title: K562 cells, HR-19011-2

city: Busan

first: Min Jung

last: Kim

address: 262, Gamcheon-ro, Seo-gu

department: Biochemistry

country: South Korea

institute: Kosin university college of medicine

description: Library name: SAMPLE 5

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform.
Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Homo sapiens (GRCh38) using HISAT v2.1.0 , based on the HISAT and Bowtie2 implementations.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9.
After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b. Gene-level and Transcript-level quantification were calculated as raw read count, FPKM and TPM
Statistical analyses of differential gene expression were performed by DESeq2 v 1.24.0 (Love. et al. 2014) using raw counts as input.
Assembly: GRCh38
Supplementary files format and content: txt files include FPKM for each Sample

source_name: Bone marrow

growth_protocol: K562 cell lines were cultured in RPMI-1640 medium (Corning Inc.) supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories) and 1× antibiotic/antimycotic solution (Invitrogen) at 37°C in a humidified atmosphere containing 5% CO2 and 95% air.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) and its integrity was verified using TapeStation RNA screentape (Agilent), ensuring RNA integrity numbers greater than 7.0 for RNA library construction.
RNA libraries were prepared from 1 µg of RNA using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.)

treatment_protocol: K562 cells were treated with either 0.1% DMSO (vehicle) or 10 µM HR-19011 for 24 h.

value: Bone marrow

value: K562 cell lines

value: Etythroleukemia

value: Wild type

tag: time


title: K562 cells, HR-19011-3

status: Public on Apr 21 2025

type: SRA

description: Library name: SAMPLE 6

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Traumatic brain injury, Patient_28, 72h post injury

city: Salzburg

first: Andreas

last: Traweger

state: Salzburg

address: Strubergasse 22

department: Tendon and Bone Regeneration

country: Austria

institute: Paracelsus Medical University

description:
Library name: Sample 17
Column name in RPM_All_Samples.csv: TBI_P028_72h

data_processing:
Sequencing was performed on an Illumina platform (NextSeq 550, 75bp, SR).
Analysis parameters were defined as follows: Sequencing adapter: RealSeq (cutadapt -a Realseq3P=TGGAATTCTC -u1). Minimum read length: 17nt. Reads quality cutoff: 30 (phred quality score). Significance level: 0.05. Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 and multiQC v1.10. Reads from all passing samples were adapter trimmed and filtered using cutadapt v3.3. Reads were then filtered for a minimum length of 17 nucleotides.
Mapping was performed with bowtie v1.3.0 and miRDeep2 v2.0.1.2, whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl allowing for two mismatches and subsequently miRBase v22.1, filtered for miRNAs of hsa only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral and then assigned to various RNA species of interest.
Statistical analysis of preprocessed NGS data was done with R v4.0 and the packages pheatmap v1.0.12, pcaMethods v1.82 and genefilter v1.72.
Differential expression analysis with edgeR v3.32 used the quasi-likelihood negative binomial generalized log-linear model functions provided by the package. The independent filtering method of DESeq2 was adapted for use with edgeR to remove low abundant miRNAs and thus optimize the false discovery rate (FDR) correction.
Assembly: GRCh38.p12
Supplementary files format and content: csv file containing reads per million (RPM) normalized values for all samples.

source_name: Blood

extract_protocol:
Total RNA was extracted from human blood samples using miRNeasy Serum/Plasma Advanced Kit (qiagen, #217204) according to manufacturer’s protocol.
Micro-RNA-seq analysis was performed by a contractor (TAmiRNA GmbH, Leberstrasse 20, 1110 Vienna, Austria) according to their customized protocol. RNA preparation and library construction was performed using Serum/Plasma Advanced Kit (Qiagen, #217204) and Biofluids Plasma/Serum miRNA Library kit (RealSeq, #600-00048) according to manufacturer’s protocol.

value: Blood

tag: Sex

value: Male


title: miR-96 KO2

city: Yangpu

first: Changgeng

last: Peng

state: Shanghai

address: Siping Road 1239

department: School of Medicine

country: China

institute: Tongji University

description:
miR-96 KO2_FPKM
FPKM. WT and miR-96 KO

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Inner ear

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: Inner ear

value: miR-96 KO

value: non


title: miR-96 KO1

description:
miR-96 KO1_FPKM
FPKM. WT and miR-96 KO


title: K562 cells, HR-19011-1

description: Library name: SAMPLE 4


title: 1528_44

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

country: USA

institute: ToxStrategies

description: Library name: Sample 44

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: This study consisted of four arms based on chemical treatment: HFPO-DA (chemical of interest), GW7647 (prototypical PPARa agonist), rosiglitazone (prototypical PPARg agonist), and APAP (prototypical cytotoxic agent). Male mice from each of the three strains (i.e., J:ARC(S), B6129SF2/J, PPARa KO) were randomly allocated based on body weight to each dose group (vehicle control, low, medium, or high) within each study arm (n = 4/dose/strain/arm). Dosing solutions of HFPO-DA, GW7647, and rosiglitazone were administered via oral gavage at a dose volume of 10 mL/kg body weight once per day for five days. The doses were as follows: 0, 3, 15, or 30 mg/kg-d HFPO-DA; 0, 5, 10, or 20 mg/kg-d GW7647; and 0, 5, 10, or 20 mg/kg-d rosiglitazone. APAP was administered to 12-hour fasted mice as a single intraperitoneal (IP) injection at 0, 150, 300, or 600 mg/kg. Feed was restored immediately after APAP dosing and mice were sacrificed 6 hours post-dose. Following the last treatment, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

value: liver

tag: strain

value: male

value: WT

tag: exposure route

value: oral

tag: exposure duration

value: 5 days

value: 10 mg/kg/day rosiglitazone


title: Traumatic brain injury, Patient_8, 7d post injury

description:
Library name: Sample 15
Column name in RPM_All_Samples.csv: TBI_P008_7d

value: Female


title: 1528_45

description: Library name: Sample 45

value: 20 mg/kg/day rosiglitazone


title: tamoxifen treated, UBCCreERT2-1

description:
UBCCreERT2-1_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO

value: tamoxifen


title: K562 cells, 0-3 (Vehicle control)

description: Library name: SAMPLE 3

value: Bone marrow

value: K562 cell lines

value: Vehicle control


title: 1528_43

description: Library name: Sample 43


title: 1528_48

description: Library name: Sample 48


title: 1528_42

description: Library name: Sample 42

value: 0 mg/kg/day rosiglitazone


title: K562 cells, 0-2 (Vehicle control)

description: Library name: SAMPLE 2

value: Etythroleukemia

value: Wild type


title: Traumatic brain injury, Patient_8, 24h post injury

description:
Library name: Sample 13
Column name in RPM_All_Samples.csv: TBI_P008_24h

value: Blood


title: Traumatic brain injury, Patient_8, 72h post injury

description:
Library name: Sample 14
Column name in RPM_All_Samples.csv: TBI_P008_72h


title: WT4

description:
WT4_FPKM
FPKM. WT and miR-96 KO

value: Inner ear

value: wild type

value: non


title: WT3

description:
WT3_FPKM
FPKM. WT and miR-96 KO


title: WT2

description:
WT2_FPKM
FPKM. WT and miR-96 KO


title: Traumatic brain injury, Patient_1, 7d post injury

description:
Library name: Sample 12
Column name in RPM_All_Samples.csv: TBI_P001_7d

value: Male


title: K562 cells, 0-1 (Vehicle control)

description: Library name: SAMPLE 1


title: Traumatic brain injury, Patient_1, 72h post injury

description:
Library name: Sample 11
Column name in RPM_All_Samples.csv: TBI_P001_72h


title: 6T-CEM,RUNX1,CUT&Tag,rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

description: Library name: Sample4

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01. Samples 6T-CEM, IgG, CUT&Tag have been submitted in GSE252992.
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: narrowPeak files
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: T-ALL cells

value: RUNX1(Abcam, ab272456)


title: 1528_41

description: Library name: Sample 41

value: liver

value: male

value: WT

value: oral

value: 5 days

value: 10 mg/kg/day rosiglitazone


title: WT1

description:
WT1_FPKM
FPKM. WT and miR-96 KO


title: 1528_40

description: Library name: Sample 40

value: 5 mg/kg/day rosiglitazone


title: Traumatic brain injury, Patient_1, 24h post injury

description:
Library name: Sample 10
Column name in RPM_All_Samples.csv: TBI_P001_24h


title: 1528_39

description: Library name: Sample 39


title: 6T-CEM,RUNX1,CUT&Tag,rep1

description: Library name: Sample3


title: 6T-CEM,ETS1,CUT&Tag,rep2

description: Library name: Sample2

value: ETS1 (Santa cruz, sc-55581)


title: Male,ΔEcad,Input

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

country: France

institute: Institut Curie

data_processing:
Reads were aligned on the mouse GRCm38 mm10 genome using bowtie2 v2.4.5.
Peaks were called using MACS2 v2.2.7.1. The algorithm parameter were set as follow: efective genome size= 1.87.10^9 bp, FDR cut-off= 1.10^-5.
Bigwig files were generated using bamcoverage function from deeptools v3.5.1.0.0. The genome was divided in bins of 20bp. Counts were normalized in bins per millions using a scaling factor of 1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: cell lines have been grown in F12-medium supplemented in 10% FBS and penicillin/streptomycin until reaching 60*10^6 cells at 70% confluency.

extract_protocol:
Cells were fixed in 10mL 0.4% PFA for 10 minutes at RT. Crosslinking reaction was stopped by addition of 1 mL 2M Glycine (pH= 8.0). Cells were resuspended in 1 mL PBS and sonicated until DNA being fragmented to an average of 400 bp. Chromatin was harvested using an anti-H3K27ac (Active motif #39133) and protein G sepharose beads. DNA was purified by protein digestion by Protein K and phenol/chloroform (1:1) extraction.
Libraries were prepared using the Illumina TruSeq ChIP library preparation kit following the manufacturer’s protocol. 2 to 3 ng of DNA were subjected to subsequent steps of end-repair, dA-tailing and ligation of TruSeq RNA UD indexes Illumina adapters. Librairies were amplified using 15 cycles on the thermocycler.

value: Melanoma

value: {delta}Ecad


title: 1528_38

description: Library name: Sample 38


title: Fracture, Patient_14, 7d post injury

description:
Library name: Sample 9
Column name in RPM_All_Samples.csv: Fx_P014_7d

value: Blood

value: Female


title: 6T-CEM,ETS1,CUT&Tag,rep1

description: Library name: Sample1


title: Female,Ecad,Input

value: Ecad


title: Fracture, Patient_14, 24h post injury

description:
Library name: Sample 7
Column name in RPM_All_Samples.csv: Fx_P014_24h


title: Jurkat day10 shSH2D1A_rep2

description: Library name: jur-D10-shSH2D1A-2

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

source_name: Jurkat

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jurkat


title: Fracture, Patient_14, 72h post injury

description:
Library name: Sample 8
Column name in RPM_All_Samples.csv: Fx_P014_72h


title: Fracture, Patient_6, 7d post injury

description:
Library name: Sample 6
Column name in RPM_All_Samples.csv: Fx_P006_7d

value: Male


title: Male,Ecad,Input


title: Jurkat day10 shSH2D1A_rep1

description: Library name: jur-D10-shSH2D1A-1

value: T-ALL cells


title: 1528_36

description: Library name: Sample 36


title: Ma_1069,Female,ΔEcad,H3K27ac


title: Fracture, Patient_6, 72h post injury

description:
Library name: Sample 5
Column name in RPM_All_Samples.csv: Fx_P006_72h


title: 1528_35

description: Library name: Sample 35

value: 0 mg/kg/day rosiglitazone


title: 1528_34

description: Library name: Sample 34

value: liver


title: Ma_1064,Female,ΔEcad,H3K27ac


title: Jurkat day10 shNC_rep2

description: Library name: jur-D10-NC-2


title: Jurkat day10 shNC_rep1

description: Library name: jur-D10-NC-1


title: 1528_33

description: Library name: Sample 33

value: male


title: Ma_1057,Female,ΔEcad,H3K27ac


title: Fracture, Patient_6, 24h post injury

description:
Library name: Sample 4
Column name in RPM_All_Samples.csv: Fx_P006_24h


title: Jurkat day8 shSH2D1A_rep2

description: Library name: jur-D8-shSH2D1A-2


title: Fracture, Patient_4, 7d post injury

description:
Library name: Sample 3
Column name in RPM_All_Samples.csv: Fx_P004_7d


title: Female,ΔEcad,Input


title: 1528_32

description: Library name: Sample 32

value: WT

value: 20 mg/kg/day rosiglitazone


title: Ma_1456,Male,ΔEcad,H3K27ac


title: Fracture, Patient_4, 72h post injury

description:
Library name: Sample 2
Column name in RPM_All_Samples.csv: Fx_P004_72h


title: Jurkat day8 shSH2D1A_rep1

description: Library name: jur-D8-shSH2D1A-1


title: 1528_37

description: Library name: Sample 37

value: oral

value: 5 days


title: 1528_31

description: Library name: Sample 31


title: Jurkat day8 shNC_rep2

description: Library name: jur-D8-NC-2


title: Fracture, Patient_4, 24h post injury

description:
Library name: Sample 1
Column name in RPM_All_Samples.csv: Fx_P004_24h


title: 1528_30

description: Library name: Sample 30


title: Ma_1062,Male,ΔEcad,H3K27ac


title: Jurkat day8 shNC_rep1

description: Library name: jur-D8-NC-1


title: Ma_1014,Female,Ecad,H3K27ac


title: 1528_28

description: Library name: Sample 28

value: 10 mg/kg/day rosiglitazone


title: 1528_29

description: Library name: Sample 29


title: Ma_1181,Male,Ecad,H3K27ac


title: 6T_CEM day10 shSH2D1A_rep2

description: Library name: c6T-D10-shSH2D1A-2


title: 1528_27

description: Library name: Sample 27


title: 6T_CEM day10 shSH2D1A_rep1

description: Library name: c6T-D10-shSH2D1A-1


title: 6T_CEM day10 shNC_rep2

description: Library name: c6T-D10-NC-2


title: KMS11,LentiV2, H3K27ac ChIP seq, biorep2

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Library name: H3K27ac_KMS11_BACH1Ctrl_rep2

data_processing:
Processed using ENCODE ChIP-seq pipeline Reads aligned to hg38 using bowtie2 and filtered for duplicates, poor quality and blacklisted regions Coverage across 20 bp windows quantified by BAMscale Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: Bigwig,narrowPeak

source_name: Haematopoietic and Lymphoid

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes (and double crosslinked with 3 mM EGS in PBS for 20min  for p300 and CBP before formaldehyde fixation), swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 200-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: chip antibody

value: H3K27ac antibody (07-360; Merck)


title: Ma_1007,Male,Ecad,H3K27ac

value: Melanoma


title: KMS11,LentiV2_BACH1g4, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_KMS11_BACH1KD_rep3


title: 1528_26

description: Library name: Sample 26


title: MuSC-Old3

city: Madiosn

first: Romeo

middle: S

last: Blanc

state: WI

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

institute: University of Wisconsin-Madison

data_processing:
The CUT&Tag samples were pre-processed with the ENCODE ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
The TrimGalore and cudadapt algorithms were used to trim adapters from the CUT&Tag
the Bowtie2 aligner was used to align reads to the mm10 reference genome.
Duplicates were then marked with the Picard algorithm and removed with samtools
The SEACR algorithm, a tool developed specifically for CUT&Tag datasets, was used to call CUT&Tag peaks with the stringent setting, and the peaks with FDR<0.05 in each sample were pooled. Pooled peaks that fell within the 5’ and 3’ boundaries of mm10 gencode gene bodies were merged into a single peak to reduce noise
Genomic features covered by CUT&Tag peaks were annotated using the ChIPseeker package in R
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: Muscle stem cells

extract_protocol:
Cells were permeabilised with 0.1% digitonin.
MuSCs were freshly isolated from young (4mos) and aged (24mos) mouse skeletal muscles. For H4K20me1 CUT&Tag, we used three young male mice and three aged male mice as individual replicate; in addition, one young and one age mouse were used as “No Antibody” control. CUT&Tag was performed following Henikoff’s group original protocol (Kaya-Okur et al., 2019). Precipitated DNA was used for a short PCR pulse (5 cycles) using one barcode pair for all samples. For quality assessment prior to library construction, PCR product was used for qPCR; libraries were balanced based on qPCR amplification. To generate library, we performed a 13 cycles PCR with individual barcode pairs for each sample, followed by AMpure XP beads (Beckman Coulter, Inc.) cleanup. Libraries were sent to GeneWiz for 150bp pair-end sequencing.

value: Muscle stem cells


title: 6T_CEM day10 shNC_rep1

description: Library name: c6T-D10-NC-1


title: MuSC-Old2


title: KMS11,LentiV2_BACH1g4, H3K27ac ChIP seq, biorep2

description: Library name: H3K27ac_KMS11_BACH1KD_rep2


title: 1528_25

description: Library name: Sample 25


title: 6T_CEM day5 shSH2D1A_rep2

description: Library name: c6T-D5_shSH2D1A_2


title: KMS11,LentiV2_BACH1g4, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_KMS11_BACH1KD_rep1


title: 1528_24

description: Library name: Sample 24

value: 5 mg/kg/day rosiglitazone


title: 6T_CEM day5 shSH2D1A_rep1

description: Library name: c6T-D5_shSH2D1A_1


title: KMS11,LentiV2, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_KMS11_BACH1Ctrl_rep3


title: Ma_1039,Female,Ecad,H3K27ac

value: Female

value: Ecad


title: KMS11, endogenous, P300 ChIP, biorep2

description: Library name: P300_KMS11_rep2

value: untreated

value: P300 antibody (PA1848, Invitrogen)


title: MuSC-Young3


title: MuSC-Young2


title: 1528_22

description: Library name: Sample 22

value: liver


title: KMS11,LentiV2, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_KMS11_BACH1Ctrl_rep1


title: KMS11, endogenous, P300 ChIP, biorep1

description: Library name: P300_KMS11_rep1


title: MM1144,LentiV2, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_MM1144_Ctrl_rep3


title: 6T_CEM day5 shNC_rep1

description: Library name: c6T-D5_shNC_1

value: T-ALL cells


title: 1528_21

description: Library name: Sample 21

value: male

value: WT


title: MuSC-Young1


title: npc_ic2_c1

city: Saint Louis

first: David

middle: H.

last: Gutmann

state: MO

address: 1 Childrens Place Suit 2130

institute: Washington University in St. Louis

data_processing:
Normalization and differential analysis were conducted using Partek Flow version 11.0.23.115. NPC samples were excluded due to low quality. Genes with average coverage <1 were excluded from differential analyses.
Differential analyses were conducted on median ratio normalized gene counts using DESeq2, comparing control astrocytes to control OPCs and GRPs and NF1-null astrocytes to NF1-null OPCs and GRPs. The threshold for differentially expressed genes was false discovery rate (FDR) ≤ 0.05, p-value ≤ 0.05, and fold change ±2.
Pathway analyses were conducted on genes upregulated in control astrocytes compared to control OPCs and GRPs, and on genes upregulated in control OPCs and GRPs compared to control astrocytes. DAVID v2023q3 was first used to convert Ensembl gene IDs into official gene symbols; pathway analyses were conducted on the converted gene lists using the annotation categories GOTERM_BP_DIRECT, GOTERM_CC_DIRECT, and GOTERM_MF_DIRECT. Bar plots of log10(FDR) and fold enrichment for selected pathways were created using Microsoft Excel version 16.79
Differential analyses were conducted on median ratio normalized gene counts using DESeq2, comparing NF1-null OPCs to control OPCs, NF1-null astrocytes to control astrocytes, and NF1-null GRPs to control GRPs. The threshold for differentially expressed genes was false discovery rate (FDR) ≤ 0.05, p-value ≤ 0.05, and fold change ±2. R studio version 2023.09.1 and dplyr version 1.1.3 were used to identify genes that were upregulated in all of NF1-null OPCs, NF1-null astrocytes, and NF1-null GRPs, as well as genes that were upregulated in all of control OPCs, control astrocytes, and control GRPs
Assembly: Ensembl release 76 (hg38)
Supplementary files format and content: The text file contains gene expression data, including gene counts, genomic coordinates, and expression metrics such as CPM and FPKM for genes.

source_name: NPC

extract_protocol:
Cells were harvested once a T25 flask reached approximately 70% confluency. Total RNA was extracted from cell pellets using NucleoSpin RNA Plus (Takara Bio Cat. Number 740984.50).
Bulk RNA sequencing; Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.

value: NPC

value: Wild-Type


title: npc_ic2_b1


title: MM1144,LentiV2, H3K27ac ChIP seq, biorep2

description: Library name: H3K27ac_MM1144_Ctrl_rep2


title: KO3

description: biotin labeled nascent RNA

data_processing:
Dual, 6nt UMIs extracted from FASTQs and subsequently used to deduplicate mapped reads, both using UMI-tools 1.1.1
Low-quality bases trimmed from 3’ ends with a cutoff score of 10, followed by adapter removal using cutadapt 1.14. Read pairs with either trimmed read falling shorter than 20nt filtered.
Read pairs mapped to combined mm10/dm6 index using BWA-MEM 0.7.17 (-L 100,5) and separated according to primary/spike genome using samtools 1.3.1
PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined
Assembly: mm10
Supplementary files format and content: bigwig containing combined count of end 1 3' mapping locations for all replicates

source_name: muscle stem cell

extract_protocol:
nascent biotin-labeled RNA was isolated from permeabilized cells, essentially as described in Elrod et al., Mol. Cell, 2019
PRO-seq libraries, essentially as described in Reimer et al., Mol. Cell, 2021

value: muscle stem cell

value: KMT5a KO


title: MM1144,LentiV2, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_MM1144_Ctrl_rep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma


title: KO2

description: biotin labeled nascent RNA


title: npc_ic2_a1


title: MuSC-Old1


title: MM1144,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_MM1144_ATF4KD_rep3

value: H3K27ac antibody (07-360; Merck)


title: 1528_18

description: Library name: Sample 18

value: oral

value: 5 days

value: 0 mg/kg/day rosiglitazone


title: npc_ic2


title: KO1

description: biotin labeled nascent RNA


title: MM1144,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep2

description: Library name: H3K27ac_MM1144_ATF4KD_rep2


title: WT3

description: biotin labeled nascent RNA


title: 1528_23

description: Library name: Sample 23

value: 5 mg/kg/day rosiglitazone


title: 1528_17

description: Library name: Sample 17


title: npc_st18_c1

value: NF1 null (homozygous c.2041C>T)


title: 6T_CEM day5 shNC_rep2

description: Library name: c6T-D5_shNC_2


title: WT2

description: biotin labeled nascent RNA


title: MM1144,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_MM1144_ATF4KD_rep1


title: 1528_16

description: Library name: Sample 16

value: PPARa KO

value: KO

value: 20 mg/kg/day rosiglitazone


title: WT1

description: biotin labeled nascent RNA


title: 1528_15

description: Library name: Sample 15

value: liver

value: male


title: 1528_20

description: Library name: Sample 20

value: WT


title: npc_st18_d1

value: NPC


title: KMS11,control, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_KMS11_Ctrl_rep3


title: npc_st18_a1


title: 1064, GRP + RC, rep3

description:
1064P_GRC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

data_processing:
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Reads were mapped to the mouse reference genome mm10 (gencode m13 version-GRCm38.p5) using STARs
STAR was also used to create the expression matrixes.
Transcript Per Million (TPM) normalized count were calculated based on library size and gene length.
Assembly: mm10
Supplementary files format and content: Tab delimited text files with raw counts for every genes and every samples
Supplementary files format and content: Tab delimited files text with TPM-Normalized counts for every genes and every samples

growth_protocol: 24hours after seeding, cells were starved for 18 hours in 0.5% FCS. Cell confluency after the starvation was at 80%.

extract_protocol:
RNA were extracted using the miRNeasy mini kit according to manufacturer protocol.
RNA sequencing libraries were prepared from 1 μg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit

treatment_protocol: Cells were treated with GRP and or RC for four hours in low serum (0.5% FCS).

value: Melanoma cell line

value: Female

tag: phenotype

value: GRPRpos

value: 10nM GRP + 1microM RC-3095


title: KMS11,control, H3K27ac ChIP seq, biorep2

description: Library name: H3K27ac_KMS11_Ctrl_rep2

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: H3K27ac antibody (07-360; Merck)


title: KMS11,control, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_KMS11_Ctrl_rep1


title: 1528_19

description: Library name: Sample 19

value: oral

value: 5 days

value: 0 mg/kg/day rosiglitazone


title: 1064, RC, rep3

description:
1064P_RC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: 1microM RC-3095


title: 1528_14

description: Library name: Sample 14

value: PPARa KO

value: KO


title: KMS11,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep3

description: Library name: H3K27ac_KMS11_ATF4KD_rep3


title: 1064, GRP, rep3

description:
1064P_G10_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: 10nM GRP


title: 1528_12

description: Library name: Sample 12

value: liver

value: male

value: 10 mg/kg/day rosiglitazone


title: grp_ic2_p2

source_name: GRP

value: GRP

value: Wild-Type


title: 1064, MOCK, rep3

description:
1064P_CTRL_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Melanoma cell line

value: Female

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: KMS11,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep1

description: Library name: H3K27ac_KMS11_ATF4KD_rep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: H3K27ac antibody (07-360; Merck)


title: 1528_11

description: Library name: Sample 11

value: oral

value: 5 days


title: grp_ic2


title: grp_ic2_e1


title: 1014-Grpr, GRP + RC, rep3

description:
1014G_GRC_3
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: 10nM GRP + 1microM RC-3095


title: grp_st18_a1

value: NF1 null (homozygous c.2041C>T)


title: 1528_10

description: Library name: Sample 10

value: liver

value: PPARa KO

value: KO


title: KMS11, endogenous, CBP ChIP, biorep2

description: Library name: CBP_KMS11_rep2

value: untreated

value: CBP antibody (ab253202, abcam)


title: KMS11,LentiV2_ATF4g3, H3K27ac ChIP seq, biorep2

description: Library name: H3K27ac_KMS11_ATF4KD_rep2


title: 1014-Grpr, RC, rep3

description:
1014G_RC_3
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: Melanoma cell line

value: 1microM RC-3095


title: 1528_09

description: Library name: Sample 9

value: male

value: 0 mg/kg/day rosiglitazone


title: grp_st18_b1

value: GRP


title: grp_ic2_c

value: Wild-Type


title: 1528_08

description: Library name: Sample 8

value: 5 mg/kg/day rosiglitazone


title: grp_st18_c1


title: 1014-Grpr, GRP, rep3

description:
1014G_G10_3
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: Female

value: GRPRpos

value: 10nM GRP


title: 1528_13

description: Library name: Sample 13

value: oral

value: 5 days

value: 20 mg/kg/day rosiglitazone


title: 1528_07

description: Library name: Sample 7

value: liver

value: PPARa KO


title: KMS11, endogenous, BACH1 ChIP, biorep3

description: Library name: BACH1_KMS11_rep3

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: untreated

value: BACH1 antibody (A303057A, Bethyl Laboratories)


title: grp_st18_d1

value: NF1 null (homozygous c.2041C>T)


title: 1014-Grpr, MOCK, rep3

description:
1014G_CTRL_3
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: Melanoma cell line

value: MOCK (DMSO 0.1percent)


title: KMS11, endogenous, BACH1 ChIP, biorep2

description: Library name: BACH1_KMS11_rep2


title: 1528_06

description: Library name: Sample 6

value: male

value: KO

value: 0 mg/kg/day rosiglitazone


title: 1014-Ctrl, GRP + RC, rep3

description:
1014C_GRC_3
Tyr::NRASQ61K/°;CMV::tGFP

value: Female

value: GRPRneg

value: 10nM GRP + 1microM RC-3095


title: opc_ic2

source_name: OPC

value: OPC

value: Wild-Type


title: KMS11, endogenous, BACH1 ChIP, biorep1

description: Library name: BACH1_KMS11_rep1


title: 1528_05

description: Library name: Sample 5

value: liver

value: PPARa KO

value: oral

value: 5 days

value: 5 mg/kg/day rosiglitazone


title: 1528_04

description: Library name: Sample 4

value: 20 mg/kg/day rosiglitazone


title: opc_ic2_c1


title: MM1144, endogenous, ATF4 ChIP, biorep2

description: Library name: ATF4_MM1144_rep2

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: untreated

value: ATF4 antibody (11815, CST)


title: MM1144, endogenous, ATF4 ChIP, biorep3

description: Library name: ATF4_MM1144_rep3


title: 1014-Ctrl, GRP, rep3

description:
1014C_G10_3
Tyr::NRASQ61K/°;CMV::tGFP

value: Melanoma cell line

value: 10nM GRP


title: 1528_03

description: Library name: Sample 3

value: male

value: KO


title: 1014-Ctrl, MOCK, rep3

description:
1014C_CTRL_3
Tyr::NRASQ61K/°;CMV::tGFP

value: Female

value: GRPRneg

value: MOCK (DMSO 0.1percent)


title: opc_ic2_a1

value: OPC

value: Wild-Type


title: KMS11, endogenous, CBP ChIP, biorep1

description: Library name: CBP_KMS11_rep1

value: CBP antibody (ab253202, abcam)


title: 1528_02

description: Library name: Sample 2

value: liver

value: PPARa KO

value: oral

value: 5 days

value: 10 mg/kg/day rosiglitazone


title: 1181-Grpr, GRP + RC, rep3

description:
1181G_GRC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Male

value: GRPRpos

value: 10nM GRP + 1microM RC-3095


title: KMS11, endogenous, ATF4 ChIP, biorep3

description: Library name: ATF4_KMS11_rep3

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: untreated

value: ATF4 antibody (11815, CST)


title: MM1144, endogenous, ATF4 ChIP, biorep1

description: Library name: ATF4_MM1144_rep1


title: 1181-Grpr, RC, rep3

description:
1181G_RC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Melanoma cell line

value: 1microM RC-3095


title: opc_st18_c1

value: OPC

value: NF1 null (homozygous c.2041C>T)


title: 1181-Grpr, GRP, rep3

description:
1181G_G10_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: 10nM GRP


title: opc_st18_b1


title: opc_st18_e1


title: 1528_01

description: Library name: Sample 1

value: liver

value: PPARa KO

value: male

value: KO

value: 0 mg/kg/day rosiglitazone


title: KMS11, endogenous, ATF4 ChIP, biorep2

description: Library name: ATF4_KMS11_rep2


title: Deac3_14d_tetralone-ABA_rep2

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

molecule: polyA RNA

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

value: Riesling

tag: deacclimation assay

tag: days

value: tetralone-ABA


title: 1014-Ctrl, RC, rep3

description:
1014C_RC_3
Tyr::NRASQ61K/°;CMV::tGFP

value: Female

value: GRPRneg


title: 1181-Grpr, MOCK, rep3

description:
1181G_CTRL_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Male

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: KMS11, endogenous, ATF4 ChIP, biorep1

description: Library name: ATF4_KMS11_rep1

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT

value: untreated

value: ATF4 antibody (11815, CST)


title: opc_st18_f1

value: OPC

value: NF1 null (homozygous c.2041C>T)


title: Deac3_14d_tetralone-ABA_rep3


title: CD4+ T cells, added with IL-12 and IL-6, 96h, biol rep 3

city: Rehovot

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm9 genome using STAR v2.4.2a (default parameters).
Counting proceeded over genes annotated in Ensembl release 82, using HTSeq-count (intersection-strict mode).
Pipeline was constructed using Snamemake
Assembly: mm9
Supplementary files format and content: countsMatrix_RemappingSamples_mm9.txt (read count matrix)

source_name: Spleen

growth_protocol: Naive CD4+ T cells were isolated from spleens of C57BL/6 female mice (age 6-8 weeks) and maintained in RPMI-1640 medium with phenol red supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, 100 unit/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 1% kanamycin, 50µM β-mercaptoethanol, and 1X MEM non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was produced using the NucleoSpin® RNA, MACHEREY-NAGEL kit. 300-400ng of total RNA was used for the construction of sequencing libraries.
33 Libraries were prepared using the INCPM-mRNA-seq. Briefly, the polyA fraction (mRNA) was purified from 300-400 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Samples were sequenced on 4 lanes of Illumina NextSeq 500. Sequencing was done on a Nextseq 75 cycles high output kit, allocating 15M reads per sample (Illumina; single read sequencing).

treatment_protocol: Cells were cultured at a concentration of 1x106 cells/ml in 6 well plates with RPMI+ 10% FBS, in the presence of plate-bound anti-CD3 (1µg/ml) and anti-CD28 (3µg/ml) for stimulation. Cells were added with the indicated treatment with cytokines at the following concentrations: IL-4 (20ng/ml, R&D), IL-12 (10ng/ml, R&D), IL-6 (20ng/ml, R&D), IL-2 (5ng/ml, R&D), and TGFb1 (10ng/ml, R&D) and cultured for 96h.

value: Spleen

value: CD4 T cells

value: female


title: 1181-Ctrl, GRP + RC, rep3

description:
1181C_GRC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Melanoma cell line

value: 10nM GRP + 1microM RC-3095


title: Deac3_14d_tetralone-ABA_rep1

value: bud

value: Riesling

value: tetralone-ABA


title: opc_ic2_b1

value: Wild-Type


title: ng2.pos_ic2_a1

source_name: NG2+ progenitor cells

value: NG2+ progenitor cells


title: Deac3_14d_Control_rep3

value: Control


title: ng2.pos_ic2_b1


title: CD4+ T cells, added with TGFb1 and IL-2, 96h, biol rep 3


title: 1181-Ctrl, RC, rep3

description:
1181C_RC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Male

value: GRPRneg

value: 1microM RC-3095


title: 1181-Ctrl, GRP, rep3

description:
1181C_G10_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: 10nM GRP


title: ng2.pos_ic2_c1


title: Deac3_14d_Control_rep2


title: CD4+ T cells, added with TGFb1 and IL-6, 96h, biol rep 3


title: CD4+ T cells, added with TGFb1 and IL-12, 96h, biol rep 3


title: Deac3_14d_Control_rep1


title: Deac3_7d_tetralone-ABA_rep3


title: CD4+ T cells, added with TGFb1 and IL-4, 96h, biol rep 3


title: ng2.pos_ic2_d1


title: 1064, GRP + RC, rep2

description:
1064P_GRC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Female

value: GRPRpos


title: 1064, RC, rep2

description:
1064P_RC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF


title: ng2.pos_st18

value: NF1 null (homozygous c.2041C>T)


title: Deac3_7d_tetralone-ABA_rep2


title: Deac3_7d_tetralone-ABA_rep1


title: 1064, MOCK, rep2

description:
1064P_CTRL_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: MOCK (DMSO 0.1percent)


title: CD4+ T cells, IL-2 added, 96h, biol rep 3

value: Spleen

value: CD4 T cells

value: female


title: CD4+ T cells, IL-6 added, 96h, biol rep 3


title: 1064, GRP, rep2

description:
1064P_G10_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Melanoma cell line


title: ng2.pos_st18_b1


title: Deac3_7d_Control_rep3

value: bud

value: Riesling


title: ng2.pos_st18_a1


title: CD4+ T cells, IL-12 added, 96h, biol rep 3


title: CD4+ T cells, added with IL-4 and IL-6, 96h, biol rep 3


title: ng2.pos_st18_c1


title: CD4+ T cells, IL-4 added, 96h, biol rep 3


title: Deac3_7d_Control_rep1


title: 1014-Grpr, RC, rep2

description:
1014G_RC_2
Tyr::NRASQ61K/°;CMV::Grpr/tGFP


title: Deac3_7d_Control_rep2


title: astro_ic2_c1

source_name: Astrocyte

value: Astrocyte

value: Wild-Type


title: CD4+ T cells, added with IL-12 and IL-6, 96h, biol rep 2


title: astro_ic2_d1


title: 1181-Ctrl, MOCK, rep3

description:
1181C_CTRL_3
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP


title: 1014-Grpr, GRP, rep2

description:
1014G_G10_2
Tyr::NRASQ61K/°;CMV::Grpr/tGFP


title: CD4+ T cells, added with IL-4 and IL-6, 96h, biol rep 2


title: astro_ic2_b1


title: Deac3_5d_tetralone-ABA_rep2

value: tetralone-ABA


title: astro_ic2


title: 1014-Ctrl, GRP + RC, rep2

description:
1014C_GRC_2
Tyr::NRASQ61K/°;CMV::tGFP

value: 10nM GRP + 1microM RC-3095


title: CD4+ T cells, added with TGFb1 and IL-2, 96h, biol rep 2


title: Deac3_5d_tetralone-ABA_rep1


title: astro_st18_a1


title: CD4+ T cells, added with TGFb1 and IL-6, 96h, biol rep 2


title: 1014-Ctrl, RC, rep2

description:
1014C_RC_2
Tyr::NRASQ61K/°;CMV::tGFP

value: GRPRneg


title: astro_st18_c1


title: 1014-Ctrl, GRP, rep2

description:
1014C_G10_2
Tyr::NRASQ61K/°;CMV::tGFP


title: CD4+ T cells, added with TGFb1 and IL-12, 96h, biol rep 2


title: 1014-Grpr, GRP + RC, rep2

description:
1014G_GRC_2
Tyr::NRASQ61K/°;CMV::Grpr/tGFP


title: astro_st18_a


title: CD4+ T cells, added with TGFb1 and IL-4, 96h, biol rep 2


title: Deac3_5d_Control_rep2

value: Control


title: 1014-Ctrl, MOCK, rep2

description:
1014C_CTRL_2
Tyr::NRASQ61K/°;CMV::tGFP


title: Deac3_3d_tetralone-ABA_rep3


title: Deac3_5d_Control_rep1


title: 1181-Grpr, GRP + RC, rep2

description:
1181G_GRC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Male


title: npc_st18_e1

value: NPC


title: CD4+ T cells, IL-2 added, 96h, biol rep 2


title: astro_st18_e1


title: CD4+ T cells, IL-6 added, 96h, biol rep 2


title: Deac3_5d_tetralone-ABA_rep3


title: 1181-Grpr, RC, rep2

description:
1181G_RC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: GRPRpos

value: 1microM RC-3095


title: 1014-Grpr, MOCK, rep2

description:
1014G_CTRL_2
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: Female

value: MOCK (DMSO 0.1percent)


title: CD4+ T cells, IL-12 added, 96h, biol rep 2

value: Spleen

value: CD4 T cells


title: 1181-Grpr, GRP, rep2

description:
1181G_G10_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Melanoma cell line

value: 10nM GRP


title: Deac3_3d_tetralone-ABA_rep1

value: bud

value: Riesling


title: CD4+ T cells, IL-4 added, 96h, biol rep 2

value: female


title: RO50579

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0) (PMID: 28091601). The “mkfastq” command was used to generate FASTQ files and the “count” command was used to generate raw gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters. Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates (PMID: 33270111). Samples from 22 patients were combined in R using the Read10X() function from Seurat package(v4.3.0) (PMID: 34062119) and an integrated Seurat object was generated. Filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) less than 20000 and had mitochondrial content less than 20 percent. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers (PMID: 26430063). Doublets were removed using scDblFinder (v1.12.0) (PMID: 35814628). The SCTransform workflow was used for count normalization, initial integration, and to identify highly variable genes (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Batch correction was performed using Harmony (v0.1.1) (PMID: 31740819). Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Celltype annotation was performed using two different approaches: 1) Seurat Reference Mapping and Label Transfer approach, Bone Marrow Atlas was downloaded from DISCO (PMID: 34791375) and was used a reference to transfer labels this data 2) Manual curation was done by gene markers to reflect the prediction results. Hematopoietic Stem Cells (HSC) were identifed by PROM1 and CD34,MultiPotent Progenitors (MPP) by TESPA1, PLEK, Granulocyte/Macrophage Progenitors (GMP) by SPINK2 and SERPINB1, Granulocytes by AZU1 and PRTN3, CD14-Mono by CD14 and S100A8, Macrophages by C1QA and C1QB, Megakaryocytes(MK) by PPBP and PF4, Classical Dendritic Cells (cDC) by CD1C and FCER1A, Plasmacytoid dendritic cells (pDCs) by IRF7 and IRF8, TCells by CD3E and CD8A, NaturalKiller Cells(NK) by NKG7 and IL2RB, Fibroblasts by COL1A1 and CXCL12, MAST cells by CPA3 and KIT, Keratin Expressing Stromal Cells(KESC) by KRT7 and KRT14 and Plasma Cells by JCHAIN
Assembly: hg38
Supplementary files format and content: Matrix fle

source_name: Bone Marrow

extract_protocol:
After evaluating for cell number, cell viability, and cell size, the appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) with a targeted cell recovery of 10,000. Single-cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2. Next GEM Single Cell 3′ reagent kit (10X Genomics, Pleasanton, CA, USA). Following cell capture and cell lysis, cDNA was synthesized and amplified.
An Illumina sequencing library was then prepared with the amplified cDNA with the Chromium™ Next GEM Single-Cell 3′ GEM, Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA, USA). The resulting library was sequenced, including cell barcode and UMI sequences, and the read lengths were 26 bp read 1 (cell barcode and UMI) and 91 bp read 2 (RNA read) were generated with Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) at the Center for Medical Genomics of the Indiana University School of Medicine.

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

tag: age

tag: race

value: Caucasian

tag: response

value: Refractory

value: Tosedostat + ARAC


title: Deac3_5d_Control_rep3

value: Control


title: 1181-Grpr, MOCK, rep2

description:
1181G_CTRL_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Male

value: GRPRpos


title: CD4+ T cells, added with IL-12 and IL-6, 96h, biol rep 1


title: RO50575

description: 10x Genomics

value: Female

value: American Indian or Alaska Native

value: CR


title: Deac3_3d_Control_rep3


title: Deac3_3d_Control_rep2


title: 1181-Ctrl, GRP + RC, rep2

description:
1181C_GRC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: GRPRneg

value: 10nM GRP + 1microM RC-3095


title: RO50562

description: 10x Genomics

value: Tosedostat + DAC


title: 1181-Ctrl, RC, rep2

description:
1181C_RC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Melanoma cell line

value: 1microM RC-3095


title: Deac3_3d_Control_rep1

value: bud

value: Riesling


title: RO50549

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: Pacific Islander


title: CD4+ T cells, added with IL-4 and IL-6, 96h, biol rep 1

value: Spleen

value: CD4 T cells

value: female


title: CD4+ T cells, added with TGFb1 and IL-2, 96h, biol rep 1


title: Deac3_0d_tetralone-ABA_rep3

value: tetralone-ABA


title: CD4+ T cells, added with TGFb1 and IL-6, 96h, biol rep 1


title: RO50528

description: 10x Genomics

value: Male

value: Caucasian

value: Refractory

value: 46,XY, t(5;12) with rearrangekemts involving 12q13

value: Benda + IDA


title: 1181-Ctrl, MOCK, rep2

description:
1181C_CTRL_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: GRPRneg

value: MOCK (DMSO 0.1percent)


title: 1181-Ctrl, GRP, rep2

description:
1181C_G10_2
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Melanoma cell line

value: 10nM GRP


title: RO50497

description: 10x Genomics

value: Female

value: GCLAC


title: RO50634

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: CR

value: IAP


title: Deac3_0d_tetralone-ABA_rep1

value: bud

value: Riesling


title: 1064, GRP + RC, rep1

description:
1064P_GRC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: GRPRpos

value: 10nM GRP + 1microM RC-3095


title: CD4+ T cells, added with TGFb1 and IL-12, 96h, biol rep 1

value: Spleen

value: CD4 T cells

value: female


title: Deac3_3d_tetralone-ABA_rep2

value: tetralone-ABA


title: RO50417

description: 10x Genomics

value: Male

value: Caucasian


title: 1064, RC, rep1

description:
1064P_RC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Melanoma cell line

value: 1microM RC-3095


title: Deac3_0d_Control_rep3

value: Control


title: CD4+ T cells, IL-2 added, 96h, biol rep 1


title: 1064, GRP, rep1

description:
1064P_G10_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Female

value: 10nM GRP


title: Deac3_0d_Control_rep2


title: RO50393

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: Refractory

value: Benda + IDA


title: RO50392

description: 10x Genomics

value: Pacific Islander

value: GCLAC


title: 1064, MOCK, rep1

description:
1064P_CTRL_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: Deac3_0d_Control_rep1

value: bud

value: Riesling


title: CD4+ T cells, IL-12 added, 96h, biol rep 1

value: Spleen

value: CD4 T cells

value: female


title: RO50377

description: 10x Genomics

value: Caucasian

value: Benda+Idarubicin


title: Deac3_0d_tetralone-ABA_rep2

value: tetralone-ABA


title: Deac2_14d_tetralone-ABA_rep3


title: 1014-Grpr, GRP + RC, rep1

description:
1014G_GRC_1
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: Melanoma cell line

value: Female

value: 10nM GRP + 1microM RC-3095


title: 1014-Grpr, RC, rep1

description:
1014G_RC_1
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: 1microM RC-3095


title: 1014-Grpr, GRP, rep1

description:
1014G_G10_1
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: 10nM GRP


title: RO50324

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: CR


title: Deac2_14d_tetralone-ABA_rep1


title: Deac2_14d_tetralone-ABA_rep2


title: CD4+ T cells, Naïve, biol rep 2

value: No treatment


title: Deac2_14d_Control_rep3

value: bud

value: Control


title: 1014-Grpr, MOCK, rep1

description:
1014G_CTRL_1
Tyr::NRASQ61K/°;CMV::Grpr/tGFP

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: CD4+ T cells, Naïve, biol rep 3

value: Spleen

value: CD4 T cells

value: female


title: RO50256

description: 10x Genomics

value: unknown


title: RO50268

description: 10x Genomics

value: Caucasian

value: Refractory

value: 4 + 3 + Sorafenib


title: CD4+ T cells, Naïve, biol rep 1


title: CD4+ T cells, added with TGFb1 and IL-4, 96h, biol rep 1


title: Deac2_14d_Control_rep2

value: Riesling


title: CD4+ T cells, IL-6 added, 96h, biol rep 1


title: RO50378

description: 10x Genomics

value: Male

value: Unknown

value: GCLAC


title: Deac2_14d_Control_rep1


title: RO50183

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: CR


title: CsA Ang-II 24h 3

city: Madrid

first: Paula

middle: Sofia

last: Yunes-Leites

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: NormCounts_RNAseq2: S18_C_A_24h_3

data_processing:
Reads were aligned first using BoWTie version 0.12.7 and then mapped to the latest Ensembl transcript set using RSEM v1.16.
Genes showing altered expression with an adjusted p < 0.05 were considered differentially expressed genes (DEGs). Only protein-coding genes were included in further analysis.
Assembly: GRCm38_91
Supplementary files format and content: .txt. Normalized counts of all detected transcripts (rows) and all samples (columns)

source_name: Aorta

growth_protocol: All mice were housed in the CNIC specific pathogen-free animal facility with controlled temperature, humidity, and light-dark cycles.

extract_protocol:
Aortas were isolated after perfusion with saline, and the perivascular tissue and the adventitia layer were removed with forceps. Aortic tissue was frozen in liquid nitrogen and homogenized with lysis buffer (Qiagen, 64204) using an automatic bead homogenizer (MagNA Lyser; Roche). Total RNA was isolated with the RNeasy MinElute Cleanup Kit (QIAGEN, 74204). Each triplicate was a pool of 3 aortas (total, 9 aortas per condition). RNA quality and purity was analyzed by Nanodrop and Bioanalyzer (Agilent 2100 Bioanalyzer RNA NanoChip). Only RNA samples with appropriate absorbance ratios were used (260/280 nm > 2.0; 230/260 nm 2.0–2.2); RNA samples with a RIN (RNA Integrity number- Bioanalyzer) below 7 were discarded.
For each condition, 1.5 μg of RNA was retro-transcribed with oligo dT priming, and the cDNA obtained was used to generate the transcriptome library. The library was sequenced using Illumina technology (Illumina Genome Analyzer IIx System). Library generation and sequencing were performed by the CNIC Genomics Unit under the supervision of Dr. Ana Dopazo.

treatment_protocol: RNAseq 1: male mice were treated with tamoxifen (1mg daily for 5 days) and, after 6 weeks, baseline BP measurements were performed. Osmotic minipumps with Ang-II (1 µg/kg/min) were implanted in Cn-Ctl and SM-Cn-/- mice in parallel, and BP was measured after 2h, 6h or 24h. Treated Cn-Ctl mice with systolic BP >130 mmHg were considered valid for analysis and were euthanized; all the SM-Cn-/- mice treated in parallel were selected for analysis. RNAseq 2: osmotic minipumps with CsA (CsA group) were implanted in WT C57BL/6J male mice. Minipumps were not implanted in control mice at this stage. After 5 days, baseline BP measurements were taken. Ang-II osmotic minipumps (1 µg/kg/min) were implanted in CsA and control mice in parallel, and BP was measured after 2h and 24h. Ang-II-treated CsA and control mice with a systolic BP >130 mmHg were considered valid for analysis and euthanized.

value: Aorta

value: male

value: Cyclosporin A 5 days and Ang-II 24h


title: 1014-Ctrl, RC, rep1

description:
1014C_RC_1
Tyr::NRASQ61K/°;CMV::tGFP

value: Melanoma cell line

value: Female

value: GRPRneg

value: 1microM RC-3095


title: CsA Ang-II 24h 2

description: NormCounts_RNAseq2: S17_C_A_24h_2


title: RO50236

description: 10x Genomics

value: Hispanic


title: Deac2_7d_Control_rep3

value: bud

value: Control


title: 1014-Ctrl, GRP, rep1

description:
1014C_G10_1
Tyr::NRASQ61K/°;CMV::tGFP

value: 10nM GRP


title: RO50176

description: 10x Genomics

value: Caucasian

value: ND

value: FLAM


title: CD4+ T cells, IL-4 added, 96h, biol rep 1

value: Spleen

value: CD4 T cells

value: female


title: CsA Ang-II 24h 1

description: NormCounts_RNAseq2: S16_C_A_24h_1

value: Aorta


title: Deac2_7d_Control_rep2

value: Riesling


title: RO50166

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: unknown

value: CR


title: 1181-Grpr, GRP + RC, rep1

description:
1181G_GRC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Melanoma cell line

value: Male

value: GRPRpos

value: 10nM GRP + 1microM RC-3095


title: CsA Ang-II 2h 3

description: NormCounts_RNAseq2: S12_C_A_2h_3

value: male

value: Cyclosporin A 5 days and Ang-II 2h


title: Deac2_7d_Control_rep1

value: bud

value: Control


title: CsA Ang-II 2h 2

description: NormCounts_RNAseq2: S11_C_A_2h_2


title: Deac2_7d_tetralone-ABA_rep3

value: tetralone-ABA


title: 1181-Grpr, RC, rep1

description:
1181G_RC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: 1microM RC-3095


title: RO50112

description: 10x Genomics

value: Female

value: American Indian or Alaska Native

value: Refractory

value: IAP


title: 1014-Ctrl, GRP + RC, rep1

description:
1014C_GRC_1
Tyr::NRASQ61K/°;CMV::tGFP

value: GRPRneg


title: CsA Ang-II 2h 1

description: NormCounts_RNAseq2: S10_C_A_2h_1

value: Aorta


title: 1181-Grpr, GRP, rep1

description:
1181G_G10_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: 10nM GRP


title: RO50130

description: 10x Genomics

value: Bone Marrow

value: Acute Myeloid leukemia (AML)

value: Caucasian


title: RO50076

description: 10x Genomics

value: Male

value: CR


title: 1181-Grpr, MOCK, rep1

description:
1181G_CTRL_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::Grpr/tGFP

value: Melanoma cell line

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: CsA basal 3

description: NormCounts_RNAseq2: S6_CsA_3

value: male

value: Cyclosporin A 5 days


title: Deac2_7d_tetralone-ABA_rep2

value: bud

value: Riesling

value: tetralone-ABA


title: Gal, TANGO2KO, Rep3

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS21

data_processing:
Sequenced reads were trimmed of adapter sequences with Trim Galore 0.6.6 using Cutadapt 1.18  and FastQC 0.11.9 (--fastqc --nextera --clip_R1 1).
Trimmed reads were quantified against the GENCODE v37 transcript sequences with custom mitochondrial transcripts (properly merged bicistronic transcripts and corrected terminal sequences) using Salmon 1.5.2 (-l A --seqBias –posBias –validateMappings).
Transcript abundances were summarised to gene-level with tximport 1.14.2 and analysed for differential changes between wild type and knockout genotypes using DESeq2 1.26.0 with independent hypothesis weighting (IHW) 1.14.0 . Gene expression changes with an adjusted p-value < 0.05 were considered significant.
Assembly: hg38
Supplementary files format and content: .xlsx spreadsheet containing differential gene expression results and normalised counts for cells grown on glucose.
Supplementary files format and content: .xlsx spreadsheet containing differential gene expression results and normalised counts for cells grown on galactose.

source_name: Breast

extract_protocol:
RNA was isolated from CAL51 cells using a miRNeasy Mini Kit (Qiagen) incorporating an on-column DNase digestion according to the manufacturers instructions.
Libraries were constructed using an Illumina Stranded mRNA preparation kit and sequenced using the NovaSeq platform by AGRF.

value: Breast

value: TANGO2 KO

value: Galactose


title: Deac2_7d_tetralone-ABA_rep1


title: CsA basal 1

description: NormCounts_RNAseq2: S4_CsA_1

value: Aorta


title: Gal, TANGO2KO, Rep2

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS20


title: Deac2_5d_tetralone-ABA_rep3


title: Deac2_5d_tetralone-ABA_rep2


title: 1014-Ctrl, MOCK, rep1

description:
1014C_CTRL_1
Tyr::NRASQ61K/°;CMV::tGFP

value: Female

value: GRPRneg


title: Gal, TANGO2KO, Rep1

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS19


title: WT Ang-II 24h 3

description: NormCounts_RNAseq2: S15_24h_3

value: Ang-II 24h


title: 1181-Ctrl, RC, rep1

description:
1181C_RC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Male

value: 1microM RC-3095


title: 1181-Ctrl, GRP, rep1

description:
1181C_G10_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Melanoma cell line

value: 10nM GRP


title: Gal, TANGO2WT, Rep3

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS18

value: TANGO2 WT


title: Deac2_5d_tetralone-ABA_rep1


title: WT Ang-II 24h 2

description: NormCounts_RNAseq2: S14_24h_2

value: male


title: 1181-Ctrl, GRP + RC, rep1

description:
1181C_GRC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: 10nM GRP + 1microM RC-3095


title: Gal, TANGO2WT, Rep2

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS17


title: Deac2_5d_Control_rep3

value: bud

value: Control


title: WT Ang-II 24h 1

description: NormCounts_RNAseq2: S13_24h_1


title: Deac2_5d_Control_rep2

value: Riesling


title: Gal, TANGO2WT, Rep1

description:
Gal_TANGO2KO_v_TANGO2WT.results.xlsx
MS16

value: Breast


title: 1057, GRP + RC, rep3

description:
1057_GRC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: GRPRpos


title: WT Ang-II 2h 3

description: NormCounts_RNAseq2: S9_2h_3

value: Ang-II 2h


title: 1057, RC, rep3

description:
1057_RC_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF


title: Deac2_5d_Control_rep1


title: Glu, TANGO2KO, Rep3

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
30_HOM3_TANGO

value: TANGO2 KO

value: Glucose


title: WT Ang-II 2h 2

description: NormCounts_RNAseq2: S8_2h_2

value: Aorta


title: CsA basal 2

description: NormCounts_RNAseq2: S5_CsA_2

value: Cyclosporin A 5 days


title: 1057, GRP rep3

description:
1057_G10_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Female


title: Glu, TANGO2KO, Rep2

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
29_HOM2_TANGO


title: WT Ang-II 2h 1

description: NormCounts_RNAseq2: S7_2h_1


title: Deac2_3d_Control_rep2


title: 1057, MOCK, rep3

description:
1057_CTRL_3
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: MOCK (DMSO 0.1percent)


title: WT basal 3

description: NormCounts_RNAseq2: S3_Basal_3

value: Non-treated


title: 1057, GRP + RC, rep2

description:
1057_GRC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Melanoma cell line


title: Glu, TANGO2KO, Rep1

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
28_HOM1_TANGO


title: Deac2_3d_Control_rep1


title: Glu, TANGO2WT, Rep3

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
27_WT3_TANGO

value: TANGO2 WT


title: WT basal 2

description: NormCounts_RNAseq2: S2_Basal_2

value: male


title: 1057, RC, rep2

description:
1057_RC_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: 1microM RC-3095


title: Glu, TANGO2WT, Rep2

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
26_WT2_TANGO


title: 1181-Ctrl, MOCK, rep1

description:
1181C_CTRL_1
Tyr::NRASQ61K/°; Cdkn2a-/-;°/°;Cdh1dF/dF;CMV::tGFP

value: Male

value: GRPRneg


title: WT basal 1

description: NormCounts_RNAseq2: S1_Basal_1


title: Glu, TANGO2WT, Rep1

description:
Glu_TANGO2KO_v_TANGO2WT.results.xlsx
25_WT1_TANGO


title: Deac2_3d_tetralone-ABA_rep2

value: bud

value: Riesling

value: tetralone-ABA


title: 1057, GRP rep2

description:
1057_G10_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: GRPRpos

value: 10nM GRP


title: Deac2_3d_tetralone-ABA_rep1


title: SM-Cn-/- Ang-II 24h 2

description: NormCounts_RNAseq1: KO_24h_2

value: CnB1-flox;Myh11-CreERT2-pos, male

value: Tamoxifen and 24h Ang-II


title: airway tissue systems - RSV infected

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description:
10x Genomics
instrument model: Illumina NovaSeq X

data_processing:
The 10X Genomics Cell Ranger pipeline (version 7.1.0) was used to perform sample demultiplexing, barcode/UMI processing, and gene counting for each cell (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: respiratory tract

growth_protocol: To start the differentiation, human ES/iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded onto Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. The differentiation of the human airway tissue systems was performed in serum-free differentiation (SFD) medium, composed of DMEM/F12 (3:1) (Cat# 044-29765, FUJIFILM Wako Pure Chemical and Cat# 11320033, Thermo Fisher Scientific) supplemented with N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), ascorbic acid (50 μg/mL, Cat# ST-72132, STEMCELL Technologies), 1× GlutaMAX (Cat# 35050-061, Thermo Fisher Scientific), 1% monothioglycerol (Cat# 195-15791, FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin (Cat# 820024, Sigma-Aldrich), and 1× penicillin/streptomycin). During days 0-1 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), and 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems). During days 1–3 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems) and 1% FBS. Between days 3–5 of differentiation, cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (Cat# 047-33763, FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (Cat# 037-24293, FUJIFILM Wako Pure Chemical) for 24 h, and then SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (Cat# 04-0034, Stemolecule) for another 24 h. During days 5–12 of differentiation, cells were cultured with SFD medium supplemented with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (Cat# AF-100-26, PeproTech), 10 ng/mL human FGF7 (Cat# AF-100-19, PeproTech), 10 ng/mL human BMP4 (Cat# 120-05ET, PeproTech), 20 ng/mL human EGF (Cat# AF-100-15, PeproTech), and all-trans retinoic acid (Cat# R2625 ATRA, Sigma-Aldrich). On day 12 of differentiation, cells were dissociated and embedded in the Matrigel Growth Factor Reduced Basement Membrane to generate organoids. During days 12–20 of the differentiation, organoids were cultured in SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA. On day 20 of differentiation, organoids were recovered from the Matrigel, and the resulting suspension of organoids (small free-floating clumps) was seeded onto Matrigel-coated cell culture plates. During days 20–30 of differentiation, organoids were cultured in SFD medium containing 50 nM dexamethasone (Cat# S1322, Selleck Chemicals), 0.1 mM 8-bromo-cAMP (Cat# 1140/50, Tocris), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (Cat# 095-03413, FUJIFILM Wako Pure Chemical).

extract_protocol:
Airway tissue systems were dissociated, and the cell concentration was adjusted to 1,000 cells/μL. The single-cell suspension, with a concentration of 1,200 cells/μL, was loaded onto a 10x Genomics Chromium Next GEM single cell G chip (10x Genomics) with enzyme mix, gel beads, and oils to generate gel beads-in-emulsion (Chromium Next GEM single cell 3’ kit v3.1) (10x Genomics).
Subsequently, reverse transcription and cDNA amplification were conducted according to the manufacturer’s instructions by using Verity thermal cycler (Thermo Fisher Scientific) for Chromium Next GEM Single Cell kit.

treatment_protocol: 0.1 MOI isolated RSV infected

value: respiratory tract

value: human iPS cells

value: iPS cell-derived airway tissue systems

value: wild type

value: RSV infected


title: Deac2_0d_tetralone-ABA_rep3


title: SM-Cn-/- Ang-II 24h 3

description: NormCounts_RNAseq1: KO_24h_3

value: Aorta


title: 1057, GRP + RC, rep1

description:
1057_GRC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: Melanoma cell line

value: Female

value: 10nM GRP + 1microM RC-3095


title: Deac2_3d_Control_rep3

value: Control


title: airway tissue systems - no virus

value: no virus


title: SM-Cn-/- Ang-II 24h 1

description: NormCounts_RNAseq1: KO_24h_1

value: male


title: 1057, RC, rep1

description:
1057_RC_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: 1microM RC-3095


title: DK8_low

city: London

first: Holly

last: Philpott

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

description: 10x genomics

data_processing:
Alignment was carried out to the GRCh38.p13 (2020-A) reference genome and filtering, barcoding, and UMI counting were performed using Cell Ranger 6.1.1 and the 10x Genomics recommended default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovial tissue

extract_protocol:
Synovial tissue was digested in 3 mL of complete RPMI (10% FBS, 1% pen/strep) containing 400 μg/ml of LiberaseTM (Roche, Basel, Switzerland) and 400 μg/mL of DNAse I for 30 minutes at 37°C while rotating at 14 rpm. Next, 100 mM EDTA was added to stop enzymatic digestion and cells were washed twice with DMEM prior to trypan exclusion for total live cell counts and viability. Cells were then aliquoted into 1.0-2.0 million cells per 1 mL of CS10 (Stemcell Technologies, Vancouver, BC, Canada), frozen at -80°C overnight in a controlled rate cell freezing container (Mr. FrostyTM) and transferred to a liquid nitrogen vapour phase storage container until use.
Synovial single cell suspensions from each patient were rapidly thawed from cryopreservation and underwent trypan exclusion to confirm viability >75% prior to library prep. Cells were prepared for cDNA amplification and chromium library construction using the 10x Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 according to manufacturer's protocol (10x Genomics)

tag: disease state

value: late-stage knee osteoarthritis

value: synovial tissue

value: low pain


title: SM-Cn-/- Ang-II 6h 3

description: NormCounts_RNAseq1: KO_6h_3

tag: tissue

value: CnB1-flox;Myh11-CreERT2-pos, male

value: Tamoxifen and 6h Ang-II


title: SM-Cn-/- Ang-II 6h 2

description: NormCounts_RNAseq1: KO_6h_2


title: DK7_high

description: 10x genomics

value: high pain


title: 1057, MOCK, rep1

description:
1057_CTRL_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

tag: cell line

value: GRPRpos

value: MOCK (DMSO 0.1percent)


title: Deac2_0d_tetralone-ABA_rep1

value: bud

value: Riesling

value: tetralone-ABA


title: Deac2_0d_Control_rep3


title: Deac2_3d_tetralone-ABA_rep3


title: DK6_high

description: 10x genomics


title: SM-Cn-/- Ang-II 6h 1

description: NormCounts_RNAseq1: KO_6h_1

value: Aorta


title: Deac2_0d_Control_rep2


title: 1057, MOCK, rep2

description:
1057_CTRL_2
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

tag: cell type

value: Melanoma cell line

value: Female


title: ΔEcad tumor, female, #7

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #7

extract_protocol:
tumors RNA were extracted using the miRNeasy mini-kit.
RNA sequencing libraries were prepared from 1 μg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit

value: melanoma primary tumor


title: DK5_high

description: 10x genomics


title: Deac2_0d_Control_rep1

tag: genotype

value: Control


title: ΔEcad tumor, female, #8

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #8


title: Deac2_0d_tetralone-ABA_rep2

tag: treatment


title: SM-Cn-/- Ang-II 2h 2

description: NormCounts_RNAseq1: KO_2h_2

tag: Sex

value: male

value: Tamoxifen and 2h Ang-II


title: DK4_low

description: 10x genomics

value: late-stage knee osteoarthritis

value: synovial tissue


title: Deac1_14d_tetralone-ABA_rep2


title: Deac1_14d_tetralone-ABA_rep3


title: SM-Cn-/- Ang-II 2h 1

description: NormCounts_RNAseq1: KO_2h_1

value: CnB1-flox;Myh11-CreERT2-pos, male


title: ΔEcad tumor, female, #5

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #5


title: DK2_high

description: 10x genomics


title: ΔEcad tumor, female, #4

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #4


title: 1057, GRP rep1

description:
1057_G10_1
Tyr::NRASQ61K/°; Cdkn2a-/-;Tyr::CreA/°;Cdh1dF/dF

value: 10nM GRP


title: SM-Cn-/- basal 3

description: NormCounts_RNAseq1: KO_Basal_3

value: Tamoxifen


title: ΔEcad tumor, female, #6

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #6


title: DK1_low

description: 10x genomics

value: low pain


title: SM-Cn-/- basal 2

description: NormCounts_RNAseq1: KO_Basal_2


title: Deac1_14d_Control_rep3


title: Dauv-1, GRP+RC, rep4

data_processing:
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Reads were mapped to the mouse reference genome hg38 (gencode 42 version-GRCh38.p13)  using STAR.
STAR was also used to create the expression matrixes.
Batch were corrected using ComBat.
Raw counts were normalized to the TPM-level.
Assembly: hg38 (gencode 42 version-GRCh38.p13)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: Cells were starved overnight 24 hours after seeding in 10% FCS. When the cells were treated, confluence was about 80%.

extract_protocol:
RNA was harvested using miRneasy mini  kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit according to manufacturer protocol.

treatment_protocol: Cells were treated with vehicle or 10nM GRP and/or 1µM RC-3095 for 4 hours

value: 10nM GRP + 1microM RC-3095


title: SM-Cn-/- basal 1

description: NormCounts_RNAseq1: KO_Basal_1


title: ΔEcad tumor, female, #2

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #2


title: Cn-Ctl Ang-II 24h 3

description: NormCounts_RNAseq1: WT_24h_3

value: CnB1-flox;Myh11-CreERT2-neg, male

value: Tamoxifen and 24h Ang-II


title: SM-Cn-/- Ang-II 2h 3

description: NormCounts_RNAseq1: KO_2h_3


title: Deac1_14d_Control_rep2

value: bud

value: Riesling


title: Dauv-1, RC, rep4

value: Melanoma cell line

value: 1microM RC-3095


title: Deac1_14d_Control_rep1


title: Dauv-1, GRP, rep4


title: ΔEcad tumor, female, #1

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #1

value: melanoma primary tumor

value: Female


title: DK3_low

description: 10x genomics


title: Cn-Ctl Ang-II 24h 2

description: NormCounts_RNAseq1: WT_24h_2

value: Aorta

value: male


title: ΔEcad tumor, Male, #8

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #8

value: Male


title: Dauv-1, MOCK, rep4

value: DMSO-MOCK


title: Deac1_7d_tetralone-ABA_rep3

value: tetralone-ABA


title: Cn-Ctl Ang-II 6h 2

description: NormCounts_RNAseq1: WT_6h_2

value: Tamoxifen and 6h Ang-II


title: Cn-Ctl Ang-II 6h 3

description: NormCounts_RNAseq1: WT_6h_3


title: Deac1_7d_tetralone-ABA_rep2


title: ΔEcad tumor, Male, #6

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #6


title: Dauv-1, GRP+RC, rep3


title: Deac1_7d_tetralone-ABA_rep1


title: Dauv-1, RC, rep3


title: Deac1_14d_tetralone-ABA_rep1


title: ΔEcad tumor, Male, #5

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #5


title: Deac1_7d_Control_rep3

value: Control


title: Dauv-1, GRP, rep3

value: 10nM GRP


title: ΔEcad tumor, female, #3

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ female_ #3


title: Cn-Ctl Ang-II 6h 1

description: NormCounts_RNAseq1: WT_6h_1


title: Cn-Ctl Ang-II 2h 3

description: NormCounts_RNAseq1: WT_2h_3

value: Tamoxifen and 2h Ang-II


title: ΔEcad tumor, Male, #7

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #7


title: ΔEcad tumor, Male, #4

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #4


title: Deac1_7d_Control_rep2


title: Cn-Ctl Ang-II 2h 2

description: NormCounts_RNAseq1: WT_2h_2

value: CnB1-flox;Myh11-CreERT2-neg, male


title: Deac1_7d_Control_rep1


title: Dauv-1, GRP+RC, rep2

value: 10nM GRP + 1microM RC-3095


title: Dauv-1, MOCK, rep3


title: ΔEcad tumor, Male, #3

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #3


title: ΔEcad tumor, Male, #2

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #2


title: Cn-Ctl basal 3

description: NormCounts_RNAseq1: WT_Basal_3

value: Tamoxifen


title: Deac1_5d_tetralone-ABA_rep3

value: bud

value: Riesling


title: Dauv-1, RC, rep2

value: Melanoma cell line

value: 1microM RC-3095


title: ΔEcad tumor, Male, #1

description:
Tyr::NrasQ61K;Cdkn2a-/+;Tyr::NRAS/°;Cdh1F/F
ΔEcad_tumor_ Male_ #1

value: melanoma primary tumor


title: Deac1_5d_tetralone-ABA_rep2


title: Cn-Ctl basal 2

description: NormCounts_RNAseq1: WT_Basal_2

value: Aorta


title: Deac1_5d_tetralone-ABA_rep1


title: Dauv-1, GRP, rep2


title: Dauv-1, MOCK, rep2


title: sam-UTD-DN0003-DRG-8

city: Richardson

first: Theodore

last: Price

state: Texas

address: 800 W. Campbell Road

institute: The University of Texas at Dallas

description:
Library name: sam-UTD-DN0003-DRG-8
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

data_processing:
Raw data were processed with the 10X SpaceRanger pipeline
Assembly: GRCh38.p10 and GRCh38.p13
Supplementary files format and content: raw and filtered gene counts matrices, cloupe files for !0x loupe browser, barcode positions/coordinates, csv file of annotated barcodes
Library strategy: Spatial Transcriptomics

source_name: dorsal root ganglia

extract_protocol:
Human DRGs were collected from neurologically dead organ donors through a collaboration with the Southwest Transplant Alliance or from AnaBios
Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain.

value: dorsal root ganglia

tag: batch


title: Ecad tumor, female, #4

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #4

value: Female


title: Dauv-1, GRP, rep1


title: Deac1_5d_Control_rep2


title: Deac1_5d_Control_rep3


title: A4573 tumor

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
10X Genomics Cell Ranger (v3.1.0) (PMID: 28091601) was used to process the fastq files to cell and gene count tables using unique molecule identifiers (UMIs) aligning to GRCh38 (compiled by 10X Genomics as 2020-A).
Downstream quality control and analysis utilized the Seurat (v4.0.4) (PMID: 34062119) pipeline. Cell Ranger-filtered data was further processed by removing genes identified in fewer than 10 cells. Cell barcodes were removed if they had greater than 50,000 UMIs, less than 10,000 UMIs, less than 2,000 genes, or greater than 5% of UMIs from mitochondria. Cell doublets were identified and removed using the scDblFinder R package (PMID: 35814628).
The gene counts were normalized using Seurat where counts are divided by each cells total counts and multiplied by 10,000 followed by natural-log transformation. The top 2,000 most variable genes were scaled with S score, G2M score, and percentage mitochondria regressed out.
Assembly: GRCh38 (compiled by 10X Genomics as 2020-A)
Supplementary files format and content: Text file containing UMIs by gene by cell (counts_matrix.txt) and text file containing metadata for each cell (cell_metadata.txt)

source_name: Tumor

extract_protocol:
Tumor tissue was thawed at 37°C and gently dissociated using an optimized Collagenase-IV/DNaseI/RPMI digestion protocol. Tumor-digest suspensions were strained through a 70µm filter membrane & washed, then treated using the ErythroClear™ Red Blood Cell Depletion Kit followed by DAPI-exclusion FACS.
3' end 10x Genomics library prep

value: Tumor

value: Ewing sarcoma


title: Dauv-1, RC, rep1


title: shA673-1c_dox_T4_rep3 [DOX_R3_T4]

city: Liège

first: Franck

last: Dequiedt

state: Liège

address: Avenue de l'hôpital, 1

department: Molecular Biology of Diseases

country: Belgium

institute: GIGA Institute

data_processing:
RNA-seq read quality was evaluated using FastQC
Sequence reads were aligned to the human genome hg19 using STAR. STAR quantMode was used to obtain raw read counts.
Assembly: hg19
Supplementary files format and content: A673_dox_raw_counts.txt is a tab-delimited file of raw RNA-Seq read counts per gene, per sample.

growth_protocol: Cells were cultured in a 37°C, 5% CO2 humidified incubator in DMEM high glucose with 10% FBS, 1% Penn/Strep, 20 µg/ml Blasticidin, 200 µg/ml zeocyn and 1 µg/ml doxycyclin

extract_protocol:
Nucleospin RNA kit (Macherey-Nagel)
Illumina TruSeq stranded mRNA

treatment_protocol: Biological replicates of shA673-1c cells were seeded in 6-well plates and treated with 5 µM ActD for 0, 1, 2 and 4h.

value: Actinomycin D

tag: time point


title: Deac1_3d_tetralone-ABA_rep3

value: tetralone-ABA


title: Ecad tumor, female, #7

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #7


title: Ecad tumor, female, #3

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #3


title: Dauv-1, GRP+RC, rep1


title: Ecad tumor, female, #6

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #6


title: Ecad tumor, female, #2

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #2


title: no template control 2

description: FFPE spatial profiling

library_source: other

data_processing:
NanoString GeoMX Platform was used for probe QC and Q3 normalization as recommended by NanoString. Then patient samples were grouped based on those with more pain and those with less pain for analysis and adjusted for ID and BMI. All microenvironment ROI subtypes were analyzed separately. For example, all ROIs of synovial intimal lining were included in one analysis, then all sublining ROIs, and then all microvessel ROIs.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files, PKC file, probe QC, Q3 normalization, metadata file
Library strategy: GeoMx Seq

molecule: other

organism: blank sample

extract_protocol:
Synovial tissue samples were processed for FFPE and constructed into a tissue microarray, so that all samples could be analyzed on a single slide. The slide was sent to NanoString for library construction and
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/


title: shA673-1c_dox_T1_rep3 [DOX_R3_T1]


title: shA673-1c_dox_T2_rep3 [DOX_R3_T2]


title: Cn-Ctl Ang-II 2h 1

description: NormCounts_RNAseq1: WT_2h_1

value: male


title: Deac1_3d_tetralone-ABA_rep1


title: sam-UTD-DN0003-DRG-4

description:
Library name: sam-UTD-DN0003-DRG-4
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: shA673-1c_dox_T0_rep3 [DOX_R3_T0]


title: Ecad tumor, female, #1

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #1


title: Deac1_3d_Control_rep3

value: Control


title: no template control 1

description: FFPE spatial profiling


title: Deac1_3d_tetralone-ABA_rep2


title: Ecad tumor, female, #8

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #8


title: Deac1_5d_Control_rep1


title: Dauv-1, MOCK, rep1

value: DMSO-MOCK


title: Ecad tumor, female, #5

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ female_ #5


title: KMS11,LentiV2_ATF4g3, ATAC-seq, biorep3

description: Library name: KMS11_ATAC_ATF4KD_rep3

data_processing:
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak, bigwig

source_name: Haematopoietic and Lymphoid

extract_protocol:
The cells were resuspended cold ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3 min. The cells were then washed in RBS containing 0.1% Tween-20 at 500 g at 4 °C before subjecting the nuclei to the transposase reaction for 30 min at 37 °C. Termination of the reaction and DNA purification was performed using Zymo DNA clean and Concentrator kit.
The purified DNA was amplified with NEBNext High-Fidelity 2x PCR Master Mix then purified and size selected twice with AMPure beads. Nextera Tn5 Transposase is employed for tagmentation.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: WT


title: shA673-1c_dox_T4_rep2 [DOX_R2_T4]


title: KMS11,LentiV2_ATF4g3, ATAC-seq, biorep2

description: Library name: KMS11_ATAC_ATF4KD_rep2


title: shA673-1c_dox_T1_rep2 [DOX_R2_T1]


title: Ecad tumor, Male, #7

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #7

value: Male


title: Deac1_3d_Control_rep1

value: bud

value: Riesling


title: Deac1_3d_Control_rep2


title: KMS11,LentiV2_ATF4g3, ATAC-seq, biorep1

description: Library name: KMS11_ATAC_ATF4KD_rep1


title: KMS11, control, ATAC-seq, biorep3

description: Library name: KMS11_ATAC_ctrl_rep3


title: shA673-1c_dox_T2_rep2 [DOX_R2_T2]


title: Deac1_0d_tetralone-ABA_rep3


title: KMS11, control, ATAC-seq, biorep2

description: Library name: KMS11_ATAC_ctrl_rep2


title: Ecad tumor, Male, #5

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #5

value: melanoma primary tumor


title: Deac1_0d_tetralone-ABA_rep1


title: shA673-1c_dox_T4_rep1 [DOX_R1_T4]


title: KMS11, control, ATAC-seq, biorep1

description: Library name: KMS11_ATAC_ctrl_rep1


title: shA673-1c_dox_T0_rep2 [DOX_R2_T0]


title: Ecad tumor, Male, #4

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #4


title: Ecad tumor, Male, #6

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #6


title: Deac1_0d_tetralone-ABA_rep2


title: Ecad tumor, Male, #3

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #3


title: Deac1_0d_Control_rep3


title: shA673-1c_dox_T1_rep1 [DOX_R1_T1]


title: respiratory organoids/RSV/PALI

description: 10x Genomics

growth_protocol: To start the differentiation, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded onto Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. The differentiation of the respiratory organoids was performed in serum-free differentiation (SFD) medium, composed of DMEM/F12 (3:1) (Cat# 044-29765, FUJIFILM Wako Pure Chemical and Cat# 11320033, Thermo Fisher Scientific) supplemented with N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), ascorbic acid (50 μg/mL, Cat# ST-72132, STEMCELL Technologies), 1× GlutaMAX (Cat# 35050-061, Thermo Fisher Scientific), 1% monothioglycerol (Cat# 195-15791, FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin (Cat# 820024, Sigma-Aldrich), and 1× penicillin/streptomycin). During days 0-1 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), and 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems). During days 1–3 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems) and 1% FBS. Between days 3–5 of differentiation, cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (Cat# 047-33763, FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (Cat# 037-24293, FUJIFILM Wako Pure Chemical) for 24 h, and then SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (Cat# 04-0034, Stemolecule) for another 24 h. During days 5–12 of differentiation, cells were cultured with SFD medium supplemented with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (Cat# AF-100-26, PeproTech), 10 ng/mL human FGF7 (Cat# AF-100-19, PeproTech), 10 ng/mL human BMP4 (Cat# 120-05ET, PeproTech), 20 ng/mL human EGF (Cat# AF-100-15, PeproTech), and all-trans retinoic acid (Cat# R2625 ATRA, Sigma-Aldrich). On day 12 of differentiation, cells were dissociated and embedded in the Matrigel Growth Factor Reduced Basement Membrane to generate organoids. During days 12–20 of the differentiation, organoids were cultured in SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA. On day 20 of differentiation, organoids were recovered from the Matrigel, and the resulting suspension of organoids (small free-floating clumps) was seeded onto Matrigel-coated cell culture plates. During days 20–30 of differentiation, organoids were cultured in SFD medium containing 50 nM dexamethasone (Cat# S1322, Selleck Chemicals), 0.1 mM 8-bromo-cAMP (Cat# 1140/50, Tocris Bioscience), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (Cat# 095-03413, FUJIFILM Wako Pure Chemical).

extract_protocol:
Respiratory organoids were dissociated, and the cell concentration was adjusted to 1,000 cells/μL. The single-cell suspension, with a concentration of 1,200 cells/μL, was loaded onto a 10x Genomics Chromium Next GEM single cell G chip (10x Genomics) with enzyme mix, gel beads, and oils to generate gel beads-in-emulsion (Chromium Next GEM single cell 3’ kit v3.1) (10x Genomics).
Subsequently, reverse transcription and cDNA amplification were conducted according to the manufacturer’s instructions by using Verity thermal cycler (Thermo Fisher Scientific) for Chromium Next GEM Single Cell kit. After adding index sequences to the library pool, the cDNA library was sequenced on the Nova-seq X platform (Illumina).

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids

value: wild type

value: RSV and palivizumab


title: shA673-1c_dox_T2_rep1 [DOX_R1_T2]

value: Ewing sarcoma

value: Actinomycin D


title: Ecad tumor, Male, #2

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #2


title: Deac1_0d_Control_rep2


title: shA673-1c_dox_T0_rep1 [DOX_R1_T0]


title: Ecad tumor, Male, #8

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #8


title: respiratory organoids/RSV/NIRS

description: 10x Genomics

value: RSV and nirsevimab


title: Ecad tumor, Male, #1

description:
Tyr::NrasQ61K;Cdkn2a-/+;°/°;Cdh1F/F
Ecad_tumor_ Male_ #1