title: CTRL_PND30-40_502

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
treatment:  CTRL
dose: --
sample ID: 502

tag: background strain

tag: age


title: P10 Input Replicate C

status: Public on Nov 04 2025

type: SRA

city: Copenhagen

first: Erkut

last: Ilaslan

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: p10-INP-C

library_source: genomic

data_processing:
Additional runs concatenated to first FastQ file. For samples with a 3rd run, these runs processed seperately.
Samples sequenced for revision were clipped to 51 bp length to preserve comparability to rest of the samples using Trim Galore --hardtrim5 51 parameter.
FastQ files trimmed using Trim Galore.
Trimmed FastQ files mapped to mm10 using bowtie1 with -m 1 parameter.
BAM files sorted using SAMtools and converted to BED format using BEDtools.
BED files from 3rd run merged to the BED files contaning 1st and 2nd runs before downstream analysis in EaSeq (http://easeq.net). Gzip compressed WIG files generated using EaSeq. Scores represent fragments per kilobasepairs per million reads.
Assembly: mm10
Supplementary files format and content: wig files containing genomic location and score of deduplicated mapped reads

molecule: genomic DNA

organism: Mus musculus

source_name: P10 oocyte

growth_protocol: Postnatal day 7 (P7), P10, and P12 CD-1 females were used for collection of growing oocyte (GO) sample pools. C57BL/6NRj females aged 4 weeks were used for collecting NSN, SN and MII oocytes. To induce superovulation for collection of these three stages, the mice received an intraperitoneal injection with 5 international units (IU) of pregnant mare serum gonadotropin (PMSG; Prospec, HOR-272) at 2pm. For NSN and SN stages, the oocytes were collected ~45 hours after the PMSG injection. For collection of MII stage oocytes, an intraperitoneal injection with 5 IU of human chorionic gonadotropin (hCG; Sigma, C1063) was given 45-48 hours following PMSG injection. Subsequently, MII oocytes were collected 66-67 hours after the PMSG injection. Mouse E14 ES cells were obtained from a stock at passage P2 equal to those used for the mouse ENCODE project and cultured following the corresponding instructions (https://www.encodeproject.org/biosamples/ENCBS171HGC/). Prior to collection, cells were passaged once on gelatinized, feeder-free plates.  Zygote, 2-Cell and 4-Cell embryos: To perform in vitro fertilization, sperm from C57BL/6NRj male mouse was collected directly from the cauda epididymis of a recently euthanized male and incubated in a 35 mm dish containing 90 µl of FERITUP preincubation media (Cosmo-Bio; KYD-002-EX) In parallel, a fertilization dish (30 mm) was prepared by placing a 90 µl droplet of human tubal fluid (HTF) medium supplemented with 2 mM reduced glutathione (Sigma; G4251), and covering it with NidOil. The HTF medium (100ml) was prepared in-house (593.8 mg NaCl (Sigma; S-5886), 35 mg KCl (Sigma; P-5405), 4.9 mg MgSO₄·7H₂O (Sigma; M-7774), 5.4 mg KH₂PO₄ (Sigma; P-5655), 57 mg CaCl₂ (Sigma; C-5670), 210 mg NaHCO₃ (Sigma; S-5761), 0.34 ml sodium lactate (Sigma; L-7900), 3.7 mg sodium pyruvate (Sigma; P-4562), 50 mg glucose (Sigma; G-6152), 49.55 mg Methyl-b-cyclodextrin (Sigma; C-4555), 0.5 ml penicillin/streptomycin (Gibco; 15140-122), 400 mg BSA (Sigma; A-7030), 0.04 ml phenol red (Sigma; P-0290), dissolved in Milli-Q water to a final volume of 100 ml). The fertilization dish was equilibrated at 37 °C in a 5% CO₂ incubator. Female C57BL/6NRj mice were superovulated via intraperitoneal injection of pregnant mare serum gonadotropin (PMSG; Prospec; HOR-272), followed 48 hours later by human chorionic gonadotropin (hCG; Sigma; CG5). The dosage of each hormone (5  IU) was administered to mice aged 4 weeks. Fifteen hours after hCG administration, the mice were euthanized, and their oviducts were dissected and placed into the fertilization dish. Cumulus-oocyte complexes were retrieved from the ampulla and transferred into the fertilization droplet. Following a 30-minute pre-incubation period, between 1 and 10 µl of motile sperm was added to the fertilization droplet. The dish was then incubated for three hours at 37 °C in 5% CO₂. To remove cumulus cells and excess sperm, embryos were washed through seven sequential droplets of Advanced KSOM medium (Sigma; MR-101) placed in a 60 mm dish, which had been pre-equilibrated under the same conditions and covered with NidOil. Zygotes were collected approximately four hours post-fertilization, at which point pronuclei were clearly visible. Embryos at the two-cell stage were collected 24 hours post-fertilization, and those at the four-cell stage were retrieved after approximately 48 hours. All samples were subsequently processed for pico-ChIP sequencing.  8-cell embryos: The same procedure was followed for superovulation and copulation as described above, but with different timing for the hormone injections: PMSG at 3pm and hCG 48h later. At 68h after the hCG injection, the females were euthanized by cervical dislocation and the ovaries with oviducts and upper uterine horns were removed and transferred for processing in a petri dish with M2 medium. One by one, the ovary was removed, the infundibulum was located and slid onto a flushing needle. Embryos were isolated by flushing M2 medium through the oviduct. 8-cell embryos were collected and washed in fresh M2 medium before Tyrode’s acid treatment, further washing in M2, and cross-linking.  Morulas and blastocysts: Follicle growth was stimulated in 3.5–4 week old females (C57BL/6NRj, Janvier Labs) by an intraperitoneal (IP) injection with 5 IU PMSG at 2pm. Around 45 h later, 5 IU hCG (Chorulon, MSD Animal Health) was IP injected to induce ovulation. Directly after hCG injection, females were housed 1:1 with stud males of the same strain for copulation. The following morning at 8am, females were removed from the males' cages and euthanized by cervical dislocation. The ovaries with oviducts and upper uterine horns were removed in one piece, placed in a microtube with 1 ml of M2 medium and immediately transferred for processing. Under a stereomicroscope, zygotes surrounded by cumulus cells were isolated from the ampulla in a petri dish with M2 medium at 37°C. To remove the cumulus cells, zygotes were briefly put in hyaluronidase solution (HYASE-10X, Vitrolife) diluted 1:10 in M2 medium. The zygotes were then washed in three consecutive wells of 0.5 ml M2 medium covered with OVOIL-100 paraffin oil (Vitrolife). Normally fertilized zygotes, identified by the presence of two pronuclei, were selected and transferred to a pre-equilibrated micro-droplet culture dish (Vitrolife) containing 25 μl of G-1 PLUS culture medium (Vitrolife) per well, covered with paraffin oil, with approximately 10 zygotes per droplet. The zygotes were incubated at 37 °C with 6% CO₂. Late morulas (n = 11) and blastocysts (n = 14) were collected at developmental day 3.5, as embryos originated from natural copulation of several mice, and therefore development was not fully synchronized. The zona pellucida was removed using Tyrode’s acid treatment, and the embryos were then washed in fresh M2 medium and cross-linked as described below (picoChIP-seq > Oocyte and embryo cross-linking).

extract_protocol:
The samples were transferred to 1.5 ml tubes. SDS/RNase-free elution buffer (20 mM Tris–HCl/pH-7.5), 50 mM NaCl, 5 mM EDTA/pH-8.0) was added to 415 µl final volume, and the aqueous phase was sequentially extracted using equal volumes of phenol:chloroform:isoamylalcohol (Invitrogen, 15593-031) and chloroform:isoamylalcohol (Sigma-Aldrich, C0549). The 400 µl of the last aqueous phase were precipitated with 1 ml ice-cold ethanol, 11 µl linear acrylamide (Thermo Fisher Scientific, AM9520) and 44 µl 1 M sodium acetate (Invitrogen, AM9740) at least overnight at -80°C. For reconstitution, the pellets were centrifuged (swing-out, 16,000 x g, 4°C), and recovered using 15 µl of Qiagen EB (10 mM Tris, Qiagen, 19086) overnight at 4°C.
Sequencing libraries were prepared using the Qiaseq ultralow input kit (Qiagen, 180492 + 180310) with modifications to minimize material loses. These included prolonged incubations during the AMPure XP bead extractions (>15 min bead/sample incubation, >15 min DNA elution) (Beckman coulter, A63881), and an increased volume of beads (1.2 volume equivalents) during the second bead extraction. Double-stranded DNA concentration was determined using the Qubit HS DNA kit (ThermoFisher Scientific, Q32851), while DNA fragment size analyses were performed with TapeStation D1000 HS (Agilent, 5067-5585). Libraries were then and pooled in equimolar amounts. Sequential AMPure XP extractions (1.2 volume equivalents) were employed to drastically reduce adapter dimers from the pool prior to sequencing.

treatment_protocol: Oocytes were cross-linked in a solution of 50 µl M2 media, 50 µl PBS (Life Technologies, 14190-094), and a final concentration of 1% w/v formaldehyde (Sigma-Aldrich, F8775). After 8 min at room temperature, 14.3 µl 1 M Glycine (Merck, 67419) was added to inactivate the fixative. After 5 min at room temperature, ice cold PBS was used to wash the oocytes three times in a 0.6 ml tube (MaxymumRecovery, Axygen), resulting in a final volume of 10 µl. The fixative was added either in droplets under the microscope, or directly in the 0.6 ml tube followed by the washes and centrifugations at 700 x g for 10 min at 4°C with careful supernatant removal. Correspondingly, liquids were mixed by droplet pipetting or by gentle tube vortexing during cross-linking and glycine inactivation. Samples were snap-frozen in liquid nitrogen before storage at -80°C. Pelleted ES cells (around 20 million) were resuspended in 20 ml of a 1 % w/v formaldehyde (Sigma-Aldrich, F8775) solution in PBS with 20 mM of sodium butyrate (Sigma-Aldrich, 19-137), cross-linked at room temperature for 8 min, and inactivated using 2.4 ml of an aqueous 1.25 M glycine (Sigma, G8790) solution. Then, the pellet was washed twice with ice cold PBS supplemented with 20 mM of sodium butyrate (650 x g, 10 min, 4°C), cells were counted, diluted, and aliquoted into 0.6 ml tubes (MaxymumRecovery, Axygen) at different cell numbers. Finally, the cells were centrifuged, the supernatant removed, leaving 10 µl, and snap-frozen in liquid nitrogen before storage at -80°C.

tag: cell type

value: P10 oocyte


title: V20-003_C1D1 Pre

city: Duarte

first: Edward

middle: C.

last: Dominguez

state: CA

address: 1500 E. Duarte Rd.

department: Toni Stephenson Lymphoma Ctr

country: USA

institute: City of Hope

library_source: transcriptomic

data_processing:
Partek Flow was utilized for data analysis. Trimming of adapters and bases for Fastq files was performed with ParteK software. Mapping to the reference index hg38 was performed with STAR.  Counts were then normalized to 1.0e4 CPM. Gene set enrichment analysis (GSEA) (Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, http://www.broad.mit.edu/gsea/) was performed using Hallmark pathways.
Assembly: quantified to hg38 - Ensembl Transcripts release 102
Supplementary files format and content: Excel file with normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll gradient and resuspended in ACK lysing buffer (Life Technologies) for red blood cell lysis. Total RNA was extracted using Homogenizer Mini Columns and the E.Z.N.A Total RNA Kit I (Omega Bio-Tek).
Pre-made libraries partial lane sequencing (PE150)

tag: diagnosis

value: DLBCL

tag: treatment

value: Voruciclib

tag: time

value: Pre-Treatment

tag: outcome

value: Progressive Disease

value: PBMC


title: V20-003_C1D1 6hr

value: Post-Treatment


title: FLUT_ADI_PND30-40_542

type: RNA

country: France

description:
treatment:  FLUT
dose: ADI
sample ID: 542

hyb_protocol: Agilent : 55 degree_C during 20 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: The R package AgiMicroRna was used to extract the TotalGenesignal value from the Agilent result files, and perform quantile normalization separately for each age group.

organism: Rattus norvegicus

source_name: Testis

label_protocol: Agilent - miRNA Complete Labeling and Hyb Kit starting from 100 ng total RNA

extract_protocol: Total RNAs were isolated from frozen testicular powder using TRIzol reagent (Invitrogen, Cergy Pontoise, France) coupled with column purification of RNA (High pure miRNA isolation kit, Roche Diagnostics, Meylan, France) and DNase treatment.

treatment_protocol: Antiandrogenic substances were administered in aqueous preparations. Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND21), the day of sexual maturation (Subset 2, puberty at PND30-40) or early adulthood (Subset 3, PND83±2). At each subset, testes were used for transcriptome and miRNome analyses. Three antiandrogenic substances were tested: Flutamide (FLUT), Prochloraz (PROC), Vinclozolin (VINC), at 3 doses. Flutamide: ADI = 0.0025mg/kg/d, NOAEL = 0.25mg/kg/d, LOAEL = 2.5mg/kg/d. Prochloraz: ADI=0.01 mg/kg/d, NOAEL=5 mg/kg/d, LOAEL=30 mg/kg/d. Vinclozolin: ADI=0.005 mg/kg/d, NOAEL=4 mg/kg/d, LOAEL=20 mg/kg/d

value: Wistar

value: postnatal day (PND) 30-40


title: VINC_LOAEL_PND21_334

description:
treatment:  VINC
dose: LOAEL
sample ID: 334

value: postnatal day (PND) 21


title: V6-005_EOT

value: CLL


title: 4-cell H2AZ Replicate A

description: Library name: 4c-AZ-200

source_name: 4-cell embryo

value: 4-cell embryo


title: NRF_ZT4_WT_rep3

city: Neuherberg

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

country: Germany

institute: helmholtz munich

data_processing:
Sequence quality was checked using FastQC and MultiQC
Adapter reads were trimmed using Trimmomatics
Reads were aligned using Salmon to mm10
Salmon quant.sf files were imported in R using tximport to generate read counts
Raw read counts were transformed by variance  stabilizing transformation (VST) method.
Assembly: mm10
Supplementary files format and content: tab-separate files containing raw read counts from Salmon
Supplementary files format and content: tab-separate files containing VST counts from DESeq2

molecule: polyA RNA

source_name: Mouse liver

growth_protocol: C57BL/6J mice were fed with chow diet

extract_protocol:
RNA was extracted using the QIAZOL reagent. 1 μg of RNA was used for library preparation.
Libraries were prepped from 1µg total RNA with the Illumina TruSeq RNA library prep kit v2 chemistry in an automated system (Agilent Bravo liquid handling) platform).

treatment_protocol: Mice were either night-restricted fed (NRF), or NRF + reduced calorie intake across the weeks with end point of 40% less calories

tag: tissue

value: Mouse liver

tag: strain

tag: genotype

value: GRfl/fl

value: Night Restricted Feeding (NR)


title: VINC_LOAEL_PND21_333

description:
treatment:  VINC
dose: LOAEL
sample ID: 333


title: NRF_ZT4_WT_rep2


title: 2-cell H2AZ Replicate A

description: Library name: 2c-AZ-200

source_name: 2-cell embryo

value: 2-cell embryo


title: VINC_LOAEL_PND21_332

description:
treatment:  VINC
dose: LOAEL
sample ID: 332


title: V6-005_C1D8


title: NRF_ZT4_WT_rep1


title: V6-005_C1D1 Pre


title: P10 H2AZ Replicate D

description: Library name: p10-AZ-80-D


title: NRF_ZT0_GRLKO_rep3

value: GRfl/fl x Alb-Cre


title: VINC_LOAEL_PND21_331

description:
treatment:  VINC
dose: LOAEL
sample ID: 331


title: 4-cell Input Replicate A

description: Library name: 4c-INP


title: VINC_NOAEL_PND21_324

description:
treatment:  VINC
dose: NOAEL
sample ID: 324


title: NRF_ZT0_GRLKO_rep2


title: CTRL_PND30-40_501

description:
treatment:  CTRL
dose: --
sample ID: 501


title: NRF_ZT4_GRLKO_rep1


title: VINC_NOAEL_PND21_323

description:
treatment:  VINC
dose: NOAEL
sample ID: 323


title: NRF_ZT0_GRLKO_rep1


title: P10 H2AZ Replicate C

description: Library name: p10-AZ-80-C

value: P10 oocyte


title: V6-004_EOT


title: V6-004_C1D8


title: NRF_ZT0_WT_rep3


title: CD8+T cell,CUMS3

city: Jinan

first: Renhui

last: Sun

state: Shandong

address: 44 Wenhua west road

country: China

institute: Shandong University

description: Library name: CUMS3

data_processing:
1 Quality control Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
2 Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
3 Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
4 Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw count for each sample

source_name: liver

extract_protocol:
RNA was extracted from CD8+T cells by TRIZOL lysis and tested for RNA integrity by quality control using Agilent 2100 bioanalyzer
Library construction by NEB: the first strand of cDNA was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotide as primer. The RNA strand was degraded by RNaseH, and the second strand of cDNA was synthesized from dNTPs under DNA polymerase I system. The purified double-stranded cDNA was end repaired, an A-tail was added, and the sequencing adapter was ligated. The cDNA of about 250-300bp was screened by AMPure XP beads, and the PCR product was purified by AMPure XP beads again

value: liver

tag: cell line

value: CD8+T cells

value: lymphocytes

value: CUMS


title: V6-004_C1D1 Pre

value: Voruciclib

value: Pre-Treatment

value: Progressive Disease

value: PBMC


title: V6-004_C1D1 6hr

value: Post-Treatment


title: NRF_ZT0_WT_rep1


title: VINC_ADI_PND21_314

description:
treatment:  VINC
dose: ADI
sample ID: 314

value: Wistar

value: postnatal day (PND) 21


title: Zygote H2AZ Replicate A

description: Library name: zyg-AZ-200

source_name: Zygote

value: Zygote


title: CD8+T cell,control3

description: Library name: control3

value: Wild type


title: CD8+T cell,CUMS1

description: Library name: CUMS1


title: KO-3

city: Xi’an

first: Huilong

last: Yin

state: Shaanxi

address: No.169, Changle West Road

institute: Fourth Military Medical University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
 After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: mm10
Supplementary files format and content: text files include FPKM values for each Sample

source_name: BMDMs

growth_protocol: Briefly, bone marrow was extracted from femur and tibia of C57BL/6 mice, and red blood cells were lysed. Resultant bone marrow cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 mg/mL streptomycin in the presence of 40 ng/mL M-CSF for 7 days prior to treatment.

extract_protocol:
Total RNA was isolated from BMDMs using Trizol
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA)

value: bone-marrow-derived macrophages


title: V229_2

value: AML


title: CD8+T cell,control2

description: Library name: control2


title: V229_3


title: KO-2


title: V6-005_C1D1 6hr

value: CLL


title: VINC_NOAEL_PND21_322

description:
treatment:  VINC
dose: NOAEL
sample ID: 322


title: VINC_ADI_PND21_313

description:
treatment:  VINC
dose: ADI
sample ID: 313


title: VINC_ADI_PND21_312

description:
treatment:  VINC
dose: ADI
sample ID: 312


title: V228_3


title: CD8+T cell,CUMS2

description: Library name: CUMS2


title: V229_1


title: CD8+T cell,control1

description: Library name: control1


title: VINC_NOAEL_PND21_321

description:
treatment:  VINC
dose: NOAEL
sample ID: 321


title: VINC_ADI_PND21_311

description:
treatment:  VINC
dose: ADI
sample ID: 311


title: P0_KOME

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: Library name: P0KOME

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.0.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx
Library strategy: CITE-seq

source_name: Liver

extract_protocol: 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) with Feature Barcode User Guide

value: Liver

value: Lin-Kit+ cells


title: WT-3

value: wild type


title: NRF_ZT0_WT_rep2

value: Mouse liver

value: GRfl/fl

value: Night Restricted Feeding (NR)


title: PROC_LOAEL_PND21_394

description:
treatment:  PROC
dose: LOAEL
sample ID: 394


title: PROC_LOAEL_PND21_392

description:
treatment:  PROC
dose: LOAEL
sample ID: 392


title: PROC_LOAEL_PND21_393

description:
treatment:  PROC
dose: LOAEL
sample ID: 393


title: WT-2


title: WT-1


title: V228_1

value: Voruciclib

value: Pre-Treatment


title: V223_2

value: Progressive Disease

value: PBMC


title: P0_Control

description: Library name: P0WT


title: Patient12_Plaque_Panel2

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

hyb_protocol: Subsequently, the samples went through a 3-day protocol including multiple steps such as deparaffinization, decrosslinking, probe hybridization, ligation, and amplification.

scan_protocol: Xenium Analyzer

data_processing:
The preprocessed samples were analyzed using the Xenium Analyzer with the instrument software version 1.5.1.2 (Patients 1-4) or 1.7.6.0 (Patients 5-12) and analysis version 1.5.0.3 (Patients 1-4) or 1.7.1.0 (Patients 5-12).
The zip archive contains:
Raw data files:  transcripts.parquet, morphology.ome.tif
Processed data files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet

label: Xenium Human Probe Set

source_name: human carotid artery tissue

label_protocol: Xenium Human Probe Set

extract_protocol: Tissue sectioning and sample preprocessing were performed according to the manufacturer’s protocol. Briefly, 5-μm FFPE sections were mounted on Xenium slides and dried to optimize adherence

tag: plaque or control

value: Plaque

tag: panel


title: PROC_LOAEL_PND21_391

description:
treatment:  PROC
dose: LOAEL
sample ID: 391

value: Wistar

value: postnatal day (PND) 21


title: V223_1


title: ND/WCR, rep2

city: Sapporo

first: Mari

last: Sato

address: Kita13 Nishi7 KIta ku

country: Japan

institute: Hokkaido University

data_processing:
The NEBNext Ultra Directional RNA protocol was used for the preparation of RNA-seq libraries and sequenced on a NovaSeq 6000 machine (Illumina), as paired-end, 150 base paires reads.
Paired-end sequencing reads from NovaSeq 6000 were subjected to adaptor-trimming and quality-trimmed with the default parameters to map the reference genome.
The sequencing reads were trimmed using Trimmomatic v0.39 with the following options: ILLUMINACLIP:TruSeq3-PE-2.fa:1:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:20:20 MINLEN:50
Trimmed  reads were aligned to the GRCm38 genome assembly using HISAT2 v2.2.1  with the following options: --dta-cufflinks
Aligned reads were sorted and indexed using Samtools v1.10
FPKMs were using Cufflinks (version2.2.1) with a transcriptome reference (Ensembl Mouse Transcript). To identify signature genes for each group, we normalized the read count matrix and performed gene-wise moderated F-tests to test whether a gene is differentially expressed across the cell groups. Signature genes for each group were identified using the following criteria: adjusted q-value < 0.05. Significance difference was defined by q-value.
Assembly: GRCm38 Ensembl release 100
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: femoral bone

extract_protocol:
Total RNA was extracted using the TRIzol Reagent.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

value: femoral bone

value: wild-type

value: NW


title: Patient12_Plaque_Panel1


title: V202_3

value: AML

value: Post-Treatment


title: ND/WCR, rep3


title: KO-1

value: bone-marrow-derived macrophages


title: PROC_NOAEL_PND21_383

description:
treatment:  PROC
dose: NOAEL
sample ID: 383


title: V228_2


title: ND/WCR, rep1


title: PROC_NOAEL_PND21_382

description:
treatment:  PROC
dose: NOAEL
sample ID: 382


title: P0_ME

description: Library name: P0ME

value: Liver

value: Lin-Kit+ cells


title: Patient11_Plaque_Panel1


title: Patient10_Plaque_Panel2


title: ND/SED, rep3

value: NS


title: V202_2


title: ND/SED, rep2


title: Patient11_Plaque_Panel2


title: PROC_NOAEL_PND21_381

description:
treatment:  PROC
dose: NOAEL
sample ID: 381


title: V046_4


title: PROC_ADI_PND21_374

description:
treatment:  PROC
dose: ADI
sample ID: 374


title: Patient10_Plaque_Panel1


title: V202_1


title: PROC_ADI_PND21_373

description:
treatment:  PROC
dose: ADI
sample ID: 373


title: ND/SED, rep1


title: Patient9_Plaque_Panel2


title: PROC_NOAEL_PND21_384

description:
treatment:  PROC
dose: NOAEL
sample ID: 384


title: Zebrafish Liver Illumina

city: Lausanne

first: James

middle: A

last: Holzwarth

state: Vaud

address: EPFL Innovation Park, G

department: NIFSAS

country: Switzerland

institute: Nestlé

data_processing:
Illumina fastx_toolbox quality control and filtering
Illumina HiSat2 mapping
PacBio lima demultiplex and remove barcodes
PacBio isoseq3 refine remove polyA and concatamers
PacBio isoseq3 cluster to cluster reads
PacBio minimap2 for mapping
stringtie to assemble into transcripts
gffcompare annotate transcripts
bedtools getfasta extract cDNA sequences
SixFrame convert to protein sequences
gtf files (generated by stringtie).  These have normalized count FPKM and TPM. The files also have information about exon coverage. Some of the transcripts identified by stringtie do not correspond to any annotated transcripts, and I have been left in the files.
Assembly: GRCz9
Supplementary files format and content: fasta files containing translated protein sequences of transcripts
Supplementary files format and content: gtf files containing normalized count FPKM and TPM

organism: Danio rerio

growth_protocol: Adult and larval zebrafish of the AB line were raised at 27.5 °C, on a 14/10 hours light/dark cycle, under standard husbandry conditions. Fertilized wild type eggs were collected via natural spawning and reared in egg water at 28.5 °C incubation up to 4 days post fertilization (dpf). Adult zebrafish euthanasia and organs sampling were carried out according to the Swiss and EU ethical guidelines based on article 22, paragraph 3 of the ordonnance on animal by-products (permit VD-H13).

extract_protocol:
Tissues were put in a Lysing Matrix D tube placed on ice. Then 600 µL of lysis buffer were added. The tubes were firmly closed and agitated for 2×60 s at speed 6 m/s on a FastPrep-24 homogenizer. Total RNA was then extracted using the Agencourt RNAdvance Tissue Kit following the provider’s recommendations. Total RNA was quantified using the Quant-iT™ RiboGreen™ RNA Assay Kit on a Spectramax M2. Total RNA quality was assessed using Fragment Analyzer-96 with DNF-471-0500 Standard Sensitivity RNA Analysis Kit.
RNA-Seq:  An amount of 500 ng of total RNA was used for each sample. A bead-based mRNA capture followed by a fragmentation, first and second strand synthesis, an end repair, and a 3`adenylation and indexed linker ligation were performed. The adapter ligated cDNA library fragments were then enriched by pPolymerase chain reaction (PCR) using 15 cycles of amplification (Illumina TruSeq Stranded mRNA protocol). Samples were then bead purified, pooled equimolar
Iso-Seq:  An amount of 300 ng of total RNA was used to prepare the Iso-Seq libraries for PacBio following exactly the Iso-Seq Express Template Preparation for Sequel and Sequel II Systems version 02 (October 2019). Libraries sizes were assessed using a FemtoPulse with FP-1002-0275 gDNA 165kb Analysis Kit. Libraries quantifications were performed using a Qubit fluorometer with Q32854 Qubit dsDNA HS Assay Kit (500×).

treatment_protocol: Muscle, brain and liver tissues were dissected, sampled and snap-frozen from male zebrafishes. In addition, 4 dpf whole larvae or tails dissected from larvae were pooled and snap-frozen

value: liver


title: PROC_ADI_PND21_372

description:
treatment:  PROC
dose: ADI
sample ID: 372


title: PROC_ADI_PND21_371

description:
treatment:  PROC
dose: ADI
sample ID: 371


title: Patient9_Plaque_Panel1


title: V046_2

value: Voruciclib


title: V046_1

value: Pre-Treatment


title: Patient8_Plaque_Panel2


title: Zebrafish Brain Illumina

source_name: brain

value: brain


title: Zebrafish Muscle Illumina

source_name: muscle

value: muscle


title: Patient8_Plaque_Panel1

value: Plaque


title: FLUT_LOAEL_PND21_364

description:
treatment:  FLUT
dose: LOAEL
sample ID: 364

value: Wistar


title: V042_4

value: Progressive Disease

value: PBMC


title: V042_3


title: Patient7_Plaque_Panel2


title: FLUT_LOAEL_PND21_363

description:
treatment:  FLUT
dose: LOAEL
sample ID: 363

value: postnatal day (PND) 21


title: Patient7_Plaque_Panel1


title: V042_2


title: Zebrafish Larvae tail Illumina

source_name: Larvae tail

value: Larvae tail


title: FLUT_LOAEL_PND21_362

description:
treatment:  FLUT
dose: LOAEL
sample ID: 362


title: V042_1

value: AML


title: FLUT_LOAEL_PND21_361

description:
treatment:  FLUT
dose: LOAEL
sample ID: 361


title: wt_5_Starved_03042020_lane5_20

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

institute: MDC-Berlin

description: Library name: 03042020_lane5_20

data_processing:
A total of 50 bp paired-end reads were aligned to the D. melanogaster reference genome (release 6) using STAR aligner (version 2.5.3a) with providing GTF annotation (dmel-all-r6.17.gtf). Reads with multiple alignments were filtered by setting outFilterMultimapNmax parameter to 1. Reads were counted per gene with parameter –quantMode GeneCounts. BAM files were converted to normalized bedgraph coverages using genomeCoverageBed command (bedtools version 2.27.1) with -scale parameter set to divide by the total number of reads and multiplied by a million. Bedgraph files were converted to tdf files (igvtools version 2.3.98) to visualize in the IGV browser.
Count tables (read counts per gene) were read into R environment and low count genes were filtered out (at least 3 read per gene in 10% of the samples analyzed together). Differential expression analysis was performed by DESeq2 package (version 1.24) by adding replicate information as batch variable. Samples that were directly compared to each other were fitted in the same DESeq2 model.
Assembly: dmel-all-r6.17.gtf
Supplementary files format and content: Tab-separated text file: read counts per gene

organism: Drosophila melanogaster

growth_protocol: Fly lines were maintained in a incubator (Panasonic, MLR-235H-PE) at 25°C with a 12 hr/12 hr light-dark cycle at 60% relative humidity.

extract_protocol:
30 heads were homogenized with an electrical stirrer with 500 μl of Trizol (Thermo Fisher; cat. no. 15596026). Chloroform was added at the ratio of 1:5 with Trizol and the solutions were mixed for 15 s by inverting the eppendorfs. After 5 min incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min. Aqueous phase was transferred to a new eppendorf from the centrifuged sample, to which isopropanol was added at 1:1 ratio of the obtained aqueous phase, vortexed briefly and incubated for 10 min at room temperature. They were then centrifuged for 10 min at 12,000 x g. Supernatant was discarded and obtained pellet was washed with 750 μl of 80% ethanol. After brief vortexing, samples were centrifuged at 8,000 x g for 5 min. Obtained supernatant was discarded and pellet was air dried for 5 min inside the hood and resuspended in RNase-free water
1 ug of RNA, obtained from fly heads was used for library preparation. Both total and mRNA quality was assessed on a 2100 Bioanalyzer (Agilent Technologies, Cat. No G2939BA) using RNA pico assay kit (Agilent RNA 6000 Pico Kit, cat. No: 5067-1513) using manufacturer's protocol. rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and library preparation for RNA-sequencing was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) following manufacturer’s protocol.

treatment_protocol: As age, sex, temperature, light-dark cycle and humidity could affect starvation response and resistance, we kept all these constant by using only male flies of age 8-9 days old at 25°C with 60% relative humidity and 12 hr light/12 hr dark cycle (unless stated otherwise). Approx. 50-60 flies were transferred to an empty fly bottle containing a tissue with 4 ml of tap water. Total number of flies for each experiment ranged from 150-250 flies for each genotype/condition tested

value: head

tag: Sex

value: male

value: 8-9 days

value: control

value: 24 hr

tag: batch


title: Patient6_Plaque_Panel2


title: V046_3

value: Post-Treatment


title: Zebrafish Larvae Illumina

source_name: Entire larvae

value: Entire larvae


title: FLUT_NOAEL_PND21_354

description:
treatment:  FLUT
dose: NOAEL
sample ID: 354


title: Patient6_Plaque_Panel1


title: chm_3_Starved_03042020_lane5_18

description: Library name: 03042020_lane5_18

value: chm MYST mutant


title: wt_5_Fed_03042020_lane5_19

description: Library name: 03042020_lane5_19

value: 0 hr


title: normal human Sinoatrial Node (SN)

city: Guangzhou

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads. Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of at least two biological replicates per group was performed by using the edgeR_3.24.3. Genes with an adjusted P-value <0.05 were assigned as differentially expressed genes (DEGs).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: EXCEL file included mRNA FPKM values for each Sample

source_name: human tissue

growth_protocol: Human iPSCs were cultured in mTesR1 medium.

extract_protocol:
total RNAs were harvested using RNeasy Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations
the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

treatment_protocol: All human samples from healthy donor and HCM patients were obtained according to institutional guidelines (Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, Guangzhou, CHINA). Written, informed consent was obtained in advance from donors. The collection and usage about the human heart tissues were conducted according to the principles of the Declaration of Helsinki and was approved by the Research Ethical Committee of the Guangdong Provincial People's Hospital.

value: human tissue

value: tissue

value: normal


title: normal human Right Ventricular (RV)


title: Patient5_Plaque_Panel2

value: Plaque


title: chm_3_Fed_03042020_lane5_17

description: Library name: 03042020_lane5_17


title: Patient5_Plaque_Panel1


title: normal Human iPSCs

source_name: cell lines

value: cell lines

value: hiPSCs


title: wt_4_Starved_03042020_lane5_16

description: Library name: 03042020_lane5_16


title: FLUT_NOAEL_PND21_352

description:
treatment:  FLUT
dose: NOAEL
sample ID: 352

value: Wistar

value: postnatal day (PND) 21


title: Patient4_Control_Panel2

value: Control


title: normal human Left Ventricular (LV)


title: wt_4_Fed_03042020_lane5_15

description: Library name: 03042020_lane5_15

value: head

value: male


title: human_EIF3M_IgG

city: Shanghai

first: Zilun

last: Wei

address: 180 Fenglin Road

department: Shanghai Institute of Cardiovascular Diseases

institute: Zhongshan Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Clip-Seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Clip-Seq reads were aligned to the UCSC rn6/hg19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create Clip-Seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing homer v4.11 with the significance cut-off q-value <=0.05
Assembly: rn6 for rat genome/hg19 for human genome
Supplementary files format and content: tab txt format
Library strategy: Clip-Seq

source_name: hPSC-CMs

growth_protocol: NRVMs were derived from embryonic rat myocardium. NRVMs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
3’ end of the RNA carries a monophosphate due to RNase A mediated cleavage; calf intestinal alkaline phosphatase (CIAP) was added to remove the monophosphate so that the RNA can be ligated to the 5’-end of adenylated 3’ linker consequently. On the other hand, 5’ end of RNA lacks a phosphate group due to RNase A cleavage, 1 ml of [ɣ-32P] ATP (Perkin Elmer, USA) was added into the immunoprecipitates. RNA was then purified and precipitated through acidic phenol, chloroform and ethanol and resuspended in 5 ml of RNase-free water.
The first few steps in sequence analysis were done by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). First, the 3’ adaptor sequences were removed from reads by using fastx_clipper. The rest was trimmed from the 3’ end so that the remaining reads have Phred quality of 25 or higher. After clipping and trimming, reads of 20nt or longer were collapsed to generate a set of unique sequences. The sequences were aligned to abundant contaminant sequences (Illumina adaptor/primer sequences and rat/human ribosomal DNA complete repeating unit, queried in GenBank accession) with GSNAP (V2021-12-17) with 10% mismatch rate137. Filtered reads that do not match to any contaminant and have sufficient sequence complexity were aligned to UCSC (the University of California, Santa Cruz) rn6 for rat genome assembly and hg19 for human with GSNAP (V2021-12-17) with options of 10% mismatch rate, no terminal clipping, and splice site annotations from RefSeq (https://www.ncbi.nlm.nih.gov/refseq/, V2022-9-16). The alignment results were filtered to leave only the single best hit with minimum edit distance (up to two edits) to obtain a set of single hit reads. Those with multiple best hits were ignored as repetitive sequences. The alignments were annotated with RefSeq (https://www.ncbi.nlm.nih.gov/refseq/, V2022-9-16), RepeatMasker (http://repeatmasker.org/, V4.1.3), miRBase (https://www.mirbase.org/, V22.1), Rfam (https://rfam.xfam.org/, V14.8) and GtRNAdb (http://gtrnadb.ucsc.edu/, V19.0) by using intersectBed of BEDTools (https://bedtools.readthedocs.io/en/latest/index.html, V2.28.0).

treatment_protocol: NRVMs grown on four 100 mm dishes were rinsed and irradiated with 600 mJ/cm of UV-B by using CL-1000 ultraviolet crosslinker (UVP). UV-irradiated cells were harvested and treated with DNase I and RNase A. 20μL eIF3m antibody (11423-1-AP, Proteintech) or IgG was used for immunoprecipitation of eIF3m-RNA complex or the negative control.

value: hPSC-CMs

tag: clip antibody

value: IgG


title: Patient4_Control_Panel1


title: Patient4_Plaque_Panel2


title: FLUT_ADI_PND21_343

description:
treatment:  FLUT
dose: ADI
sample ID: 343

source_name: Testis


title: FLUT_ADI_PND21_344

description:
treatment:  FLUT
dose: ADI
sample ID: 344


title: Patient4_Plaque_Panel1


title: chm_5_Fed_03042020_lane5_13

description: Library name: 03042020_lane5_13

value: 8-9 days


title: human_EIF3M_CLIP


title: FLUT_ADI_PND21_342

description:
treatment:  FLUT
dose: ADI
sample ID: 342


title: Patient3_Control_Panel2


title: Day 60 iPSC-derived spinal cord organoid

city: Parkville

first: Samantha

middle: Katherine

last: Barton

state: Victoria

address: 30 Royal Parade

country: Australia

institute: The Florey Institute of Mental Health and Neuroscience

description: Library name: Cs0202

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq fastq files were processed using 10x CellRanger v 8.0.1 flex pipeline.
Assembly: GRCh38
Supplementary files format and content: tab separated values files and matrix files

extract_protocol:
Day-60 human iPSC-derived spinal cord organoids were dissociated into single cells by incubation with papain (20 U/ml) at 37 °C for 60 min. Following enzymatic digestion, the cell suspension was washed with a DNase–protease inhibitor solution and centrifuged at 300 g for 5 min. The resulting single-cell pellet was immediately used for 10x Genomics single-cell RNA-sequencing library preparation.
scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell Fixed RNA Sample Preparation kit 10x Genomics P/N 1000414) as per manufacturer’s protocol. Library prep and sequencing were performed by the Australian Genome Research Facility, and data were generated with the Illumina BCL Convert 4.1.5 pipeline.

treatment_protocol: spinal cord organoid differentiation

value: induced pluripotent stem cell

value: WT

value: spinal cord organoid differentiation


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di6N animal, stimulated

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

institute: National Institutes of Health

description: Library name: Di6N2.stim

data_processing:
Fastq files were pre-processed and filtered using ScaleBio Seq Suite: RNA, a cloud-based pipeline on the basepair cloud using nextflow version 23.10.0 and Mmul_10 for rhesus macaque or GRCh38 for human as the reference genome.
The Seurat standard preprocessing and clustering workflow was performed for dimensionality reduction and clustering. Briefly, raw counts were normalized, and the top 2,000 highly variable genes were selected using Seurat’s FindVariableFeatures with vst.
RunPCA was performed on the variable genes and an SNNgraph was created with FindNeighbors with 20 principal components as determined by an Elbowplot. Clusters were generated with Findclusters and RunUMAP was used to produce the visualization.
Filtered barcode, features, and matrix files were used to create rds objects then merged with unique identifiers. Data were analyzed and statistical testing was performed using Seurat V5.0.0 for both macaque and human samples.
Assembly: GRCh38/Mmul_10
Supplementary files format and content: Hda5 format, containing counts and barcodes/UMIs

organism: Macaca mulatta

source_name: Granuloma

growth_protocol: Healthy male Indian-origin rhesus macaques aged ~3 years from the National Institute of Allergy and Infectious Diseases breeding colony on Morgan Island, South Carolina were used in this experiment.

extract_protocol:
Granuloma samples were processed with the ScaleBio Low Input Fixation protocol for single cell RNA sequencing with the ScaleBio Sample Fixation Kit (Scale Biosciences #2020001) with additional fixation time required for BSL3 procedures.
Fixed frozen samples were thawed on ice, counted, resuspended in Wash Buffer at 2000 cells per μL and processed with the ScaleBio Single cell RNA sequencing Kit v1.1 (Cat #950884) and laboratory protocol RevA NOV2023 from ScaleBiosciences. Approximately 10,000 cells were added per well to the RT-barcode plate on ice.

treatment_protocol: These animals were treated with isotype control rhesus macaque IgG (Nonhuman Primate Reagent Resource RRID:AB_2716330) at 10mg/kg on weeks 0, 2, 4, 6, 8, 9, 10, 11, and 12 via intravenous infusion and intratracheal instillation. Rhesus macaques were anesthetized with ketamine and dexmedetomidine and 2 ml of physiological saline containing ~25 CFU of Mtb H37Rv was bronchoscopically instilled into the lower right lobe of the lungs. Stimulated samples also received MHC-I and MHC-II MTB300 Mtb peptide megapools which were added at 1μg/mL and 2μg/mL, respectively.

value: Granuloma


title: FLUT_NOAEL_PND21_353

description:
treatment:  FLUT
dose: NOAEL
sample ID: 353


title: wt_3_Starved_03042020_lane4_11

description: Library name: 03042020_lane4_11

value: control

value: 24 hr


title: FLUT_ADI_PND21_341

description:
treatment:  FLUT
dose: ADI
sample ID: 341


title: chm_2_Fed_03042020_lane5_12

description: Library name: 03042020_lane5_12

value: chm MYST mutant

value: 0 hr


title: CTRL_PND21_304

description:
treatment:  CTRL
dose: --
sample ID: 304


title: Patient3_Control_Panel1


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di6N animal

department: National Institute of Allergy and Infectious Diseases

description: Library name: Di6N2


title: wt_3_Fed_03042020_lane4_10

description: Library name: 03042020_lane4_10


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di6N animal, stimulated

description: Library name: Di6N.stim


title: Patient3_Plaque_Panel2

value: Plaque


title: chm_4_Starved_03042020_lane4_9

description: Library name: 03042020_lane4_9


title: FLUT_NOAEL_PND21_351

description:
treatment:  FLUT
dose: NOAEL
sample ID: 351

value: Wistar


title: CTRL_PND21_303

description:
treatment:  CTRL
dose: --
sample ID: 303

value: postnatal day (PND) 21


title: Patient3_Plaque_Panel1


title: CTRL_PND21_302

description:
treatment:  CTRL
dose: --
sample ID: 302


title: skin_sham_rep_4

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description: Library name: 24-05-19-w03

data_processing:
the reads were aligned to mm10 genome using STAR and reads were counted using htseq-count
Assembly: mm10
Supplementary files format and content: tab separated text files (tsv) with raw read counts per mgi-annotated genes

source_name: skin

extract_protocol:
The tissue samples were subjected to RNA extraction using the Qiagen RNeasy mini kit.
Illumina TruSeq RNA

treatment_protocol: Homozygous CD11c-IL-17Aind/ind mice were exposed to radon, once to 539.0 ± 2.8 kBq/m³ or at 10 consecutive workdays to 39.2 ± 2.0 kBq/m³ radon activity concentration.

value: skin

value: sham


title: chm_5_Starved_03042020_lane5_14

description: Library name: 03042020_lane5_14

value: head

value: male


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di6N animal

description: Library name: Di6N


title: chm_4_Fed_03042020_lane4_8

description: Library name: 03042020_lane4_8


title: Patient2_Control_Panel1

value: Control


title: Patient2_Control_Panel2


title: CTRL_PND21_301

description:
treatment:  CTRL
dose: --
sample ID: 301


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di5F animal, stimulated

description: Library name: Di5F2.stim


title: wt_2_Starved_03042020_lane4_7

description: Library name: 03042020_lane4_7

value: 8-9 days


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di5F animal

description: Library name: Di5F2


title: Patient2_Plaque_Panel2


title: wt_2_Fed_03042020_lane4_6

description: Library name: 03042020_lane4_6


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di5F animal, stimulated

description: Library name: Di5F.stim


title: skin_radon_rep_4

description: Library name: 24-05-19-w01

value: radon


title: skin_sham_rep_3

description: Library name: 24-05-19-m04


title: chm_2_Starved_03042020_lane4_5

description: Library name: 03042020_lane4_5


title: Patient2_Plaque_Panel1


title: wt_1_Starved_03042020_lane4_4

description: Library name: 03042020_lane4_4


title: skin_radon_rep_2

description: Library name: 06-04-19-w03


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di4D animal, stimulated

description: Library name: Di4D2.stim


title: Patient1_Control_Panel2


title: wt_1_Fed_03042020_lane4_3

description: Library name: 03042020_lane4_3


title: Patient1_Control_Panel1


title: R. macaque granuloma single-cell RNAseq, replicate 2 of Di4D animal

description: Library name: Di4D2


title: chm_1_Starved_03042020_lane4_2

description: Library name: 03042020_lane4_2


title: Patient1_Plaque_Panel2


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di4D animal, stimulated

description: Library name: Di4D.stim


title: skin_sham_rep_2

description: Library name: 05-04-19-w01


title: skin_sham_rep_1

description: Library name: 05-04-19-m06


title: chm_1_Fed_03042020_lane4_1

description: Library name: 03042020_lane4_1


title: skin_radon_rep_3

description: Library name: 24-05-19-m05


title: Patient1_Plaque_Panel1


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di4D animal

description: Library name: Di4D


title: LN95UGTKO-4

status: Public on Nov 03 2025

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

description: Library name: LN95UGTKO-4

data_processing:
The sequencing reads are mapped to the hg19 genome assembly using HISAT2 (v2.1.0), and alignment statistics are recorded in a summary file.
The resulting BAM files are processed with HTSeq-count to quantify gene expression using the GENCODE v29lift37 annotation.
Assembly: hg19
Supplementary files format and content: Gene Count Files (e.g htseq-count.strandno.sorted.LN95-1.txt) - Each line represents a gene ID (GENCODE v29lift37) and its corresponding read count

source_name: Prostate

growth_protocol: LNCaP95 and LN95(UGT2B17KO) cells were cultured in RPMI1640 media containing 10% charstripped serum. Cells were split when reached 90% confluency.

extract_protocol:
Total RNA was extracted from cells using the Purelink RNA mini kit (Invitrogen) following the manufacturer's standard protocol.
Library Construction for DNBseq Sequencing: Total RNA was enriched for mRNA using Oligo(dT) selection, followed by fragmentation and reverse transcription into cDNA. The cDNA was then subjected to end repair, A-tailing, and adaptor ligation, followed by PCR amplification. Amplified DNA was denatured into single strands and circularized to generate the sequencing library. Finally, DNA nanoballs (DNBs) were synthesized and sequenced on the DNBseq platform.

treatment_protocol: There is no treatment to the cells before RNA extraction.

value: Prostate

value: prostate cancer

value: UGT2B17 KO


title: R. macaque granuloma single-cell RNAseq, replicate 1 of Di5F animal

description: Library name: Di5F

value: Granuloma


title: LN95-2

description: Library name: LN95-2

value: WT


title: TGF-Tg-2

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

description:
Library name: SH10X-35
10x Genomics

data_processing:
Base call files were demultiplexed into FASTQ files using Cell Ranger (v 7.1.0). Sequences were aligned to the mouse reference genome GRCm39.
Assembly: GRCm39
Supplementary files format and content: RDS

source_name: Lung

extract_protocol:
Lung sample were digested in an enzymatic cocktail (collagenase I/dispase II) with DNase I using a gentleMACS Octo Dissociator.
For single cell RNA sequencing lung tissue was filtered through 40 μm filters, and viable cells were counted using a Countess II automated cell counter (Thermo). Single cell barcoding and complementary DNA (cDNA) library preparation were performed according to the manufacturer’s protocol (Single Cell 3′ Reagent Kits v3, 10x Genomics, USA), and run on the Chromium X. Reverse transcription was performed at 53 °C for 45 min and cDNA was amplified for 12 cycles using a BioRad C1000 Touch thermocycler. We performed cDNA size selection using SpriSelect beads (Beckman Coulter, USA) and cDNA quality was confirmed with an Agilent Bioanalyzer High Sensitivity DNA chip. DNA fragmentation, end-repair, A-tailing, and ligation of sequencing adapters were performed per the manufacturer’s protocol (10x Genomics, USA). The cDNA libraries were sequenced on a NovaSeq 6000 platform.

treatment_protocol: Bleomycin-induced mouse and doxycyclin-induced mouse

value: Lung

value: lung single suspension cell

value: TGF-B Tg+

value: doxycycline


title: TGF-Tg-3

description:
Library name: SH10X-36
10x Genomics


title: hpMSC-derived EV small RNA 1

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

country: South Korea

institute: CHA University

description: Library name: hpMSC_EV1

data_processing:
Reads were mapped to GRCh38 using subread aligner
Readcount extraction was performed using featureCounts with miRBase v22.1 human annotation
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts

source_name: Extracellular vesicle

growth_protocol: hpMSCs were maintained in α-MEM supplemented with 10% fetal bovine serum, 100 mg/mL each of penicillin and streptomycin, 25 ng/mL FGF4, and 1 mg/mL heparin. For EV isolation, FBS was replaced with EV-depleted FBS. At ~90% confluence, cells were washed with PBS and incubated in α-MEM for 48 h. Conditioned medium was collected, and EVs were isolated using qEV.

extract_protocol:
total RNA and small RNA were extracted using BGI protocols
RNA libraries were prepared for sequencing using BGI protocols

value: Extracellular vesicle

value: Human Placenta-Derived Mesenchymal Stem Cells


title: TGF WT-C2

description:
Library name: SH10X-32
10x Genomics

value: Vehicle


title: TGF WT-C1

description:
Library name: SH10X-31
10x Genomics


title: TGF-Tg-1

description:
Library name: SH10X-34
10x Genomics


title: PF4-Cd74-KO-Bleoymcin-D14-3

description:
Library name: SH10X-48
10x Genomics

value: Cd74fl/fl, Pf4iCre

value: Bleoymcin


title: PF4-Cd74-KO-Bleoymcin-D14-2

description:
Library name: SH10X-47
10x Genomics


title: skin_radon_rep_1

description: Library name: 05-04-19-w04

value: skin


title: PF4-Cd74-KO-Bleoymcin-D14-1

description:
Library name: SH10X-46
10x Genomics


title: LN95-1

description: Library name: LN95-1


title: PF4-Cd74-WT-Bleoymcin-D14-2

description:
Library name: SH10X-44
10x Genomics

value: Cd74wt/wt, Pf4iCre


title: PF4-Cd74-WT-Bleoymcin-D14-1

description:
Library name: SH10X-43
10x Genomics


title: TGF WT-C3

description:
Library name: SH10X-33
10x Genomics


title: SPC-Mif-KO-Bleomycin-D14-2

description:
Library name: SH10X-41
10x Genomics

value: Mif fl/fl, SftpcCreER2

value: Tamoxifen, Bleoymcin


title: SPC-Mif-KO-Bleomycin-D14-3

description:
Library name: SH10X-42
10x Genomics


title: SPC-Mif-KO-Bleomycin-D14-1

description:
Library name: SH10X-40
10x Genomics


title: SPC-Mif-WT-Bleomycin-D14-2

description:
Library name: SH10X-38
10x Genomics

value: Corn oil, Bleoymcin


title: SPC-Mif-WT-Bleomycin-D14-3

description:
Library name: SH10X-39
10x Genomics


title: CX3CR1-Cd74-KO-Bleoymcin-3

description:
Library name: SH10X-29
10x Genomics

value: Cd74fl/fl, Cx3cr1CreERT2


title: SPC-Mif-WT-Bleomycin-D14-1

description:
Library name: SH10X-37
10x Genomics


title: LN95UGTKO-3

description: Library name: LN95UGTKO-3

value: Prostate

value: prostate cancer

value: UGT2B17 KO


title: CX3CR1-Cd74-WT-Bleoymcin-4

description:
Library name: SH10X-27
10x Genomics

value: Lung

value: lung single suspension cell


title: CX3CR1-Cd74-WT-Bleoymcin-3

description:
Library name: SH10X-26
10x Genomics


title: CX3CR1-Cd74-KO-Control-1

description:
Library name: SH10X-28
10x Genomics

value: Tamoxifen, Vehicle


title: SPC-Cul3-KO(+mt)-Bleoymcin-D10-2

description:
Library name: SH10X-24
10x Genomics

value: Cul3fl/fl, SftpcCreER2, ROSA26mTmG


title: CX3CR1-Cd74-WT-Control-1

description:
Library name: SH10X-25
10x Genomics

value: Corn oil, Vehicle


title: SPC-Cul3-KO(+mt)-Bleoymcin-D10-1

description:
Library name: SH10X-23
10x Genomics


title: SPC-Cul3-WT(+mt)-Bleoymcin-D10-2

description:
Library name: SH10X-21
10x Genomics

value: Cul3wt/wt, SftpcCreER2, ROSA26mTmG


title: SPC-Cul3-WT(+mt)-Bleoymcin-D10-1

description:
Library name: SH10X-20
10x Genomics


title: SPC-Cul3-WT(+mt)-Control-D10-1

description:
Library name: SH10X-19
10x Genomics


title: SPC-Cul3-KO(+mt)-Control-D10-1

description:
Library name: SH10X-22
10x Genomics


title: CX3CR1-Cd74-WT-Bleoymcin-2

description:
Library name: SH10X-16
10x Genomics


title: CX3CR1-Cd74-KO-Bleoymcin-1

description:
Library name: SH10X-17
10x Genomics


title: SPC-Cul3-KO-Bleomycin-D14-2

description:
Library name: SH10X-14
10x Genomics

value: Cul3fl/fl, SftpcCreER2


title: CX3CR1-Cd74-KO-Bleoymcin-2

description:
Library name: SH10X-18
10x Genomics


title: SPC-Cul3-KO-Bleomycin-D14-1

description:
Library name: SH10X-13
10x Genomics


title: SPC-Cul3-WT-Bleomycin-D14-2

description:
Library name: SH10X-11
10x Genomics

value: Corn oil, Bleomycin


title: SPC-Cul3-WT-Bleomycin-D14-1

description:
Library name: SH10X-10
10x Genomics


title: SPC-Cul3-WT-Control-D14-1

description:
Library name: SH10X-9
10x Genomics


title: SPC-Cul3-KO-Control-D14-1

description:
Library name: SH10X-12
10x Genomics


title: DDT KO-Bleoymcin-1

description:
Library name: SH10X-7
10x Genomics

value: DDT KO

value: Bleoymcin


title: DDT KO-Bleoymcin-2

description:
Library name: SH10X-8
10x Genomics


title: DDT KO-Control-1

description:
Library name: SH10X-5
10x Genomics

value: Vehicle


title: DDT KO-Control-2

description:
Library name: SH10X-6
10x Genomics


title: DDT WT-Bleoymcin-2

description:
Library name: SH10X-4
10x Genomics

value: WT


title: DDT WT-Control-2

description:
Library name: SH10X-2
10x Genomics


title: DDT WT-Control-1

description:
Library name: SH10X-1
10x Genomics


title: DDT WT-Bleoymcin-1

description:
Library name: SH10X-3
10x Genomics


title: siOct4_48h_6

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

description: Library name: siOct4_48h_6

data_processing:
libraries were demultiplexed using bcl2fastq
adapters were trimmed with cutadapt
read were aligned using STAR
read counts were calculated with rsem
Assembly: mm10
Supplementary files format and content: TPM counts

source_name: ES cells

growth_protocol: ES cells were grown in DMEM supplemented with 15% FCS and 0.01ug/mL LIF on gelatin coated plasticware and mitomycin C-inactivated MEF feeder

extract_protocol:
cells were trypsinised, MEFs were adsorbed on non-treated plasticware for 20 minutes. Cells were washed once in PBS and lysed in TRIzol. Total RNAs were purified by pheno-chloroform extraction and precipitated.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification, following NOVOGENE library construction workflow using Novogene stranded RNAkit: 250~300bp insert, stranded specific library (directional)

treatment_protocol: 1µg/mL dox + control or oct4 siRNA

value: ES cells

value: cells carrying a doxycycline-inducible gata6 expression cassette

value: oct4 siRNA + 1µg/mL dox


title: siOct4_48h_5

description: Library name: siOct4_48h_5


title: siCTL_48h_5

description: Library name: siCTL_48h_5

value: control siRNA + 1µg/mL dox


title: siCTL_48h_6

description: Library name: siCTL_48h_6


title: siOct4_48h_3

description: Library name: siOct4_48h_3


title: siCTL_48h_4

description: Library name: siCTL_48h_4


title: siOct4_48h_4

description: Library name: siOct4_48h_4


title: siCTL_48h_3

description: Library name: siCTL_48h_3


title: siOct4_48h_2

description: Library name: siOct4_48h_2


title: CX3CR1-Cd74-WT-Bleoymcin-1

description:
Library name: SH10X-15
10x Genomics

value: Cd74fl/fl, Cx3cr1CreERT2

value: Corn oil, Bleoymcin


title: siCTL_48h_1

description: Library name: siCTL_48h_1


title: siCTL_48h_2

description: Library name: siCTL_48h_2


title: siOct4_48h_1

description: Library name: siOct4_48h_1


title: ChAT-eGFP+ adipose cells, cold 2

first: Alexander

middle: J

last: Knights

state: MO

address: 4515 McKinley Ave

institute: Washington University

description:
Library name: Cold2
10x Genomics

data_processing:
Following sequencing, raw data were aligned to the GRCm38 (mm10) mouse genome using STAR, then pre-processing (demultiplexing, barcode processing, gene counting and aggregation) was performed using Cell Ranger software v3.1.0. Aligned pre-processed data were read from Cell Ranger into Seurat (v4.2.0) using the CreateSeuratObject function, with removal of cells containing less than 100 genes (min.features = 100) and removal of genes found in less than 10 cells (min.cells = 10). Low quality, dying or doublet cells were defined as having less than 200 or greater than 5000 genes or having greater than 7.5% of genes derived from mitochondrial transcripts. These cells were filtered out during pre-processing. Cell cycle regression was not performed. An elbow plot was used to determine the optimal number of principal components for post-processing (dims = 1:25). Unsupervised clustering was performed using a resolution of 0.1, then non-linear dimensionality reduction was undertaken via Uniform Manifold Approximation and Projection (UMAP).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Inguinal subcutaneous white adipose tissue (IWAT) was immediately harvested after CO2 euthanasia, finely minced, then digested to yield the stromal vascular fraction (SVF). Digestion was performed as previously reported, in a Collagenase D solution (1.5 U/mL) and Dispase II (2.4 U/mL) supplemented with 10 mM CaCl2 for 20 minutes in a 37°C water bath with agitation. Digested tissues were washed with phosphate-buffered saline (PBS) and filtered through a 100 μm strainer, then the filtrate was centrifuged at 500 x g for 5 minutes to pellet SVF cells and remove the floating adipocyte layer. Red blood cells were lysed with ddH2O then SVF cells were stained with TOPRO3 viability dye in FACS buffer (cold PBS containing 2% fetal bovine serum and 1 mM EDTA).  SVF cells from wild-type C57BL6/J mice were used as unstained and fluorescence-minus-one controls in cell sorting. Live ChAT-eGFP+ singlet cells were sorted into DMEM media using a BD FACS Aria III with a 100 μm nozzle. Cells were submitted to 10x Genomics scRNAseq at ~1000 cells/uL (total of ~10,000 cells per sample)
Library construction was performed in accordance with 10x Genomics 3' GEX instructions.

treatment_protocol: Mice were housed in a temperature- and humidity-controlled chamber at thermoneutrality (30C) for three weeks then either kept at thermoneutrality for a further four hours, or transferred to 4C (cold) for four hours, before harvest.

value: ChAT-eGFP+ cells from the adipose stromal vascular fraction

value: ChATBAC-eGFP

value: 3wks thermoneutrality then 4h cold (4C)


title: ChAT-eGFP+ adipose cells, thermoneutrality 1

description:
Library name: Thermo1
10x Genomics

source_name: Inguinal subcutaneous white adipose tissue

value: 3wks thermoneutrality then 4h thermoneutrality


title: ChAT-eGFP+ adipose cells, cold 1

description:
Library name: Cold1
10x Genomics

value: Inguinal subcutaneous white adipose tissue


title: ChAT-eGFP+ adipose cells, thermoneutrality 2

description:
Library name: Thermo2
10x Genomics


title: LSK cells, YODA1, rep2

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

description:
Library name: YODA1_S2
10x Genomics

data_processing:
The scRNA-seq libraries were constructed using the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were pooled and sequenced on Illumina Novaseq 6000, generating 150 bp paired-end reads.
The mouse reference genome GRCm38 v92 was used for mapping reads.
The R package Seurat (v. 4.3.0) was utilized to process the profiles of cell expression.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
LSK cells were harvested from the bone marrow of vehicle and Yoda1-treated mice
LSK cells from the bone marrow of mice were sorted into 1.5 mL tubes. Cell suspensions were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System.

treatment_protocol: Mice were subjected intraperitoneally to Yoda1 for 2 weeks

value: Bone marrow

value: LSK cells

value: Bone marrow cells


title: LSK cells, Control, rep2

description:
Library name: CON_S2
10x Genomics

value: Control


title: IL-2 Timecourse GEX Library

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: IL-2 Timecourse GEX Library

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, hashes.tsv, matrix_HTO.mtx - Barcodes, features and counts for HTO.
Supplementary files format and content: Cellranger output files: cells.tsv, genes.tsv, matrix_rna.mtx -Barcodes, features and counts for RNA

source_name: Spleen

extract_protocol:
Tregs were isolated from Foxp3IRES-GFP mice. Immunocytes were released from spleens using mechanical disruption followed by filtering and washes in phenol red-free DMEM containing 10mM HEPES (Gibco) and 2% fetal calf serum (FCS). Red blood cells in spleen samples were lysed before filtering using ACK lysis buffer (Gibco, ref A10492-01). Tregs were sorted as PI-Dump [CD19-CD8a-CD11c-NK1.1]-CD4+TCRb+GFP+ , and sent to the Broad Institute Genomics Platform for encapsulation and 10x Genomics protocols.
Encapsulation was performed on the 10X Chromium instrument (10x Genomics). Libraries were prepared using Chromium Single Cell 3′reagents kit v2 according to manufacturer’s protocol at the Broad

value: Spleen

value: CD4+ T cells

value: In vivo IL2 treatment, 1 to 128hr

tag: hashtag assignment

value: hashtag 2, 128hr IL2-treated; hashtag 4, 128hr PBS-treated; hashtag 5, 64hr IL2-treated; hashtag 6, 24hr IL2-treated; hashtag 8, 16hr IL2-treated; hashtag 9, 8hrs IL2-treated; hashtag 10, 4hr IL2-treated; hashtag 11, 2hr IL2-treated; hashtag 12, 2h PBS-treated; hashtag 13, 1hr IL2-treated.


title: IL-2 Timecourse HTO library

description: Library name: IL-2 Timecourse HTO library

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Cellranger output files: cells.tsv, hashes.tsv, matrix_HTO.mtx - Barcodes, features and counts for HTO.
Supplementary files format and content: Cellranger output files: cells.tsv, genes.tsv, matrix_rna.mtx -Barcodes, features and counts for RNA
Library strategy: CITE-Seq


title: CD8, EPZ, 8days, biol rep4

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: EPZ_rep4
14_DOT1Li_WT4_10uM

data_processing:
51-bp paired-end reads were aligned against the mouse reference genome (Ensembl build 38) using Tophat (version 2.1, bowtie version 1.1).
Tophat was supplied with a Gene Transfer File (GTF, Ensembl version 77) and was supplied with the following parameters: “prefilter-multihits –no-coverage-search – bowtie1 –library-type fr-firststrand”.
To count the number of reads per gene, a custom script which is based on the same ideas as HTSeq-count has been used.
A list of the total number of uniquely mapped reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Assembly: mm10
Supplementary files format and content: Tab delineated Excel workbook with raw counts for each sample

source_name: Isolated CD8 T cell

growth_protocol: Isolated and activated (aCD3/aCD28) on day 0, then expanded for 8 days in RPMI, 10 % heat-inactivated FBS, 2 mM L-glutamine, 28.6 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 10 mM HEPES, P/S. Cells were cultured at 37C and 5% CO2.

extract_protocol:
1x10e6 were suspended in RLT supplemented with 2-mercapthoethanol and snap frozen. Total RNA was isolated with the RNAeasy mini kit (Qiagen). Samples with an RNA integrity number >8 were subjected to library preparation
cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina)

treatment_protocol: DOT1L-WT and DOT1L-KO cells were treated with 4-hydroxytamoxifen (10 nM) on day 0. DMSO & EPZ-5676 cells were treated every 2 days with 0.1% DMSO or 10 mM EPZ-5676.

value: wt;wt;het

value: male

value: Isolated CD8 T cell

value: day 8


title: CD8, EPZ, 8days, biol rep2

description:
Library name: EPZ_rep2
12_DOT1Li_WT2_10uM

value: female


title: LSK cells, YODA1, rep1

description:
Library name: YODA1_S1
10x Genomics

value: WT


title: CD8, EPZ, 8days, biol rep3

description:
Library name: EPZ_rep3
13_DOT1Li_WT3_10uM


title: CD8, DMSO, 8days, biol rep4

description:
Library name: DMSO_rep4
10_DOT1Li_WT4_DMSO

value: DMSO 0.1%


title: CD8, EPZ, 8days, biol rep1

description:
Library name: EPZ_rep1
11_DOT1Li_WT1_10uM


title: CD8, DMSO, 8days, biol rep1

description:
Library name: DMSO_rep1
7_DOT1Li_WT1_DMSO


title: CD8, DOT1L-WT, 8days, biol rep 3

description:
Library name: WT_rep3
6_RCM2_WT8

value: het;wt;het


title: CD8, DOT1L-WT, 8days, biol rep 2

description:
Library name: WT_rep2
5_RCM2_WT7


title: CD8, DOT1L-WT, 8days, biol rep 1

description:
Library name: WT_rep1
4_RCM2_WT6


title: CD8, DMSO, 8days, biol rep3

description:
Library name: DMSO_rep3
9_DOT1Li_WT3_DMSO


title: CD8, DMSO, 8days, biol rep2

description:
Library name: DMSO_rep2
8_DOT1Li_WT2_DMSO


title: CD8, DOT1L-KO, 8days, biol rep 1

description:
Library name: KO_rep1
1_RCM2_KO1

value: het;hom;het


title: CD8, DOT1L-KO, 8days, biol rep 3

description:
Library name: KO_rep3
3_RCM2_KO3


title: CD8, SGC, 8days, biol rep2

description:
Library name: SGC_rep2
6_DOT1Li_SGC_WT2_10uM

extract_protocol:
1x10e6 were suspended in RLT supplemented with 2-mercapthoethanol and snap frozen. Total RNA was isolated with the RNAeasy mini kit (Qiagen). 2 ug total RNA (in RLT buffer) isolated from S. cerevisae was added as a reference. Samples with an RNA integrity number >6 were subjected to library preparation
cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina)

treatment_protocol: Treated every 2 days with 0.1% DMSO or 10 mM SGC-0946


title: CD8, SGC, 8days, biol rep3

description:
Library name: SGC_rep3
7_DOT1Li_SGC_WT3_10uM


title: CD8, DMSO, 8days, biol rep4

description:
Library name: DMSO_rep4
4_DOT1Li_SGC_WT4_DMSO


title: CD8, SGC, 8days, biol rep1

description:
Library name: SGC_rep1
5_DOT1Li_SGC_WT1_10uM


title: CD8, DMSO, 8days, biol rep3

description:
Library name: DMSO_rep3
3_DOT1Li_SGC_WT3_DMSO


title: IL2_2h_Ctrl

description: Library name: IL2_2h_Ctrl

library_source: genomic single cell

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v2.1).
Hashtag processing followed the original recommendations of the ASAP-seq paper (Mimitou et al, Nature Biotech, 2021), using asap_to_kite (https://github.com/caleblareau/asap_to_kite) to process FASTQs files for downstream quantification by the bustools and kite workflows {Melsted et al, Nature Biotech 2021; Booeshagi et al, bioRxiv, 2022}. We used the HTODemux() (Stoeckius et al, Genome Biology, 2018)  function in the Seurat package (v4.0.2) (Hao et al, Cell, 2021) to remove doublets and call hashtag identities.
To enable comparisons across conditions and datasets, we used a common set of Treg-specific open chromatin regions, defined previously (Chowdhary et al., 2023) by supplementing pan-immunocyte OCRs from the ImmGen consortium(Yoshida et al., 2019) with additional peaks from Treg spleen and colon scATAC-seq data in (Chowdhary et al., 2023). To arrive at the final peak set, we also called peaks on the data generated in this study, using Archr v1.0.1(Granja et al., 2021) and MACS2 v2.2.7.1(Zhang et al., 2008) to call fixed-width peaks of 250bp within cell clusters. Any new OCRs not overlapping with the previous peak sets were added to the final merged peak set used for downstream analysis.
scATACseq data analysis was performed using Signac v1.4(Stuart et al., 2021). For quality control, only cells with at least 1x103 fragments per cell (depending on sequencing depth of experiment), greater than 25 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05 were retained for further analysis. Putative doublets identified by ArchR v1.0.1(Granja et al., 2021) and non-Treg, non-Tconv contaminant cells were also removed. We used the latent semantic indexing approach as previously described (Cusanovich et al., 2018; Stuart et al., 2019). Binarized count matrices were normalized using the term frequency-inverse document frequency (TF-IDF) transformation and reduced in dimensionality by singular value decomposition (SVD). As the first component was highly correlated with sequencing depth, SVD components 2-30 were used to generate a shared nearest neighbor (SNN) graph for clustering and as input into UMAP(McInnes et al., 2018) with cosine distance metric for visualization.
Assembly: mm10
Supplementary files format and content: .mtx ATAC counts matrices, peaks.txt files have OCR locations, barcodes.txt files have cell barcodes
Supplementary files format and content: fragments.tsv.gz files have raw ATAC fragments, fragments.tsv.gz.tbi files are index of fragments files
Supplementary files format and content: MetaData.txt files have relevant metadata, including hashtag/sample assignment (condition column; each unique value is a different biological replicate), cell population assignment, UMAP coordinates.
Supplementary files format and content: Hashtag_Counts.txt files contain raw counts of ASAPseq hashtags by cell barcode for cells included in ATAC counts matrices

extract_protocol:
Tregs were isolated from Foxp3IRES-GFP mice. Immunocytes were released from spleens using mechanical disruption followed by filtering and washes in phenol red-free DMEM containing 10mM HEPES (Gibco) and 2% fetal calf serum (FCS). Red blood cells in spleen samples were lysed before filtering using ACK lysis buffer (Gibco, ref A10492-01). CD4+ T cells were enriched using negative magnetic selection using the Dynabeads Untouched Mouse CD4 Cells Kit (ThermoFisher Scientific, cat#11415D). Tregs were sorted as DAPI- Dump (CD19, Cd11c, Cd8)- CD4+ TCRb+ GFP+ .
Nuclei isolation, transposition, GEM generation, and library construction targeting capture of 10000 cells were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics) with modifications to allow sample hashtagging (see below). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 to a final median depth of approximately 20-30,000 paired-end reads per cell. Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v2.1). To include multiple experimental conditions in the same scATAC run, we hashtagged cells using a modification of the ASAP-seq strategy (Mimitou et al., 2021) for low cell input primary cell samples. Before sorting, cells were hashtagged with mouse TotalSeqA DNA-barcoded hashtag antibodies at the same time as staining with fluorophore-conjugated antibodies (BioLegend). Cells were sorted into RPMI + 5% FCS in DNA Lo-Bind tubes (Eppendorf, cat # 022431021). After spinning down for 5 min at 500g in a refrigerated centrifuge at 4°C, cells were resuspended in 100 μl chilled 0.1x Omni Lysis buffer (1x Omni Lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute/IGEPAL, 0.01% Digitonin, 1% BSA in nuclease free water) diluted 1:10 in Wash/Lysis Dilution Buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 1% BSA in nuclease free water), gently mixed by pipetting, and incubated on ice for 6.5 min. Following lysis, 100 μl chilled wash buffer was added and gently mixed by pipetting. Cells were spun down for 5 min at 500g at 4°C, all but 5 μl of supernatant was removed, and 45 μl of chilled 1x nuclei buffer (10x Genomics) was added without mixing. After one more centrifugation step at 500g, 4°C for 5 min, supernatant was removed, and samples were resuspended in 7ul 1x nuclei buffer for cell counting and input into transposition, barcoding, and library preparation according to the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Modifications to the original 10X protocol were made as described in the original ASAP-seq publication (Mimitou et al., 2021) and as detailed at https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf. Briefly, 0.5 μl of 1uM BOA bridge oligo was spiked into the barcoding reaction. During GEM incubation, an additional 5 min incubation at 40°C was added to the beginning of the protocol. 43.5 instead of 40.5 μl of Elution Solution I was added during silane bead elution to recover 43 μl. 40 μl was used for SPRI clean up as indicated in the protocol, while 3 μl was set aside. During SPRI cleanup, the supernatant was saved. The bead bound fraction was processed as in the protocol, while for the supernatant fraction, 32 μl SPRI was added for 5 min. Beads were collected on a magnet, washed twice with 80% ethanol, and eluted in 42 μl EB. This 42 μl was combined with the 3 μl set aside from the previous step as input into the HTO indexing reaction. HTO Indexing PCR was run with partial P5 and indexed Rpxx primers (https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf) as: 95°C 3 min, 12-14 cycles of (95°C 20 sec, 60°C 30 sec, 72°C 20 sec), 72°C 5 min. The PCR product was cleaned up with 1.6X SPRI purification for quantification and sequencing alongside ATAC libraries.

value: Treg

value: Male


title: CD8, DMSO, 8days, biol rep1

description:
Library name: DMSO_rep1
1_DOT1Li_SGC_WT1_DMSO


title: LSK cells, Control, rep1

description:
Library name: CON_S1
10x Genomics

value: Bone marrow

value: LSK cells

value: Bone marrow cells


title: CD8, SGC, 8days, biol rep2, INP

description:
Library name: SGC_INP_rep2
input_M2_SGC

data_processing:
51-bp paired-end reads were mapped to a hybrid genome made from concatenating the mouse mm10 genome (Ensembl GRCm38) with the yeast sacCer3 genome.
Mapping was performed using BWA-MEM (version 0.7.17-r1188) with the option ‘-M’ and filtered for a mapping quality of 10. Duplicate alignments were removed using MarkDuplicates from the Picard toolset (version 3.0.0) with the option ‘-REMOVE_DUPLICATES true’.
Paired-end reads were then converted to fragments by reading in mapped, properly paired reads using the GenomicAlignments R/Bioconductor package (release 3.17). Peaks were called using MACS2 version 2.2.7.1 using samples pooled by treatment and pooled input samples as the ‘control’ argument using the options ‘-f BEDPE -g mm --keep-dup all --broad’. Peaks detected on yeast chromosomes were removed.
Genomic bigwig tracks were generated for both individual samples and samples pooled by treatment from fragments mapping to the mouse genome using a custom R script using the ‘coverage’ function from the GenomicRanges R/Bioconductor package. The track heights were multiplied by a factor ‘1x10e6 / number of yeast reads’ for values to represent ‘coverage per million yeast reads’ to allow quantitative comparisons. Signal values per peak were obtained by using the BigWigFile-method of the ‘summary’ function in the rtracklayer R/Bioconductor package.
For aggregate visualization of coverage data the tornadoplot R/GitHub package was used and TSS/exons were determined using the EnsDb.Mmusculus.v75 R/Bioconductor package. To calculate distances to the first internal exon, exons within a gene were first collapsed to disjoint ranges using the ‘reduce’ function from the GenomicRanges R/Bioconductor package. The distance was then taken as the number of basepairs between the 3’ end of the most 5’ exon and the 5’ end of the subsequent exon for genes that have at least 2 distinct exons.
Assembly: mm10, sacCer3
Supplementary files format and content: bigWig (per sample), broadPeak (per treatment), Excel Workbook (with normalized peak counts per sample)

extract_protocol:
Cells were fixed with 1% methanol free formaldehyde for 10 minutes & quenched with 125 mM glycine for 5 minutes. Quenced cells were lysed in 50 mM Tris-HCl pH8, 10 mM EDTA pH8, 1 % SDS + protease inhibitor cocktail, and sonicated for 3 minutes (30sec on, 30 sec off) on the Bioruptor PICO. Yeast chromatin was spiked in (1:1000 based on DNA concentration) prior to immunoprecipitation to allow for downstream normalization.
The library was prepped using the KAPA genomic DNA prep Hyper, purified and quantified using the Bioanalyzer DNA 7500.

treatment_protocol: Treated every 2 days with 0.1% DMSO, 10 mM EPZ-5676 or 10 mM SGC-0946

tag: spike-in organism

value: Saccharomyces cerevisiae


title: CD8, SGC, 8days, biol rep1, INP

description:
Library name: SGC_INP_rep1
input_M1_SGC


title: CD8, DMSO, 8days, biol rep2, INP

description:
Library name: DMSO_INP_rep2
input_M2_DMSO


title: CD8, EPZ, 8days, biol rep2, IP

description:
Library name: EPZ_IP_rep2
H3K79me2_M2_EPZ

tag: chip antibodies

value: anti-H3K79me2 (04-835 Sigma), anti-HA-12CA5 (17 03 2019 NKI; in-house)


title: CD8, DMSO, 8days, biol rep1, INP

description:
Library name: DMSO_INP_rep1
input_M1_DMSO

tag: cell type


title: CD8, DMSO, 8days, biol rep2, IP

description:
Library name: DMSO_IP_rep2
H3K79me2_M2_DMSO


title: CD8, DOT1L-KO, 8days, biol rep 2

description:
Library name: KO_rep2
2_RCM2_KO2


title: CD8, SGC, 8days, biol rep1, IP

description:
Library name: SGC_IP_rep1
H3K79me2_M1_SGC


title: CD8, EPZ, 8days, biol rep1, IP

description:
Library name: EPZ_IP_rep1
H3K79me2_M1_EPZ


title: Cortex_Null_Rep4

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Sequence quality was assessed using FastQC v 0.11.2, and quality trimming was done using Trimmomatic39. RNA-seq reads were aligned to the mm10 genome using STAR v.2.5.240and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis.
Output bam files were converted into bigwig track files to display coverage throughout the genome (in CPM)
Assembly: mm10
Supplementary files format and content: normalized bigWig

source_name: Cortex

extract_protocol:
RNA was isolated using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Ribosomal RNA was depleted following instructions from the NEBNext rRNA Depletion Kit v2 (NEB; E7400L). RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB; E7770L).

value: Cortex

value: Mecp2 null


title: Cortex_Null_Rep6


title: Cortex_Null_Rep5


title: Cortex_Null_Rep2


title: Cortex_Null_Rep3


title: CD8, DMSO, 8days, biol rep1, IP

description:
Library name: DMSO_IP_rep1
H3K79me2_M1_DMSO

value: wt;wt;het

value: male


title: CD8, SGC, 8days, biol rep4

description:
Library name: SGC_rep4
8_DOT1Li_SGC_WT4_10uM

value: Isolated CD8 T cell

value: day 8


title: Cortex_Null_Rep1


title: CD8, DMSO, 8days, biol rep2

description:
Library name: DMSO_rep2
2_DOT1Li_SGC_WT2_DMSO


title: Cortex_WT_Rep5

value: WT


title: Cortex_WT_Rep6


title: Cortex_WT_Rep4


title: Cortex_WT_Rep2


title: Cortex_WT_Rep3


title: CD8, EPZ, 8days, biol rep2, INP

description:
Library name: EPZ_INP_rep2
input_M2_EPZ


title: 56_Cortex_RNAPolII_Flox_KA_Rep2_input

data_processing:
reads were trimmed using Cutadapt v4.1 with parameters --nextseq-trim=30 --minimum-length=20, then aligned to the mm10 mouse genome assembly and dm6Drosophilagenome assembly for spike-in read mapping using Bowtie2 v2.2.636with parameters --sensitive --no-unal.
BigWig files were normalized using Drosophila spike-in.
Assembly: mm10
Supplementary files format and content: spike-in normalized bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA hyperprep kit. 1 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles for AFF4 ChIP, 9 cycles for RNAPolII ChIP, and 9 cycles for inputs on the thermocycler. Post amplification libraries were size selected at 200-400bp in length using KAPA pure beads from Roche. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Camk2a-Cre>Aff4 fl/fl

value: Kainic acid injected


title: Cortex_WT_Rep1


title: CD8, EPZ, 8days, biol rep1, INP

description:
Library name: EPZ_INP_rep1
input_M1_EPZ


title: 54_Cortex_RNAPolII_Flox_Saline_Rep2_input

value: Saline injected


title: 53_Cortex_RNAPolII_Flox_Saline_Rep1_input


title: CD8, SGC, 8days, biol rep2, IP

description:
Library name: SGC_IP_rep2
H3K79me2_M2_SGC


title: 52_Cortex_RNAPolII_Cre_KA_Rep2_input


title: 51_Cortex_RNAPolII_Cre_KA_Rep1_input


title: 50_Cortex_RNAPolII_Cre_Saline_Rep2_input


title: 49_Cortex_RNAPolII_Cre_Saline_Rep1_input


title: 48_Cortex_AFF4_Flox_KA_Rep2_input


title: 47_Cortex_AFF4_Flox_KA_Rep1_input


title: 46_Cortex_AFF4_Flox_Saline_Rep2_input


title: 45_Cortex_AFF4_Flox_Saline_Rep1_input


title: 44_Cortex_AFF4_Cre_KA_Rep2_input


title: 43_Cortex_AFF4_Cre_KA_Rep1_input


title: 41_Cortex_AFF4_Cre_Saline_Rep1_input


title: 42_Cortex_AFF4_Cre_Saline_Rep2_input


title: 37_Cortex_RNAPolII_WT_Rep3_input

value: Wildtype


title: 39_Cortex_RNAPolII_Null_Rep2_input


title: 38_Cortex_RNAPolII_Null_Rep1_input


title: 35_Cortex_RNAPolII_WT_Rep1_input


title: 34_Cortex_AFF4_Null_Rep3_input


title: 55_Cortex_RNAPolII_Flox_KA_Rep1_input


title: 36_Cortex_RNAPolII_WT_Rep2_input


title: 33_Cortex_AFF4_Null_Rep2_input


title: 27_Cortex_RNAPolII_Flox_KA_Rep1

tag: chip ab

value: RNAPolII (CST, 14958S)


title: 26_Cortex_RNAPolII_Flox_Saline_Rep2

tag: treatment


title: 28_Cortex_RNAPolII_Flox_KA_Rep2


title: 31_Cortex_AFF4_WT_Rep3_input


title: 32_Cortex_AFF4_Null_Rep1_input


title: 29_Cortex_AFF4_WT_Rep1_input


title: 22_Cortex_RNAPolII_Cre_Saline_Rep2


title: 21_Cortex_RNAPolII_Cre_Saline_Rep1


title: 24_Cortex_RNAPolII_Cre_KA_Rep2


title: 20_Cortex_AFF4_Flox_KA_Rep2

value: AFF4 (Bosterbio, M03824)


title: 30_Cortex_AFF4_WT_Rep2_input


title: 40_Cortex_RNAPolII_Null_Rep3_input


title: 19_Cortex_AFF4_Flox_KA_Rep1


title: 18_Cortex_AFF4_Flox_Saline_Rep2


title: 14_Cortex_AFF4_Cre_Saline_Rep2


title: 12_Cortex_RNAPolII_Null_Rep3


title: 15_Cortex_AFF4_Cre_KA_Rep1


title: 10_Cortex_RNAPolII_Null_Rep1


title: 9_Cortex_RNAPolII_WT_Rep3


title: 5_Cortex_AFF4_Null_Rep2


title: 6_Cortex_AFF4_Null_Rep3


title: 25_Cortex_RNAPolII_Flox_Saline_Rep1


title: 8_Cortex_RNAPolII_WT_Rep2


title: 4_Cortex_AFF4_Null_Rep1


title: 23_Cortex_RNAPolII_Cre_KA_Rep1


title: sox2_xen_rep1

data_processing:
raw data files format and content: R1 files contain the 1st read, R2 the UMI and R3 the second read (is sequenced as paired end)
Libraries were demultiplexed  using bcl2fastq and adapters trimmed using cutadapt
Reads were aligned to the mm10 genome using bowtie2 in local mode
UMIs were added to the SAM RX tag using AnnotateBamWithUmis, duplicates and reads with MAPQ < 30 filtered using SAMtools
Assembly: mm10
Supplementary files format and content: txt file containing ChIPseq (RPM) for 42403 GATA6 binding sites throughout the ES > iXEN conversion

source_name: XEN cells

growth_protocol: ES cells were grown in DMEM supplemented with 15% FCS and 0.01ug/mL LIF on gelatin coated plasticware and mitomycin C-inactivated MEF feeders. XEN cells were cultured in the same condition but without LIF.

extract_protocol:
cells were trypsinised, MEFs were adsorbed on non-gelatinized plasticware for 20 minutes. Cells were washed once in PBS, pelleted and fixed in PBS-2 mM DSG for 50 min followed by 10 min in PBS-1%PFA.
Chromatin Immunoprecipitation was carried out against GATA6, SOX17, OCT4, SOX2, ESRRB and ESRRA as described in material and methods.
Libraries were constructed using the NEBNext Ultra II DNA library prep kit using 0.6 μM annealed adapters for ligaXon
Custom designed Y/forked adapters based on Illumina Truseq indexes with 6-8nt UMI 3’ of the index sequence were used

treatment_protocol: 1ug/mL doxycycline was added to the cell-culture media

value: XEN cells

value: no treatment

tag: antibody


title: sox2_xen_rep2


title: 3_Cortex_AFF4_WT_Rep3


title: 1_Cortex_AFF4_WT_Rep1


title: sox2_d4_rep1

value: ES cells

value: cells carrying a doxycycline-inducible gata6 expression cassette

value: dox

tag: time point


title: 2_Cortex_AFF4_WT_Rep2

tag: tissue

value: Cortex


title: sox2_d4_rep2

tag: strain


title: sox2_d2_rep2


title: 16_Cortex_AFF4_Cre_KA_Rep2

tag: genotype


title: 17_Cortex_AFF4_Flox_Saline_Rep1


title: sox2_d4_rep1_2

tag: cell line


title: 13_Cortex_AFF4_Cre_Saline_Rep1


title: old hpMSC-treated 2

description:
Library name: old-treated2
TN1505R0200-1

data_processing:
Reads were mapped to GRCm38 using TopHat
The read counts were normalized to the fragments per kilobase of exon per million (FPKM)
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes raw counts

source_name: hippocampus

extract_protocol:
Mouse brains were snap-frozen in liquid nitrogen. Brains were sliced on a pre-chilled mouse brain matrix using a razor blade. From each slice, the hippocampus was carefully dissected. Hippocampal total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using at Theragen Bio protocl

value: hippocampus

tag: group

value: old

tag: agent

value: hpMSC-treated


title: sox2_d1_rep1


title: sox2_d1_rep2


title: old hpMSC-treated 3

description:
Library name: old-treated3
TN1505R0201-1


title: 11_Cortex_RNAPolII_Null_Rep2

value: Mecp2 null


title: old hpMSC-treated 1

description:
Library name: old-treated1
TN1505R0199-1


title: sox2_d016_rep2


title: 7_Cortex_RNAPolII_WT_Rep1


title: old sham 3

description:
Library name: old-sham3
TN1505R0198-1

value: sham


title: sox2_d008_rep2


title: old sham 2

description:
Library name: old-sham2
TN1505R0197-1


title: sox2_d008_rep1


title: sox2_d0_rep2


title: old sham 1

description:
Library name: old-sham1
TN1505R0196-1


title: young control 3

description:
Library name: young3
TN1505R0195-1

value: young

value: control


title: sox2_d0_rep2_2


title: sox2_d2_rep1


title: young control 1

description:
Library name: young1
TN1505R0193-1


title: sox17_xen_rep2


title: PCLS-FC+4IPP-2

description:
Library name: JN10X-HP8
10x Genomics

data_processing:
Base call files were demultiplexed into FASTQ files using Cell Ranger (v 7.1.0). Sequences were aligned to the human reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: RDS

extract_protocol:
Human PCLS specimens were harvested 5 days after treatment with the FC, with or without 4-IPP. For each experimental group, three PCLS slices were pooled to generate sufficient nuclei for library preparation and sequencing.Nuclei were isolated from human snap frozen lung tissue using the Chromium10x genomics nuclei isolation kit, per manual.
An aliquot of nuclei was stained with 0.4% trypan blue stain and DAPI and subsequently counted with the Thermo Fisher countess II FL. Samples with > 90% viability were used for downstream analysis. Approximately 20,000 nuclei per sample were loaded onto chip M and processed with the Chromium X controller. Barcoding and DNA (cDNA) library preparation was performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3' HT Kit v3.1). Quality of the cDNA was assessed at 2 time points with the Agilent Bioanalyzer High sensitivity DNA chip. The cDNA libraries were sequenced on the Novaseq 6000, using a Hiseq paired end 100bp sequencing configuration.

treatment_protocol: Samples were treated with vehicle (DMSO) or Fibrotic cocktail (FC) [5 ng/ml recombinant transforming growth factor-β (TGF-β) (240-B, R&D Systems), 5 μM platelet-derived growth factor-AB (PDGF-AB) (PHG0134, GIBCO), 10 ng/ml tumor necrosis factor-α (TNF-α) (210-TA, R&D Systems), and 5 μM 1-Oleoyl lysophosphatidic acid (LPA) (62215, Cayman Chemical)] +/- 50μM 4-IPP drugs in 500 ul of 0.25% DMEM w 1% pen-strep.

value: Lung

value: lung single suspension cell


title: PCLS-FC-2

description:
Library name: JN10X-HP7
10x Genomics


title: sox17_xen_rep1


title: sox17_d4_rep2


title: PCLS-Control-2

description:
Library name: JN10X-HP5
10x Genomics

value: fibrotic cocktail (FC)


title: sox17_d4_rep1


title: PCLS-4IPP-2

description:
Library name: JN10X-HP6
10x Genomics


title: PCLS-FC-1

description:
Library name: JN10X-HP3
10x Genomics


title: PCLS-FC+4IPP-1

description:
Library name: JN10X-HP4
10x Genomics


title: sox2_d016_rep1


title: sox17_d2_rep2


title: sox17_d2_rep1


title: PCLS-Control-1

description:
Library name: JN10X-HP1
10x Genomics

value: Vehicle


title: sox17_d1_rep2


title: PCLS-4IPP-1

description:
Library name: JN10X-HP2
10x Genomics


title: sox17_d1_rep1


title: sox17_d016_rep2