title: 25931X3 25931_RAW264.7_Control_6h_3

first: Hamid

last: Ghandehari

state: Ut

address: 36 S Wasatch Dr

department: Molecular Pharmaceutics

institute: Univeristy of Utah

description: Library name: 25931X3

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 1112 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

growth_protocol: RAW 264.7 cells were cultured in RPMI media supplemented with 10% FBS. The cells were maintained at 37 °C in 5% CO2 incubator.

extract_protocol:
The total RNA of the cells was collected in RNase-free water using the Qiagen RNeasy Miniprep Kit. The sample was treated with DNase to remove DNA and stored at -80°C. RNA concentration was measured with a Qubit RNA HS Assay Kit (Fisher Scientific #Q32855).  RNA quality was evaluated with an Agilent Technologies RNA ScreenTape Assay (5067-5579 and 5067-5580). All samples were ensured to have an RNA quantity of over 25 ng/µL and an RNA integrity number (RIN) between 9 and 10 before sequencing.
The library was generated using the NEB Next Ultra II Directional RNA Library Prep with Poly(A) mRNA Isolation kit for Illumina sequencing

treatment_protocol: SNPs were treated at their non-toxic concentration to the cells and kept for 6 hours before RNA extraction.

value: Mouse macrophage

value: Control


title: GFPb1_1.5h_rep1_ATACseq

status: Public on Apr 01 2026

type: SRA

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

country: USA

institute: University of Colorado

description:
Library name: g90-1
GFPb1_1.5h_REP1.mLb.clN.sorted.bam

library_source: genomic

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/atacseq v2.1.2.
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome with the GENCODE v38 genome annotation file. Reads located in the ENCODE hg38 blacklist v2 region were removed.
Supplementary files format and content: .csv, consensus peaks raw counts of all samples
Supplementary files format and content: .bigWig, merged replicate ATAC-seq tracks of each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: hiPSCs

extract_protocol:
All steps from nuclei isolation through library preparation were performed by Novogene Co., Ltd. using their standardized, optimized ATAC-seq workflow.
The final ATAC-seq libraries were quantified, quality-controlled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end, 150 bp) by Novogene Co., Ltd.

tag: cell line

value: hiPSCs


title: 25931X2 25931_RAW264.7_Control_6h_2

city: Salt Lake City

description: Library name: 25931X2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: treatment


title: Fed B6 mouse hypothalamus sample 3

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

description:
Library name: RNAseq_Ctrl3
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt

data_processing:
RNA-seq Aligned with HISAT2 with the parameter ‘-x’.
Gene expression counted with Rsubread::featureCounts.
EdgeR differential expression analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq: EdgeR Output with CPM normalized counts, tab delimited.
Supplementary files format and content: rSubread gene-level counts, tab delimited.

source_name: Hypothalamus

extract_protocol:
Qiagen RNeasy kit.
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human, mouse, rat).

treatment_protocol: Fed, fasted 24h, fasted 72 hours, 72 hours fasted with cold treatment (18C), 1h refed after 72h fast, 12h refed after 72h fast, 1 month refed after 72h fast.

tag: tissue

value: Hypothalamus

tag: genotype

value: WT

value: Fed

tag: batch


title: Fed B6 mouse hypothalamus 1 month refed control sample 3

description:
Library name: RNAseq_Fed_RNA_3
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: Fed B6 mouse hypothalamus 1 month refed control sample 2

description:
Library name: RNAseq_Fed_RNA_2
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: Fed B6 mouse hypothalamus sample 2

description:
Library name: RNAseq_Ctrl2
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt


title: GFPb1_1h_rep2_ATACseq

description:
Library name: g60-2
GFPb1_1h_REP2.mLb.clN.sorted.bam


title: HPR033

city: Denver

first: Evans

last: Fernandez

address: 1400 Jackson St.

institute: National Jewish

description:
Library name: HPR033
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files compressed with gzip
Supplementary files format and content: Integrated Seurat object

source_name: PBMC

extract_protocol:
Single-cell suspensions were prepared from peripheral blood mononuclear cell samples following standard dissociation and filtration protocols to obtain high-quality, viable cells. Cell viability was confirmed to be greater than 85% using trypan blue exclusion. The concentration of each sample was adjusted to approximately 1,500–2,000 cells/µL to achieve the recommended target of up to 5,000 cells per sample for on-chip multiplexing using the 10x Genomics Chromium platform. Prior to loading, samples were inspected under a microscope to ensure the absence of debris and cell aggregates.
Following the recovery of the Gel Beads-In-Emulsions, the emulsions were broken, and barcoded complementary deoxyribonucleic acid was purified and amplified using the 10x Genomics GEM-X Universal Library Construction Kit. For on-chip multiplexing, each reaction was limited to approximately 5,000 cells per sample, ensuring comparable cell input and ribonucleic acid content across all multiplexed samples. Libraries were dual-indexed, pooled, and sequenced on an Illumina NextSeq 2000. Sequencing depth was adjusted to achieve approximately 20,000 reads per cell, depending on experimental design and transcriptome complexity.

value: PBMC

tag: phenotype

value: HP

tag: Sex

value: Male

tag: race

value: White

tag: ethnicity

value: NotHispanicOrLatino

tag: age


title: Fed B6 mouse hypothalamus 1 month refed control sample 4

description:
Library name: RNAseq_Fed_RNA_4
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: GFPb1_1h_rep1_ATACseq

description:
Library name: g60-1
GFPb1_1h_REP1.mLb.clN.sorted.bam


title: GFPb1_1h_rep3_ATACseq

description:
Library name: g60-3
GFPb1_1h_REP3.mLb.clN.sorted.bam


title: 25931X1 25931_RAW264.7_Control_6h_1

description: Library name: 25931X1


title: HPR028

description:
Library name: HPR028
10x Genomics

value: Female


title: HPR029

description:
Library name: HPR029
10x Genomics


title: HPR031

description:
Library name: HPR031
10x Genomics


title: Fed B6 mouse hypothalamus 1 month refed control sample 5

description:
Library name: RNAseq_Fed_RNA_5
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: 25928X2 25928_RAW264.7_MSNP_6h_2

description: Library name: 25928X2

value: MSNP


title: GFPb1_0.5h_rep2_ATACseq

description:
Library name: g30-2
GFPb1_0.5h_REP2.mLb.clN.sorted.bam


title: 25930X2 25930_RAW264.7_HMSNP_6h_2

description: Library name: 25930X2

value: HMSNP


title: GFPb1_0.5h_rep3_ATACseq

description:
Library name: g30-3
GFPb1_0.5h_REP3.mLb.clN.sorted.bam


title: Rif1 sKO-3

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

country: China

institute: WuHan University

description: Library name: sample6

data_processing:
raw sequence reads were initially trimmed using Trim Galore
Trimmed sequence reads were mapped to mm39 using HISAT2
Read count extraction were performed using FeatureCounts
Assembly: mm39
Supplementary files format and content: count maritx for six samples

molecule: polyA RNA

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Enriching mRNA using mRNA Capture Beads (oligo dT magnetic beads).

value: testis

value: sKO


title: 25930X1 25930_RAW264.7_HMSNP_6h_1

description: Library name: 25930X1


title: 25930X3 25930_RAW264.7_HMSNP_6h_3

description: Library name: 25930X3


title: HPR032

description:
Library name: HPR032
10x Genomics

value: HispanicOrLatino


title: 25928X3 25928_RAW264.7_MSNP_6h_3

description: Library name: 25928X3

value: Mouse macrophage


title: Rif1 sKO-2

description: Library name: sample5


title: GFPb1_0.5h_rep1_ATACseq

description:
Library name: g30-1
GFPb1_0.5h_REP1.mLb.clN.sorted.bam


title: HPR027

description:
Library name: HPR027
10x Genomics


title: 25928X1 25928_RAW264.7_MSNP_6h_1

description: Library name: 25928X1


title: GFPb1_0h_rep2_ATACseq

description:
Library name: g0-2
GFPb1_0h_REP2.mLb.clN.sorted.bam


title: 25927X2 25927_RAW264.7_SNP50_6h_2

description: Library name: 25927X2


title: HPR025

description:
Library name: HPR025
10x Genomics


title: Rif1 WT-3

description: Library name: sample3

value: wild type


title: Rif1 sKO-1

description: Library name: sample4


title: GFPb1_0h_rep1_ATACseq

description:
Library name: g0-1
GFPb1_0h_REP1.mLb.clN.sorted.bam

value: hiPSCs


title: HPR026

description:
Library name: HPR026
10x Genomics


title: GFPb1_0h_rep3_ATACseq

description:
Library name: g0-3
GFPb1_0h_REP3.mLb.clN.sorted.bam


title: Rif1 WT-1

description: Library name: sample1


title: Rif1 WT-2

description: Library name: sample2


title: 25927X3 25927_RAW264.7_SNP50_6h_3

description: Library name: 25927X3


title: 25927X1 25927_RAW264.7_SNP50_6h_1

description: Library name: 25927X1


title: HPR024

description:
Library name: HPR024
10x Genomics


title: HPR023

description:
Library name: HPR023
10x Genomics


title: HPR019

description:
Library name: HPR019
10x Genomics


title: C57BL/6 mouse hippocampus, Cd4

city: Seattle

first: Joe

last: Lim

state: WA

address: 4225 Roosevelt Way NE, Suite 100

institute: University of Washington

description:
Library name: Sample9
Column name in raw counts "Cd_counts.txt": Cd4

data_processing:
HISAT2 v2.2.1
SAMtools v1.2
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using RNA-Bee (Tel-Test, Friendswood, TX) following the manufacturer's protocol.
Poly-A enrichment was performed for RNA sequencing.

value: Hippocampus

value: Wild type

value: Vehicle


title: Inr region HARPE (14nt, with TATA) - replicate 2 in cells

city: La Jolla

first: James

middle: T.

last: Kadonaga

state: California

address: 9500 Gilman Dr

department: Molecular Biology

institute: University of California, San Diego

description:
Library name: HARPE_Inr14-TATA_inCells_rep2
reporter RNA and plasmid DNA

library_source: other

data_processing:
Paired-end (PE100) sequences were required to have a perfect match to the 10-nt sequences immediately upstream and downstream of the randomized Inr region, which was required to be exactly 10 nt or 14 nt (for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively). Sequences were also required to have a perfect match to the 10-nt sequences immediately upstream and downstream of the randomized barcode region, which was required to be exactly 15 nt or 17 nt (for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively). All reads containing a match to the selection pattern were deemed usable and trimmed for sequences outside the randomized region.
Conversion tables from barcode to Inr variant were built by paired-end sequencing of amplicons from the starting plasmid libraries. Both read 1 and read 2 were required to pass the above screening criteria. Barcodes that were associated with multiple Inr variants were discarded (this was rare given the complexity of the 15-nt and 17-nt regions used). DNA and RNA datasets for all Inr HARPE experiments were matched to their corresponding barcode-to-Inr conversion tables.
For the DNA datasets, we only used sequences with a minimum absolute read count of 10 and a minimum relative count of 0.2 or 0.75 reads per million (RPM; for experiments with the 10-nt or 14-nt randomized Inr libraries, respectively) so that low-confidence variants would not be included in the analyses. RNA dataset sequences were then matched to their corresponding DNA dataset.
The transcription strength for each Inr sequence variant was defined as the RNA read count (in RPMs) divided by the DNA read count (in RPMs). Inr variants associated with multiple barcodes were combined, and their transcription strengths were computed as the average transcription strength across multiple barcodes.
Supplementary files format and content: txt files (15) containing the processed sequencing data [each Inr region variant and its corresponding barcode, DNA and RNA read counts, and the computed transcription strengths ("score")] for each sample
Supplementary files format and content: SVR model files (7)
Supplementary files format and content: Python script for use of the SVR models

molecule: other

source_name: HeLa S3

growth_protocol: HeLa cells were maintained at 37°C and 5% CO2 in DMEM (ATCC) supplemented with 10% FBS (ATCC), 50 U/mL penicillin (Thermo Fisher Scientific), and 50 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
HARPE DNA/RNA extraction and processing: RNA transcripts from cells or from in vitro transcription reactions were extracted with Trizol or Trizol LS (Thermo Fisher Scientific), respectively. Total RNA (120 μg per condition for cell transfection experiments, or the entirety of each condition for in vitro transcription experiments) was processed as described in Vo ngoc et al. (2020, 2023). Briefly, the following steps were performed. First, contaminating plasmid DNA was removed with the TURBO DNA-free Kit (Thermo Fisher Scientific). Next, the RNA was subjected to reverse transcription with SuperScript III Reverse Transcriptase (Thermo Fisher Scientific) and treatment with RNase H (New England Biolabs). The resulting cDNA was size-selected on a 6% (w/v) polyacrylamide-8 M urea gel with fluorescently-labeled size markers. The size-selected cDNAs and HARPE plasmid DNAs were used as templates to generate DNA amplicons for Illumina sequencing (RNA and DNA datasets, respectively). In the cell-based HARPE experiments, the DNA datasets were obtained with plasmid DNA samples that were extracted post-transfection as described in van Arensbergen et al. (2017). Briefly, cells were treated with trypsin, washed with PBS, and then incubated in 500 µL nuclear extraction buffer [10 mM NaCl, 2 mM MgCl2, 10 mM Tris-HCl (pH 7.8), 5 mM DTT, 0.5% NP40] on ice for 5 min. Nuclei were pelleted at 7,000 x g and washed twice with 1 mL nuclear extraction buffer. DNA was then extracted with ZymoPURE Plasmid Miniprep Kit (Zymo Research).
HARPE library construction: Custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequences corresponding to nucleotides +19 to +34 (relative to the SCP1 +1 TSS; the SCP1 DPR and mutDPR promoter backbones required different primers) were used to amplify the randomized barcode regions. Custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequences corresponding to nucleotides −44 to −23 or −40 to −23 (relative to the SCP1 +1 TSS; the SCP1 TATA and mutTATA promoter backbones required different primers) were used to pair each barcode with its corresponding Inr variant. Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (New England Biolabs), which match the Illumina Read2-primer sequence present on the HARPE plasmid and corresponding cDNA. NGS PCR amplicons were size-selected on native 6% (w/v) polyacrylamide gels prior to Illumina sequencing.

treatment_protocol: Transcription of HARPE libraries: HeLa cells were transfected with HARPE libraries using Lipofectamine 3000 (Thermo Fisher Scientific) as recommended by the manufacturer. For HARPE experiments performed in vitro, the products from 6 or 12 (for the 14-nt or 10-nt Inr libraries, respectively; the reactions were scaled according to to the number of independent transformants in each library) standard in vitro transcription reactions were combined. Standard reactions were performed as follows. DNA template (500 ng) was incubated with HeLa nuclear extract (prepared as described in Dignam et al. 1983) for preinitiation complex assembly at 30 °C for 1 hour in 46 μL of transcription buffer [20 mM HEPES-K+ (pH 7.6), 50 mM KCl, 6 mM MgCl2, 1.25% (w/v) polyvinyl alcohol, 1.25% (w/v) polyethylene glycol, 0.5 mM DTT, 3 mM ATP, 0.02 mM EDTA, and 2% (v/v) glycerol]. rNTPs (4 μL; 0.4 mM final concentration of each rNTP) were added to initiate transcription. The reaction was incubated at 30 °C for 20 min and terminated by the addition of 150 μL of Stop Mix [20 mM EDTA, 200 mM NaCl, 1% (w/v) SDS, 0.3 mg/mL glycogen]. Proteinase K (5 μL; 2.5 mg/mL) was added, and the mixture was incubated at 30 °C for 15 min. All HARPE experiments were performed independently at least two times to ensure reproducibility of the data.

value: HeLa S3

tag: biosource type

value: HeLa cells


title: Inr region HARPE (14nt, with TATA) - replicate 1 in cells

description:
Library name: HARPE_Inr14-TATA_inCells_rep1
reporter RNA and plasmid DNA


title: Inr region HARPE (14nt, with DPR) - replicate 2 in cells

description:
Library name: HARPE_Inr14-DPR_inCells_rep2
reporter RNA and plasmid DNA


title: HPR021

description:
Library name: HPR021
10x Genomics

value: PBMC

value: HP


title: C57BL/6 mouse hippocampus, Cd5

description:
Library name: Sample10
Column name in raw counts "Cd_counts.txt": Cd5


title: 25926X2 25926_RAW264.7_SNP100_6h_2

description: Library name: 25926X2


title: 25926X3 25926_RAW264.7_SNP100_6h_3

description: Library name: 25926X3


title: HPR017

description:
Library name: HPR017
10x Genomics

value: White

value: NotHispanicOrLatino


title: 25926X1 25926_RAW264.7_SNP100_6h_1

description: Library name: 25926X1


title: C57BL/6 mouse hippocampus, Cd2

description:
Library name: Sample7
Column name in raw counts "Cd_counts.txt": Cd2


title: HPR015

description:
Library name: HPR015
10x Genomics

value: Female


title: Inr region HARPE (14nt, with DPR) - replicate 1 in cells

description:
Library name: HARPE_Inr14-DPR_inCells_rep1
reporter RNA and plasmid DNA


title: C57BL/6 mouse hippocampus, Cd3

description:
Library name: Sample8
Column name in raw counts "Cd_counts.txt": Cd3


title: D3_9AM_erbb3_DD0624

city: Cincinnati

first: Bo

last: Li

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: D3_9AM_erbb3_DD0624
10x Genomics

data_processing:
Raw sequencing data were processed with Cell Ranger multi v9.0.0 (10x Genomics) using reference mm10 (GRCm39-2024-A) and the 10x Genomics Chromium Mouse Transcriptome Probe Set v1.1.1. Demultiplexing, read alignment, UMI counting, and feature-barcode matrix generation were performed according to the manufacturer’s instructions.
Assembly: GRCm39 (mm10), 10x Genomics reference-2024-A
Supplementary files format and content: Matrix Market format (.mtx.gz) containing UMI counts; accompanying barcodes file (.tsv.gz) and gene annotation file (.tsv.gz)

source_name: uterus (day 3 of pregnancy)

extract_protocol:
Sample preparation was performed using the GEM-X Flex Sample Preparation v2 Kit (1000781, 10x Genomics) according to the manufacturer’s protocol. Endometrial tissues (~25 mg) from Erbb3f/f and Erbb3d/d females were dissected on ice, finely minced, and fixed in Fixation Buffer B for 16 h at 4 °C. Samples were subsequently washed with PBS, quenched in Quenching Buffer B, and enzymatically dissociated in Dissociation Solution containing collagenase I, collagenase IV, and P&S at 37 °C for 40 min with intermittent pipetting. The resulting cell suspensions were passed through a 40 μm strainer, washed, and either processed immediately for library construction or stabilized with Enhancer and 50% glycerol for storage at −80 °C. Single-cell libraries were generated using the Chromium Next GEM Single Cell 3’ Gene Expression Flex v2 kit (10x Genomics) and sequenced on an Illumina platform.
Single-cell suspensions were processed using the 10x Genomics Chromium Flex Gene Expression workflow, following the manufacturer’s instructions. Libraries were constructed with the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

value: uterus (day 3 of pregnancy)

value: Endometrial cells


title: C57BL/6 mouse hippocampus, Cd1

description:
Library name: Sample6
Column name in raw counts "Cd_counts.txt": Cd1


title: HPR014

description:
Library name: HPR014
10x Genomics

value: Male


title: day 3 Erbb3d/d uterine stromal cells; rep4

description: Library name: RB3DD4

data_processing:
Reads were aligned to the mouse reference genome mm10 (GRCm38) using HISAT2 with default parameters (command: hisat2 -x mm10 -1 R1 -2 R2 -S sample.sam). Uniquely mapped reads were extracted, converted to BAM, sorted, and indexed with SAMtools. Gene-level counts were obtained using HTSeq-count with the NCBI annotation GTF file. Expression levels (FPKM) were estimated using StringTie.
Assembly: Mus musculus mm10 (GRCm38)
Supplementary files format and content: Count tables in plain text format (*.count_data.txt), containing gene-level read counts for each sample.

source_name: uterus

extract_protocol:
Total RNA was extracted from uterine stromal cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
mRNA was enriched using poly(A) selection, and RNA-seq libraries were prepared with the Plant and Animal Eukaryotic mRNA (WOBI) kit following the manufacturer’s protocol. Libraries were non-directional and sequenced on an Illumina NovaSeq X Plus platform with a paired-end 150 bp strategy (PE150). Each sample generated ~6 Gb of raw data with Q30 ≥ 85%.

value: uterus

value: mouse uterine stromal cells


title: Inr region HARPE (10nt, with DPR) - replicate 2 in vitro

description:
Library name: HARPE_Inr10-DPR_inVitro_rep2
reporter RNA and plasmid DNA

value: HeLa nuclear extract


title: Inr region HARPE (10nt, with TATA) - replicate 2 in vitro

description:
Library name: HARPE_Inr10-TATA_inVitro_rep2
reporter RNA and plasmid DNA


title: day 3 Erbb3d/d uterine stromal cells; rep3

description: Library name: RB3DD3


title: D3_9AM_erbb3_FF0701

description:
Library name: D3_9AM_erbb3_FF0701
10x Genomics


title: HPR012

description:
Library name: HPR012
10x Genomics


title: C57BL/6 mouse hippocampus, vehicle5

description:
Library name: Sample5
Column name in raw counts "Cd_counts.txt": Ctr5


title: Inr region HARPE (10nt, with DPR) - replicate 1 in vitro

description:
Library name: HARPE_Inr10-DPR_inVitro_rep1
reporter RNA and plasmid DNA


title: HPR013

description:
Library name: HPR013
10x Genomics


title: C57BL/6 mouse hippocampus, vehicle3

description:
Library name: Sample3
Column name in raw counts "Cd_counts.txt": Ctr3


title: Inr region HARPE (10nt, with TATA) - replicate 1 in vitro

description:
Library name: HARPE_Inr10-TATA_inVitro_rep1
reporter RNA and plasmid DNA


title: C57BL/6 mouse hippocampus, vehicle4

description:
Library name: Sample4
Column name in raw counts "Cd_counts.txt": Ctr4


title: HPR011

description:
Library name: HPR011
10x Genomics


title: day 3 Erbb3d/d uterine stromal cells; rep2

description: Library name: RB3DD2


title: C57BL/6 mouse hippocampus, vehicle2

description:
Library name: Sample2
Column name in raw counts "Cd_counts.txt": Ctr2


title: day 3 Erbb3d/d uterine stromal cells; rep1

description: Library name: RB3DD1


title: MEG01 cells, ID1 antibody, replicate 2

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

description: Library name: Sample 4

data_processing:
Filtering: Raw reads were filtered using fastp (verion 0.23.4)
Mapping: Clean reads were mapped to hg38 using bowtie2 (version 2.2.5)
Peak calling: MACS3 (version 3.0.1) was used to call peak with the significance cut-off q-value <= 0.01
Assembly: hg38
Supplementary files format and content: Read coverage in BigWig format; Narrow peaks in bed format.
Library strategy: CUT&Tag

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: AML cells

tag: antibody

value: ID1 (Proteintech, #67827-1-1g)


title: MEG01 cells, ID1 antibody, replicate 1

description: Library name: Sample 3


title: HPR009

description:
Library name: HPR009
10x Genomics


title: HPR007

description:
Library name: HPR007
10x Genomics


title: JPHZ-3

city: Nantong

first: Shi

last: Yiyu

address: 19，Qixiu St

institute: Nantong University

description: Library name: Sample 9

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: Colon

growth_protocol: C57BL/6 male mice (18-22 g) purchased from Chengdu Dossy Experimental Animals Co., ltd were acclimated for 1 week under standard laboratory conditions.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer's instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
Sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit, with barcodes added to each library. Library fragments were purified using the AMPure XP system, and library quality was assessed via the Agilent Bioanalyzer.

treatment_protocol: To induce ulcerative colitis (UC), 40 mice were given 3% dextran sodium sulfate (DSS) in drinking water for 4 days, followed by 2% DSS for 6 days, while 8 normal control mice received only distilled water. After successful modeling, UC mice were divided into 5 groups: model group (saline gavage), olsalazine group (200 mg/kg gavage), and JPHZW low/medium/high-dose groups (50/100/200 mg/kg gavage). All groups were treated daily for 7 days, with normal and model groups receiving saline. Before tissue collection, mice fasted for 24 hours (with free access to water) and were euthanized by eye blood collection. Colonic tissues were then harvested and stored in liquid nitrogen for transcriptome sequencing.

value: Colon

value: C57BL/6 48 mice

value: the administration of JPHZW and olsalazine to UC mice


title: HPR010

description:
Library name: HPR010
10x Genomics


title: JPHZ-1

description: Library name: Sample 7


title: C57BL/6 mouse hippocampus, vehicle1

description:
Library name: Sample1
Column name in raw counts "Cd_counts.txt": Ctr1

value: Hippocampus

value: Wild type

value: Vehicle


title: CMK cells, ID1 antibody, replicate 1

description: Library name: Sample 1

source_name: CMK

value: CMK


title: SCC-9,sh-ZIC2,rep3

city: Shijiazhuang City

first: Xingyue

last: Ma

state: Hebei

address: No. 383, Zhongshan East Road, Chang'an District, Shijiazhuang City, Hebei Province

institute: Stomatological Hospital of Hebei Medical University

description: Library name: Sample12

data_processing:
Library quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies Inc, California, USA, 5067-4626).
Library concentration was measured using PicoGreen staining with the Quantifluor-ST fluorometer (Promega, Madison, Wisconsin, USA, E6090; Quant-iT PicoGreen dsDNA Assay Kit, Invitrogen, California, USA, P7589).
The effective library concentration was quantified via qPCR (StepOnePlus Real-Time PCR System, Thermo Scientific, Waltham, Massachusetts, USA).
Multiplexed DNA libraries were normalized and combined in equal volumes. The pooled libraries were serially diluted and quantified before being sequenced in PE150 mode on an Illumina sequencer.
Assembly: hg38
Supplementary files format and content: Processed data files format and content:tad-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Csv files include FPKM values for each Sample.

source_name: tongue

growth_protocol: HN6 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the NEBNext Ultra II RNA Library Prep Kit for Illumina, and a total RNA amount of ≥1 μg was selected for sequencing library construction.
mRNA with polyA tails was enriched using Oligo(dT) beads and then randomly fragmented. The fragmented mRNA was used as a template for cDNA synthesis with random oligonucleotide primers. The synthesized cDNA was purified, followed by end repair, addition of a single "A" nucleotide at the 3' ends, and ligation of sequencing adapters. cDNA fragments of approximately 400–500 bp were selected using AMPure XP beads. The selected fragments were then PCR-amplified and purified again using AMPure XP beads to generate the final sequencing library.

value: tongue

value: tongue squamous cell carcinoma cell

value: ZIC2 knockdown


title: day 3 Erbb3f/f uterine stromal cells; rep4

description: Library name: RB3FF4


title: day 3 Erbb3f/f uterine stromal cells; rep2

description: Library name: RB3FF2


title: HPR005

description:
Library name: HPR005
10x Genomics

value: PBMC

value: HP

value: Female

value: White

value: NotHispanicOrLatino


title: CMK cells, ID1 antibody, replicate 2

description: Library name: Sample 2

value: AML cells


title: JPHZ-2

description: Library name: Sample 8


title: SCC-9,sh-ZIC2,rep2

description: Library name: Sample11


title: UCmodel-3

description: Library name: Sample 6

value: UC mice


title: Brainstem_infected_rep7

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

description: Library name: TC_infected_7

data_processing:
After sequencing, fastq files were aligned to the Mus musculus reference genome from Ensembl (Ensembl 105, December 2021) using STAR (version 2.7.9a) with the option “- -quantMode GeneCounts” to extract the raw counts for each gene, and all count files were concatenated into a single file.
The count file and a descriptive sample file were loaded into our in-house R Shiny application “EyeDVseq” for analysis: the genes with a total count below 10 across samples were filtered out and the differential gene expression analysis was performed using the version 1.40.2 DESeq integrated into EyeDVseq, comparing OIR-Norm as control and OIR-CIH as the condition.
The resulting gene list was then filtered, with |Log2(Fold Change)| > 0.5 and pAdj-values < 0.05 being considered significant.
Assembly: GRCm38 Ensembl release 105
Supplementary files format and content: Comma-separated file including raw counts for all Samples
Supplementary files format and content: Comma-separated file containing all Samples metadata

source_name: Brainstem

growth_protocol: Male hemizygous transgenic mice expressing human ACE2 under the K18 promotor (B6.Cg-Tg(K18-ACE2)2Prlmn/J (K18-hACE2) were infected with 2.4 x 104 plaque-forming units (PFU) of SARS-CoV2 by intranasal inoculation. The SARS-CoV-2 strain (GenBank MW322968) was isolated from a patient with COVID-19 hospitalized at the Pitié-Salpêtrière University Hospital

extract_protocol:
TG and brainstem were harvested from infected (n=21) and mock (n=10) mice. Tissues were either immediately immerged in RNAlater (Fischer Scientific) and stored at -80°C until use or directly stored at -80°C until use.  RNA was extracted using the NuceloSpin RNA kit (Macherey-Nagel) according to the Midi protocol in the manufacturer's instructions. RNA quality was confirmed using a Bioanalyzer RNA Analysis kit (Agilent).
RNA sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded mRNA Library Prep kit (Illumina)

treatment_protocol: Under xylazine/ketamine anesthesia (xylazine 10mg/kg, ketamine 100 mg/kg; 0.1ml/10g), male K18-hACE2 mice (11- to 22-week-old; n=25) were infected with 2.4 x 104 plaque-forming units (PFU) of SARS-CoV2 by intranasal inoculation (12-17l). K18 hACE2 mice (n=18) intranasally inoculated with an equal volume of HNE buffer were used as a mock-infection control.

value: Brainstem


title: HPR004

description:
Library name: HPR004
10x Genomics

value: HispanicOrLatino


title: HPR001

description:
Library name: HPR001
10x Genomics

value: Male


title: day 3 Erbb3f/f uterine stromal cells; rep1

description: Library name: RB3FF1

value: uterus

value: mouse uterine stromal cells


title: UCmodel-2

description: Library name: Sample 5

value: Colon

value: C57BL/6 48 mice


title: day 3 Erbb3f/f uterine stromal cells; rep3

description: Library name: RB3FF3


title: SCC-9,sh-ZIC2,rep1

description: Library name: Sample10

value: tongue


title: HPR003

description:
Library name: HPR003
10x Genomics


title: UCmodel-1

description: Library name: Sample 4


title: Brainstem_infected_rep6

description: Library name: TC_infected_6


title: SCC-9,sh-NC,rep3

description: Library name: Sample9

value: tongue squamous cell carcinoma cell

value: NC


title: Brainstem_infected_rep5

description: Library name: TC_infected_5


title: HCCLM3 cells, DMSO, replicate3

city: Chengdu City

first: Huizhen

last: Zou

address: No. 270, Tianhui Road, Rongdu Avenue, Jinniu District

institute: The General Hospital of Western Theater Command PLA

description: Library name: D3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols.

value: Human hepatocellular carcinoma cells

value: WT

value: DMSO for 24h


title: SCC-9,sh-NC,rep2

description: Library name: Sample8


title: Brainstem_infected_rep3

description: Library name: TC_infected_3


title: Brainstem_infected_rep4

description: Library name: TC_infected_4


title: Brainstem_infected_rep2

description: Library name: TC_infected_2


title: HCCLM3 cells, DMSO, replicate2

description: Library name: D2


title: HN6,sh-ZIC2,rep2

description: Library name: Sample5

value: ZIC2 knockdown


title: Control-3

description: Library name: Sample 3

value: control


title: HN6,sh-ZIC2,rep1

description: Library name: Sample4


title: HCCLM3 cells, GAC, replicate3

description: Library name: G3

value: ginkgolic acid 10μM for 24h


title: HCCLM3 cells, DMSO, replicate1

description: Library name: D1


title: Control-2

description: Library name: Sample 2


title: HCCLM3 cells, GAC, replicate1

description: Library name: G1


title: SCC-9,sh-NC,rep1

description: Library name: Sample7


title: HN6,sh-ZIC2,rep3

description: Library name: Sample6


title: neo teno, neosn, rep3

city: New York

first: Alice

middle: H.

last: Huang

state: NY

department: Orthopedic Surgery

institute: Columbia University

description: Library name: neo.9

data_processing:
Obtained fastq files were pseudo aligned to the Mus musculus genome (GRCm39, Ensembl) with the Mac terminal using Kallisto within the Conda environment. Counts per million (CPM) were log2 transformed, filtered to remove transcripts corresponding to zero read counts across all samples, and normalized using trimmed mean of M values (TMM) method.53 Principal component analysis was performed on filtered, normalized counts using stats v.4.3.1. Filtered, normalized CPM were used to generate contrast matrices between selected groups and fit to a linear model using limma v.3.56.2. Contrasts were used to identify differentially expressed genes using a global method, Bonferroni correction, adjusted p value < 0.01, and a log fold change of 2.54 Gene set enrichment analysis (GSEA) was performed using MSigDB collection for Mus musuculus M5 (ontology gene sets) and GSEAbase v.1.62.0. Normalized, filtered CPM and LogFC for pairwise comparisons were used to perform GSEA.55 Pathway analysis inference was performed using DEGs and PROGENy, a collection of pathways with weighted target genes, following the method described in.56 The Multivariate Linear Model method was used to fit gene expression with PROGENy pathways and the resulting t-values of the slopes are used as pathway scores.
Assembly: GRCm39
Supplementary files format and content: file is in xlsx format, contains read counts per million for each gene name indicated in the first column, for all samples.

source_name: primary cells

growth_protocol: Either 3 (neonatal) or 4 (adult) tendons were digested for 2.5h in 1.5ml centrifuge tubes with 1mg/ml collagenase IV and 5mg/ml collagenase I (Worthington Biochemical, cat: LS004188 andLS004196, respectively) in serum-free Dulbecco’s Modified Eagle Medium (Fisher, ref: 11965-092) with 1% penicillin/streptomycin in incubators at 5% CO2 and atmospheric O2. 200ul of digestion solution was used per tendon and scaled up accordingly. To facilitate the release of cells from the matrix, the neonatal tendons are pulse vortexed for 10s and the adult tendons are pipetted 5 times, every 30 min, throughout the digestion.  Tendon cells were cultured by plating cells from the 3 digested neonatal tendons or the 4 digested adult tendons per 1 well of a 6-well tissue culture treated plate, previously coated with 1ml of 0.1% gelatin (STEMCELL Technologies, cat: 07903). When 80% confluency was reached, cells were passaged 1:3, twice in total, followed by transfer to -80°C in freezing medium (15% FBS, 7.5% DMSO in DMEM) overnight in isopropanol freezing containers (Fisher: 5100-0001) and transferred to liquid N2 the following morning

extract_protocol:
Trizol/chloroform extraction was used to isolate RNA.  The RNA integrity number (RIN) and concentration was assessed with the Bioanalyzer pico chip at the Columbia University Molecular Pathology Shared Resource. Standard RNA-seq on total RNA with polyA tail mRNA selection was completed by Azenta Life Sciences (20M reads per sample) with Illumina 2x150bp technology, with all samples having RIN scores >6.
NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: 25K thawed tendon cells cultured for 3 days were treated with 1ml of complete DMEM + 1ml of either T cell media alone (+1% P/S) or adult/neonatal stimulated supernatants, before RNAseq processing. Samples adult.1-3 are adult tendon cells treated with T cell media, adult.4-6 are adult tendon cells treated with adult stimulated supernatant, adult.7-9 adult tendon cells treated with neonatal stimulated supernatant. Neo.1-3 are neonatal tendon cells treated with T cell media, neo.4-6 are neonatal tendon cells treated with adult stimulated supernatant and neo.7-9 are neonatal tendon cells treated with neonatal stimulated supernatant.

value: tendon

value: fibroblasts

value: Neo SN


title: Control-1

description: Library name: Sample 1


title: T3_2

city: Beijing

first: Jichang

address: No. 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

description: Library name: Sample12

data_processing:
The sequence quality of raw reads was assessed using FastQC (Version 0.12.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences and low-quality bases were trimmed using Fastp (Version 0.22.0) with parameters (-q 15 -u 40 -l 25). The resulting reads were aligned using Hisat2 (Version 2.2.1) with paramters (--no-mixed- -no-discordant) . Read count extraction were performed using FeatureCounts (Version 2.0.6).
Assembly: primary assembly GRCh38.p14/GENCODE 3 Human Release 45
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primary Human CD8+T

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Primary Human CD8+T

value: wt


title: neo teno, neosn, rep1

description: Library name: neo.7


title: Brainstem_infected_rep1

description: Library name: TC_infected_1

value: Brainstem


title: HCCLM3 cells, GAC, replicate2

description: Library name: G2


title: Brainstem_mock_rep3

description: Library name: TC_control_3

value: HNE Buffer


title: HN6,sh-NC,rep1

description: Library name: Sample1


title: Brainstem_mock_rep1

description: Library name: TC_control_1


title: trigeminal_ganglion_infected_rep5

description: Library name: TG_infected_5

source_name: Trigeminal ganglion

value: Trigeminal ganglion


title: T2_2

description: Library name: Sample11


title: neo teno, neosn, rep2

description: Library name: neo.8


title: neo teno, adultsn, rep2

description: Library name: neo.5

value: Adult SN


title: trigeminal_ganglion_infected_rep3

description: Library name: TG_infected_3


title: PA+IL-6_sIL-6R1

city: Takatsuki, Osaka

first: Yasuhiko

last: Ueda

address: 2-7 Daigaku-machi

country: Japan

institute: Osaka Medical and Pharmaceutical University

description: Library name: PA+Complex 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic, and the filtered reads were mapped to the human reference genome (hg38) using HISAT2 (version 2.1.0). Transcript abundance was quantified as fragments per kilobase of exon per million mapped fragments (FPKM) using Cufflinks (version 2.2.1).
Assembly: Human reference genome hg38 (GRCh38)
Supplementary files format and content: All data are provided in tab-delimited Excel format with gene symbols and annotations.

source_name: LSECs

growth_protocol: LSECs (Sciencell) were maintained in endothelial culture medium (ECM) supplemented with 5% fetal bovine serum (FBS), 1% endothelial cell growth supplement, and antibiotics in humidified atmosphere with 5% 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using QuickGene_AutoS RNA Cultured Cell Kit (Kurabo). 8-29 ng/μl of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq mRNA HT Library Prep Kit (Takara Bio) following manufacturer's protocols

treatment_protocol: LSECs were cultured overnight in serum-free medium with or without palmitic acid (PA) (Sigma), and subsequently stimulated with IL-6/sIL-6R complex (R&D systems) for 1 hour to evaluate trans-signaling activation and gene expression profiles. Four experimental conditions were tested: Control (untreated), PA (12-hour PA treatment), Complex (1-hour IL-6/sIL-6R complex stimulation), and PA+Complex (12-hour PA pretreatment followed by 1-hour IL-6/sIL-6R complex stimulation).

value: LSECs

value: Palmitic acid (12 hours) + IL-6/sIL-6R complex (1 hour)


title: T1_2

description: Library name: Sample10


title: HN6,sh-NC,rep3

description: Library name: Sample3

value: tongue

value: tongue squamous cell carcinoma cell

value: NC


title: C3_2

description: Library name: Sample9

value: Control


title: neo teno, Tmedia, rep1

description: Library name: neo.1

value: WT

value: T cell media


title: Brainstem_mock_rep2

description: Library name: TC_control_2


title: neo teno, adultsn, rep1

description: Library name: neo.4

value: tendon


title: neo teno, adultsn, rep3

description: Library name: neo.6

value: fibroblasts


title: HN6,sh-NC,rep2

description: Library name: Sample2


title: PA+IL-6_sIL-6R3

description: Library name: PA+Complex 3


title: C2_2

description: Library name: Sample8


title: PA+IL-6_sIL-6R2

description: Library name: PA+Complex 2


title: trigeminal_ganglion_infected_rep4

description: Library name: TG_infected_4


title: neo teno, Tmedia, rep2

description: Library name: neo.2


title: neo teno, Tmedia, rep3

description: Library name: neo.3


title: IL-6_sIL-6R3

description: Library name: Complex 3

value: IL-6/sIL-6R complex - 1h


title: trigeminal_ganglion_infected_rep2

description: Library name: TG_infected_2


title: C1_2

description: Library name: Sample7

value: Primary Human CD8+T


title: T3-1

description: Library name: Sample6

source_name: Primary Human CD4+T

value: Primary Human CD4+T

value: wt


title: adult teno, neosn, rep3

description: Library name: adult.9

value: Neo SN


title: IL-6_sIL-6R1

description: Library name: Complex 1


title: T2_1

description: Library name: Sample5


title: trigeminal_ganglion_infected_rep1

description: Library name: TG_infected_1

value: Trigeminal ganglion


title: T1_1

description: Library name: Sample4


title: adult teno, neosn, rep2

description: Library name: adult.8


title: trigeminal_ganglion_mock_rep3

description: Library name: TG_control_3

value: HNE Buffer


title: IL-6_sIL-6R2

description: Library name: Complex 2

value: LSECs


title: trigeminal_ganglion_mock_rep2

description: Library name: TG_control_2


title: PA2

description: Library name: PA 2

value: Palmitic acid - 12h


title: adult teno, neosn, rep1

description: Library name: adult.7


title: C3_1

description: Library name: Sample3


title: C2_1

description: Library name: Sample2


title: adult teno, adultsn, rep2

description: Library name: adult.5

value: Adult SN


title: PA1

description: Library name: PA 1


title: 777_IgG

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 40
NEBNext Ultra II DNA Library Prep Kit for Illumina

data_processing:
Alignment using bowtie2 to the appropriate genome (mm10 or hg19)
Filtered using samtools (MAPQ>30)
Deduplicated using picard
Normalized for ecoli spike in
Bigwig files generated using deeptools bamCoverage and scaled based on ecoli spike in normalization factor
Supplementary files format and content: bigwig files
Library strategy: CUT&RUN

source_name: Brain

extract_protocol:
Nuclei isolation using lysis buffer, 40um filtering, followed by overnight incubation with antibody indicated. Following Mnase cleavage in calcium buffer, reaction was stopped and DNA was purified using the Zymo ChIP DNA Clean and Concentrator Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Brain

tag: region

value: dHpc

tag: group

value: NP

tag: virus

value: IgG


title: adult teno, adultsn, rep3

description: Library name: adult.6

value: WT


title: Control3

description: Library name: Control 3


title: 776_IgG

description:
Library name: Sample 39
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: PA3

description: Library name: PA 3


title: E46_F1

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 93
Illumina

data_processing:
We aligned scRNA-seq reads to the GRCh38 human genome reference and quantified them using a Cellranger (version 5.0). DoubletDetection was used to filter out doublets (Gayoso and Shor, 2025) Cells with high mitochondrial read proportion (>20%) and more than 6,000 detected genes were filtered out . Data from each sample was normalized and scaled using the Scanpy (v1.9.8) pp.log1p function and principal components were calculated using the Scanpy (v1.9.8) tl.pca function. Uniform Manifold Approximation and Projection (UMAP) was calculated on the data using the by calculating nearest principal component neighbors with the Scanpy (v1.9.8) pp.neighbors function and embedding using Scanpy (v1.9.8) tl.umap function. Leiden clusters were determined using the Scanpy (v1.9.8) tl.leiden function. Differentially expressed genes determined using Mast, in addition to canonical marker genes, were used to annotate clusters (Finak et al., Genome Bio. 2015). Clusters were initially annotated as epithelial, immune and stromal before each of these populations was subclustered for further annotation. In some subclusterings where batch effects were evident in the clustering, Harmony was employed to generate a batch-corrected dimensionally-reduced space using Scanpy’s (v1.9.8) external.pp.harmony_integrate function.
Assembly: Human GRCh38
Supplementary files format and content: h5ad files

source_name: Primary gastric tumor

extract_protocol:
Tissue samples were collected from the patients who had biopsies one day prior to cycle 1, one day before cycle 2 and 1 day before cycle 7. All tissue samples were from the primary gastric tumor which was endoscopically mapped so the same region of the tumor was sampled at each biopsy.
For tissue samples, if tumor purity was estimated to be more than 40% after pathological reviews, tumor DNA and RNA were extracted by using a QIAamp Mini Kit (Qiagen, Hilden, Germany) according to the manufactures’ instructions for transcriptome sequencing. Concentration, 260/280 and 260/230nm ratios were measured with ND1000 spectrophotometer (Nanodrop Technologies, Thermo-Fisher Scientific) and then DNA/RNA was quantified using a Qubit fluorometer (Life Technologies).

value: Primary gastric tumor


title: 774_IgG

description:
Library name: Sample 38
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: C1_1

description: Library name: Sample1

value: Control


title: Control2

description: Library name: Control 2


title: trigeminal_ganglion_mock_rep1

description: Library name: TG_control_1


title: E46_B

description:
Library name: Sample 92
Illumina


title: adult teno, adultsn, rep1

description: Library name: adult.4

value: tendon

value: fibroblasts


title: adult teno, Tmedia, rep3

description: Library name: adult.3

value: T cell media


title: ChIP-SMAD2/3-TGFβ-input

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

description: Library name: SMAD2/3-TGFβ-input

data_processing:
Raw ChIP-seq reads were subjected to basic quality control including removal of sequencing adapters and low quality bases or reads using TrimGalore (v0.6.10). Clean reads were mapped to the human reference genome (hg38) using bowtie2 (v2.5.1, --maxins 700, --no-unal, --no-mixed, --no-discordant). Reads mapped to mitochondrial genome or unlocalized scaffolds were removed. Reads with mapping score below 30 were also discarded. Uniquely mapped and non-duplicated reads were finally retained. Peak calling was conducted using MACS2 (v2.2.8, --nomodel, --keep-dup all, --gsize hs, --broad, --broad-cutoff 0.01, --qvalue 0.01). Coverage tracks for each sample were generated using bamCompare function in deepTools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig files with normalized ChIP-seq signal

source_name: HUVEC

extract_protocol:
ChIP assay was performed using SimpleChIP Enzymatic chromatin IP Kit (CST, 9003S). HUVECs were fixed with 1% formaldehyde for 10 min, followed by quenching in 125 mM glycine. After washing two times in ice-cold PBS, the cell pellest were lysised in 8 ml buffer A on ice. The cell nuclei were resuspended in 8 ml buffer B, then washed two times in 1 ml ChIP buffer and sonicated for 10 min using covaris S220. 10 μg chromatin were suspended in 500 ul ChIP buffer with proteinase inhibitor, supplied with pretreated protein G magnetic beads at 4°C for 1 h. The chromatin supernatant were added with anti-SMAD2/3 (Abcam, ab202445) and incubated at 4°C overnight. The bound chromatin were further combined with pretreated protein G magnetic beads at 4°C for 2 h, then washed three times with ChIP buffer and one time with ChIP buffer supplemented with 0.3 M NaCl. The complex of chromatin and magnetic beads were resuspended in 150 ul ChIP elution buffer and eluted by 1200 rpm at 65°C for 30 min. IP product were finally de-crosslinked by RNase A at 37°C for 2 h and proteinase K at 65°C overnight.
ChIP-seq libraries were prepared according to the standard protocol of NEBNext Ultra DNA library Prep Kit (NEB, E7645B).

treatment_protocol: HUVECs were treated with 10 ng/ml TGFβ2 or not for 24 h.

value: HUVEC


title: E46_F2

description:
Library name: Sample 94
Illumina


title: 768_IgG

description:
Library name: Sample 37
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 767_IgG

description:
Library name: Sample 36
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: mCherry


title: 760_IgG

description:
Library name: Sample 35
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E45_F2

description:
Library name: Sample 91
Illumina


title: E45_F1

description:
Library name: Sample 90
Illumina


title: ChIP-SMAD2/3-TGFβ

description: Library name: SMAD2/3-TGFβ


title: adult teno, Tmedia, rep1

description: Library name: adult.1


title: adult teno, Tmedia, rep2

description: Library name: adult.2


title: X90

description:
Library name: Sample 15
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)

data_processing:
FastQ files were processed with the 10X Genomics Cell Ranger pipeline (v7.1.0) to demultiplex reads, align them to the mouse genome (mm10-2020-A), remove PCR duplicates, and generate gene expression matrices. Cell Ranger filtered outputs were analyzed using Seurat v4.3.026, and mitochondrial RNA content per cell was calculated using the GRCm39 (mm10) genome annotation and regressed out using SCTransform normalization protocol included in the Seurat toolkit with 20 principal components (PCs) and a resolution of 0.1. To estimate ambient RNA and correct for background contamination, the SoupX (v1.6.2) package27 was used for each sample using raw and filtered feature matrices from the Cell Ranger output. Heterotypic doublets were identified and removed using DoubletFinder (v2)28 to ensure the integrity of singlet datasets. Filtered singlet datasets were then re-normalized and integrated using the same Seurat SCTransform v2 workflow mentioned above. Cell clusters were annotated using a combination of expert curation based on published marker genes29–35, and label transfer from hippocampal reference datasets, including the Allen Brain Map and Broad Institute resources34,36
Assembly: GRCm39 (mm10)
Supplementary files format and content: filtered features, genes, and barcodes for each sample used directly for SCTranscform and SoupX pipeline

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated using a modified version of a sucrose density gradient isolation protocol25. Briefly, thawed tissues were placed in 1 mL of lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 0.1 mM EDTA, 10 mM Tris-HCl pH 8, 1 mM DTT, 0.1% Triton X-100) with 50 μL of 25 U/mL RNase inhibitor (Takara #2313B) in a dounce homogenizer (Wheaton #357538). Homogenization was performed with 20 strokes using a tight pestle. Another 1 mL of lysis buffer was added, followed by an additional 10 strokes. The resulting 2 mL homogenate was transferred to a 15 mL Open-Top Thinwall Polypropylene Tube (Beckman-Coulter #361707). The homogenizer and pestle were rinsed with 2 mL of lysis buffer, and this wash was combined with the homogenate for a total of 4 mL. The homogenate was carefully underlaid with 9 mL of sucrose solution (1.8 M sucrose, 3 mM magnesium acetate, 1 mM DTT, 10 mM Tris-HCl pH 8) and ultracentrifuged at 24,000 rpm for 1 hour at 4 °C using a Sorvall™ WX+ centrifuge. After centrifugation, the supernatant and debris at the interface were gently removed. The nuclear pellet was resuspended in 1 mL of resuspension buffer (0.02% bovine serum albumin in DPBS with 25 μL of 25 U/mL RNase inhibitor) and incubated on ice for 10 minutes. The suspension was passed through a 35 μm nylon mesh filter (Corning #352235) into a 1.5 mL RNase/DNase-free microcentrifuge tube and centrifuged at 2600 x g for 10 minutes at 4 °C. Supernatants were discarded, and nuclei were resuspended in 200 μL of resuspension buffer. A 10 μL aliquot of the nuclei suspension was stained with Trypan Blue to assess quality and concentration using a Countess 3 Automated Cell Counter. Nuclei suspensions were loaded onto a Chromium Single Cell 3′ chip (10X Genomics, v3) and processed according to the manufacturer's protocol, targeting 10,000 nuclei.
Single-nuclei libraries were generated using the 10X Chromium Next GEM Single Cell 3′ v3.1 (Dual Index) protocol (CG000315 Rev A). Libraries were pooled, loaded onto a single 10B 100 Cycle Flowcell, and sequenced using an Illumina NovaSeq 6000 system to generate 25-30,000 paired-end 2 × 100 bp reads.

value: StressPP


title: X88

description:
Library name: Sample 14
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)

value: ControlPP


title: 755_IgG

description:
Library name: Sample 33
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: Control1

description: Library name: Control 1

value: LSECs


title: ChIP-SMAD2/3-ctrl-input

description: Library name: SMAD2/3-ctrl-input


title: E45_B

description:
Library name: Sample 89
Illumina


title: ChIP-SMAD2/3-ctrl

description: Library name: SMAD2/3-ctrl


title: 757_IgG

description:
Library name: Sample 34
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E44_F2

description:
Library name: Sample 88
Illumina


title: X87

description:
Library name: Sample 13
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: 777_H3K4me3Q5dop

description:
Library name: Sample 32
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 616

description:
Library name: Sample 8
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: hg19
Supplementary files format and content: csv file with normalized counts containing all samples (human dorsal subiculum)

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 and Illumina Stranded mRNA Prep

value: subiculum

value: Parous

tag: births

tag: ruvs k_value


title: X77

description:
Library name: Sample 12
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)

value: Brain


title: 774_H3K4me3Q5dop

description:
Library name: Sample 30
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: dHpc


title: 560

description:
Library name: Sample 7
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv

value: NP


title: X75

description:
Library name: Sample 11
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: E44_B

description:
Library name: Sample 86
Illumina


title: 768_H3K4me3Q5dop

description:
Library name: Sample 29
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: X73

description:
Library name: Sample 10
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: 505

description:
Library name: Sample 5
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: E43_F1

description:
Library name: Sample 85
Illumina


title: E44_F1

description:
Library name: Sample 87
Illumina


title: X72

description:
Library name: Sample 9
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: 776_H3K4me3Q5dop

description:
Library name: Sample 31
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: X70

description:
Library name: Sample 8
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: E43_B

description:
Library name: Sample 84
Illumina


title: 484

description:
Library name: Sample 4
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: 760_H3K4me3Q5dop

description:
Library name: Sample 27
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 767_H3K4me3Q5dop

description:
Library name: Sample 28
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: X66

description:
Library name: Sample 7
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: 532

description:
Library name: Sample 6
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: 442

description:
Library name: Sample 2
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: 757_H3K4me3Q5dop

description:
Library name: Sample 26
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: X63

description:
Library name: Sample 6
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: E42_F1

description:
Library name: Sample 82
Illumina


title: 755_H3K4me3Q5dop

description:
Library name: Sample 25
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 461

description:
Library name: Sample 3
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: E42_B

description:
Library name: Sample 81
Illumina


title: X43

description:
Library name: Sample 5
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: E41_F2

description:
Library name: Sample 80
Illumina


title: NP12_IgG

description:
Library name: Sample 23
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: IgG


title: Valeriasen-treated bio rep 3

city: Boston

first: Timothy

last: Yu

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
Library name: Sample 12
column name in all_counts_hg38.Rmatrix.txt: Val3

data_processing:
Reads were cleaned by Novogene using in-house perl scripts to remove low quality and adapter-containing reads.
Reads were aligned to hg38 using the Spliced Transcripts Alignment to a Reference (STAR) open-source software.
The featureCounts function in the Rsubread (1.22.2) package was used to generate read counts.
Assembly: hg38
Supplementary files format and content: Text file contains raw counts for all samples

source_name: WT-iPS Neuron

extract_protocol:
RNA was isolated at DIV 29 using the PureLink RNA Mini Kit (Thermo Fisher Scientific).
RNA libraries were prepared at Novogene using the Fast RNA-seq Lib Prep Kit V2 from Abclonal.

tag: cell type

value: WT-iPS Neuron

value: WT

value: Valeriasen


title: Valeriasen-treated bio rep 2

description:
Library name: Sample 11
column name in all_counts_hg38.Rmatrix.txt: Val2

tag: treatment


title: X35

description:
Library name: Sample 3
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)

tag: tissue


title: NP11_IgG

description:
Library name: Sample 22
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 258

description:
Library name: Sample 1
Illumina Stranded mRNA Prep
NormalizedCounts_NPvsPreg_8subj_RUVs4.csv


title: NP9_IgG

description:
Library name: Sample 24
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: NP10_IgG

description:
Library name: Sample 21
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E40_F2

description:
Library name: Sample 77
Illumina

value: Primary gastric tumor


title: X31

description:
Library name: Sample 2
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: Tominersen-treated bio rep 3

description:
Library name: Sample 9
column name in all_counts_hg38.Rmatrix.txt: Tom3

tag: genotype

value: Tominersen


title: Valeriasen-treated bio rep 1

description:
Library name: Sample 10
column name in all_counts_hg38.Rmatrix.txt: Val1


title: E41_F1

description:
Library name: Sample 79
Illumina


title: X27

description:
Library name: Sample 1
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)

tag: batch


title: E40_F1

description:
Library name: Sample 76
Illumina


title: Tominersen-treated bio rep 2

description:
Library name: Sample 8
column name in all_counts_hg38.Rmatrix.txt: Tom2


title: 210_IgG

description:
Library name: Sample 19
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E41_B

description:
Library name: Sample 78
Illumina


title: ELS9_dHpc

description:
Library name: Sample 232
TruSeq RNA Library Prep Kit v2

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples


title: 213_IgG

description:
Library name: Sample 20
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E40_B

description:
Library name: Sample 75
Illumina


title: ELS6_dHpc

description:
Library name: Sample 231
TruSeq RNA Library Prep Kit v2


title: ELS5_dHpc

description:
Library name: Sample 230
TruSeq RNA Library Prep Kit v2


title: E39_F2

description:
Library name: Sample 74
Illumina


title: Tominersen-treated bio rep 1

description:
Library name: Sample 7
column name in all_counts_hg38.Rmatrix.txt: Tom1


title: Tofersen-treated bio rep 3

description:
Library name: Sample 6
column name in all_counts_hg38.Rmatrix.txt: Tof3

value: Tofersen


title: E42_F2

description:
Library name: Sample 83
Illumina


title: 196_IgG

description:
Library name: Sample 17
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: Tofersen-treated bio rep 2

description:
Library name: Sample 5
column name in all_counts_hg38.Rmatrix.txt: Tof2


title: 203_IgG

description:
Library name: Sample 18
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E39_B

description:
Library name: Sample 72
Illumina


title: X37

description:
Library name: Sample 4
10x Chromium Next GEM Single Cell 3' v3.1 (Dual Index)


title: Tofersen-treated bio rep 1

description:
Library name: Sample 4
column name in all_counts_hg38.Rmatrix.txt: Tof1


title: ELS18_dHpc

description:
Library name: Sample 228
TruSeq RNA Library Prep Kit v2


title: ELS4_dHpc

description:
Library name: Sample 229
TruSeq RNA Library Prep Kit v2


title: ELS16_dHpc

description:
Library name: Sample 227
TruSeq RNA Library Prep Kit v2


title: E38_F2

description:
Library name: Sample 71
Illumina


title: 206_IgG

description:
Library name: Sample 16
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E39_F1

description:
Library name: Sample 73
Illumina


title: 198_IgG

description:
Library name: Sample 15
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: Naive bio rep 3

description:
Library name: Sample 3
column name in all_counts_hg38.Rmatrix.txt: Naive3


title: ELS15_dHpc

description:
Library name: Sample 226
TruSeq RNA Library Prep Kit v2


title: Naive bio rep 2

description:
Library name: Sample 2
column name in all_counts_hg38.Rmatrix.txt: Naive2


title: E38_B

description:
Library name: Sample 69
Illumina


title: E37_F2

description:
Library name: Sample 68
Illumina


title: ELS13_dHpc

description:
Library name: Sample 225
TruSeq RNA Library Prep Kit v2


title: 194_IgG

description:
Library name: Sample 14
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E38_F1

description:
Library name: Sample 70
Illumina


title: ELS12_dHpc

description:
Library name: Sample 224
TruSeq RNA Library Prep Kit v2


title: 192_IgG

description:
Library name: Sample 13
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: ChIP-H3K79me2-TGFβ-rep3-input

description: Library name: H3K79me2-TGFβ-rep3-input

data_processing:
Raw ChIP-seq reads were subjected to basic quality control including removal of sequencing adapters and low quality bases or reads using TrimGalore (v0.6.10). Clean reads were mapped to the human reference genome (hg38) using bowtie2 (v2.5.1, --maxins 700, --no-unal, --no-mixed, --no-discordant). Reads mapped to mitochondrial genome or unlocalized scaffolds were removed. Reads with mapping score below 30 were also discarded. Uniquely mapped and non-duplicated reads were finally retained. Peak calling was conducted using MACS2 (v2.2.8, --nomodel, --keep-dup all, --gsize hs, --broad, --broad-cutoff 0.01, --qvalue 0.01). Coverage tracks with replicates merged for each group were generated using bamCoverage function in deepTools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig files with normalized ChIP-seq signal

extract_protocol:
ChIP assay was performed using SimpleChIP Enzymatic chromatin IP Kit (CST, 9003S). HUVECs were fixed with 1% formaldehyde for 10 min, followed by quenching in 125 mM glycine. After washing two times in ice-cold PBS, the cell pellest were lysised in 8 ml buffer A on ice. The cell nuclei were resuspended in 8 ml buffer B, then washed two times in 1 ml ChIP buffer and sonicated for 10 min using covaris S220. 10 μg chromatin were suspended in 500 ul ChIP buffer with proteinase inhibitor, supplied with pretreated protein G magnetic beads at 4°C for 1 h. The chromatin supernatant were added with anti-H3K79me2 (Abcam, ab3594) and incubated at 4°C overnight. The bound chromatin were further combined with pretreated protein G magnetic beads at 4°C for 2 h, then washed three times with ChIP buffer and one time with ChIP buffer supplemented with 0.3 M NaCl. The complex of chromatin and magnetic beads were resuspended in 150 ul ChIP elution buffer and eluted by 1200 rpm at 65°C for 30 min. IP product were finally de-crosslinked by RNase A at 37°C for 2 h and proteinase K at 65°C overnight.
ChIP-seq libraries were prepared according to the standard protocol of NEBNext Ultra DNA library Prep Kit (NEB, E7645B).

tag: cell line

value: HUVEC


title: NP9_H3K4me3Q5dop

description:
Library name: Sample 12
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: NP12_H3K4me3Q5dop

description:
Library name: Sample 11
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: ChIP-H3K79me2-TGFβ-rep2-input

description: Library name: H3K79me2-TGFβ-rep2-input


title: E37_F1

description:
Library name: Sample 67
Illumina


title: NP11_H3K4me3Q5dop

description:
Library name: Sample 10
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: ChIP-H3K79me2-TGFβ-rep1-input

description: Library name: H3K79me2-TGFβ-rep1-input


title: E36_F2

description:
Library name: Sample 65
Illumina


title: ELS10_dHpc

description:
Library name: Sample 222
TruSeq RNA Library Prep Kit v2


title: Naive bio rep 1

description:
Library name: Sample 1
column name in all_counts_hg38.Rmatrix.txt: Naive1


title: ChIP-H3K79me2-TGFβ-rep3

description: Library name: H3K79me2-TGFβ-rep3

value: anti-H3K79me2 (Abcam, ab3594)


title: dHpc_132

description:
Library name: Sample 221
Illumina Stranded mRNA Prep


title: 213_H3K4me3Q5dop

description:
Library name: Sample 8
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: StressPP


title: ELS11_dHpc

description:
Library name: Sample 223
TruSeq RNA Library Prep Kit v2


title: ChIP-H3K79me2-TGFβ-rep2

description: Library name: H3K79me2-TGFβ-rep2


title: E36_B

description:
Library name: Sample 63
Illumina


title: NP10_H3K4me3Q5dop

description:
Library name: Sample 9
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E37_B

description:
Library name: Sample 66
Illumina


title: 210_H3K4me3Q5dop

description:
Library name: Sample 7
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: ChIP-H3K79me2-TGFβ-rep1

description: Library name: H3K79me2-TGFβ-rep1


title: 203_H3K4me3Q5dop

description:
Library name: Sample 6
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E36_F1

description:
Library name: Sample 64
Illumina


title: dHpc_131

description:
Library name: Sample 220
Illumina Stranded mRNA Prep


title: dHpc_130

description:
Library name: Sample 219
Illumina Stranded mRNA Prep


title: E35_F2

description:
Library name: Sample 62
Illumina


title: 206_H3K4me3Q5dop

description:
Library name: Sample 4
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: ControlPP


title: E35_B

description:
Library name: Sample 60
Illumina


title: dHpc_128

description:
Library name: Sample 217
Illumina Stranded mRNA Prep

value: PupSensitized


title: E35_F1

description:
Library name: Sample 61
Illumina


title: ChIP-H3K79me2-ctrl-rep2-input

description: Library name: H3K79me2-ctrl-rep2-input


title: ChIP-H3K79me2-ctrl-rep1-input

description: Library name: H3K79me2-ctrl-rep1-input


title: 196_H3K4me3Q5dop

description:
Library name: Sample 5
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: dHpc_126

description:
Library name: Sample 215
Illumina Stranded mRNA Prep


title: dHpc_127

description:
Library name: Sample 216
Illumina Stranded mRNA Prep


title: dHpc_129

description:
Library name: Sample 218
Illumina Stranded mRNA Prep


title: ChIP-H3K79me2-ctrl-rep1

description: Library name: H3K79me2-ctrl-rep1


title: 198_H3K4me3Q5dop

description:
Library name: Sample 3
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E34_F1

description:
Library name: Sample 59
Illumina


title: 194_H3K4me3Q5dop

description:
Library name: Sample 2
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: E34_B

description:
Library name: Sample 58
Illumina


title: dHpc_125

description:
Library name: Sample 214
Illumina Stranded mRNA Prep


title: ChIP-H3K79me2-ctrl-rep2

description: Library name: H3K79me2-ctrl-rep2


title: E33_F1

description:
Library name: Sample 57
Illumina


title: RNA-TGFβ2-treated-rep2

description: Library name: TGFβ-rep2

data_processing:
Raw sequencing reads were first subjected to quality control including removal of sequencing adapters and low quality bases or reads using TrimGalore (v0.6.10). Trimmed clean reads were then aligned to the human reference genome (hg38) using STAR (v2.7.10b), and multi-mapped reads were filtered out. Raw reads count for each gene was quantified using featureCounts (v2.0.6). Differentially expressed genes were identified using DESeq2 package (v1.40.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

extract_protocol:
HUVECs were collected at 24 h following TGFβ2 treatment or not. Then, total RNA was extracted using FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01).
RNA-seq libraries were prepared according to the standard protocol of VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604).


title: dHpc_124

description:
Library name: Sample 213
Illumina Stranded mRNA Prep


title: 192_H3K4me3Q5dop

description:
Library name: Sample 1
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: X777

description:
Library name: Sample 256
Illumina Stranded mRNA Prep


title: RNA-TGFβ2-treated-rep3

description: Library name: TGFβ-rep3


title: E33_B

description:
Library name: Sample 56
Illumina


title: E32_F2

description:
Library name: Sample 55
Illumina


title: X776

description:
Library name: Sample 255
Illumina Stranded mRNA Prep


title: dHpc_123

description:
Library name: Sample 212
Illumina Stranded mRNA Prep


title: RNA-ctrl-rep3

description: Library name: ctrl-rep3


title: dHpc_122

description:
Library name: Sample 211
Illumina Stranded mRNA Prep


title: RNA-ctrl-rep2

description: Library name: ctrl-rep2


title: X774

description:
Library name: Sample 254
Illumina Stranded mRNA Prep


title: dHpc_121

description:
Library name: Sample 210
Illumina Stranded mRNA Prep


title: E32_F1

description:
Library name: Sample 54
Illumina


title: input

city: shanghai

first: wang

middle: si

last: qi

address: Lane 485-11, Nan Chen Road, Baoshan District, Shanghai, China

department: School of Life Sciences, Shanghai University

institute: Shanghai University

description: Library name: input

data_processing:
Raw sequencing reads were quality-checked using FastQC, and low-quality reads and adapter sequences were trimmed using Trim Galore. Clean reads were aligned to the mouse reference genome (mm10) using Bowtie, followed by PCR duplicate removal with Picard tools. Peak calling was performed using MACS with IgG as a control, and peaks were annotated to genomic features using Homer. BigWig files were generated using deepTools for visualization in IGV, and differentially enriched regions were identified using DiffBind.
Assembly: mm10 (Mus musculus reference genome)
Supplementary files format and content: The processed data includes peak files in BED format and signal tracks in BigWig format for visualization.

growth_protocol: C2C12 myoblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a 5% CO₂ incubator. To induce differentiation into myotubes, cells were switched to DMEM containing 2% horse serum when reaching 90% confluence and maintained for 4–5 days until multinucleated myotubes were observed.

extract_protocol:
First, harvest cells and wash them with 1xPBS. Then, resuspend the cells in RIP buffer and incubate on ice for 20 min. Next, centrifuge the cell suspension at 15,000 x g for 15 min at 4 °C to clarify the lysate. After that, wash the beads three times with RIP buffer, add the cell supernatant to the beads, and incubate with rotation at 4 °C for 2 h. Subsequently, remove the beads and incubate the supernatant with the corresponding antibody for 2 h. Finally, wash the sample three times and extract RNA for detection.
After immunoprecipitation, the enriched DNA was purified using the QIAquick PCR purification kit (Qiagen). DNA was then end-repaired, A-tailed, and ligated to indexed adapters. The ligated DNA was amplified by PCR, and the resulting libraries were purified using the QIAquick PCR purification kit. Library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified by qPCR. The libraries were then sequenced on the Illumina HiSeq 3000 platform, generating 150 bp paired-end reads.

treatment_protocol: No additional treatment was applied

value: myotube

value: Wild-type


title: dHpc_120

description:
Library name: Sample 209
Illumina Stranded mRNA Prep

value: Brain


title: RNA-TGFβ2-treated-rep1

description: Library name: TGFβ-rep1


title: RNA-ctrl-rep1

description: Library name: ctrl-rep1


title: YTHDF

description: Library name: YTHDF


title: X773

description:
Library name: Sample 253
Illumina Stranded mRNA Prep

value: dHpc


title: X771

description:
Library name: Sample 252
Illumina Stranded mRNA Prep

value: NP


title: dHpc_119

description:
Library name: Sample 208
Illumina Stranded mRNA Prep


title: X768

description:
Library name: Sample 251
Illumina Stranded mRNA Prep


title: dHpc_118

description:
Library name: Sample 207
Illumina Stranded mRNA Prep


title: dHpc_117

description:
Library name: Sample 206
Illumina Stranded mRNA Prep

value: PP


title: X766

description:
Library name: Sample 249
Illumina Stranded mRNA Prep

value: mCherry


title: X767

description:
Library name: Sample 250
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, INCB000262, animal 71

city: San Diego

first: Joshua

last: Wollam

address: 9761 W. Canyon Ter. Unit 1

institute: Escient Pharmaceuticals

description: Library name: An_71_Skin_20220823_S69

data_processing:
Partek Flow Software, version 7.0
Alignment was performed using STAR with mouse reference genome GRCm39. Ensembl Transcripts release 107 was used for gene feature annotation.
For normalization of transcript counts, CPM (Counts per million of reads) and add 0.0001 normalization method was applied.
Data was filtered by “Lowest average coverage = 1”, before applying differential expression algorithm.
Partek-based GSA was used to determine differentially expressed genes between sample set comparisons.  Different P-value cutoffs were used to filter for significantly differentially expressed genes between different sample set comparisons.
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Annotated excel of CPM plus 0.0001

source_name: skin

extract_protocol:
RNA was harvested using RNAeasy Mini Plus Kits (Qiagen).  1 ug total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kits (Roche) following manufacturer's protocols.

value: skin

tag: genetic background

value: MRGPRX2 Knock-in

tag: Sex

value: Male

tag: treatment (topical)

value: HDM+SEB

tag: treatment (oral)


title: skin, biopsy, HDM+SEB, INCB000262, animal 72

description: Library name: An_72_Skin_20220823_S70


title: skin, biopsy, HDM+SEB, INCB000262, animal 70

description: Library name: An_70_Skin_20220823_S68


title: dHpc_116

description:
Library name: Sample 205
Illumina Stranded mRNA Prep


title: X763

description:
Library name: Sample 248
Illumina Stranded mRNA Prep


title: sec12-4 ino2Δ ino4Δ (FKY4418) 3

type: RNA

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

institute: National Research Institute of Brewing

description: Gene expression data

hyb_protocol: 5 ug of cRNA were hybridized for 4 hr at 45℃ on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Operating Software(GCOS) v1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Saccharomyces cerevisiae

source_name: sec12-4 ino2Δ ino4Δ (FKY4418)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: sec12-4 (FKY4415 MATa sec12-4, his3, leu2, ade2, lys2, trp1, ura3, bar1-1) and sec12-4 ino2Δ ino4Δ (FKY4418 MAT a sec12-4, his3, leu2, lys2, trp1, ura3, bar1-1, ino2Δ::HIS3, ino4Δ::LEU2) cells were grown to log phase at 25°C in YPD medium.

extract_protocol: Total RNA was extracted by the hot phenol extraction method (Carlson and Botstein, 1982) and cleaned up on RNeasy columns (Qiagen)) .

treatment_protocol: Cells grown in YPD medium were not treated.

tag: strain/genotype

value: sec12-4 ino2{delta} ino4{delta} (FKY4418)


title: skin, biopsy, HDM+SEB, INCB000262, animal 69

description: Library name: An_69_Skin_20220823_S67


title: skin, biopsy, HDM+SEB, INCB000262, animal 68

description: Library name: An_68_Skin_20220823_S66


title: sec12-4 ino2Δ ino4Δ (FKY4418) 1

description: Gene expression data


title: WT liver, IL-1

city: Hiroshima

first: Yoshihiro

last: Tsuchiya

state: Hiroshima

address: 4-13-1 Ushita Higashi Higashi-ku

department: Department of Nutrition and Health Promotion

institute: Hiroshima Jogakuin University

hyb_protocol: Gene-expression profiling was performed with the GeneChip Mouse Genome 430 2.0 Array (Affymetrix) according to the manufacturer's instructions.

scan_protocol: Arrays were scanned according to the manufacturer's instructions.

data_processing:
Processed data matrix provided by submitter in four columns: ID_REF, WT_saline, TNF, and IL1.
Processed expression value

source_name: WT mouse liver, IL-1-treated

label_protocol: Samples were prepared and labeled according to the manufacturer's instructions for the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

growth_protocol: treatment protocol Male mice were maintained under standard specific pathogen-free conditions and analyzed at 8 weeks of age.

extract_protocol: Total RNA was extracted from liver tissues using TRIzol Reagent (Invitrogen) and further purified using RNeasy MinElute Spin Columns (Qiagen).

treatment_protocol: For acute inflammatory stimulation, 8-week-old male mice were administered saline (vehicle), mouse TNFα (BioLegend), or mouse IL-1β (BioLegend) once by intra-venous injection (7.5 μg/kg) and euthanized 4 h after injection.

value: liver


title: X757

description:
Library name: Sample 246
Illumina Stranded mRNA Prep


title: dHpc_114

description:
Library name: Sample 203
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, INCB000262, animal 67

description: Library name: An_67_Skin_20220823_S65


title: X760

description:
Library name: Sample 247
Illumina Stranded mRNA Prep


title: sec12-4 ino2Δ ino4Δ (FKY4418) 2

description: Gene expression data


title: sec12-4 (FKY4415) 2

description: Gene expression data


title: sec12-4 (FKY4415) 3

description: Gene expression data


title: WT liver, TNF

source_name: WT mouse liver, TNF-treated

value: TNF


title: X755

description:
Library name: Sample 245
Illumina Stranded mRNA Prep


title: dHpc_115

description:
Library name: Sample 204
Illumina Stranded mRNA Prep

value: PregnancyOnly


title: skin, biopsy, HDM+SEB, INCB000262, animal 66

description: Library name: An_66_Skin_20220823_S64


title: sec12-4 (FKY4415) 1

description: Gene expression data


title: dHpc_113

description:
Library name: Sample 202
Illumina Stranded mRNA Prep


title: dHpc_112

description:
Library name: Sample 201
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, INCB000262, animal 65

description: Library name: An_65_Skin_20220823_S63


title: X752

description:
Library name: Sample 244
Illumina Stranded mRNA Prep


title: Liver from 6-week-old male Tg-IKKβΔhep mouse

description: Representative liver sample used for exploratory microarray analysis.

hyb_protocol: Labeled target was hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array according to the manufacturer’s instructions.

scan_protocol: Arrays were washed, stained, and scanned according to the manufacturer’s standard Affymetrix protocol.

data_processing: Raw CEL files were imported into GeneSpring and processed using Affymetrix MAS5.0-based analysis. The processed data deposited to GEO are normalized probe set expression values exported from GeneSpring.

source_name: liver

label_protocol: Biotin-labeled target was prepared according to the manufacturer’s standard protocol for the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

growth_protocol: Male mice were maintained under standard specific pathogen-free conditions and analyzed at 6 weeks of age.

treatment_protocol: No treatment was applied.

value: Tg-IKK{beta}{delta}hep

value: male

tag: age

value: 6 weeks


title: WT liver, saline

source_name: WT mouse liver, saline-treated

value: saline


title: X751

description:
Library name: Sample 243
Illumina Stranded mRNA Prep

value: Brain

tag: region


title: dHpc_111

description:
Library name: Sample 200
Illumina Stranded mRNA Prep

value: dHpc

tag: group


title: skin, biopsy, HDM+SEB, INCB000262, animal 64

description: Library name: An_64_Skin_20220823_S62


title: dHpc_110

description:
Library name: Sample 199
Illumina Stranded mRNA Prep

value: MatingOnly

tag: virus


title: X748

description:
Library name: Sample 242
Illumina Stranded mRNA Prep

value: PP


title: Liver from 6-week-old male Tg mouse

value: Tg


title: skin, biopsy, HDM+SEB, INCB000262, animal 63

description: Library name: An_63_Skin_20220823_S61

value: skin


title: dHpc_107

description:
Library name: Sample 198
Illumina Stranded mRNA Prep


title: Liver from 6-week-old male IKKβΔhep mouse

value: IKK{beta}{delta}hep


title: X740

description:
Library name: Sample 240
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, INCB000262, animal 62

description: Library name: An_62_Skin_20220823_S60

value: MRGPRX2 Knock-in

value: Male


title: X745

description:
Library name: Sample 241
Illumina Stranded mRNA Prep

value: mCherry


title: dHpc_106

description:
Library name: Sample 197
Illumina Stranded mRNA Prep


title: Liver from 6-week-old male IKKβF/F mouse

value: IKK{beta}F/F


title: skin, biopsy, HDM+SEB, INCB000262, animal 61

description: Library name: An_61_Skin_20220823_S59

value: HDM+SEB


title: dHpc_105

description:
Library name: Sample 196
Illumina Stranded mRNA Prep


title: skin, biopsy, HDM+SEB, INCB000262, animal 60

description: Library name: An_60_Skin_20220823_S58

value: vehicle


title: dHpc_104

description:
Library name: Sample 195
Illumina Stranded mRNA Prep

value: PregnancyOnly


title: X739

description:
Library name: Sample 239
Illumina Stranded mRNA Prep


title: MOLM13-5TDMSO

city: Lausanne

first: Vincent

last: Roh

address: Bugnon 25A

country: Switzerland

institute: SIB

description: Library name: MOLM13-5TDMSO

data_processing:
Sequencing quality was evaluated with FastQC v.0.11.5. The reads were mapped to the UCSC hg19 human reference genome with the TopHat v.2.0.11 software. Alignment summary metrics were obtained with PicardTools v.1.141.
The table of gene counts, with the number of reads mapping to each gene feature of UCSC hg19, was prepared with HTSeq v0.6p1.
Assembly: hg19
Supplementary files format and content: raw_counts_DNA_MOLM_4samples.xlsx: table of gene counts for samples MOLM13-P-1, MOLM13-1TBU, MOLM13-3TBU, MOLM13-5TBU, in xlsx format
Supplementary files format and content: Molm13_Parental_genecounts_strandedreverse.txt: gene counts for sample MOLM13-P-2 in txt format
Supplementary files format and content: Molm13_DMSO_t1_genecounts_strandedreverse.txt: gene counts for sample MOLM13-1TDMSO in txt format
Supplementary files format and content: Molm13_DMSO_t3_genecounts_strandedreverse.txt: gene counts for sample MOLM13-3TDMSO in txt format
Supplementary files format and content: Molm13_DMSO_t5_genecounts_strandedreverse.txt: gene counts for sample MOLM13-5TDMSO in txt format

growth_protocol: MOLM13 cell lines were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium containing L-glutamine and 25 mM HEPES (REF:52400-025, Gibco, Life Technologies Europe B.V.) supplemented with 10–20% fetal bovine serum (FBS) (REF:10270-106, Gibco, Life Technologies Europe B.V.) and 1% penicillin‒streptomycin (REF: P0781, Gibco, Life Technologies Europe B.V.). Cells were incubated at 37 °C in a 5% CO2-humidified atmosphere according to the supplier’s recommendations.

extract_protocol:
RNA was extracted using PureLink RNA Mini kit (Invitrogen, Thermo Scientific, Wilmington, DE, USA) according to manufacturers' recommendations. Concentration and purity were evaluated on an ND-1000 spectrophotometer.
Library construction and sequencing were performed at the iGE3 Genomics Platform – CMU (Geneva, Switzerland) using the TruSeq RNA Library Prep Kit.
Sequencing was done on a Illumina HiSeq 2000 platform.

value: MOLM13 cells after the 5th treatment course with DMSO


title: skin, biopsy, HDM+SEB, vehicle, animal 59

description: Library name: An_59_Skin_20220823_S57


title: dHpc_103

description:
Library name: Sample 194
Illumina Stranded mRNA Prep


title: MOLM13-3TDMSO

description: Library name: MOLM13-3TDMSO

value: MOLM13 cells after the 3rd treatment course with DMSO


title: skin, biopsy, HDM+SEB, vehicle, animal 58

description: Library name: An_58_Skin_20220823_S56


title: skin, biopsy, HDM+SEB, vehicle, animal 57

description: Library name: An_57_Skin_20220823_S55


title: dHpc_102

description:
Library name: Sample 193
Illumina Stranded mRNA Prep


title: MOLM13-1TDMSO

description: Library name: MOLM13-1TDMSO

value: MOLM13 cells after the 1st treatment course with DMSO


title: X717

description:
Library name: Sample 236
Illumina Stranded mRNA Prep

value: Brain


title: X725

description:
Library name: Sample 237
Illumina Stranded mRNA Prep

value: dHpc


title: MOLM13-P-2

description: Library name: MOLM13-P_2

value: MOLM13 cells (MOLM13-P, parental)


title: X707

description:
Library name: Sample 235
Illumina Stranded mRNA Prep

value: PP


title: dHpc_101

description:
Library name: Sample 192
Illumina Stranded mRNA Prep

value: MatingOnly


title: X726

description:
Library name: Sample 238
Illumina Stranded mRNA Prep


title: MOLM13-1TBU

data_processing:
Software to map the reads to the UCSC hg19 human reference genome: TopHat v.2.0.11
Software to estimate the read counts for each gene: HTSeq v0.6p1.
Assembly: hg19
Supplementary files format and content: Table of raw gene counts for each gene (rows) and each sample (columns)

growth_protocol: 4.0 x106 MOLM13 suspension cells were seeded in T25 flasks. Cells were treated with 20 uM, 8 uM DMF or DMSO at days 0 and 2. 2 days after the second treatment the cells were distributed into 96-well plates at 10.000 c/well and treated with Busulfan

extract_protocol:
mRNA was extracted by pelleting the cells grown under optimal growth conditions after each respective treatment. RNA was extracted using PureLink RNA Mini kit (Invitrogen, Thermo Scientific, Wilmington, DE, USA) according to manufacturers' recommendations.
Library construction and sequencing were performed at the iGE3 Genomics Platform – CMU (Geneva, Switzerland) using the TruSeq RNA Library Prep Kit.

tag: disease state

value: acute myeloid leukemia

value: MOLM13 cells after the 1st treatment course with busulfan


title: skin, biopsy, HDM+SEB, vehicle, animal 55

description: Library name: An_55_Skin_20220823_S54

value: skin

value: MRGPRX2 Knock-in


title: MOLM13-5TBU

value: MOLM13 cells after the 5th treatment course with busulfan


title: skin, biopsy, HDM+SEB, vehicle, animal 52

description: Library name: An_52_Skin_20220823_S51

value: Male


title: VTA_131

description:
Library name: Sample 191
Illumina Stranded mRNA Prep

value: VTA

value: NP

tag: ruvs k_value


title: X704

description:
Library name: Sample 234
Illumina Stranded mRNA Prep

value: mCherry


title: MOLM13-P


title: skin, biopsy, HDM+SEB, vehicle, animal 54

description: Library name: An_54_Skin_20220823_S53

value: HDM+SEB

value: vehicle


title: MOLM13-3TBU

value: MOLM13 cells after the 3rd treatment course with busulfan


title: VTA_129

description:
Library name: Sample 189
Illumina Stranded mRNA Prep

value: Brain


title: skin, biopsy, HDM+SEB, vehicle, animal 53

description: Library name: An_53_Skin_20220823_S52


title: X701

description:
Library name: Sample 233
Illumina Stranded mRNA Prep

value: dHpc


title: VTA_122

description:
Library name: Sample 187
Illumina Stranded mRNA Prep