL6 (10 ng/ml; Peprotech), SCF (50 ng ml/ml; Peprotech) and 1% penicillin–streptomycin–glutamine (Gibco).

extract_protocol:
RNA was extracted from HSPC/Lin– BM cells with an Arcturus Picopure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer's instructions. RNA from mouse primary AML samples was extracted with TRIzol reagent (Thermo Fisher Scientific). RNA from human cell lines was extracted with an RNeasy kit (Qiagen) according to the manufacturer's instructions.
An RNA-seq library was generated with a TruSeq Stranded mRNA Sample Prep Kit (Illumina) and sequenced on the Illumina HiSeq2000 v4 platform with 75-bp paired-end sequencing.An RNA-seq library was generated with a TruSeq Stranded mRNA Sample Prep Kit (Illumina) and sequenced on the Illumina HiSeq2000 v4 platform with 75-bp paired-end sequencing.

value: bone marrow

value: lineage negative HSPC

tag: condition

value: 6 weeks post-pIpC


title: Mouse DSMX47 4E


title: Mouse DSMX47 4F


title: Mouse DSMX47 4H


title: HSC001_TGFB1+COLCOAT_4day_R4_2

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E790
HSC001_TGFB1+COLCOAT_4day

data_processing:
Base-calling software: Bcl2fastq2 with Version 2.20.0.422-2
Exon quantification pipeline (version 2.5, (51)) with STAR (version 2.7.3a)
PISCES (GitHub - Novartis/pisces) to quantify gene expression.
Assembly: hg38 with ensembl version 98
Supplementary files format and content: tab-delimited file includes raw count for each sample

source_name: HSC

growth_protocol: Primary HSCs were obtained from Lonza and grown in collagen-coated flasks in human stellate cell growth medium (Lonza, MCST250) supplemented with 50 mM 2-Phospho-L-ascorbic acid (Merck, 49752).

extract_protocol:
Total RNA was extracted with Trizol
PolyA selected mRNA library

treatment_protocol: The medium was changed the following day and cells were incubated in the same low FBS medium with addition of TGF-β (Gibco, PHG9214), for 24h (qPCR), 4 and 7 days (RNA-seq).

value: HSC


title: HSC001_TGFB1+NOCOAT_7day_R3_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E785
HSC001_TGFB1+NOCOAT_7day


title: HSC001_UNTREATED+COLCOAT_4day_R4_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E789
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_TGFB1+NOCOAT_7day_R2_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E784
HSC001_TGFB1+NOCOAT_7day


title: HSC001_UNTREATED+NOCOAT_7day_R3_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E782
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_TGFB1+COLCOAT_4day_R2_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E778
HSC001_TGFB1+COLCOAT_4day


title: HSC001_UNTREATED+NOCOAT_7day_R1_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E780
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_UNTREATED+NOCOAT_7day_R2_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E781
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_TGFB1+COLCOAT_4day_R1_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E777
HSC001_TGFB1+COLCOAT_4day


title: HSC001_TGFB1+COLCOAT_4day_R3_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E779
HSC001_TGFB1+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R3_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E776
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R2_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E775
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R1_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E774
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R4_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E789
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_TGFB1+NOCOAT_7day_R3_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E785
HSC001_TGFB1+NOCOAT_7day


title: HSC001_TGFB1+NOCOAT_7day_R2_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E784
HSC001_TGFB1+NOCOAT_7day


title: HSC001_UNTREATED+NOCOAT_7day_R3_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E782
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_TGFB1+NOCOAT_7day_R1_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E783
HSC001_TGFB1+NOCOAT_7day


title: HSC001_UNTREATED+NOCOAT_7day_R1_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E780
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_TGFB1+COLCOAT_4day_R1_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E777
HSC001_TGFB1+COLCOAT_4day


title: HSC001_UNTREATED+NOCOAT_7day_R2_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E781
HSC001_UNTREATED+NOCOAT_7day


title: HSC001_TGFB1+COLCOAT_4day_R2_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E778
HSC001_TGFB1+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R2_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E775
HSC001_UNTREATED+COLCOAT_4day


title: HSC001_UNTREATED+COLCOAT_4day_R3_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E776
HSC001_UNTREATED+COLCOAT_4day


title: HA3

city: London

first: Yazead

last: Buhidma

state: London

address: 1 Wakefield Street

department: Department of Neurodegenerative Diseases

institute: University College London

description:
Library name: Sample 15
10X Genomics

data_processing:
The resulting gene count table was analysed using the Seurat package (version 4.4). Quality control was performed to remove low-quality cells based on the number of detected genes and unique molecular identifiers (UMIs). Cells with an unusually high number of UMIs, suggesting potential doublet events, were also excluded using scDblFinder. Using SCTransform, gene expression data were normalised to adjust for differences in sequencing depth between cells and scaled to correct for cell-to-cell variation in total UMI count. Data were also normalised to remove confounding sources of variation such as mitochondrial mapping percentage, post-mortem delay, age of death, and batch number.
Assembly: hg38
Supplementary files format and content: Farrell_seurat_object is an RDS file containing barcodes and gene counts for each nuclei sequenced. The data within has been preprocessed for mitochondrial gene %, features above and below standard limits, as well as being scaled, normalised, and centred.  Unprocessed data files (i.e. Farrell_barcodes, features & matrix) only contain features & gene counts.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Tissue was transferred directly onto ice-cold sucrose buffer and homogenised by hand. The homogenate was layered on top of a sucrose cushion and nuclei were recovered after centrifugation. Nuclei were resuspended in PBS containing BSA (to prevent clumping) and RNase inhibitors, counted and diluted to 1,000 nuclei/μl.
Sequencing libraries were prepared using the “single cell 3’ library kit v3” with the Chromium instrument (10X Genomics). Aiming to obtain libraries for ~5,000 independent nuclei per sample. Libraries were sequenced on an Illumina NovaSeq6000 instrument (UCL Genomics), to an average of at least 100,000 reads/nucleus. Raw sequencing data were processed through the software CellRanger (10X Genomics) to assign each transcript read to its respective nucleus, we performed alignment to the transcriptome, counting reads, and processing of the unique molecular identifier tag to reduce PCR bias

value: Brain

value: Female

tag: disease

value: Healthy control


title: EOAD3

description:
Library name: Sample 16
10X Genomics

value: Early-onset Alzheimer's Disease


title: HA4

description:
Library name: Sample 13
10X Genomics

value: Male


title: DSAD2

description:
Library name: Sample 12
10X Genomics

value: Down Syndrome


title: DSAD3

description:
Library name: Sample 14
10X Genomics


title: DSAD7

description:
Library name: Sample 11
10X Genomics


title: HSC001_TGFB1+NOCOAT_7day_R1_2

description:
Library name: GSM-AAE083-220720_A00871_0363_AHGFKFDRX2-GX_IL_LIB_22_E783
HSC001_TGFB1+NOCOAT_7day


title: EOAD4

description:
Library name: Sample 10
10X Genomics


title: DSAD5

description:
Library name: Sample 9
10X Genomics


title: EOAD1

description:
Library name: Sample 8
10X Genomics


title: HA1

description:
Library name: Sample 7
10X Genomics


title: HSC001_TGFB1+COLCOAT_4day_R4_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E790
HSC001_TGFB1+COLCOAT_4day


title: DSAD1

description:
Library name: Sample 6
10X Genomics


title: EOAD2

description:
Library name: Sample 2
10X Genomics


title: DSAD6

description:
Library name: Sample 3
10X Genomics


title: DSAD8

description:
Library name: Sample 1
10X Genomics


title: SFTPC-2 | 024 | CD68+

city: Boston

first: John

middle: C

last: Kennedy

state: MA

address: 300 Longwood Ave, 5th floor

department: Division of Pulmonary Medicine

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
An Illumina NovaSeq 6000 was used for pair-end sequencing (27 x 27) of libraries, after which the obtained data was processed and filtered for quality. FASTQ files for each ROI were demultiplexed and converted to digital count conversion (DCC) files using the GeoMx NGS Pipeline (version 2.3.4) application.
Supplementary files format and content: The DCCs were transferred to the GeoMx DSP Data Analysis 5 Suite, which was used to align ROIs with raw and Q3 (3rd quartile of all selected targets) normalized counts of all targets. Q3 normalization uses the top 25% of expressors to normalize across ROIs, which makes this strategy robust to changes in expression of individual genes and suited for making comparisons across ROIs.
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Clinically obtained Formalin Fixed Parafin Embeded (FFPE) lung biopsy samples were obtained and assembled into a tissue microarray consisting of 8 individual FFPE lung biopsy samples that were each ~1cmx 1cm in size.
Sample processing was done in conjunction with the Nanostring Technology Access Program (TAP) lab, following the the GeoMx DSP user manuals for GeoMx DSP slide preparation (MAN-10150-05), GeoMx DSP sample collection (SEV-00087-05), GeoMx DSP library preparation (MAN-10153-05) and GeoMx DSP data analysis (SEV-00090-05). In brief, tissue slides were baked at 60°C for 1h in a drying oven after which they were deparaffinized and rehydrated using a Leica Biosystems FFPE BOND RX. RNA targets were exposed using proteinase K solution followed by fixation using 10% NBF. After unloading the tissue slides from the Leica Biosystems BOND RX, they were incubated overnight with the RNA probe mix (Whole Transcriptome Atlas, which consists of in situ hybridization probes with UV photocleavable oligonucleotide barcodes). Tissues were then washed and stained with the visualization markers: panCK-488 at 1:500 (Invitrogen, NBP2- 33200AF488), ABCA3-647 at 1:100 (Sevenhills, WMAB17G524 conjugated with the Alexa-647 labeling kit, Thermo A20186), CD68-594 at 1:400 (Santa Cruz, sc-20060AF647) and SYTO 83 at 1:25 (Fisher, S11364). Tissue slides were then loaded in and scanned with the GeoMx DSP instrument.
In conjunction with our pathologist, we selected three alveolar macrophage predominant regions of interest (ROIs) per sample using the immunohistochemistry markers on the slide and the H&E staining of the neighboring slide as guide.
Serial UV illumination of each ROI was used to collect the probe barcodes from the different ROIs. Using the i5/i7 dual-indexing system of Illumina, each ROI was uniquely indexed.

value: Lung

tag: age at_biopsy_(months)

tag: phenotype

value: DIP-like

tag: male/female (m/f)

value: F


title: SFTPC-2 | 022 | CD68+

tag: tissue


title: HSC001_TGFB1+COLCOAT_4day_R3_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E779
HSC001_TGFB1+COLCOAT_4day


title: SFTPC-2| 023 | CD68+


title: POP | 021 | CD68+

value: intra-alveolar Macs

value: M


title: HSC001_UNTREATED+COLCOAT_4day_R1_1

description:
Library name: GSM-AAE083-220711_A00871_0360_AHF5MTDMXY-GX_IL_LIB_22_E774
HSC001_UNTREATED+COLCOAT_4day


title: POP| 020 | CD68+


title: POP | 019 | CD68+


title: SMPD1 | 017 | CD68+


title: SMPD1 | 018 | CD68+


title: SMPD1 | 016 | CD68+


title: DIP-2| 014 | CD68+


title: NPC2 | 012 | CD68+


title: NPC2 | 011 | CD68+


title: HA2

description:
Library name: Sample 5
10X Genomics


title: SFTPC-1 | 009 | CD68+


title: SFTPC-1 | 008 | CD68+


title: DSAD4

description:
Library name: Sample 4
10X Genomics


title: GRN| 006 | CD68+


title: SFTPC-1 | 007 | CD68+


title: GRN | 005 | CD68+


title: DIP-1 | 003 | CD68+


title: DIP-1 | 002 | CD68+


title: DIP-1 | 001 | CD68+

value: Desqumative Interstitial Penumonia (DIP)-like


title: EFT620

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Exon quantification pipeline (version 2.5, with STAR (version 2.7.3a); PISCES (GitHub - Novartis/pisces) to quantify gene expression.
Assembly: Ensembl version 98
Supplementary files format and content: Gene count table

source_name: Liver

growth_protocol: Human liver biopsy samples.

treatment_protocol: Samples obtained at the time of bariatric surgery.

value: Liver


title: RVO178


title: YRI137


title: XSP436


title: NVS675


title: DIP-2 | 015 | CD68+


title: AKE602


title: OYE145


title: MUH937


title: NPC2| 010 | CD68+


title: WVK235


title: DIP-2 | 013 | CD68+


title: WEW415


title: WZG609


title: DJG504


title: FHC603


title: HNK873


title: XNG554


title: GRN | 004 | CD68+


title: NSF317


title: UIX583


title: UMD368


title: GWX459


title: DWS954


title: XVC832


title: CNR595


title: TTQ135


title: PWQ681


title: FAO468


title: BQG343


title: SBB944


title: WAH911


title: YDJ237


title: RKT482


title: HPF205


title: ZTZ746


title: GNO731


title: YNL310


title: IPZ774


title: ZZX516


title: AWX180


title: ADI555


title: MSD301


title: ABZ370


title: HNR861


title: IRP509


title: WQI320


title: ENP459


title: CJU592


title: CCA245


title: CCL865


title: BMO617


title: AUR380


title: EFW637


title: PYQ514


title: XTI939


title: TWJ769


title: EUU581


title: HML208


title: AEK876


title: EEJ113


title: JNK936


title: ERH825


title: DNM623


title: TPT236


title: KAV782


title: QYJ155


title: NWX937


title: DPS177


title: LAH821


title: CMW958


title: QZV338


title: TAB580


title: HDN490


title: CCU357


title: SXI255


title: TVO619


title: UBH208


title: QMA457


title: XSP695


title: YNE987


title: LSG225


title: HKE922


title: GNK557


title: RVT473


title: HOI855


title: HTS420


title: QFU156


title: WLW163


title: HMU541


title: GTX889


title: YOX147


title: BVJ928


title: VBL165


title: DXN914


title: NWU655


title: YFH298


title: YMK964


title: IMD704


title: LOT902


title: CFH377


title: OTW294


title: OUX828


title: FYS787


title: AUT782


title: JLG297


title: AQB432


title: EYC308


title: SRC524


title: YXK696


title: YHL587


title: BGB414


title: JFF518


title: ABJ468


title: TKR960


title: ALF449


title: CIW710


title: GKM743


title: KIU550


title: KHJ333


title: VNQ333


title: SPM565


title: BDR489


title: LUK585


title: IOW123


title: ZOD179


title: TPZ888


title: RYZ258


title: HIY471


title: DNL679


title: PXJ190


title: UTB432


title: RPC773


title: TLT507


title: GNI484


title: TDW443


title: DDT659


title: UHV721


title: WRY133


title: UXJ402


title: YSZ301


title: ADE464


title: KUV229


title: YIU233


title: ASX665


title: YSU419


title: QDY893


title: PGH821


title: KXW719


title: IQG997


title: GBP913


title: IOA210


title: MJN217


title: MMJ737


title: OQG452


title: ZKP780


title: ESJ967


title: TTG258


title: WNN537


title: WCG168


title: PFX974


title: QTT156


title: DTH947


title: ALD943


title: PUF962


title: UDT182


title: ONT897


title: HDW632


title: YVA544


title: ZQQ777


title: CVW854


title: YXW946


title: DGQ395


title: CUG491


title: FUG307


title: FND585


title: QJY851


title: BIW515


title: EJK173


title: WVX781


title: ZKD805


title: ACO747


title: WIZ538


title: UAO361


title: KFY268


title: XFO277


title: XPI774


title: FKY810


title: XYG500


title: REK696


title: EXK318


title: KQC337


title: GYZ241


title: IBF935


title: LUH941


title: DDX442


title: BRE547


title: RFN819


title: SIT901


title: JVQ477


title: XTU916


title: PWY153


title: XDI475


title: QKK716


title: NJM268


title: MYN546


title: RZD705


title: QJW266


title: PND513


title: VCO315


title: SPI488


title: VRE722


title: OXK164


title: CQW242


title: SQP633


title: YHB234


title: XPP673


title: END612


title: EJV194


title: YPG840


title: DCR810


title: KZR101


title: LQF210


title: GDJ739


title: VVI446


title: UHL541


title: XQE847


title: JTN948


title: DNMT1 knockdown,#2

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

data_processing:
Raw sequencing data was preprocessed using Ktrim software to remove adapters and low quality cycles; PCR duplicates were removed using in-house programs; the clean reads were subsequently aligned to the human reference genome (GRCh38/hg38) using STAR software
FeatureCount was then used to quantify gene expressions (e.g., raw read counts); the raw read counts for shNC and shDNMT1/shDNMT3B were analyzed using DESeq2 to mine differentially expressed genes; genes with Benjamini-Hochberg adjusted p-values lower than 0.05 and at least 1.5-fold changes in expression between shNC and shDNMT1/shDNMT3B were considered as differentially expressed
Assembly: NCBI GRCh38
Supplementary files format and content: Matrix for raw read counts for all genes in each sample

growth_protocol: HT29 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol:
RNA of HT29 cells was extracted with Direct-zol RNA Miniprep Kit (ZYMO) after adding TRIzol™ Reagent (Invitrogen) ; Concentration was detected by Nanodrop and quality was assessed using 1.5% agarose gel.
A total of 1ug RNA were used to preprare the whole transcriptome library with MGIEasy rRNA Depletion Kit (MGI) and VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme). Concentration of library was detected with Qubit dsDNA HS Assay Kit and size was detected using Agilent High Sensitivity D1000 ScreenTape System.

treatment_protocol: HT29 cells with stable knockdown of DNMT1/DNMT3B were obtained using lentiviruses and selected using puromycin (1μg/ml) for 3 passage

tag: cell type

value: colorectal cancer cell

value: DNMT1 knockdown

value: puromycin selection


title: DNMT1 knockdown,#3

tag: genotype


title: C2

city: Shanghai

last: Tian

address: South Chongqing Road

institute: Shanghai Jiao Tong University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
Bowtie2 (v2.3.4.3) was applied to align the clean reads to the reference gene set.
Expression level of gene was calculated by RSEM (v1.3.1).
Differential expression analysis was performed using the DESeq2 (v1.4.5).
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and FPKM values.

source_name: Th2 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer’s protocols.

tag: model

value: Bleomycin-induced SSc (BLM-SSc)

value: Th2 cells

value: WT

tag: treatment


title: C1


title: D1

value: DMSO


title: PNT686


title: JFL906


title: FSM684


title: UDF695


title: YKD902


title: JWQ775


title: DNMT3B knockdown,#2

tag: cell line

value: DNMT3B knockdown


title: DNMT1 knockdown,#1


title: Control,#3

value: Control


title: DNMT3B knockdown,#1


title: REI423


title: VBR963


title: DNMT3B knockdown,#3


title: KQF393


title: CLU626


title: QKY201


title: HYC397


title: Control,#1


title: IL28 CD8 T cells, NOD Sh2b3 -/- + anti-IL2, 24hr

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

description: Library name: IL28

data_processing:
Sequences were quality assess with FastQC (v0.119.9).
Sequences were filtered with AdapterRemoval (v2.3.2) to remove poor quality sequences (score <30, length <15, ambiguous >1).
Sequences were aligned to the mouse genome (GRCm39 releast 106) with STAR (v2.7.9a).
Sequences were quality assessed with samtools flagstat (v1.7) and Picard (v2.42.2).
Alignments were filtered with samtools to remove PCR duplicates, unmapped, non-primary and poor-quality alignments (MAPQ < 30).
High quality alignments were quantified in gene exons using Subread featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts with genes as rows and samples as columns

source_name: Spleen

growth_protocol: Naïve CD8 T cells were isolated (negative selection) from the spleens of OT-I Sh2b3+/+ and Sh2b3-/- mice before being plated at 1e6 cells/mL in a 12 well plate.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Kit or the Zymo Quick-RNA Microprep Kit
NovoGene mRNA-Seq

treatment_protocol: Cells were stimulated with 10 ug/mL plate-bound anti-CD3 and 5 ug/mL soluble anti-CD28 with or without 10 ug/mL blocking anti-IL-2 for 24 hours at 37 C.

value: Spleen

tag: mouse strain

value: NOD

value: Purified Naive OT-I CD8 T Cells

value: NOD Sh2b3 -/-


title: Control,#2


title: SDR783


title: D2


title: IL27 CD8 T cells, NOD Sh2b3 -/- + anti-IL2, 24hr

description: Library name: IL27


title: WGK828


title: AXJ903


title: SLR4892


title: IL25 CD8 T cells, NOD Sh2b3 -/- + anti-IL2, 24hr

description: Library name: IL25


title: IL24 CD8 T cells, WT + anti-IL2, 24hr

description: Library name: IL24

value: Wild Type


title: IL23 CD8 T cells, WT + anti-IL2, 24hr

description: Library name: IL23


title: JUT827


title: IL21 CD8 T cells, WT + anti-IL2, 24hr

description: Library name: IL21


title: IL26 CD8 T cells, NOD Sh2b3 -/- + anti-IL2, 24hr

description: Library name: IL26


title: QTB333


title: XCC841


title: NIV336


title: HOY965


title: IL22 CD8 T cells, WT + anti-IL2, 24hr

description: Library name: IL22


title: AR9 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR9


title: HKD846


title: AR6 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR6


title: ROL427


title: AR8 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR8


title: AR60 CD8 T cells, NOD Sh2b3 -/-, 24hr

description: Library name: AR60


title: AR59 CD8 T cells, KO, 24hr

description: Library name: AR59


title: AR7 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR7


title: AR54 CD8 T cells, WT, 24hr

description: Library name: AR54


title: QCX420


title: LMT575


title: AR53 CD8 T cells, WT, 24hr

description: Library name: AR53


title: OXX116


title: AR5 CD8 T cells, WT, 0hr

description: Library name: AR5


title: KCX451


title: KFZ933


title: AR34 CD8 T cells, WT, 0hr

description: Library name: AR34


title: AR4 CD8 T cells, WT, 0hr

description: Library name: AR4


title: ZOD891


title: AR40 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR40


title: AR39 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR39


title: JDH172


title: AR33 CD8 T cells, WT, 0hr

description: Library name: AR33


title: SEG748


title: WXI496


title: MRA483


title: AR29 CD8 T cells, NOD Sh2b3 -/-, 6hr

description: Library name: AR29


title: YJW923


title: AR3 CD8 T cells, WT, 0hr

description: Library name: AR3


title: RJR816


title: AR28 CD8 T cells, NOD Sh2b3 -/-, 6hr

description: Library name: AR28


title: AR27 CD8 T cells, NOD Sh2b3 -/-, 6hr

description: Library name: AR27


title: YYD440


title: AR26 CD8 T cells, NOD Sh2b3 -/-, 6hr

description: Library name: AR26


title: AR25 CD8 T cells, WT, 6hr

description: Library name: AR25


title: AR23 CD8 T cells, WT, 6hr

description: Library name: AR23


title: TTC-466 DBD+ RNASeq rep 1

city: Columbus

first: Ariunaa

last: Bayanjargal

state: OH

address: 700 Children's Dr

institute: Nationwide Childrens Hospital

description:
iEFDBDpvsiEF197.complete.txt.gz
iEFDBDp_comb.bw.gz

data_processing:
Low-quality reads (q < 10) and adapter sequences were trimmed
Aligned to hg19 genome using STAR
Reads were counted
Differential analysis performed using DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig files of combined replicates for visualization
Supplementary files format and content: Text files of differential analysis run with DESeq2.

source_name: pulmonary metastasis a cervical tumor

growth_protocol: TTC466 cells were grown at 37C, 5% CO2 in DMEM with 10% fetal bovine serum, 1% P/S/Q, and 1% sodium pyruvate.

extract_protocol:
Total RNAwere extracted using RNeasy Extraction Kit.
cDNA libraries were prepared from total RNA with TruSeq Stranded mRNA Kit (Illumina 20020594)

treatment_protocol: For knockdown of endogenous EWS::ERG in TTC466, cells were infected with RNAi virus and subsequently infected with the cDNA-containing virus to rescue the cells. After 48 hours, cells were selected with puromycin (1 μg/ul) and hygromycin (150 μg/ul); and allowed to grow for ~10 days prior to collection

value: pulmonary metastasis a cervical tumor

value: Ewing sarcoma cell line

value: KD + DBD+ rescue

value: DBD+ rescue


title: TTC-466 DBD+ RNASeq rep 2


title: TTC-466 DBD+ RNASeq rep 3


title: TTC-466 DBD RNASeq rep 3

description:
iEFDBDvsiEF197.complete.txt.gz
iEFDBD_comb.bw.gz

value: KD + DBD rescue

value: DBD rescue


title: OKQ881

value: Liver


title: AR30 CD8 T cells, NOD Sh2b3 -/-, 6hr

description: Library name: AR30


title: TTC-466 DBD RNASeq rep 1


title: AR22 CD8 T cells, WT, 6hr

description: Library name: AR22


title: TTC-466 wtEF RNASeq rep 3

description:
iEF714vsiEF197.complete.txt.gz
iEF714_comb.bw.gz

value: KD + wtEF rescue

value: wtEF rescue


title: AR21 CD8 T cells, WT, 6hr

description: Library name: AR21


title: AR20 CD8 T cells, NOD Sh2b3 -/-, 2hr

description: Library name: AR20


title: TTC-466 wtEF RNASeq rep 1


title: AR19 CD8 T cells, NOD Sh2b3 -/-, 2hr

description: Library name: AR19


title: KYL112


title: TTC-466 KD RNASeq rep 1

value: KD of EWS::ERG

value: empty vector rescue


title: AR18 CD8 T cells, NOD Sh2b3 -/-, 2hr

description: Library name: AR18


title: TTC-466 KD RNASeq rep 3


title: AR157 CD8 T cells, NOD Sh2b3 -/-, 24hr

description: Library name: AR157


title: TTC-466 KD RNASeq rep 2


title: TTC-466 DBD+ CTCF CnT rep 5

description:
peaks_iERGDBDp_CTCF_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iERGDBDp_CTCF_scaled_comb.bw.gz

data_processing:
Quality control on raw sequencing reads were performed with FastQC (v0.11.4)
Adapter sequences and/or low quality reads were trimmed using trim_galore (0.4.4_dev)
Reads were aligned to human (hg19) and spike-in Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genomes using Bowtie2 (v2.3.4.3)
SamTools (v1.9) (H. Li et al., 2009) was used to convert sam to bam with ‘-bq 10’ option.
Cut and Tag reads were spike-in normalized using DESeq2’s median ratio method (Anders & Huber, 2010)
Spike-in normalized tracks were generated and averaged across biological replicates using deep-Tools (Ramírez et al., 2016).
Peaks were called with spike-in normalization and their corresponding IgG as controls accounting for variation between the biological replicates using MACS2 (v 2.2.7.1) (Zhang et al., 2008), DiffBind (v2.14.0) (Ross-Innes et al., 2012; Stark & Brown, 2011) and DESeq2 (v1.26.0)(Love, Huber, & Anders, 2014).
Assembly: hg19 and E.coli
Supplementary files format and content: Final peak list generated with following thresholds: FRD < 0.05, logFC > 8, counts > 80, IDR < 0.01.
Supplementary files format and content: Bigwig files of combined replicates for visualization.
Library strategy: CUT&Tag

extract_protocol:
Total DNA (digested with Tn5) was purified using Phenol/Chloroformextraction followed by Ethanol precipitation
CUT&Tag libraries were prepared with NEBNext HiFi 2x PCR Master Mix (NEB M0541S) and indexed primers (Buenrostro, J.D. et al, Nature, 2015)


title: AR158 CD8 T cells, NOD Sh2b3 -/-, 24hr

description: Library name: AR158


title: AR24 CD8 T cells, WT, 6hr

description: Library name: AR24


title: AR16 CD8 T cells, NOD Sh2b3 -/-, 2hr

description: Library name: AR16


title: TTC-466 DBD+ CTCF CnT rep 9


title: TTC-466 DBD+ CTCF CnT rep 6


title: AR156 CD8 T cells, NOD Sh2b3 -/-, 24hr

description: Library name: AR156


title: AR154 CD8 T cells, WT, 24hr

description: Library name: AR154


title: TTC-466 DBD CTCF CnT rep 6

description:
peaks_iERGDBD_CTCF_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iERGDBD_CTCF_scaled_comb.bw.gz


title: TTC-466 DBD CTCF CnT rep 9


title: TTC-466 DBD RNASeq rep 2


title: AR153 CD8 T cells, WT, 24hr

description: Library name: AR153


title: TTC-466 DBD CTCF CnT rep 5


title: TTC-466 wtEF RNASeq rep 2


title: AR2 CD8 T cells, WT, 0hr

description: Library name: AR2


title: AR152 CD8 T cells, WT, 24hr

description: Library name: AR152


title: AR17 CD8 T cells, NOD Sh2b3 -/-, 2hr

description: Library name: AR17


title: TTC-466 KD CTCF CnT rep 9

description:
peaks_iERG197_CTCF_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iERG197_CTCF_scaled_comb.bw.gz


title: AR15 CD8 T cells, WT, 2hr

description: Library name: AR15


title: AR14 CD8 T cells, WT, 2hr

description: Library name: AR14


title: TTC-466 KD CTCF CnT rep 5


title: TTC-466 KD CTCF CnT rep 6


title: TTC-466 DBD+ H3K27ac CnT rep 10

description:
peaks_iEFDBDp_K27ac_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iEFDBDp_K27ac_scaled_comb.bw.gz


title: AR138 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR138


title: TTC-466 DBD+ H3K27ac CnT rep 9


title: AR137 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR137


title: AR133 CD8 T cells, WT, 0hr

description: Library name: AR133


title: TTC-466 DBD H3K27ac CnT rep 10

description:
peaks_iERGDBD_K27ac_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iEFDBD_K27ac_scaled_comb.bw.gz


title: AR136 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR136


title: TTC-466 DBD H3K27ac CnT rep 9


title: TTC-466 DBD+ H3K27ac CnT rep 6


title: TTC-466 DBD+ H3K27ac CnT rep 5


title: AR131 CD8 T cells, WT, 0hr

description: Library name: AR131


title: AR135 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR135


title: AR132 CD8 T cells, WT, 0hr

description: Library name: AR132


title: TTC-466 DBD H3K27ac CnT rep 5


title: AR13 CD8 T cells, WT, 2hr

description: Library name: AR13


title: TTC-466 KD H3K27ac CnT rep 9

description:
peaks_iERG197_K27ac_fdr05_idr01_meanT80_FC8.narrowPeak.gz
iEF197_K27ac_scaled_comb.bw.gz


title: TTC-466 KD H3K27ac CnT rep 10


title: AR11 CD8 T cells, WT, 2hr

description: Library name: AR11


title: AR12 CD8 T cells, WT, 2hr

description: Library name: AR12


title: AR10 CD8 T cells, NOD Sh2b3 -/-, 0hr

description: Library name: AR10


title: TTC-466 KD H3K27ac CnT rep 6


title: AR1 CD8 T cells, WT, 0hr

description: Library name: AR1


title: TTC-466 KD H3K27ac CnT rep 5


title: TTC-466 DBD+ FLAG CnT rep 6

description:
peaks_iERGDBDp_FLAG_fdr05_idr01_meanT80_FC8.narrowPeak
iERGDBDp_FLAG_scaled_comb.bw


title: AR134 CD8 T cells, WT, 0hr

description: Library name: AR134


title: MycTG_33320

city: Basel

first: Daniel

middle: J

last: Ham

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
Library name: Sample 15
bulk RNAseq

data_processing:
FASTQ files were aligned to the indexed mouse transcriptome mm10 using Salmon (version 1.1.0) with the flags validateMappings, seqBias and gcBias.
Assembly: mm10
Supplementary files format and content: Salmon output quant.sf file, contains plain-text, tab-separated

source_name: Gastrocnemius

extract_protocol:
GAS muscles were pulverized on a metal block cooled with liquid nitrogen before lysis and RNA extraction using the RNeasy Fibrous Tissue Mini Kit (74704, Qiagen)
Libraries were prepared using the TruSeq stranded mRNA library kit (20020595, Illumina) starting from 200 ng of RNA

value: Gastrocnemius

value: HSA-MycTG


title: TTC-466 DBD+ FLAG CnT rep 10


title: TTC-466 DBD+ FLAG CnT rep 5


title: TTC-466 DBD H3K27ac CnT rep 6


title: MycTG_33531

description:
Library name: Sample 14
bulk RNAseq


title: TTC-466 DBD+ FLAG CnT rep 2


title: MycTG_33529

description:
Library name: Sample 12
bulk RNAseq


title: MycTG_33319

description:
Library name: Sample 13
bulk RNAseq


title: TTC-466 DBD FLAG CnT rep 10

description:
peaks_iERGDBD_FLAG_fdr05_idr01_meanT80_FC8.narrowPeak
iERGDBD_FLAG_scaled_comb.bw


title: MycTG_32932

description:
Library name: Sample 9
bulk RNAseq


title: TTC-466 DBD FLAG CnT rep 5


title: MycTG_32740

description:
Library name: Sample 11
bulk RNAseq


title: TTC-466 DBD FLAG CnT rep 6


title: MycTG_33528

description:
Library name: Sample 8
bulk RNAseq


title: TTC-466 KD FLAG CnT rep 5


title: TTC-466 DBD FLAG CnT rep 2


title: CON_33321

description:
Library name: Sample 7
bulk RNAseq

value: CON


title: TTC-466 KD FLAG CnT rep 2


title: TTC-466 KD FLAG CnT rep 10


title: TTC-466 KD FLAG CnT rep 6


title: CON_33322

description:
Library name: Sample 4
bulk RNAseq


title: MycTG_33325

description:
Library name: Sample 10
bulk RNAseq


title: CON_32931

description:
Library name: Sample 2
bulk RNAseq


title: CON_33532

description:
Library name: Sample 5
bulk RNAseq


title: CON_33533

description:
Library name: Sample 6
bulk RNAseq


title: CON_33324

description:
Library name: Sample 1
bulk RNAseq


title: CON_33527

description:
Library name: Sample 3
bulk RNAseq


title: HSA-MycKO_17260

description:
Library name: Sample 7
bulk RNAseq

value: HSA-MycKO


title: HSA-MycKO_17259

description:
Library name: Sample 6
bulk RNAseq


title: ZNF469_clone3.4_ZNF469_DOX_rep2

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Alignment with Bowtie (V2.3.4.3) against hg38 with following parameters: --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 --mm; Data filtering steps: All alignments were filtered for unmapped and duplicated reads; Additional processing: Peak calling was performed using MACS2 (2.2.5) with following parameters: -g hs -p 0.01 --nomodel --shift 0 --extsize 70 --keep-dup all -B –SPMR. Reproducible peak sets were called using the IDR procedure, if no biological replicates were available pseudo-replicates were used, as implemented in the ENCODE ChIP-seq pipeline (v2.2.2). Resulting reproducible peak sets were merged and reads per sample counted using Rsubread (2.10.5). All downstream analysis was performed using R 4.2.1 Bigwig signal tracks were generated using bamCoverage from Deeptools (3.5.1.) with following parameters  --extendReads --centerReads -bs 1 –ignoreDuplicates
Assembly: hg38
Supplementary files format and content: gzipped peak calling result of dZF_DOX group
Supplementary files format and content: gzipped peak calling result of DOX group
Library strategy: CUT&RUN

growth_protocol: Cells were grown in standard growth media supplemented with 50 mM 2-Phospho-L-ascorbic acid (Merck, 49752).

extract_protocol:
Following CUT&RUN Immunoprecipitation, DNA was extracted using phenol/chloroform/isoamyl alcohol followed by ethanol precipitation.
NEB DNA Ultra II

treatment_protocol: Following transfection, cells were stimulated with doxycycline (1 microgram/mL) for 24 hours prior to starting CUT&RUN.

tag: chip antibody


title: ZNF469_clone3.4_ZNF469_DOX_rep3


title: HSA-MycKO_31862

description:
Library name: Sample 8
bulk RNAseq


title: HSA-MycKO_17258

description:
Library name: Sample 5
bulk RNAseq


title: CON_31619

description:
Library name: Sample 4
bulk RNAseq


title: ZNF469_clone3.4_ZNF469_DOX_rep1


title: ZNF469_clone3.1_ZNF469_dZF_DOX_rep3


title: CON_17564

description:
Library name: Sample 2
bulk RNAseq


title: ZNF469_clone3.1_ZNF469_dZF_DOX_rep2


title: CON_17257

description:
Library name: Sample 1
bulk RNAseq


title: CON_17565

description:
Library name: Sample 3
bulk RNAseq


title: ZNF469_clone3.1_ZNF469_dZF_DOX_rep1


title: HSC131_ZNF469_ZNFAb_R3

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Alignment with Bowtie (V2.3.4.3) against hg38 with following parameters: --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 --mm; Data filtering steps: All alignments were filtered for unmapped and duplicated reads; Additional processing: Peak calling was performed using MACS2 (2.2.5) with following parameters: -g hs -p 0.01 --nomodel --shift 0 --extsize 70 --keep-dup all -B –SPMR. Reproducible peak sets were called using the IDR procedure, if no biological replicates were available pseudo-replicates were used, as implemented in the ENCODE ChIP-seq pipeline (v2.2.2). Resulting reproducible peak sets were merged and reads per sample counted using Rsubread (2.10.5). All downstream analysis was performed using R 4.2.1 Bigwig signal tracks were generated using bamCoverage from Deeptools (3.5.1.) with following parameters  --extendReads --centerReads -bs 1 –ignoreDuplicates
Assembly: hg38
Supplementary files format and content: Differential peak abundance result file in text format
Library strategy: CUT&RUN

growth_protocol: Cells were obtained from Lonza and grown in collagen-coated flasks in human stellate cell growth medium (Lonza, MCST250) supplemented with 50 mM 2-Phospho-L-ascorbic acid (Merck, 49752).

extract_protocol:
Following CUT&RUN assay, DNA was extracted using phenol/chloroform/isoamyl alcohol followed by ethanol precipitation.
NEB DNA Ultra II Kit

treatment_protocol: Cells were electroporated with RNPs for non-targeting or ZNF469 targeting gRNAs and expanded until day 12 for CUT&RUN.

value: HSC


title: AKT-MycKO_14d_34908

description:
Library name: Sample 23
bulk RNAseq

value: AKT-MycKO


title: HSC131_ZNF469_ZNFAb_R2


title: HSC131_ZNF469_ZNFAb_R1


title: AKT-MycKO_14d_34306

description:
Library name: Sample 21
bulk RNAseq


title: HSC131_ZNFAb_hNTO_R3


title: AKT-MycKO_14d_34173

description:
Library name: Sample 20
bulk RNAseq


title: AKT_14d_35228

description:
Library name: Sample 19
bulk RNAseq

value: AKT


title: HSC131_ZNFAb_hNTO_R2


title: AKT_14d_35118

description:
Library name: Sample 18
bulk RNAseq


title: HSC131_ZNFAb_hNTO_R1


title: HSC131_ZNF469_H3K27ac_R3

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Alignment with Bowtie (V2.3.4.3) against hg38 with following parameters: --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700 --mm; Data filtering steps: All alignments were filtered for unmapped and duplicated reads; Additional processing: Peak calling was performed using MACS2 (2.2.5) with following parameters: -g hs -p 0.01 --nomodel --shift 0 --extsize 70 --keep-dup all -B –SPMR. Reproducible peak sets were called using the IDR procedure, if no biological replicates were available pseudo-replicates were used, as implemented in the ENCODE ChIP-seq pipeline (v2.2.2). Resulting reproducible peak sets were merged and reads per sample counted using Rsubread (2.10.5). All downstream analysis was performed using R 4.2.1 Bigwig signal tracks were generated using bamCoverage from Deeptools (3.5.1.) with following parameters   --extendReads --centerReads -bs 1 –ignoreDuplicates
Assembly: hg38
Supplementary files format and content: gzipped peakcalling text result file
Supplementary files format and content: Differential peak abudance result in text format
Library strategy: CUT&RUN

value: liver

value: HSC electroporated with a pooled set of guide RNAs targeting ZNF469 gene


title: AKT_14d_34910

description:
Library name: Sample 17
bulk RNAseq


title: HSC131_ZNF469_H3K27ac_R2


title: AKT_14d_34305

description:
Library name: Sample 16
bulk RNAseq


title: HSC131_hNTO_H3K27ac_R3

value: HSC electroporoated with non-targeting gRNA


title: AKT-MycKO_3d_36319

description:
Library name: Sample 14
bulk RNAseq


title: AKT-MycKO_3d_35545

description:
Library name: Sample 13
bulk RNAseq


title: HSC131_hNTO_H3K27ac_R1


title: AKT_3d_36751

description:
Library name: Sample 12
bulk RNAseq


title: HSC131_ZNF469_H3K27ac_R1


title: AKT_3d_35546

description:
Library name: Sample 11
bulk RNAseq


title: AKT_3d_35542

description:
Library name: Sample 10
bulk RNAseq


title: AKT-MycKO_14d_34404

description:
Library name: Sample 22
bulk RNAseq


title: AKT_3d_35539

description:
Library name: Sample 9
bulk RNAseq


title: HSC001_H3K27ac_R1

value: no treatment


title: HSC001_H3K27ac_R3


title: HSC001_H3K27ac_R2


title: DNM623_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 2, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 3, stage: NASH_F23, sex: F

data_processing:
Base-calling software: Bcl2fastq2 with Version2.20.0.422-2; Alignment with Bowtie (V2.3.4.3) against hg38 with following parameters: --wrapper basic-0 -X2000 –mm; Data filtering steps: All alignments were filtered for unmapped and duplicated reads; Additional processing: Peak calling was performed using MACS2 (2.2.5) with following parameters: -g hs -p 0.01 --nomodel --shift 0 --extsize 70 --keep-dup all -B –SPMR. Reproducible peak sets were called using the IDR procedure, if no biological replicates were available pseudo-replicates were used, as implemented in the ENCODE ChIP-seq pipeline (v2.2.2). Resulting reproducible peak sets were merged and reads per sample counted using Rsubread (2.10.5). All downstream analysis was performed using R 4.2.1 Bigwig signal tracks were generated using bamCoverage from Deeptools (3.5.1.) with following parameters  --extendReads --centerReads -bs 1 –ignoreDuplicates
Assembly: hg38
Supplementary files format and content: peak read count table
Library strategy: CUT&RUN

growth_protocol: Human liver biopsy samples

tag: steatosis

tag: balloning

tag: lobular inflammation

tag: lobular necrosis

tag: fibrosis nas_tidy

tag: Stage

tag: Sex

value: F


title: MycKO_3d_36750

description:
Library name: Sample 8
bulk RNAseq

value: MycKO


title: QDY893_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 1, fibrosis_nas_tidy: 0, stage: NAFL, sex: F

value: Liver

value: NAFL


title: MycKO_3d_35543

description:
Library name: Sample 6
bulk RNAseq


title: MycKO_3d_35540

description:
Library name: Sample 5
bulk RNAseq


title: MycKO_3d_36321

description:
Library name: Sample 7
bulk RNAseq


title: CON_3d_36116

description:
Library name: Sample 4
bulk RNAseq


title: JDH172_nash_f1_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: AKT-MycKO_3d_36322

description:
Library name: Sample 15
bulk RNAseq


title: NWX937_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: HSC131_hNTO_H3K27ac_R2


title: FB2

description:
Library name: P29404_1019
neurosphere_rawCounts.csv

data_processing:
For LCM samples, reads were aligned and mapped to reference transcriptome mm10 using STAR V 2.3
For in vitro samples, Salmon/1.6.0 was used to create an index on the transcriptome Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl.
DESeq2 package version 1.34.0 was used to analyze RNA-seq data, including differential gene expression
Assembly: mouse mm10 for STAR, Mus_musculus.GRCm39.cdna.all (release-107) from Ensembl for Salmon
Supplementary files format and content: merged_LCM.csv contains normalized counts per sample
Supplementary files format and content: neurosphere_rawCounts.csv contains raw counts per sample

source_name: cultured sphere

value: cultured sphere

value: in vitro

tag: time

value: adult


title: FB3

description:
Library name: P29404_1020
neurosphere_rawCounts.csv


title: CON_3d_36114

description:
Library name: Sample 3
bulk RNAseq

value: Gastrocnemius


title: MB5

description:
Library name: P29404_1017
neurosphere_rawCounts.csv


title: YJW923_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F

value: NOR


title: FB1

description:
Library name: P29404_1018
neurosphere_rawCounts.csv


title: CON_3d_35544

description:
Library name: Sample 2
bulk RNAseq

value: CON


title: MB4

description:
Library name: P29404_1016
neurosphere_rawCounts.csv


title: CON_3d_35541

description:
Library name: Sample 1
bulk RNAseq


title: MB3

description:
Library name: P29404_1015
neurosphere_rawCounts.csv


title: EJV194_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M

value: M


title: CVW854_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: FB4

description:
Library name: P29404_1021
neurosphere_rawCounts.csv


title: ALD943_nash_f23_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: FB5

description:
Library name: P29404_1022
neurosphere_rawCounts.csv


title: MB2

description:
Library name: P29404_1014
neurosphere_rawCounts.csv


title: LA3_scRNA_seq

city: Lebanon

first: Leena

last: Abdullah

state: NH

address: 1 Medical Center Dr

institute: Dartmouth College

description: 10X Genomics

data_processing:
10x 3’ v3.1 data were processed using the Cell Ranger count (v6.0.1) to generate gene expression matrices for downstream processing.
processed data files format and content: Tab-separated values files and matrix files
Assembly: mm10

extract_protocol:
Cells were loaded on to a 10x Genomics Chip G targeting 10,000 cells/sample and processed using the 10x Genomics NextGEM 3’ v3.1 chemistry (PN 1000268). Libraries were prepared according to manufacturer's instructions and sequenced using NextSeq2000 paired-end 100 cycle kits (Illumina), targeting 25,000 reads/cell (Read1: 28 cycles; Read2: 90 cycles; Index1: 10 cycles; Index2: 10 cycles).
After 7 days of infection, CARLIN mice (LA1, LA2, LA3) were euthanized, and their spleens were harvested. The spleens were mashed and filtered to get a single cell suspension. Next, Erythrocytes were depleted and the samples were enriched for CD8+ T cells. The enriched CD8+ T cells were stained and finally, live, OVA-Tetramer-BV421 and OVA-Tetramer-PE double positive CD8+ T cells were sorted.

value: Spleen

value: CD8+ T cells

value: CARLIN (RRID:MMRRC_067061-JAX) x KH2/iCas9 (RRID:IMSR_JAX:029415) . The F1 generation (LA1,LA2,LA3) is heterozygous for the CARLIN barcode, tetO-Cas9 and rtTa locus.

value: mouse was infected with VSV-OVA for 7 days


title: LA1_scRNA_seq

description: 10X Genomics


title: IgG, CUT&RUN assay, Hepa1-6 cells

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
fastq.gzc evaluation of the quality of the original data.Trim-galore was used to trim the sequences.
bowtie2 was used to map reads against the reference genome. Aligned SAM files were converted to BAM format and sorted using Samtools (v1.3.1).
Signal distribution (peak calling) was identified by MACS2, using input as control if input exists. BAM coverage computation, heatmap and profile of peak coverage were made using deeptools.
Peak and motif annotation results were generated by HOMER. Statistical analyses and function enrichment analyses were condcuted using respective R packages.
Assembly: GRCm38/mm10
Supplementary files format and content: bw: IgG_sort.bw
Library strategy: CUT&RUN

source_name: Hepa1-6 cells

growth_protocol: Hepa1-6 cells were cultured in DMEM containing 10% FBS.

extract_protocol:
CUT&RUN assay was performed by usingthe Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (VAZYME，HD102)
CUT&RUN library

treatment_protocol: Hepa1-6 cells were infected with ad-FLAG-ALKBH5 adenovirus overnight.

value: Hepa1-6 cells

value: Hepatcoyte

value: Ad-ALKBH5-FLAG infection

tag: antibody

value: IgG


title: LA2_scRNA_seq

description: 10X Genomics

tag: tissue


title: LUK585_nor_H3K27ac_cutrun

value: Liver

value: F


title: ALKBH5-FLAG-2, CUT&RUN assay, Hepa1-6 cells

data_processing:
Fastqc evaluation of the quality of the original data.Trim-galore was used to trim the sequences.
bowtie2 was used to map reads against the reference genome. Aligned SAM files were converted to BAM format and sorted using Samtools (v1.3.1), then the BAM files were merged and further sorted to create a consolidated BAM file for downstream analysis.
Signal distribution (peak calling) was identified by MACS2, using input as control if input exists. BAM coverage computation, heatmap and profile of peak coverage were made using deeptools.
Peak and motif annotation results were generated by HOMER. Statistical analyses and function enrichment analyses were condcuted using respective R packages.
Assembly: GRCm38/mm10
Supplementary files format and content: tdf: A5_merge_sort.bam.tdf; bw: IgG_sort.bw
Library strategy: CUT&RUN

tag: cell type


title: ALKBH5-FLAG, CUT&RUN assay, Hepa1-6 cells

data_processing:
fastq.gzc evaluation of the quality of the original data.Trim-galore was used to trim the sequences.
bowtie2 was used to map reads against the reference genome.  Aligned SAM files were converted to BAM format and sorted using Samtools (v1.3.1), then the BAM files were merged and further sorted to create a consolidated BAM file for downstream analysis.
Signal distribution (peak calling) was identified by MACS2, using input as control if input exists. BAM coverage computation, heatmap and profile of peak coverage were made using deeptools.
Peak and motif annotation results were generated by HOMER. Statistical analyses and function enrichment analyses were condcuted using respective R packages.
Assembly: GRCm38/mm10
Supplementary files format and content: tdf: A5_merge_sort.bam.tdf; bw: IgG_sort.bw
Library strategy: CUT&RUN

value: FLAG


title: RYZ258_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F

value: NAFL


title: Human Tfh cells Tfh1 -TCR

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

country: Australia

institute: QIMR Berghofer

description: 10x Genomics

library_source: other

data_processing:
Single cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger software v6.0.1  (10x Genomics) against the human reference genome, with default parameters. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control of the data, normalization, integration, clustering and sub-clustering was done using Seurat version 4.0.2.
Gene set enrichment analysis software was used to identify significantly enriched gene ontology terms
Assembly: GRCh38 v 2.7.1a
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: blood

extract_protocol:
PBMCs were isolated from whole blood via density centrifugation with Ficoll-Paque prior to cryopreservation. PBMC samples were thawed in RPMI 1640 (Gibco) containing 10% FCS and 0.02% Benzonase. 1E6 PBMCs were stained for viability with Propidium iodide (PI) and live cells were sorted on BD FACSAria™ III Cell Sorter into 2% FBS/PBS and counted on hemocytometer
Up to 10 000 cells were loaded into each lane of Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Gel Bead-in-Emulsion (GEMs) generated in Chromium Controller. 3’ Gene Expression Libraries were then generated according to manufacturer’s instructions. Generated libraries were sequenced in a NextSeq 550 System using High Output Kit (150 Cycles) with the following parameters read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles, read 2: 98 cycles

value: blood

value: Tfh cells

tag: library type

value: TCR


title: Human Tfh cells Tfh2 -TCR

description: 10x Genomics


title: ASX665_nash_f0_H3K27ac_cutrun

description: steatosis: 3, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: Human Tfh cells Tfh17 -TCR

description: 10x Genomics


title: WNN537_nafl_H3K27ac_cutrun


title: Human Tfh cells PD1 neg -TCR

description: 10x Genomics


title: CUT&Tag_H3K4me1

city: Buffalo

first: Dahong

state: Other

address: 955 Main Street

department: Biochemistry

institute: SUNY Buffalo

data_processing:
Reads were aligned to mouse m31reference with hisat2 or bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
Assembly: m31
Supplementary files format and content: bw files that are used for visulization
Library strategy: CUT&Tag

source_name: rod

extract_protocol:
RNA was extracted by the Qiagen Micro-plus kit
CUT&Tag libraries were generated according to published protocols  Hatice S Kaya-Okur, Steven Henikoff 2020. Bench top CUT&Tag. protocols.io; ATAC-seq libraries were generated according to Chen et al., 2021, Nat. Commun.; RNA-seq libraries were generated according to the commertical instructions

value: rod

tag: genotype

value: Nrl>Tomato


title: Human Tfh cells Tfh2 -GEX

description: 10x Genomics

value: mRNA


title: CUT&Tag_H3K27me3


title: Human Tfh cells Tfh1 -GEX

description: 10x Genomics


title: Human Tfh cells Tfh17 -GEX

description: 10x Genomics


title: MB1

description:
Library name: P29404_1013
neurosphere_rawCounts.csv

extract_protocol:
RNA extraction was performed with Qiagens RNeasy micro RNA kit. 1ng of RNA was used for cDNA and amplified for 15 cycles.
cDNA libraries were made using the protocol Smart-seq2 for sensitive full-length transcriptome profiling in single cells. cDNA libraries were tagmented using home-made Tn5 enzyme and amplified for 11 cycles. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects and Nextera dual indexes (Illumina).

value: cultured sphere

tag: treatment

value: in vitro

value: adult


title: CUT&Tag_H3K27ac


title: QTT156_nafl_H3K27ac_cutrun


title: 12579_C_KidnFtl_Indtrm, rep1

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

state: CA

address: 750 Gateway Boulevard

department: CRADI

institute: Amgen

description:
Library name: 00012579
12579_C_KidnFtl_Indtrm

data_processing:
Transcript and gene level quantification was performed with Salmon. Gene level counts were normalized and assessed for differential expression using the DESeq2 R package. Differentially expressed genes (DEGs) were classified as having a log2(fold-change from a vector control) > 0.5 and an adjusted p-value < 0.001. Genes were only included for analysis if at least one sample had a count of twenty or higher. Each molecule or control condition had four replicates with the exception of IgG-scFv [1, 2] which had one sample excluded for failing NGS quality control. A principal component analysis was performed using normalized gene counts for all DEGs as defined above. Gene set enrichment was performed using the gprofiler2 R package with a focus on Reactome and Gene Ontology Biological Process gene set databases.
Assembly: hg38
Supplementary files format and content: Comma-separated text file includes Salmon count values for each gene by each sample

growth_protocol: Culturing, transfection and expression conditions were performed as described in Li et al. 2022 (DOI: 10.1016/j.xpro.2022.101428). In brief, HEK293-6E suspension cells (National Research Council of Canada) were cultured at 36C, 5% CO2, 85% humidity in 24 deep-well blocks containing 4 mL of culture per well in FreeStyle F-17 based media (Gibco Cat# A1383502), with a feed supplement of Tryptone-N1 (Organotechnie Cat# 19553) and glucose added to initiate antibody production 12 hours after transient PEI transfection of antibody expression plasmids.

extract_protocol:
Cell samples were collected from cultures on day 2 post-transfection of a transient batch expression. Total RNA was purified using TRIzol reagent (Invitrogen Cat# 15596026), and column purified using an RNeasy 96 kit (Qiagen Cat# 74181) with on-column DNA digestion using RNase-Free DNase I (Qiagen Cat# 79254).
RNA sequencing libraries were constructed with the TruSeq Stranded RNA sample preparation kit (Illumina Cat# RS-122-9004DOC).

treatment_protocol: Each sample was transiently transfected with either an empty vector control, a no DNA control, or plasmids encoding one of five secreted antibody or antibody-derived multispecific molecules. No DNA samples were provided water instead of DNA during PEI transfection. Vector samples were provided an empty expression plasmid that did not contain any antibody sequence, but does contain a glutamine synthetase selectable marker. mAb [1] and mAb [2] are samples that were provided with two monocistronic plasmids each expressing one chain of a secreted IgG designed to bind proprietary targets #1 and #2 respectively. IgG-scFv [1, 2] samples were provided with the same sequences as mAb [1] samples, but with the heavy-chain expressing plasmid including a C-terminal fusion of scFv sequence designed to bind proprietary target #2. [Fab*scFv]-heteroFc [1, 2] samples were provided with three monocistronic plasmids each expressing one chain of the three-chain [Fab*scFv]-heteroFc bispecific antibody format with the Fab arm containing an Fv domain designed to bind proprietary target #1 and the scFv domain designed to bind proprietary target #2. [Fab*scFv]-heteroFc [2, 1] samples are equivalent but with the Fab domain designed to bind proprietary target #2 and the scFv domain designed to bind proprietary target #1.

value: mAb [1]


title: Human Tfh cells PD1 neg -GEX

description: 10x Genomics


title: 12578_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012578
12578_C_KidnFtl_Indtrm

value: mAb [2]


title: CUT&Tag_CTCF


title: 12576_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012576
12576_C_KidnFtl_Indtrm

value: [Fab*scFv]-heteroFc [1, 2]


title: 12577_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012577
12577_C_KidnFtl_Indtrm

value: IgG-scFv [1, 2]


title: KFZ933_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F

value: Liver

value: NOR


title: ATAC-seq_KO_3

data_processing:
Reads were aligned to mouse m31reference with hisat2 or bowtie2 (v2.3.5; --very-sensitive, pair-end mode)
Reads were depleted for those aligned to mitochondria (egrep -v chrM) and for multi-mapped reads with samtools (v1.9)
Uniquely mapped reads were further depleted for PCR duplicates with picard (MarkDuplicates REMOVE_DUPLICATES=true)
peak calling was performed with macs2 (v2.2.6; pair-end mode -f BAMPE)
Assembly: m31
Supplementary files format and content: bw files that are used for visulization

value: Nrl>CTCF-loxP, Tomato


title: ATAC-seq_KO_2


title: CMW958_nash_f1_H3K27ac_cutrun

description: steatosis: 1, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F

value: F


title: 12573_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012573
12573_C_KidnFtl_Indtrm


title: 12574_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012574
12574_C_KidnFtl_Indtrm

value: Vector


title: WZG609_nash_f23_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 0, fibrosis_nas_tidy: 2, stage: NASH_F23, sex: F


title: 12571_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012571
12571_C_KidnFtl_Indtrm


title: 12572_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012572
12572_C_KidnFtl_Indtrm


title: ALF449_nafl_H3K27ac_cutrun

value: NAFL


title: ATAC-seq_KO_1


title: ATAC-seq_control_8


title: UIX583_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: LOT902_nor_H3K27ac_cutrun


title: 12569_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012569
12569_C_KidnFtl_Indtrm

value: [Fab*scFv]-heteroFc [2, 1]


title: 12568_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012568
12568_C_KidnFtl_Indtrm


title: ATAC-seq_control_7

value: rod


title: ATAC-seq_control_6

value: Nrl>Tomato


title: 12575_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012575
12575_C_KidnFtl_Indtrm


title: 12566_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012566
12566_C_KidnFtl_Indtrm


title: OUX828_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: 12565_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012565
12565_C_KidnFtl_Indtrm


title: ATAC-seq_control_5


title: 12563_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012563
12563_C_KidnFtl_Indtrm


title: 12564_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012564
12564_C_KidnFtl_Indtrm


title: 12562_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012562
12562_C_KidnFtl_Indtrm


title: ATAC-seq_control_4


title: ATAC-seq_control_3


title: UDF695_nash_f1_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: HPF205_nash_f0_H3K27ac_cutrun

description: steatosis: 1, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: F


title: 12570_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012570
12570_C_KidnFtl_Indtrm


title: 12559_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012559
12559_C_KidnFtl_Indtrm


title: 12560_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012560
12560_C_KidnFtl_Indtrm


title: 12558_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012558
12558_C_KidnFtl_Indtrm


title: 12557_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012557
12557_C_KidnFtl_Indtrm


title: ATAC-seq_control_2


title: 12555_C_KidnFtl_Indtrm, rep1

description:
Library name: 00012555
12555_C_KidnFtl_Indtrm

value: No DNA


title: 12556_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012556
12556_C_KidnFtl_Indtrm


title: UXJ402_nash_f1_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 2, lobular_necrosis: 1, fibrosis_nas_tidy: 1, stage: NASH_F1, sex: F


title: JNK936_nafl_H3K27ac_cutrun

description: steatosis: 1, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: PXJ190_nash_f23_H3K27ac_cutrun

description: steatosis: 2, balloning: 2, lobular_inflammation: 2, lobular_necrosis: 2, fibrosis_nas_tidy: 3, stage: NASH_F23, sex: F


title: RNA-seq_KO_3


title: 12554_C_KidnFtl_Indtrm, rep2

description:
Library name: 00012554
12554_C_KidnFtl_Indtrm


title: 12567_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012567
12567_C_KidnFtl_Indtrm


title: HNK873_nor_H3K27ac_cutrun

description: steatosis: 0, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NOR, sex: F


title: GNI484_nafl_H3K27ac_cutrun


title: 12553_C_KidnFtl_Indtrm, rep3

description:
Library name: 00012553
12553_C_KidnFtl_Indtrm


title: RNA-seq_KO_2


title: 12552_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012552
12552_C_KidnFtl_Indtrm


title: 12561_C_KidnFtl_Indtrm, rep4

description:
Library name: 00012561
12561_C_KidnFtl_Indtrm


title: NIV336_nafl_H3K27ac_cutrun

description: steatosis: 3, balloning: 0, lobular_inflammation: 0, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NAFL, sex: F


title: RNA-seq_KO_1


title: multiplexed samples (blastoids; 0mM/4mM dm-aKG), HTO

city: Copenhagen

first: Jan

middle: Jakub

last: Żylicz

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

country: Denmark

institute: University of Copenhagen

description:
Hashtag-derived oligonucleotide (HTO): Cell Hashing library: R1 file contains cell barcode and UMI; R2 file contains Hashtag Antibody Derived Tag reads
EXP3_barcodes.tsv.gz
EXP3_features.tsv.gz
EXP3_matrix.mtx.gz

data_processing:
Initial processing of scRNA-seq data was performed using Cell Ranger (v 6.1.2; 10X Genomics). Dual-indexed RNA and single-indexed hashtag oligo (HTO) libraries were processed in separate instances of cellranger mkfastq, using bcl2fastq (v2.20.0.422; Illumina).
FASTQ files were aligned to the human reference genome (GRCh38, v 2020-A as provided by 10x Genomics) with cellranger count (--expect-cells=9500).
Resulting filtered feature-barcode matrices were loaded into Seurat (v 4.3.0), ignoring features that are detected in less than 3 cells. HTO assay was normalized with centered log-ratio (CLR) transformation, and Seurat's HTODemux function (with default parameters) was used to assign single cells back to their sample origins, resulting in 6012 (EXP2) and 10400 (EXP3) cells classified as singlets.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: filtered feature-barcode matrix (combined gene expression and HTO counts, per experiment) in Market Exchange Format: EXP[23]_{barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz}

molecule: protein

source_name: H9 (WA09, WiCell)

growth_protocol: nESC cultured in PXGL were collected by incubation for 3 min with Accutase (Merck Sigma Aldrich, A6964) and were depleted from the feeder layer by incubation on 0.1% gelatin for at least 60 min. Single cells were plated at a density of 80-85 cells per micro-well of a 24-well AggreWell™ 400 plate in N2B27 supplemented with Y27632 (10 μM, Axon Medchem, Axon1683) to aggregate for 16h. Subsequently, half medium was changed with 2x PALLY consisting of N2B27 supplemented with PD0325901 (1 μM, Axon Medchem, Axon 1408), A83-01 (1 μM, Axon MedChem, Axon 1421), hLIF (10 ng/mL, Qkine, Qk036), oleoyl-L-α-lysophosphatidic acid sodium salt (LPA, 1 μM, Merck Sigma Aldrich, L7260) and Y27632 (10 μM, Axon Medchem, Axon1683). 24 hours later, half medium was changed with 1x PALLY. After 48h of PALLY culture, blastoids were maintained for 56 hours in LY medium consisting of N2B27 supplemented with LPA (1 μM, Merck Sigma Aldrich, L7260) and Y27632 (10 μM, Axon Medchem, Axon1683).

extract_protocol:
120h single cavity blastoid structures were selected by mouth pipetting. 40h aggregates and 120h blastoids were dissociated into a single cell suspension by incubation with a mixture of TrypLE™ 10x (1x, Thermo Fisher Scientific, A1217701) and Accutase (Merck Sigma Aldrich, A6964) for about 10 to 20 minutes respectively with intermittent pipetting. Each sample was incubated with 0.5 μg of unique hashtag antibody for 20 min on ice. TotalSeq hashtag antibodies (A0251-A0256, Biolegend) were used to multiplex the samples (DOI: 10.1126/sciadv.adg4055). All samples were sorted on a BD FACSymphony S6 (BD Bioscences) resulting in a total cell recovery of around 8000 or 1600 cells, for mRNA2 and mRNA3 respectively, which were loaded onto a Chromium Next GEM chip (10x Genomics).
Library preparation was performed according to the Chromium Next GEM Single Cell 3’ v3.1 user guide with the addition of the hashtag library for demultiplexing. Combined libraries were sequenced using the NextSeq2000 P2-100 kit (Illumina) with Paired-end sequencing

treatment_protocol: Treatment of blastoid induction with dm-αKG was performed by directly diluting dimethyl 2-oxoglutarate (4mM, Merck Sigma Aldrich, 349631) in the culture medium. The medium was then equilibrated for 2-3 hours at 37°C in hypoxic conditions (5% CO2, 5% O2) before use.

tag: cell line

value: H9 (WA09, WiCell)

value: human embryonic stem cells

value: mixed sample (non-demultiplexed):0mM/4mM dm-aKG

value: HTO

tag: hto

value: TotalSeq-A0255 anti-human Hashtag 5, TotalSeq-A0256 anti-human Hashtag 6


title: multiplexed samples (blastoids; 0mM/4mM dm-aKG), GEX

description:
gene expression (GEX): 3' mRNA library: R1 file contains cell barcode and UMI; R2 file contains transcript
EXP3_barcodes.tsv.gz
EXP3_features.tsv.gz
EXP3_matrix.mtx.gz

value: mRNA


title: multiplexed samples (aggregates/blastoids; 0mM/4mM dm-aKG), HTO

description:
Hashtag-derived oligonucleotide (HTO): Cell Hashing library: R1 file contains cell barcode and UMI; R2 file contains Hashtag Antibody Derived Tag reads
EXP2_barcodes.tsv.gz
EXP2_features.tsv.gz
EXP2_matrix.mtx.gz

value: TotalSeq-A0251 anti-human Hashtag 1, TotalSeq-A0252 anti-human Hashtag 2, TotalSeq-A0253 anti-human Hashtag 3, TotalSeq-A0254 anti-human Hashtag 4


title: TLT507_nafl_H3K27ac_cutrun

value: Liver

tag: chip antibody


title: multiplexed samples (aggregates/blastoids; 0mM/4mM dm-aKG), GEX

description:
gene expression (GEX): 3' mRNA library: R1 file contains cell barcode and UMI; R2 file contains transcript
EXP2_barcodes.tsv.gz
EXP2_features.tsv.gz
EXP2_matrix.mtx.gz


title: ATAC-seq_control_1


title: hiTSC d3, 4mM dm-αKG, rep3

data_processing:
Paired-end reads were aligned with STAR (v 2.7.2d) to the reference genome GRCh38.p13 with gene annotations from GENCODE release 32 (`--sjdbGTFfile gencode.v32.annotation.gtf`) and option `--quantMode GeneCounts` was set to count the number of reads per gene while mapping.
The 4th column of each sample's "ReadsPerGene.out.tab" file (corresponding to counts for the 2nd read strand aligned with RNA) was extracted and combined to a joint counts matrix.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.

growth_protocol: Naive ESC were cultured on gelatin-coated plates including a feeder layer of gamma-irradiated DR4 mouse embryonic fibroblasts (MEFs) (ATCC, SCRC-1045) in tt2iLGö medium. tt2iLGö medium consists of N2B27 basal medium supplemented with PD0325901 (1 μM, Axon Medchem, Axon 1408), CHIR99021 (0.3 μM, Axon Medchem, Axon1386), Gö 6983 (2 μM, Axon Medchem, Axon 2466) and human leukemia inhibitory factor (hLIF, 10 ng/mL, Qkine, Qk036)(Guo, von Meyenn et al. 2017). N2B27 basal medium contains DMEM/F12 with Glutamax (50%, Thermo Fisher Scientific, 31331028), neurobasal medium (50%, Fisher Scientific, 11570556), N2 supplement (1x, Merck Sigma Aldrich, SCM012), B27 supplement (0.5x, Thermo Fisher Scientific, 17504044), 2-mercaptoethanol (0.2 mM, Thermo Fisher Scientific, 31350010), and GlutaMAX™ (0.75 mM, Thermo Fisher Scientific, 25030024). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂) and passaged as single cells every three to four days. Cells were cultured for 24 hours with Y27632 (10 μM, Axon Medchem, Axon1683) after passaging. Medium was changed daily.

extract_protocol:
RNA was collected and extracted using the Qiagen RNeasy Mini Kit (Qiagen, 74104) with on column DNAse treatment.
Libraries for sequencing were prepared using 500ng of total RNA and the NEBNext Poly(A) mRNA and NEBNext UltraII stranded RNA-seq library preparation kit. 10 cycles of amplification were performed.

treatment_protocol: Naive ESC were depleted from the feeder layer by incubating the single cell suspension on 0.1% gelatin for 45-75 min. Cells then were seeded at a density of 1.8 x10³ cells per cm² in a 6-well plate pre-coated with ECMatrix™-511 Silk E8 Laminin Substrate (Merck Sigma Aldrich, CC161) in tt2iLGö medium for 48 hours. Medium was changed to tt2iLGö supplemented with 0 or 4mM dm-αKG or 1uM A-485 for 24h before cells were collected for mRNA-seq or induced towards hiTSC. Briefly, media was changed to hiTSC medium consisting of N2B27 supplemented with Bovine Serum Albumin (BSA) (0.3%, Sigma, A3294), heat-inactivated Fetal Bovine Serum (HI-FBS) (0.2%, Thermo Fisher Scientific, 12389782), Insulin-Transferrin-Selenium-Ethanolamine (ITS-X) (1x, Gibco, 51500), L-ascorbic acid (1.5 μg/ml, Sigma, A8960-5G), recombinant human EGF (50 ng/ml , Qkine, Qk011), CHIR99021 (2 μM, Axon MedChem, Axon 1386), A83-01 (0.5 μM, Axon MedChem, Axon 1421), SB431542 (1 μM, Axon MedChem, Axon 1661), Valproic Acid (VPA) (0.8 mM, Axon MedChem, Axon 3127), and Y-27632 (10 μM, Axon MedChem, Axon 1683). Cells were cultured in hypoxic conditions (5% CO₂, 5% O₂).

value: human induced trophoblast stem cells day 3

value: 4mM dm-aKG


title: YMK964_nash_f0_H3K27ac_cutrun

description: steatosis: 2, balloning: 1, lobular_inflammation: 1, lobular_necrosis: 0, fibrosis_nas_tidy: 0, stage: NASH_F0, sex: M

tag: steatosis

value: M


title: RNA-seq_control_8


title: RNA-seq_control_6


title: RNA-seq_control_5


title: hiTSC d3, 0mM dm-αKG, rep3

value: DMSO