title: Control patient 10 Visit 3 Tissue Input Control

status: Public on Aug 03 2026

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: C3-10 Tissue IC

data_processing:
To analyze the MeDIP-seq data, high-quality reads from MeDIP-seq were aligned to the human reference genome (GRCH38/hg38) using bwa-mem2. Mapped reads were processed using MEDIPS R package58 to compute genome-wide methylation signals in every 300bp sliding window. The resulting count data were normalized using the trimmed mean of M-values (TMM) methods to account for differences in library size across samples. Peaks whose midpoint was located from 2000bp upstream to 500bp downstream of transcription start sites (TSS) were defined as promoter peaks. The promoter methylation level was quantified by averaging the Relative Methylation Score (RMS) across all windows covering promoter region. RMS is a normalized metric that adjusts for sequencing read coverage and CpG density, enabling cross-sample and locus-level comparisons. For differential methylation analysis, DMRs in both tissue and cfDNA were first identified separately within the exercise and control groups by comparing pre- and post-intervention using a generalized linear model (GLM)-based approach in MEDIPS package, which utilizes the edgeR framework to model over-dispersed count data via a negative binomial distribution73. FDR correction was performed using Benjamini–Hochberg (BH). However, no windows met the adjusted p-value threshold of 0.05 during DMR detection from tissue-derived DNA. Therefore, in this study, DMRs were defined as regions with a minimum coverage of 5 reads per window, an absolute log2 fold change (|log2FC|) ≥2, and an unadjusted p-value < 0.01for both cfDNA- and tissue-derived datasets. Exercise-induced DMRs (eDMRs) were identified based on two criteria: (1) DMRs that appeared exclusively in the exercise group but not in the control group, and (2) DMRs that were detected in both groups but exhibited opposite methylation changes between pre- and post-intervention. Therefore, the identified eDMRs not only capture the time-dependent methylation changes but also reflect exercise intervention.
Assembly: hg38
Supplementary files format and content: Each .rds file contains the corresponding MEDIP R object.

source_name: colonic tissues

extract_protocol:
Genome-wide DNA methylation profiling was performed using MeDIP-seq on both colonic biopsy tissue DNA and cfDNA, following the published methods
genomic DNA was sheared to 200-600bp fragments, denatured to single strands, and immunoprecipitated with a monoclonal antibody against 5-methylcytosine. The enriched methylated DNA fragments were then subjected to high-throughput sequencing using Illumina HiSeq platform

value: colonic tissues


title: WD1297-well-differentiated-liposarcoma

status: Public on Aug 04 2026

type: RNA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: cDNA was hybridized to HG U113A oligonucleotide arrays (Affymetrix, Inc.).

scan_protocol: Fluorescence was measured by laser confocal scanner (Agilent) and converted to signal intensity by means of Affymetrix Microarray Suite v5 software.

data_processing: CEL files were processed and normalized using gcrma methods implemented in the BioConductor package gcrma. Citation: Wu J, Gentry RIwcfJMJ (2023). gcrma: Background Adjustment Using Sequence Information. R package version 2.72.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: surgical specimen

label_protocol: cDNA was synthesized in the presence of oligo(dT)24-T7 from Genset Corp. cRNA was prepared using biotinylated UTP and CTP.

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

tag: tissue

value: well-differentiated liposarcoma

tag: tumor site

value: retroperitoneal

tag: tumor grade

value: low

tag: treatement

value: surgery


title: WD1340-well-differentiated-liposarcoma


title: Control patient 10 Visit 3 Tissue 5mC

type: SRA

description: Library name: C3-10 Tissue 5mC

library_source: genomic

molecule: genomic DNA


title: Control patient 10 Visit 3 cfDNA 5mC

description: Library name: C3-10 cfDNA 5mC

source_name: Serum

value: Serum


title: Nasal turbinate, LacZ, d1133, rep1

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description:
Library name: EK-Hamst-NT-LacZ-113-1_R1_001
Hamst_NT_LacZd113_rep1

library_source: transcriptomic

data_processing:
Low quality nucleotides and adapter sequences were removed from raw reads using trimmomatic PE (v. 0.36; PE, LEADING:3, TRAILING:3, MINLEN:36).
Reads were mapped to golden Syrian hamster genome (BCM_Maur_2.0) using STAR aligner (v. 2.7.9a).
Gene-level count matrix (counts.hamster_NT_RNAseq.txt) was produced using analyzeRepeats function (analyzeRepeats.pl rna GCF_017639785.1/genomic.gtf -raw) in homer (v4.10).
Assembly: Mesocricetus auratus (golden Syrian hamster) genome BCM_Maur_2.0
Supplementary files format and content: Tab-delimited text file containing transcript refSeq ID, transcript information (chromosome/scaffold, start, end, strand, length) and raw counts for each sample.

molecule: polyA RNA

organism: Cricetulus griseus

source_name: Nasal turbinates

growth_protocol: Both female and male Golden Syrian hamsters (Envigo/Inotiv) were used in the study. The animals were housed in temperature and humidity-controlled conditions, with a 12 h light/dark cycle. They were provided ad libitum access to food and water and were used in experiments after a 7-day acclimatization period.

extract_protocol:
frozen tissue samples were homogenized in TRIzolä (Invitrogen) reagent using Precellys lysing kit (CKmix) and the Precellys 24 instrument (Bertin) according to the manufacturer’s instructions
Library preparation was performed at Azenta Life Sciences using poly-A selection

treatment_protocol: Hamsters were anesthetized with isoflurane (induction 4.5%, 450 mL oxygen, maintenance 2% isoflurane, 200 mL air, Vet Medic Animal Health Oy). Hamsters were vaccinated i.n. by pipetting a total of 100 µL of diluted vaccine (50 µL to each nostril). Hamsters received either a prime dose and one booster (2 vac) or prime dose and two boosters (3 vac).All vaccinations were given 14 days after the previous one.

value: Nasal turbinates

tag: time point

tag: genotype

value: WT

tag: Sex

value: Female

tag: treatment

value: Adeno-LacZ intra-nasal

tag: batch


title: Control patient 10 Visit 3 cfDNA Input Control

description: Library name: C3-10 cfDNA IC


title: Bcell-rich region for FL-pt9 ROI A15

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: tFL_TMA_A_20250520_A15_Bcell

data_processing:
Cell segmentation was performed using the MESMER model of DeepCell version 0.12.2(Van Valen et al. 2016; Greenwald et al. 2022), with maxima_threshold set to 0.075 and interior_threshold set to 0.05. The nuclear channel input of MESMER was SYTO13. The membrane channel input of MESMER was a summation of CD3 and CD68. For each marker, the pixel value within the area of each cell, determined by the segmentation mask, was summed and then divided by the area of each cell, and the resulting cell-size scaled sum was set as the expression value for a given marker. Each cell from each core was identified by unique cell label and tissue ID.
Cell phenotyping was performed through iterative rounds of clustering and annotating processes with PhenoGraph based on the phenotyping marker enrichment profiles(Levine et al. 2015). Clustering results were plotted as heatmaps showing the Z-score of each marker within each cluster, and were annotated based on the combination of markers that had the highest Z-score in that cluster. PAX5, CD3 and CD68 were used to annotate the general cell types of B/tumor, T and myeloid cells, respectively. Cells that showed unclear marker enrichment patterns were annotated as “Other” cells.
After an initial round of clustering with PhenoGraph was performed, clusters with clear enrichment patterns were annotated, while clusters with mixed patterns underwent additional rounds of iterative clustering and annotation until all identifiable cells were annotated. To visualize and confirm the assigned annotations, Mantis Viewer(Schiemann et al. 2020) was used to overlay the annotations onto the segmentation mask and the marker image, for visual inspection. A segmentation mask for each annotated cell population was iteratively generated, and these masks were re-uploaded to the GeoMx to guide cell-type specific genome-wide transcriptome extraction.
Assembly: (v1.0) Human NGS Whole Transcriptome Atlas RNA
Supplementary files format and content: Excel containing AOI expression counts and metadata
Library strategy: Spatial Transcriptomics

source_name: Lymph Node

extract_protocol:
FFPE tissue slides were baked in an oven (VWR, 10055-006) at 70°C for 1 hr and thoroughly deparaffinized by immersing in xylenes for 2× 5 minutes. The slides were then rehydrated by a series of graded solutions using a linear stainer (Leica Biosystems, ST4020), with each step proceeding for 3 minutes: 3× xylene, 2× 100% ethanol (EtOH), 2× 95% EtOH, 1× 80% EtOH, 1× 70% EtOH, 3× UltraPure water (Invitrogen 10977-023), and finally left in UltraPure water (Invitrogen 10977-023). Unless otherwise specified, all washes mentioned below were with gentle agitation. Antigen retrieval was performed at 97°C for 20 minutes with pH 9 Target Retrieval Solution (Agilent, S236784-2) using a PT Module (ThermoFisher, A80400012), after which the slides were cooled to room temperature on the benchtop and washed once in 1× PBS for 5 minutes. The RNA probe staining cocktail was prepared according to the Nanostring RNA slide Prep kit (Nanostring, 121300313) using the Nanostring Human Whole Transcriptome Atlas detection probe set (Nanostring, 121401102). The RNA probe cocktail was applied to the tissue slides, covered with a hybridization cover slip (EMS Diasum, 70329-40), and incubated at 37oC for 18 hrs. After hybridization, the tissue slides were first washed twice in Stringent Wash Buffer (mixing 4x SSC (Millipore Sigma, S6639) 1:1 with 100% formamide (Millipore Sigma, 344206-1L-M)) for 5 mins each at 37oC, and twice with 2x SSC for 5 mins each at room temperature (RT) on an orbital shaker .  Tissues were then stained with antibodies against PAX5, CD3 and CD68 for 1 hr at RT, in dark, followed by SYTO13 (100nM) for 10 mins at RT, in dark. The slides were then washed twice in 2x SSC for 2 mins each at RT and scanned on the GeoMx for ROI selection. One 660x660 μm square ROI was drawn in each core, resulting in a total of 72 ROI across the two TMA. Fibrotic areas were excluded from ROI selection for each core. ROIs were selected to achieve the maximum possible coverage of both intra- and inter-follicular regions in cores with distinct follicular structures, while in cores lacking clear follicular structures, ROIs were chosen based on the most representative antibody staining patterns. The spatial coordinates of each ROI were then recorded and used to register the ROI segmentation mask.
After transcriptome capture, unique molecular barcodes for the RNA probes were aspirated from each cell population to 96-well collection plates (Nanostring, 100473). Collection plates were then dried according to Nanostring instructions. Sequencing libraries were prepared by first resuspending each aspirate in 10 µL UltraPure water (Invitrogen 10977-023) and uniquely indexed with the Illumina i5×i7 dual indexing system as part of the Nanostring NGS library preparation kits (Nanostring, 121400201 & 121400202 & 121400203 & 121400204). PCR reactions were performed as follows: 37oC for 30 mins, 50oC for 10 mins, 95oC for 3 mins, followed by 18 cycles of 95oC for 15 s, 65oC for 50 s, 68oC for 30s, followed by a final extension of 68oC for 5 mins and hold indefinitely at 12oC. Next, 4 µL of PCR product from each well of the same plate was pooled and purified with AMPure XP beads (Beckman Coulter A63881) according to Nanostring’s instructions. Finally, QC was performed for the library with the Agilent TapeStation. Equal concentrations of each sub-library were pooled and 5% of PhiX sequencing control (Illumina FC-110-3002) was added to the library. The mixture was then subjected to paired-end sequencing with the NextSeq 2000 platform.

value: Lymph Node

tag: sample id

tag: patient id

tag: disease binary

value: FL

tag: disease fine


title: Nasal turbinate, LacZ, d57, rep3

description:
Library name: EK-Hamst-NT-LacZ-57-3_R1_001
Hamst_NT_LacZd57_rep3

value: Male


title: Nasal turbinate, LacZ, d57, rep2

description:
Library name: EK-Hamst-NT-LacZ-57-2_R1_001
Hamst_NT_LacZd57_rep2


title: Control patient 8 Visit 3 Tissue 5mC

description: Library name: C3-8 Tissue 5mC


title: Nasal turbinate, LacZ, d57, rep1

description:
Library name: EK-Hamst-NT-LacZ-57-1_R1_001
Hamst_NT_LacZd57_rep1


title: Control patient 8 Visit 3 cfDNA 5mC

description: Library name: C3-8 cfDNA 5mC


title: Nasal turbinate, LacZ, d43, rep2

description:
Library name: EK-Hamst-NT-LacZ-43-2_R1_001
Hamst_NT_LacZd43_rep2


title: Control patient 7 Visit 3 cfDNA Input Control

description: Library name: C3-7 cfDNA IC


title: Control patient 8 Visit 3 Tissue Input Control

description: Library name: C3-8 Tissue IC


title: Nasal turbinate, LacZ, d43, rep1

description:
Library name: EK-Hamst-NT-LacZ-43-1_R1_001
Hamst_NT_LacZd43_rep1


title: DD1360-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

value: high


title: Control patient 7 Visit 3 cfDNA 5mC

description: Library name: C3-7 cfDNA 5mC


title: Control patient 6 Visit 3 Tissue Input Control

description: Library name: C3-6 Tissue IC


title: Nasal turbinate, d0, rep3

description:
Library name: EK-Hamst-NT-d0-3_R1_001
Hamst_NT_noXd0_rep3

value: Non


title: Nasal turbinate, d0, rep2

description:
Library name: EK-Hamst-NT-d0-2_R1_001
Hamst_NT_noXd0_rep2


title: Nasal turbinate, d0, rep4

description:
Library name: EK-Hamst-NT-d0-4_R1_001
Hamst_NT_noXd0_rep4


title: Control patient 6 Visit 3 Tissue 5mC

description: Library name: C3-6 Tissue 5mC


title: Control patient 6 Visit 3 cfDNA 5mC

description: Library name: C3-6 cfDNA 5mC


title: Control patient 6 Visit 3 cfDNA Input Control

description: Library name: C3-6 cfDNA IC


title: Nasal turbinate, coS, d113, rep4

description:
Library name: EK-Hamst-NT-coS-113-4_R1_001
Hamst_NT_coSd113_rep4

value: Adeno-coS intra-nasal


title: Control patient 5 Visit 3 Tissue 5mC

description: Library name: C3-5 Tissue 5mC

value: colonic tissues


title: Nasal turbinate, coS, d113, rep3

description:
Library name: EK-Hamst-NT-coS-113-3_R1_001
Hamst_NT_coSd113_rep3


title: Control patient 5 Visit 3 cfDNA Input Control

description: Library name: C3-5 cfDNA IC


title: Nasal turbinate, coS, d113, rep2

description:
Library name: EK-Hamst-NT-coS-113-2_R1_001
Hamst_NT_coSd113_rep2


title: Control patient 5 Visit 3 cfDNA 5mC

description: Library name: C3-5 cfDNA 5mC


title: Nasal turbinate, coS, d57, rep5

description:
Library name: EK-Hamst-NT-coS-57-5_R1_001
Hamst_NT_coSd57_rep5


title: Control patient 3 Visit 3 Tissue Input Control

description: Library name: C3-3 Tissue IC


title: Control patient 3 Visit 3 Tissue 5mC

description: Library name: C3-3 Tissue 5mC


title: Nasal turbinate, coS, d113, rep1

description:
Library name: EK-Hamst-NT-coS-113-1_R1_001
Hamst_NT_coSd113_rep1


title: Nasal turbinate, coS, d57, rep4

description:
Library name: EK-Hamst-NT-coS-57-4_R1_001
Hamst_NT_coSd57_rep4


title: Control patient 3 Visit 3 cfDNA Input Control

description: Library name: C3-3 cfDNA IC


title: Nasal turbinate, coS, d57, rep3

description:
Library name: EK-Hamst-NT-coS-57-3_R1_001
Hamst_NT_coSd57_rep3


title: Nasal turbinate, coS, d57, rep2

description:
Library name: EK-Hamst-NT-coS-57-2_R1_001
Hamst_NT_coSd57_rep2


title: Control patient 3 Visit 3 cfDNA 5mC

description: Library name: C3-3 cfDNA 5mC


title: Nasal turbinate, coS, d57, rep1

description:
Library name: EK-Hamst-NT-coS-57-1_R1_001
Hamst_NT_coSd57_rep1


title: Control patient 2 Visit 3 Tissue Input Control

description: Library name: C3-2 Tissue IC


title: Control patient 2 Visit 3 Tissue 5mC

description: Library name: C3-2 Tissue 5mC


title: Control patient 2 Visit 3 cfDNA Input Control

description: Library name: C3-2 cfDNA IC


title: Nasal turbinate, coS, d43, rep5

description:
Library name: EK-Hamst-NT-coS-43-5_R1_001
Hamst_NT_coSd43_rep5


title: Nasal turbinate, coS, d43, rep4

description:
Library name: EK-Hamst-NT-coS-43-4_R1_001
Hamst_NT_coSd43_rep4


title: Nasal turbinate, coS, d43, rep3

description:
Library name: EK-Hamst-NT-coS-43-3_R1_001
Hamst_NT_coSd43_rep3


title: Control patient 2 Visit 3 cfDNA 5mC

description: Library name: C3-2 cfDNA 5mC


title: Nasal turbinate, coS, d43, rep2

description:
Library name: EK-Hamst-NT-coS-43-2_R1_001
Hamst_NT_coSd43_rep2


title: Exercise patient 11 Visit 3 Tissue 5mC

description: Library name: E3-11 Tissue 5mC


title: Exercise patient 11 Visit 3 cfDNA Input Control

description: Library name: E3-11 cfDNA IC


title: Nasal turbinate, coS, d43, rep1

description:
Library name: EK-Hamst-NT-coS-43-1_R1_001
Hamst_NT_coSd43_rep1


title: HT29_MYC_AID_IAA_SLAM_rep3

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

country: China

institute: Shenzhen University

description:
Library name: HT29_MYC_AID_IAA_SLAM_rep3
HT29_MYC_AID_Ctrl_SLAM_rep3_Tcreadcount_RPM.txt

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on DNBseq G400 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from DNBseq G400 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include transcript count for each sample.

growth_protocol: HT29 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum. LoVo cells were maintained in F12K medium supplemented with 10% fetal bovine serum. For selection of AID clones, Cells transfected with indicated plasmids were cultured with 2 ug/ml puromycin and 5 ug/ml blasticidin.

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Acute degradation of MYC in AID cells was induced by auxin (IAA) treatment, cells were then harvested for transcriptome analysis. For conditional knock-out of Myc in intestinal stem cells, Mycf/f ; Lgr5-CreERT2 mice were intraperitoneally injected with Tamoxifen (TAM) dissolved in corn oil (80mg/kg) daily for there consecutive days, three days post last injection mice were sacrificed and intestinal crypt was harvested for transcriptome analysis.

tag: cell line

tag: cell type

value: Colorectal cancer cell

value: IAA


title: Exercise patient 11 Visit 3 cfDNA 5mC

description: Library name: E3-11 cfDNA 5mC


title: Exercise patient 9 Visit 3 Tissue Input Control

description: Library name: E3-9 Tissue IC


title: HT29_MYC_AID_IAA_rep3

description:
Library name: HT29_MYC_AID_IAA_rep3
HT29_MYC_AID_Ctrl_IAA_rep3_matrix.txt


title: Nasal turbinate, LacZ, d1133, rep3

description:
Library name: EK-Hamst-NT-LacZ-113-3_R2_001
Hamst_NT_LacZd113_rep3


title: Exercise patient 9 Visit 3 cfDNA Input Control

description: Library name: E3-9 cfDNA IC


title: Exercise patient 9 Visit 3 cfDNA 5mC

description: Library name: E3-9 cfDNA 5mC


title: LoVo_MYC_AID_IAA_rep3

description:
Library name: LoVo_MYC_AID_IAA_rep3
LoVo_MYC_AID_Ctrl_IAA_rep3_matrix.txt

source_name: LoVo

value: LoVo


title: HT29_siFOXP1_rep3

description:
Library name: HT29_siFOXP1_rep3
HT29_siCtrl_siFOXP1_rep3_matrix.txt


title: LoVo_MYC_AID_Ctrl_rep3

description:
Library name: LoVo_MYC_AID_Ctrl_rep3
LoVo_MYC_AID_Ctrl_IAA_rep3_matrix.txt

value: Ctrl


title: Exercise patient 8 Visit 3 Tissue Input Control

description: Library name: E3-8 Tissue IC


title: Exercise patient 8 Visit 3 Tissue 5mC

description: Library name: E3-8 Tissue 5mC


title: HT29_siCtrl_rep3

description:
Library name: HT29_siCtrl_rep3
HT29_siCtrl_siFOXP1_rep3_matrix.txt

value: siCtrl


title: Exercise patient 8 Visit 3 cfDNA Input Control

description: Library name: E3-8 cfDNA IC

value: Serum


title: HT29_ETS2_AID_IAA_rep3

description:
Library name: HT29_ETS2_AID_IAA_rep3
HT29_ETS2_AID_Ctrl_IAA_rep3_matrix.txt


title: HT29_ETS2_AID_Ctrl_rep3

description:
Library name: HT29_ETS2_AID_Ctrl_rep3
HT29_ETS2_AID_Ctrl_IAA_rep3_matrix.txt


title: Exercise patient 7 Visit 3 Tissue Input Control

description: Library name: E3-7 Tissue IC


title: Exercise patient 7 Visit 3 Tissue 5mC

description: Library name: E3-7 Tissue 5mC


title: pfoa_EC5_72_rep2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

description: Library name: SF_407

data_processing:
The  quality assessment of all RNA-Seq datasets was conducted using FastQC v0.12.1
Trimming of reads, including removal of low-quality ends and adapters, was performed using cutadapt v4.4_dev with Python 3.8.10 with default parameters.
the trimmed and adapter-clipped raw reads underwent a second round of quality checks using FastQC v0.12.1
The RNA sequencing reads were aligned to the human reference genome assembly GRCh38 using the HISAT2 algorithm and its corresponding genome indexes.
Transcript abundance was determined using the featurecounts function from the Rsubread package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample. EnsemblID on the rows and samples on the columns.

growth_protocol: THP-1 cells (ATCC TIB-202, USA) were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% FBS (Gibco, USA) (culture media). Cells were cultured in 75 cm2 flasks at a density < 1 × 106 cells/ml. Cells were differentiated in 12 well plates, with 500,000 cells/ well (127,000 cells/cm2), in the culture media supplemented with 50 nM of phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, USA) for 48h

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, Germany) according to vendor’s instructions. RNA quality was assessd by Bioanalyzer. Only high quality samples were sequenced.
Novogene NGS RNA Library Prep Set (PT042)

value: macrophage

value: WT

value: PFOA

tag: time

tag: replicate

tag: concentration

tag: concentration unit

value: nM


title: pfoa_EC5_72_rep3

description: Library name: SF_408


title: pfoa_EC5_72_rep1

description: Library name: SF_406


title: Exercise patient 5 Visit 3 Tissue 5mC

description: Library name: E3-5 Tissue 5mC

tag: tissue


title: pfoa_EC5_48_rep3

description: Library name: SF_360


title: pfoa_EC5_48_rep1

description: Library name: SF_358


title: pfoa_EC5_48_rep2

description: Library name: SF_359


title: Exercise patient 4 Visit 3 Tissue Input Control

description: Library name: E3-4 Tissue IC


title: Exercise patient 4 Visit 3 cfDNA Input Control

description: Library name: E3-4 cfDNA IC


title: pfoa_EC5_24_rep1

description: Library name: SF_310


title: Exercise patient 4 Visit 3 cfDNA 5mC

description: Library name: E3-4 cfDNA 5mC


title: pfoa_EC20_72_rep3

description: Library name: SF_402


title: Exercise patient 3 Visit 3 Tissue Input Control

description: Library name: E3-3 Tissue IC


title: pfoa_EC20_72_rep2

description: Library name: SF_401


title: Exercise patient 3 Visit 3 Tissue 5mC

description: Library name: E3-3 Tissue 5mC


title: pfoa_EC20_72_rep1

description: Library name: SF_400


title: Exercise patient 3 Visit 3 cfDNA Input Control

description: Library name: E3-3 cfDNA IC


title: pfoa_EC20_48_rep3

description: Library name: SF_354


title: Exercise patient 3 Visit 3 cfDNA 5mC

description: Library name: E3-3 cfDNA 5mC


title: pfoa_EC20_48_rep2

description: Library name: SF_353


title: Exercise patient 2 Visit 3 Tissue Input Control

description: Library name: E3-2 Tissue IC


title: Mac-rich region for FL-pt11-A ROI A10

description: Library name: tFL_TMA_A_20250520_A10_Mac

value: Lymph Node

value: FL


title: Nasal turbinate, LacZ, d1133, rep2

description:
Library name: EK-Hamst-NT-LacZ-113-2_R1_001
Hamst_NT_LacZd113_rep2

value: Nasal turbinates

value: Male

value: Adeno-LacZ intra-nasal


title: pfoa_EC20_48_rep1

description: Library name: SF_352


title: Exercise patient 2 Visit 3 Tissue 5mC

description: Library name: E3-2 Tissue 5mC


title: pfoa_EC20_24_rep3

description: Library name: SF_306


title: Exercise patient 2 Visit 3 cfDNA Input Control

description: Library name: E3-2 cfDNA IC


title: pfoa_EC20_24_rep2

description: Library name: SF_305


title: Exercise patient 2 Visit 3 cfDNA 5mC

description: Library name: E3-2 cfDNA 5mC


title: pfoa_EC20_24_rep1

description: Library name: SF_304


title: Exercise patient 1 Visit 3 Tissue Input Control

description: Library name: E3-1 Tissue IC


title: pfoa_EC10_72_rep3

description: Library name: SF_405


title: pfoa_EC10_72_rep2

description: Library name: SF_404


title: Exercise patient 1 Visit 3 cfDNA Input Control

description: Library name: E3-1 cfDNA IC


title: pfoa_EC10_72_rep1

description: Library name: SF_403


title: Exercise patient 11 Visit 3 Tissue Input Control

description: Library name: E3-11 Tissue IC


title: Exercise patient 1 Visit 3 cfDNA 5mC

description: Library name: E3-1 cfDNA 5mC


title: pfoa_EC10_48_rep3

description: Library name: SF_357


title: Control patient 10 Visit 1 Tissue Input Control

description: Library name: C1-10 Tissue IC


title: HT29_MYC_AID_Ctrl_rep3

description:
Library name: HT29_MYC_AID_Ctrl_rep3
HT29_MYC_AID_Ctrl_IAA_rep3_matrix.txt


title: HT29_MYC_AID_Ctrl_SLAM_rep3

description:
Library name: HT29_MYC_AID_Ctrl_SLAM_rep3
HT29_MYC_AID_Ctrl_SLAM_rep3_Tcreadcount_RPM.txt


title: Exercise patient 9 Visit 3 Tissue 5mC

description: Library name: E3-9 Tissue 5mC


title: pfoa_EC10_48_rep2

description: Library name: SF_356


title: Control patient 10 Visit 1 cfDNA 5mC

description: Library name: C1-10 cfDNA 5mC


title: pfoa_EC10_24_rep2

description: Library name: SF_308


title: Control patient 8 Visit 1 Tissue Input Control

description: Library name: C1-8 Tissue IC


title: Control patient 8 Visit 1 Tissue 5mC

description: Library name: C1-8 Tissue 5mC


title: pfoa_control_72_rep3

description: Library name: SF_411


title: pfoa_EC10_24_rep1

description: Library name: SF_307


title: Control patient 8 Visit 1 cfDNA 5mC

description: Library name: C1-8 cfDNA 5mC


title: Control patient 8 Visit 1 cfDNA Input Control

description: Library name: C1-8 cfDNA IC


title: Control patient 7 Visit 1 cfDNA Input Control

description: Library name: C1-7 cfDNA IC


title: pfoa_control_48_rep3

description: Library name: SF_363


title: Control patient 7 Visit 1 cfDNA 5mC

description: Library name: C1-7 cfDNA 5mC


title: pfoa_control_48_rep2

description: Library name: SF_362


title: pfoa_control_72_rep2

description: Library name: SF_410


title: Control patient 6 Visit 1 Tissue Input Control

description: Library name: C1-6 Tissue IC


title: pfoa_control_72_rep1

description: Library name: SF_409


title: pfoa_control_48_rep1

description: Library name: SF_361


title: Control patient 6 Visit 1 Tissue 5mC

description: Library name: C1-6 Tissue 5mC


title: pfoa_control_24_rep3

description: Library name: SF_315


title: Control patient 6 Visit 1 cfDNA Input Control

description: Library name: C1-6 cfDNA IC


title: pfoa_control_24_rep2

description: Library name: SF_314


title: pfoa_control_24_rep1

description: Library name: SF_313


title: Control patient 6 Visit 1 cfDNA 5mC

description: Library name: C1-6 cfDNA 5mC


title: Control patient 5 Visit 1 Tissue Input Control

description: Library name: C1-5 Tissue IC


title: 82_cl_pfesa_EC5_72_rep3

description: Library name: SF_251


title: Control patient 5 Visit 1 Tissue 5mC

description: Library name: C1-5 Tissue 5mC


title: Exercise patient 1 Visit 3 Tissue 5mC

description: Library name: E3-1 Tissue 5mC


title: 82_cl_pfesa_EC5_72_rep2

description: Library name: SF_247


title: Control patient 5 Visit 1 cfDNA Input Control

description: Library name: C1-5 cfDNA IC


title: 82_cl_pfesa_EC5_72_rep1

description: Library name: SF_243


title: Control patient 5 Visit 1 cfDNA 5mC

description: Library name: C1-5 cfDNA 5mC


title: 82_cl_pfesa_EC5_48_rep3

description: Library name: SF_167


title: Control patient 3 Visit 1 Tissue Input Control

description: Library name: C1-3 Tissue IC


title: 82_cl_pfesa_EC5_48_rep2

description: Library name: SF_163


title: Control patient 3 Visit 1 Tissue 5mC

description: Library name: C1-3 Tissue 5mC


title: 82_cl_pfesa_EC5_48_rep1

description: Library name: SF_159


title: Control patient 10 Visit 1 Tissue 5mC

description: Library name: C1-10 Tissue 5mC


title: Control patient 3 Visit 1 cfDNA Input Control

description: Library name: C1-3 cfDNA IC


title: Control patient 10 Visit 1 cfDNA Input Control

description: Library name: C1-10 cfDNA IC


title: 82_cl_pfesa_EC5_24_rep3

description: Library name: SF_83


title: pfoa_EC10_48_rep1

description: Library name: SF_355


title: Control patient 3 Visit 1 cfDNA 5mC

description: Library name: C1-3 cfDNA 5mC


title: pfoa_EC10_24_rep3

description: Library name: SF_309


title: 82_cl_pfesa_EC5_24_rep2

description: Library name: SF_79


title: Control patient 2 Visit 1 Tissue Input Control

description: Library name: C1-2 Tissue IC


title: 82_cl_pfesa_EC5_24_rep1

description: Library name: SF_75


title: Control patient 2 Visit 1 cfDNA Input Control

description: Library name: C1-2 cfDNA IC


title: Control patient 2 Visit 1 Tissue 5mC

description: Library name: C1-2 Tissue 5mC


title: 82_cl_pfesa_EC20_72_rep3

description: Library name: SF_249


title: Control patient 2 Visit 1 cfDNA 5mC

description: Library name: C1-2 cfDNA 5mC


title: Nasal turbinate, coS, d113, rep5

description:
Library name: EK-Hamst-NT-coS-113-5_R1_001
Hamst_NT_coSd113_rep5

value: Female

value: Adeno-coS intra-nasal


title: 82_cl_pfesa_EC20_72_rep2

description: Library name: SF_245


title: 82_cl_pfesa_EC20_72_rep1

description: Library name: SF_241


title: Exercise patient 11 Visit 1 Tissue Input Control

description: Library name: E1-11 Tissue IC

value: colonic tissues


title: 82_cl_pfesa_EC20_48_rep3

description: Library name: SF_165


title: Exercise patient 11 Visit 1 Tissue 5mC

description: Library name: E1-11 Tissue 5mC


title: Exercise patient 11 Visit 1 cfDNA Input Control

description: Library name: E1-11 cfDNA IC


title: 82_cl_pfesa_EC20_48_rep2

description: Library name: SF_161


title: 82_cl_pfesa_EC20_48_rep1

description: Library name: SF_157


title: 82_cl_pfesa_EC20_24_rep3

description: Library name: SF_81


title: Exercise patient 11 Visit 1 cfDNA 5mC

description: Library name: E1-11 cfDNA 5mC


title: Exercise patient 9 Visit 1 Tissue Input Control

description: Library name: E1-9 Tissue IC


title: DD693-dedifferentiated-liposarcoma

value: dedifferentiated liposarcoma

tag: tumor site

value: retroperitoneal

tag: tumor grade

value: high

tag: treatement

value: surgery


title: Exercise patient 9 Visit 1 cfDNA Input Control

description: Library name: E1-9 cfDNA IC

value: Serum


title: 82_cl_pfesa_EC20_24_rep2

description: Library name: SF_77

value: macrophage

tag: genotype


title: DD6213-dedifferentiated-liposarcoma


title: 82_cl_pfesa_EC10_72_rep3

description: Library name: SF_250

value: WT

tag: treatment


title: Exercise patient 9 Visit 1 Tissue 5mC

description: Library name: E1-9 Tissue 5mC


title: 82_cl_pfesa_EC20_24_rep1

description: Library name: SF_73


title: Exercise patient 9 Visit 1 cfDNA 5mC

description: Library name: E1-9 cfDNA 5mC


title: Exercise patient 8 Visit 1 Tissue Input Control

description: Library name: E1-8 Tissue IC


title: 82_cl_pfesa_EC10_72_rep2

description: Library name: SF_246


title: 82_cl_pfesa_EC10_72_rep1

description: Library name: SF_242


title: Exercise patient 8 Visit 1 Tissue 5mC

description: Library name: E1-8 Tissue 5mC


title: Exercise patient 8 Visit 1 cfDNA Input Control

description: Library name: E1-8 cfDNA IC


title: 82_cl_pfesa_EC10_48_rep3

description: Library name: SF_166


title: 82_cl_pfesa_EC10_48_rep2

description: Library name: SF_162


title: Exercise patient 8 Visit 1 cfDNA 5mC

description: Library name: E1-8 cfDNA 5mC


title: 82_cl_pfesa_EC10_48_rep1

description: Library name: SF_158


title: Exercise patient 7 Visit 1 Tissue Input Control

description: Library name: E1-7 Tissue IC


title: 82_cl_pfesa_EC10_24_rep3

description: Library name: SF_82


title: Exercise patient 7 Visit 1 Tissue 5mC

description: Library name: E1-7 Tissue 5mC


title: Exercise patient 7 Visit 1 cfDNA Input Control

description: Library name: E1-7 cfDNA IC


title: 82_cl_pfesa_EC10_24_rep2

description: Library name: SF_78


title: 82_cl_pfesa_EC10_24_rep1

description: Library name: SF_74


title: Exercise patient 7 Visit 1 cfDNA 5mC

description: Library name: E1-7 cfDNA 5mC


title: Exercise patient 5 visit 1 cfDNA Input Control

description: Library name: E1-5 cfDNA IC


title: 82_cl_pfesa_control_72_rep1

description: Library name: SF_244


title: Bcell-rich region for FL-pt58 ROI A33

description: Library name: tFL_TMA_A_20250520_A33_Bcell


title: Exercise patient 5 visit 1 Tissue 5mC

description: Library name: E1-5 Tissue 5mC


title: 82_cl_pfesa_control_72_rep2

description: Library name: SF_248


title: 82_cl_pfesa_control_72_rep3

description: Library name: SF_252


title: Exercise patient 5 visit 1 cfDNA 5mC

description: Library name: E1-5 cfDNA 5mC


title: Others-rich region for FL-pt58 ROI A33

description: Library name: tFL_TMA_A_20250520_A33_Others


title: human_esc_cell_rna_3

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: human_esc_cell_rna_3

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

tag: lab

value: Skop


title: 82_cl_pfesa_control_48_rep3

description: Library name: SF_168

value: nM


title: Exercise patient 8 Visit 3 cfDNA 5mC

description: Library name: E3-8 cfDNA 5mC


title: Exercise patient 4 Visit 1 Tissue Input Control

description: Library name: E1-4 Tissue IC


title: 82_cl_pfesa_control_48_rep2

description: Library name: SF_164


title: Exercise patient 5 Visit 3 Tissue Input Control

description: Library name: E3-5 Tissue IC


title: 82_cl_pfesa_control_48_rep1

description: Library name: SF_160


title: Exercise patient 4 Visit 1 Tissue 5mC

description: Library name: E1-4 Tissue 5mC


title: 82_cl_pfesa_control_24_rep3

description: Library name: SF_84


title: Exercise patient 4 Visit 1 cfDNA 5mC

description: Library name: E1-4 cfDNA 5mC


title: 82_cl_pfesa_control_24_rep2

description: Library name: SF_80


title: Exercise patient 4 Visit 1 cfDNA Input Control

description: Library name: E1-4 cfDNA IC


title: 82_cl_pfesa_control_24_rep1

description: Library name: SF_76


title: Exercise patient 3 Visit 1 Tissue 5mC

description: Library name: E1-3 Tissue 5mC


title: adona_EC5_72_rep3

description: Library name: SF_239

value: Branched ADONA


title: adona_EC5_72_rep2

description: Library name: SF_235


title: Exercise patient 3 Visit 1 cfDNA Input Control

description: Library name: E1-3 cfDNA IC


title: Exercise patient 3 Visit 1 Tissue Input Control

description: Library name: E1-3 Tissue IC


title: Exercise patient 3 Visit 1 cfDNA 5mC

description: Library name: E1-3 cfDNA 5mC


title: adona_EC5_48_rep3

description: Library name: SF_155


title: Exercise patient 2 Visit 1 cfDNA Input Control

description: Library name: E1-2 cfDNA IC


title: adona_EC5_48_rep2

description: Library name: SF_151


title: adona_EC5_48_rep1

description: Library name: SF_147


title: Exercise patient 2 Visit 1 Tissue 5mC

description: Library name: E1-2 Tissue 5mC


title: adona_EC5_24_rep3

description: Library name: SF_71


title: adona_EC5_24_rep2

description: Library name: SF_67


title: Exercise patient 1 Visit 1 Tissue 5mC

description: Library name: E1-1 Tissue 5mC


title: Exercise patient 1 Visit 1 cfDNA Input Control

description: Library name: E1-1 cfDNA IC


title: Exercise patient 2 Visit 1 cfDNA 5mC

description: Library name: E1-2 cfDNA 5mC


title: Exercise patient 1 Visit 1 cfDNA 5mC

description: Library name: E1-1 cfDNA 5mC


title: adona_EC20_72_rep2

description: Library name: SF_233


title: adona_EC20_48_rep3

description: Library name: SF_153


title: adona_EC20_48_rep2

description: Library name: SF_149


title: Normal sample of patient 8209

description: Library name: PT 8209 Normal

data_processing:
Briefly, duplicated reads were removed with the deduplicate_bismark tool, and methylation levels were determined using bismark_methylation_extractor. Methylated regions were then annotated with annotatePeaks.pl from the HOMER package (https://pmc.ncbi.nlm.nih.gov/articles/PMC2898526/).
Assembly: hg19
Supplementary files format and content: HypoDMRs_hypo.bed: Hypometheloation peaks
Supplementary files format and content: HyperDMRs_hypo.bed: Hypermetheloation peaks

extract_protocol:
Genomic DNA was extracted from paired normal and tumor colonic tissues of 3 patients with LS–associated CRC.
Briefly, 100–500 ng of high-quality genomic DNA from each sample was digested with the MspI restriction enzyme. Fragmented DNA was then end-repaired, A-tailed, and ligated to methylated sequencing adapters to prevent artificial unmethylated cytosines during amplification. The adapter-ligated DNA fragments were size-selected to enrich for 40–220 bp fragments, followed by bisulfite conversion using a commercial bisulfite conversion kit, which converts unmethylated cytosines to uracils while leaving methylated cytosines unmodified. The converted DNA was PCR amplified, purified, and sequenced on the Illumina HiSeq platform.


title: adona_EC20_48_rep1

description: Library name: SF_145


title: Tumor sample of patient 2726

description: Library name: PT 2726 Tumor


title: Normal sample of patient 2726

description: Library name: PT 2726 Normal


title: Muscle, DHT, Nega, rep4

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: Library name: Mouse_DHT_Nega_rep4

data_processing:
To align the reads, the mm10 (for mouse) or  GRCm38 (for human) reference genomes were employed, utilizing Bowtie2 with the default parameters. Removal of duplicated reads was carried out using Samtools (rmdup). Subsequent analysis focused solely on the uniquely mapped reads.
BigWig files were generated using `bamCoverage` in deepTools (version 3.4.1) with the following options: `--binSize 100 --normalizeUsing CPM`.
To identify AR peaks across samples, peak calling was performed with MACS2 on BAM files merged from biological replicates (n = 4). Peak calling for AR was performed against the corresponding control sample using MACS2 with a P-value cutoff of 0.01 and the following options: --call-summits --nomodel --nolambda.
Assembly: mm10, GRCm38
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: biceps brachii muscle

extract_protocol:
Cryosections (10 µm thick) were individually transferred to wells of a µ-Plate 96 Well Bottom plate (Ibidi, Cat# 89626). Sections were fixed for 5 min in 4% paraformaldehyde prepared in PBS containing 0.3% Triton X-100 and subsequently washed with PBS. Nonspecific binding was blocked sequentially with 5% goat serum in PBS. The sections were incubated overnight at 4°C with the primary antibody diluted in  5% goat serum in PBS. The sections were then incubated with the ChIL probe in PBS containing M.O.M. Protein Concentrate (Vector Laboratories,Cat# BMK-2202) and NaCl at a final concentration of 0.5 M.
ChIL-seq libraries were generated using a previously described ChIL protocol (Harada et al., 2018), with several modifications. The Tn5-binding and fill-in reactions were extended to 1 and 2 hours, respectively. T7 RNA polymerase from Toyobo was used at 100 U per well, and the libraries were amplified by 15 cycles of PCR. Amplified libraries were purified using a DNA Clean & Concentrator column (Zymo Research, Cat# D4013), followed by size selection with AMPure beads (Beckman Coulter, Cat# A63880) at a bead-to-sample volume ratio of 0.5. The resulting libraries had an average fragment-size range of 200 to 500 bp.

value: biceps brachii muscle

tag: Sex

value: male

value: DHT for 2h


title: Muscle, DHT, Nega, rep5

description: Library name: Mouse_DHT_Nega_rep5


title: adona_EC10_72_rep3

description: Library name: SF_238


title: Muscle, DHT, Nega, rep3

description: Library name: Mouse_DHT_Nega_rep3


title: adona_EC10_72_rep2

description: Library name: SF_234


title: Muscle, DHT, Nega, rep2

description: Library name: Mouse_DHT_Nega_rep2


title: adona_EC10_72_rep1

description: Library name: SF_230


title: Muscle, DHT, H3K27ac, rep4

description: Library name: Mouse_DHT_H3K27ac_rep4

tag: chil antibody

value: H3K27ac (MAB, Cat# MABI0309)


title: adona_EC10_48_rep3

description: Library name: SF_154


title: adona_EC10_48_rep2

description: Library name: SF_150


title: adona_EC10_48_rep1

description: Library name: SF_146


title: Muscle, DHT, H3K27ac, rep1

description: Library name: Mouse_DHT_H3K27ac_rep1


title: adona_EC10_24_rep3

description: Library name: SF_70


title: Muscle, DHT, AR, rep8

description: Library name: Mouse_DHT_AR_rep8

value: AR (Abcam, Cat# ab108341)


title: adona_EC10_24_rep2

description: Library name: SF_66


title: adona_EC10_24_rep1

description: Library name: SF_62


title: Muscle, DHT, AR, rep6

description: Library name: Mouse_DHT_AR_rep6


title: adona_control_72_rep3

description: Library name: SF_240


title: Muscle, DHT, AR, rep5

description: Library name: Mouse_DHT_AR_rep5


title: Muscle, DHT, AR, rep7

description: Library name: Mouse_DHT_AR_rep7


title: adona_control_72_rep2

description: Library name: SF_236


title: Muscle, DHT, Nega, rep1

description: Library name: Mouse_DHT_Nega_rep1


title: Exercise patient 2 Visit 1 Tissue Input Control

description: Library name: E1-2 Tissue IC


title: adona_EC5_72_rep1

description: Library name: SF_231


title: adona_control_72_rep1

description: Library name: SF_232


title: Muscle, DHT, AR, rep4

description: Library name: Mouse_DHT_AR_rep4


title: Exercise patient 1 Visit 1 Tissue Input Control

description: Library name: E1-1 Tissue IC


title: adona_EC5_24_rep1

description: Library name: SF_63


title: adona_control_48_rep3

description: Library name: SF_156


title: adona_EC20_72_rep3

description: Library name: SF_237


title: Muscle, DHT, AR, rep3

description: Library name: Mouse_DHT_AR_rep3


title: adona_control_48_rep2

description: Library name: SF_152


title: Muscle, DHT, AR, rep2

description: Library name: Mouse_DHT_AR_rep2


title: adona_EC20_72_rep1

description: Library name: SF_229


title: Tumor sample of patient 8209

description: Library name: PT 8209 Tumor


title: Tumor sample of patient 9677

description: Library name: PT 9677 Tumor


title: Normal sample of patient 9677

description: Library name: PT 9677 Normal


title: adona_control_24_rep3

description: Library name: SF_72


title: Muscle, DHT, AR, rep1

description: Library name: Mouse_DHT_AR_rep1


title: adona_control_48_rep1

description: Library name: SF_148


title: Muscle, control, Nega, rep2

description: Library name: Mouse_Control_Nega_rep2


title: adona_EC20_24_rep3

description: Library name: SF_69


title: adona_control_24_rep2

description: Library name: SF_68


title: adona_control_24_rep1

description: Library name: SF_64


title: Muscle, control, AR, rep8

description: Library name: Mouse_Control_AR_rep8


title: Muscle, control, AR, rep7

description: Library name: Mouse_Control_AR_rep7


title: Muscle, control, AR, rep6

description: Library name: Mouse_Control_AR_rep6


title: pfesa_bp1_EC5_72_rep2

description: Library name: SF_223


title: pfesa_bp1_EC5_72_rep3

description: Library name: SF_227


title: adona_EC20_24_rep2

description: Library name: SF_65


title: adona_EC20_24_rep1

description: Library name: SF_61


title: Muscle, control, H3K27ac, rep4

description: Library name: Mouse_Control_H3K27ac_rep4


title: Muscle, control, Nega, rep1

description: Library name: Mouse_Control_Nega_rep1


title: pfesa_bp1_EC5_48_rep2

description: Library name: SF_139


title: pfesa_bp1_EC5_72_rep1

description: Library name: SF_219


title: pfesa_bp1_EC5_48_rep3

description: Library name: SF_143


title: Muscle, control, H3K27ac, rep3

description: Library name: Mouse_Control_H3K27ac_rep3


title: Muscle, control, H3K27ac, rep2

description: Library name: Mouse_Control_H3K27ac_rep2


title: pfesa_bp1_EC5_48_rep1

description: Library name: SF_135


title: pfesa_bp1_EC5_24_rep3

description: Library name: SF_59


title: Muscle, control, AR, rep5

description: Library name: Mouse_Control_AR_rep5


title: Muscle, control, AR, rep3

description: Library name: Mouse_Control_AR_rep3


title: pfesa_bp1_EC5_24_rep2

description: Library name: SF_55


title: Muscle, control, AR, rep4

description: Library name: Mouse_Control_AR_rep4


title: Muscle, control, H3K27ac, rep1

description: Library name: Mouse_Control_H3K27ac_rep1


title: pfesa_bp1_EC20_72_rep3

description: Library name: SF_225


title: pfesa_bp1_EC5_24_rep1

description: Library name: SF_51


title: Muscle, control, AR, rep2

description: Library name: Mouse_Control_AR_rep2


title: Muscle, control, AR, rep1

description: Library name: Mouse_Control_AR_rep1


title: pfesa_bp1_EC20_72_rep2

description: Library name: SF_221


title: Endometriosis lesion, IL-33 treated, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep4

city: Kingston

first: Katherine

middle: B

last: Zutautas

state: Ontario

address: 18 Stuart St. Rm 853

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

description: Library name: F157

data_processing:
Adaptor sequences and low-quality score bases from the 3′ end (Phred score < 30) were first trimmed using Trimmomatic. Reads shorter than 32 bp were discarded.
Reads were aligned to the GRCm38 assembly of the Mus musculus reference genome using STAR and gene-level read counts were obtained using HTSeq with parameters -m intersection-nonempty -stranded=reverse. Lowly expressed genes were excluded, with an average read count lower than 10 across all samples.
Raw counts were normalized using the trimmed mean of M-values (TMM) method implemented in edgeR and transformed to log2 counts per million (log2CPM) using the voom function in the limma R package.
Assembly: GRCm38
Supplementary files format and content: csv file containing raw counts for each sample

source_name: Endometriosis lesion

extract_protocol:
RNA was isolated from snap frozen mouse endometriosis lesions with the Total RNA Purification Plus Kit (Norgen Biotek, 48300)
RNA libraries for RNAseq were prepared using NEBNext UltraExpress RNA Library Prep Kit as per manufacturers guidelines

treatment_protocol: To generate endometriosis lesions, uterine punch biopsies (4mm) are taken from donor mice and adhered to the inner peritoneal wall of recipients using a veterinary adhesive. Mice were 12-16wks old. 7-days following endometriosis induction, mice were treated with 3 intraperitoneal injections of IL-33 (1ug) or PBS administered every other day across 6 days. In the event of ILC2 adoptive transfer (with either 120,000 or 250,000 cells), ILC2s were administered via intraperitoneal injection the day before IL-33 injections. In the event of lesion transfer experiments, endometrial fragments used for endometriosis induction were transplanted across genotypes - ie. Nmur1iCre-eGFP lesion fragments were placed in Nmur1iCre-eGFPId2fl/fl recipients and vice versa. Genotype specified in column F denotes the genotype of the endometriosis fragment.

value: Endometriosis lesion

value: Nmur1iCre-eGFP Id2fl/fl

value: Endometriosis-induction, IL-33 injection, PBS injection


title: pfesa_bp1_EC20_72_rep1

description: Library name: SF_217


title: pfesa_bp1_EC20_48_rep3

description: Library name: SF_141


title: Endometriosis lesion, IL-33 treated, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep3

description: Library name: F154


title: Endometriosis lesion, IL-33 treated, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep2

description: Library name: F151


title: pfesa_bp1_EC20_48_rep2

description: Library name: SF_137


title: Muscle, DHT, H3K27ac, rep3

description: Library name: Mouse_DHT_H3K27ac_rep3


title: Endometriosis lesion, IL-33 treated, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep1

description: Library name: F147


title: pfesa_bp1_EC20_48_rep1

description: Library name: SF_133


title: pfesa_bp1_EC20_24_rep3

description: Library name: SF_57


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_250k, Nmur1iCre-eGFP Id2fl/fl, rep4

description: Library name: F158

value: Endometriosis-induction, IL-33 injection, ILC2 adoptive transfer with 250,000 cells


title: Muscle, DHT, H3K27ac, rep2

description: Library name: Mouse_DHT_H3K27ac_rep2


title: pfesa_bp1_EC20_24_rep2

description: Library name: SF_53


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_250k, Nmur1iCre-eGFP Id2fl/fl, rep3

description: Library name: F156


title: pfesa_bp1_EC10_72_rep3

description: Library name: SF_226


title: pfesa_bp1_EC20_24_rep1

description: Library name: SF_49


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_250k, Nmur1iCre-eGFP Id2fl/fl, rep2

description: Library name: F152


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_250k, Nmur1iCre-eGFP Id2fl/fl, rep1

description: Library name: F148


title: pfesa_bp1_EC10_72_rep2

description: Library name: SF_222


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFPId2fl/fl lesion in Nmur1iCre-eGFP, rep4

description: Library name: F112


title: pfesa_bp1_EC10_72_rep1

description: Library name: SF_218


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFPId2fl/fl lesion in Nmur1iCre-eGFP, rep3

description: Library name: F110


title: pfesa_bp1_EC10_48_rep3

description: Library name: SF_142


title: pfesa_bp1_EC10_48_rep2

description: Library name: SF_138


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFPId2fl/fl lesion in Nmur1iCre-eGFP, rep2

description: Library name: F107


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFPId2fl/fl lesion in Nmur1iCre-eGFP, rep1

description: Library name: F104


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFP lesion in Nmur1iCre-eGFP Id2fl/fl, rep2

description: Library name: F135


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFP lesion in Nmur1iCre-eGFP Id2fl/fl, rep3

description: Library name: F138


title: pfesa_bp1_EC10_24_rep1

description: Library name: SF_50


title: pfesa_bp1_EC10_24_rep3

description: Library name: SF_58


title: pfesa_bp1_EC10_48_rep1

description: Library name: SF_134


title: pfesa_bp1_EC10_24_rep2

description: Library name: SF_54


title: pfesa_bp1_control_72_rep3

description: Library name: SF_228


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFP lesion in Nmur1iCre-eGFP Id2fl/fl, rep4

description: Library name: F141


title: Endometriosis lesion, IL-33 treated, lesion transfer, Nmur1iCre-eGFP lesion in Nmur1iCre-eGFP Id2fl/fl, rep1

description: Library name: F134


title: Endometriosis lesion, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep4

description: Library name: F126

value: Endometriosis-induction, PBS injection


title: Endometriosis lesion, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep3

description: Library name: F122


title: pfesa_bp1_control_72_rep2

description: Library name: SF_224


title: pfesa_bp1_control_72_rep1

description: Library name: SF_220


title: Endometriosis lesion, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep2

description: Library name: F120


title: pfesa_bp1_control_48_rep3

description: Library name: SF_144


title: Endometriosis lesion, PBS treated, Nmur1iCre-eGFP Id2fl/fl, rep1

description: Library name: F119


title: pfesa_bp1_control_48_rep1

description: Library name: SF_136


title: pfesa_bp1_control_48_rep2

description: Library name: SF_140


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_120k, Nmur1iCre-eGFP Id2fl/fl, rep1

description: Library name: F75

value: Endometriosis-induction, IL-33 injection, ILC2 adoptive transfer with 120,000 cells


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_120k, C57Bl/6J, rep3

description:
Library name: 2RR
Column name in raw_counts.csv: S2RR


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_120k, C57Bl/6J, rep1

description:
Library name: 2L
Column name in raw_counts.csv: S2L


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP, rep4

description: Library name: F50


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_120k, Nmur1iCre-eGFP Id2fl/fl, rep2

description: Library name: F78


title: Endometriosis lesion, IL-33 treated, ILC2 adoptive transfer_120k, C57Bl/6J, rep2

description:
Library name: 2R
Column name in raw_counts.csv: S2R


title: pfhps_EC5_72_rep2

description: Library name: SF_211

value: PFHpS


title: pfesa_bp1_control_24_rep1

description: Library name: SF_52

value: macrophage


title: pfhps_EC5_72_rep3

description: Library name: SF_215

value: WT


title: pfhps_EC5_72_rep1

description: Library name: SF_207


title: pfesa_bp1_control_24_rep2

description: Library name: SF_56


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP, rep2

description: Library name: F41


title: pfesa_bp1_control_24_rep3

description: Library name: SF_60


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP, rep3

description: Library name: F47


title: Endometriosis lesion, IL-33 treated, Id2fl/fl, rep4

description: Library name: F69


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP, rep1

description: Library name: F39


title: pfhps_EC5_48_rep2

description: Library name: SF_127


title: pfhps_EC5_48_rep3

description: Library name: SF_131


title: pfhps_EC5_48_rep1

description: Library name: SF_123


title: pfhps_EC5_24_rep3

description: Library name: SF_47


title: Endometriosis lesion, IL-33 treated, Id2fl/fl, rep2

description: Library name: F57


title: Endometriosis lesion, IL-33 treated, Id2fl/fl, rep3

description: Library name: F59


title: pfhps_EC5_24_rep2

description: Library name: SF_43


title: pfhps_EC20_72_rep3

description: Library name: SF_213


title: Endometriosis lesion, IL-33 treated, Id2fl/fl, rep1

description: Library name: F54


title: pfhps_EC20_72_rep2

description: Library name: SF_209


title: pfhps_EC5_24_rep1

description: Library name: SF_39


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP Id2fl/fl, rep 2

description: Library name: F44


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP Id2fl/fl, rep 3

description: Library name: F51


title: pfhps_EC20_48rep3

description: Library name: SF_129


title: pfhps_EC20_72_rep1

description: Library name: SF_205


title: Endometriosis lesion, IL-33 treated, C57Bl/6J, rep 4

description:
Library name: 1RR
Column name in raw_counts.csv: S1RR


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP Id2fl/fl, rep 1

description: Library name: F42


title: Endometriosis lesion, IL-33 treated, Nmur1iCre-eGFP Id2fl/fl, rep 4

description: Library name: F53


title: pfhps_EC20_48rep2

description: Library name: SF_125


title: pfhps_EC20_48rep1

description: Library name: SF_121


title: Endometriosis lesion, IL-33 treated, C57Bl/6J, rep 2

description:
Library name: 1R
Column name in raw_counts.csv: S1R


title: Endometriosis lesion, IL-33 treated, C57Bl/6J, rep 3

description:
Library name: 1N
Column name in raw_counts.csv: S1N


title: Endometriosis lesion, IL-33 treated, C57Bl/6J, rep1

description:
Library name: 1L
Column name in raw_counts.csv: S1L


title: pfhps_EC20_24_rep3

description: Library name: SF_45


title: pfhps_EC20_24_rep2

description: Library name: SF_41


title: pfhps_EC20_24_rep1

description: Library name: SF_37


title: pfhps_EC10_72_rep2

description: Library name: SF_210


title: pfhps_EC10_72_rep3

description: Library name: SF_214


title: CD11c+ OVA-pulsed BMDCs, wildtype, Rep 4

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

country: Germany

institute: University Leipzig

description: Library name: GA_15

data_processing:
Demultiplexing with bcl2fastq software (Illumina, v2.20)
Trimming and polishing using FASTP (PMID: 30423086)
Reads were mapped against the mouse reference genome (mm10) using HISAT2
Stringtie and the R package Ballgown (PMID: 27560171) were employed for transcript quantification.
DESeq2 (PMID:25516281) normalization.
Assembly: T2Tmouse
Supplementary files format and content: Tab-delimited textfiles containing raw counts
Supplementary files format and content: Comma-delimitet textfiles containing normalized counts

source_name: lung

extract_protocol:
RNA was extracted using the RNeasy Kit (Qiagen)
150 ng of total RNA using the Watchmaker RNA library prep kit with Polaris depletion (Watchmaker Genomics) according to the instructions of the manufacturer.

value: lung

value: bone marrow-derived dendritic cell

value: dendritic cell


title: CD11c+ OVA-pulsed BMDCs, Cd97-/-, Rep 3

description: Library name: GA_14


title: CD11c+ OVA-pulsed BMDCs, wildtype, Rep 3

description: Library name: GA_13


title: CD11c+ OVA-pulsed BMDCs, Cd97-/-, Rep 2

description: Library name: GA_12


title: pfhps_EC10_72_rep1

description: Library name: SF_206

value: nM


title: pfhps_EC10_48_rep3

description: Library name: SF_130


title: CD11c+ OVA-pulsed BMDCs, wildtype, Rep 2

description: Library name: GA_11


title: pfhps_EC10_48_rep2

description: Library name: SF_126


title: pfhps_EC10_48_rep1

description: Library name: SF_122


title: CD11c+ OVA-pulsed BMDCs, wildtype, Rep 1

description: Library name: GA_09


title: CD11c+ OVA-pulsed BMDCs, Cd97-/-, Rep 1

description: Library name: GA_10


title: pfhps_EC10_24_rep3

description: Library name: SF_46


title: pfhps_EC10_24_rep2

description: Library name: SF_42


title: TAC REFLEX heart cells (CD45− GFP−, CD45− GFP+, CD45+ GFP−, CD45+ GFP+), Tag

city: Shimotsuke

first: Takayuki

last: Isagawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

description:
Library name: sample2
Single-cell suspensions were prepared from TAC-operated Cdh5-CreERT2;REFLEX mouse hearts. GFP-positive and GFP-negative cells from both CD45-positive and CD45-negative fractions were pooled for library preparation and sequencing. GFP-positive REFLEX-labeled interacting cells were subsequently selected for downstream analyses.

library_source: transcriptomic single cell

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of sample IsagawaWTA3 were processed as follows. Adapter trimming, quality filtering, and phase-shift base removal of sequencing data was performed by using Cutadapt 4.1. Filtered cell barcode and cDNA reads were annotated and mapped to reference genome (build GRCm39 release-107) by using STARsolo (2.7.10b) and known BD Rhapsody cell barcodes by the following parameters:–clipAdapterType CellRanger4 –outSAMmultNmax 1 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMultimapScoreRange 0 –seedSearchStartLmax 30 –soloType CB_UMI_Complex –soloUMIdedup NoDedup –soloMultiMappers Rescue –soloFeatures Gene GeneFull –soloCBmatchWLtype EditDist_2 –soloUMIlen 8 –soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA –soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 –soloUMIposition 3_10_3_17. We do not perform UMI compression because BD Rhapsody UMI length (8-base and directly attatched polyT) is not sufficient to avoid UMI collision (minimum 10-base is required, Perukhov et al Genome Biol 2018). Resulted non-umi count data was converted to genes x cells matrix file and inflection threshold of the barcode rank plot was detected by using DropletUtils package in R version 4.3.1 (2023-06-16). Valid cell barcodes and backgrounds from inflection threshold * 0.9 to inflection threshold * 1.1 were separated by Dropkick package (Heiser et al Genome Biol 2022).
For STAR index build, small RNA annotations were filtered out from gencode.vM30 gtf file.
Assembly: GRCm39 release-107
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: heart

growth_protocol: Cdh5-CreERT2;REFLEX mice were maintained under specific pathogen-free conditions.

extract_protocol:
Hearts were harvested, dissociated into single-cell suspensions, and CD45-positive and CD45-negative fractions were isolated by FACS.
Pooled single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow for cDNA and/or hashtag library amplification (Shichino S., bioRxiv, 2021). 150 ng of amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

treatment_protocol: Mice were subjected to transverse aortic constriction (TAC).

value: heart

value: Cdh5-CreERT2; REFLEX reporter

value: Transverse aortic constriction (TAC)


title: Microglia, WT_Saline rep3

city: Shanghai

first: Wang

last: Hanqi

address: 800 Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

description:
Library name: WT_Saline_3
Column names in  1_genes_fpkm_expression.txt: WT_Saline_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

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: brain

value: microglia

value: Saline


title: pfhps_control_72_rep3

description: Library name: SF_216


title: Microglia, WT_Saline rep2

description:
Library name: WT_Saline_2
Column names in  1_genes_fpkm_expression.txt: WT_Saline_2


title: TAC REFLEX heart cells(CD45− GFP−, CD45− GFP+, CD45+ GFP−, CD45+ GFP+), WTA

description:
Library name: sample1
Single-cell suspensions were prepared from TAC-operated Cdh5-CreERT2;REFLEX mouse hearts. GFP-positive and GFP-negative cells from both CD45-positive and CD45-negative fractions were pooled for library preparation and sequencing. GFP-positive REFLEX-labeled interacting cells were subsequently selected for downstream analyses.


title: pfhps_EC10_24_rep1

description: Library name: SF_38


title: pfhps_control_72_rep2

description: Library name: SF_212


title: Microglia, WT_Saline rep1

description:
Library name: WT_Saline_1
Column names in  1_genes_fpkm_expression.txt: WT_Saline_1


title: pfhps_control_72_rep1

description: Library name: SF_208


title: Microglia, WT_LPS rep2

description:
Library name: WT_LPS_2
Column names in  1_genes_fpkm_expression.txt: WT_LPS_2

value: LPS


title: pfhps_control_48_rep2

description: Library name: SF_128


title: Microglia, WT_LPS rep3

description:
Library name: WT_LPS_3
Column names in  1_genes_fpkm_expression.txt: WT_LPS_3


title: Microglia, WT_LPS rep1

description:
Library name: WT_LPS_1
Column names in  1_genes_fpkm_expression.txt: WT_LPS_1


title: pfhps_control_48_rep3

description: Library name: SF_132


title: pfhps_control_48_rep1

description: Library name: SF_124


title: Microglia, KO_LPS rep3

description:
Library name: KO_LPS_3
Column names in  1_genes_fpkm_expression.txt: FPR2KO_LPS_3


title: pfhps_control_24_rep3

description: Library name: SF_48


title: Microglia, KO_LPS rep2

description:
Library name: KO_LPS_2
Column names in  1_genes_fpkm_expression.txt: FPR2KO_LPS_2


title: pfhps_control_24_rep2

description: Library name: SF_44


title: Microglia, KO_LPS rep1

description:
Library name: KO_LPS_1
Column names in  1_genes_fpkm_expression.txt: FPR2KO_LPS_1


title: CLP cell, HuFl and AKK, recipient mice 3, scRNAseq

city: Bethesda

first: Guangpu

last: Shi

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

description: Library name: HuFl_AKK3_CLP

data_processing:
Sequencing data were processed with Cell Ranger v9.0.1 (10x Genomics) for demultiplexing and alignment to the Mus musculus reference (GRCm39, Genome Reference Consortium, 2024). Cell doublets were detected and removed using Scrublet v0.2.3. Cells exhibiting high mitochondrial transcript content (≥ 5%) or abnormal gene counts (< 500 or > 8000) were excluded. Expression data were log-normalized and scaled using the Scanpy v1.11.0 in Python v3.10. Dimensionality reduction was performed using Principal Component Analysis (PCA) followed by Uniform Manifold Approximation and Projection (UMAP), and cell clusters were identified with the Leiden algorithm. Cell type annotation was based on computational classification using SingleR v2.8.0 with mouse immune reference data from celldex::ImmGenData v1.16.0 in R v4.4, as well as the expression of canonical cell type marker genes.
Assembly: GRCm39
Supplementary files format and content: filtered_feature_bc_matrix

source_name: lamina propria

extract_protocol:
Cells from colon lamina propria were abeled and sorted for live CD45+ and CD4+ populations. Hash-tagged samples were pooled at equal ratios within each experimental group, combining CD45+ and CD4+ fractions at 1:1 ratio to enrich for CD4+ T cells.
Pooled cells were resuspended in PBS with 0.04% BSA and loaded onto a 10x Genomics Chromium X instrument at 700-1200 cells/µL for single cell 5’ gene expression profiling. Libraries were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) following the manufacturer’s protocol.

value: lamina propria

value: primary cells

value: immune cell

tag: hashtag ids


title: pfesa_bp2_EC5_72_rep3

description: Library name: SF_203


title: pfhps_control_24_rep1

description: Library name: SF_40

value: PFHpS


title: CLP cell, HuFl and AKK, recipient mice 2, scRNAseq

description: Library name: HuFl_AKK2_CLP


title: pfesa_bp2_EC5_72_rep2

description: Library name: SF_199

value: macrophage


title: CLP cell, HuFl and AKK, recipient mice 1, scRNAseq

description: Library name: HuFl_AKK1_CLP


title: CLP cell, HuFl and PBS, recipient mice 3, scRNAseq

description: Library name: HuFl_PBS3_CLP


title: pfesa_bp2_EC5_72_rep1

description: Library name: SF_195

value: WT


title: pfesa_bp2_EC5_48_rep3

description: Library name: SF_119


title: CLP cell, HuFl and PBS, recipient mice 2, scRNAseq

description: Library name: HuFl_PBS2_CLP


title: pfesa_bp2_EC5_48_rep2

description: Library name: SF_115


title: pfesa_bp2_EC5_48_rep1

description: Library name: SF_111


title: CLP cell, HuFl and PBS, recipient mice 1, scRNAseq

description: Library name: HuFl_PBS1_CLP


title: pfesa_bp2_EC5_24_rep3

description: Library name: SF_35


title: R_Saline_sTREM2_4

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description:
Library name: Sample 59
mRNA expression in mouse striatum

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. Genes expressed in ≤3 cells were removed. Cells were filtered using dataset-specific thresholds for detected genes, UMI counts, and mitochondrial content: LID (nFeature_RNA 300–4,000; nCount_RNA <20,000; percent.mt <5%), LID_PLX (nFeature_RNA 300–5,000; nCount_RNA <15,000; percent.mt <1%), and LID_sTREM2 (nFeature_RNA 300–6,000; nCount_RNA <35,000; percent.mt <5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.2.2 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: striatum

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: striatum

value: Male

tag: age


title: R_Saline_sTREM2_3

description:
Library name: Sample 58
mRNA expression in mouse striatum


title: R_Saline_sTREM2_2

description:
Library name: Sample 57
mRNA expression in mouse striatum


title: R_Saline_sTREM2_1

description:
Library name: Sample 56
mRNA expression in mouse striatum


title: pfesa_bp2_EC5_24_rep1

description: Library name: SF_27

tag: cell line


title: pfesa_bp2_EC20_72_rep3

description: Library name: SF_201

tag: cell type


title: pfesa_bp2_EC5_24_rep2

description: Library name: SF_31

tag: time


title: R_Saline_GFP_3

description:
Library name: Sample 54
mRNA expression in mouse striatum


title: pfesa_bp2_EC20_72_rep2

description: Library name: SF_197

tag: replicate


title: pfesa_bp2_EC20_72_rep1

description: Library name: SF_193

tag: concentration


title: 3D muscle construct, SnC cocultured, biol rep3

city: Seoul

first: Tae-Hwan

last: Gil

address: 46, Gaeunsa 2-gil, Seongbuk-gu, Seoul, Republic of Korea

country: South Korea

institute: Korea university, College of Medicine

description: Library name: SnC_co3

data_processing:
A quality control of raw sequencing data was performed using FastQC
Sequenced reads were trimmed for adapter sequences and low-quality filtered using bbduk
Then the clean reads were mapped to the reference genome using STAR
The quantification of reads was processed using HTSeq-count
The Read Counts were processed based on TMM+CPM normalization method using using Python “conorm” package
Assembly: Mus musculus reference genome GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file containing raw read counts per gene for this sample

source_name: 3D muscle model

growth_protocol: C2C12 myoblasts were embedded within muscle tissue–derived extracellular matrix (mdECM). growth media consisted of DMEM (Corning, CV-01-090-17, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, #16140071, USA) and 100 U/ml penicillin and 100 µg/ml streptomycin (P/S; Gibco, #15140122, USA). The cells were cultured in growth media.  for 2 days at 37 ℃ in 5% CO2 for 2days.

extract_protocol:
To isolate RNA from muscle stem cells and 3D muscle tissues, TRIzol™ Reagent (Invitrogen, #15596018, USA) and the RNA Mini-Prep Kit (Zymo Research, #R2052, USA) were used according to the manufacturer's protocol. 100ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen) according to the manufacturer’s instructions. Briefly, an oligo-dT primer containing an Illumina-compatible sequence was used for first-strand cDNA synthesis, followed by RNA removal and second-strand synthesis primed by a random primer containing an Illumina linker sequence. Double-stranded libraries were purified using magnetic beads and PCR-amplified to add full Illumina adapter sequences. Sequencing was performed as single-end 75 bp reads on an Illumina NextSeq 550.

treatment_protocol: After 2 days, to induce differentiation, the medium was replaced with a muscle differentiation media composed of DMEM supplemented with 10% equine serum (Cytiva, #SH3007403, USA) and 100 U/ml penicillin and 100 µg/ml streptomycin for 10 days

value: 3D muscle model

value: myoblast

value: myogenic differentiation media


title: 3D muscle construct, SnC cocultured, biol rep2

description: Library name: SnC_co2


title: R_Saline_GFP_4

description:
Library name: Sample 55
mRNA expression in mouse striatum


title: 3D muscle construct, SnC cocultured, biol rep1

description: Library name: SnC_co1


title: pfesa_bp2_EC20_48_rep3

description: Library name: SF_117

tag: concentration unit

value: nM


title: R_Saline_GFP_1

description:
Library name: Sample 52
mRNA expression in mouse striatum

tag: tissue


title: R_Saline_GFP_2

description:
Library name: Sample 53
mRNA expression in mouse striatum


title: 3D muscle construct, irradiated, biol rep2

description: Library name: SnC_2


title: Saline_sTREM2_4

description:
Library name: Sample 51
mRNA expression in mouse striatum

value: lesioned saline-treated sTREM2-injected


title: pfesa_bp2_EC20_48_rep2

description: Library name: SF_113


title: 3D muscle construct, irradiated, biol rep3

description: Library name: SnC_3


title: 3D muscle construct, irradiated, biol rep1

description: Library name: SnC_1


title: 3D muscle construct, normal. biol rep3

description: Library name: Ctrl_3


title: Others-rich region for FL-pt11-A ROI A10

description: Library name: tFL_TMA_A_20250520_A10_Others

value: Lymph Node

tag: sample id

tag: patient id

tag: disease binary

value: FL

tag: disease fine


title: pfesa_bp2_EC20_48_rep1

description: Library name: SF_109

tag: genotype

tag: treatment


title: Saline_sTREM2_3

description:
Library name: Sample 50
mRNA expression in mouse striatum

tag: Sex


title: 3D muscle construct, normal, biol rep2

description: Library name: Ctrl_2


title: 3D muscle construct, normal, biol rep1

description: Library name: Ctrl_1


title: pfesa_bp2_EC20_24_rep3

description: Library name: SF_33


title: Ahrfl/fl VillinCre+, Female, rep4

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

description: Library name: V337

data_processing:
Sequencing reads were mapped to the Ensembl reference mouse transcriptome GRCm39 cDNA (v113) using kallisto (v0.51.1) and were subsequently quantified as read counts and tpm at the gene level by the R package tximport (v1.34.0) based on the Ensembl GRCm39 v113 GTF annotation file.
A total of 21,462 protein-coding genes were selected for downstream analysis.
Assembly: Ensembl GRCm39 mouse reference transcriptome cDNA (v113)
Supplementary files format and content: tab-delimited text file includes raw counts of all analyzed protein-coding genes for each sample
Supplementary files format and content: tab-delimited text file includes tpm values of all analyzed protein-coding genes for each sample

source_name: duodenum

extract_protocol:
Total RNA was isolated from tissue samples using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
Sequencing libraries were generated from total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer's standard protocol.

treatment_protocol: Mice were fed a HFD for 12 weeks. After sacrifice, the mice were flushed with PBS and intestines were extracted. The intestine was cut into sections, duodenum, jejunum and ileum, from which the duodenum was taken for analysis.

value: duodenum

value: female

value: 12 weeks HFD

value: Ahrfl/fl-Villin- Cre+

value: AAV8-PCSK9 overexpression +12w HFD


title: Ahrfl/fl VillinCre+, Female, rep1

description: Library name: V332


title: Ahrfl/fl VillinCre+, Female, rep3

description: Library name: V336


title: Saline_sTREM2_1

description:
Library name: Sample 48
mRNA expression in mouse striatum


title: Ahrfl/fl VillinCre+, Female, rep2

description: Library name: V335


title: Ahrfl/fl VillinCre−, Female, rep4

description: Library name: V329

value: Ahrfl/fl-Villin- Cre-


title: Saline_sTREM2_2

description:
Library name: Sample 49
mRNA expression in mouse striatum


title: pfesa_bp2_EC20_24_rep2

description: Library name: SF_29

value: macrophage


title: Ahrfl/fl VillinCre−, Female, rep2

description: Library name: V327


title: Ahrfl/fl VillinCre−, Female, rep3

description: Library name: V328


title: pfesa_bp2_EC20_24_rep1

description: Library name: SF_25

value: WT


title: L_DOPA_sTREM2_4

description:
Library name: Sample 47
mRNA expression in mouse striatum

value: striatum

value: lesioned L-DOPA-treated sTREM2-injected


title: pfesa_bp2_EC10_72_rep3

description: Library name: SF_202


title: Ahrfl/fl VillinCre−, Female, rep1

description: Library name: V323


title: L_DOPA_sTREM2_3

description:
Library name: Sample 46
mRNA expression in mouse striatum

value: Male


title: pfesa_bp2_EC10_72_rep2

description: Library name: SF_198


title: Ahrfl/fl VillinCre+, Male, rep4

description: Library name: V321

value: male


title: L_DOPA_sTREM2_2

description:
Library name: Sample 45
mRNA expression in mouse striatum


title: Ahrfl/fl VillinCre+, Male, rep3

description: Library name: V320


title: pfesa_bp2_EC10_72_rep1

description: Library name: SF_194


title: L_DOPA_sTREM2_1

description:
Library name: Sample 44
mRNA expression in mouse striatum


title: pfesa_bp2_EC10_48_rep2

description: Library name: SF_114


title: pfesa_bp2_EC10_48_rep3

description: Library name: SF_118


title: Saline_GFP_4

description:
Library name: Sample 43
mRNA expression in mouse striatum

value: lesioned saline-treated GFP-injected


title: Ahrfl/fl VillinCre+, Male, rep1

description: Library name: V317


title: Ahrfl/fl VillinCre−, Male, rep2

description: Library name: V312


title: Ahrfl/fl VillinCre−, Male, rep4

description: Library name: V315


title: Ahrfl/fl VillinCre−, Male, rep3

description: Library name: V314


title: Saline_GFP_3

description:
Library name: Sample 42
mRNA expression in mouse striatum


title: Ahrfl/fl VillinCre+, Male, rep2

description: Library name: V319


title: Ahrfl/fl VillinCre−, Male, rep1

description: Library name: V311


title: Nasal turbinate, LacZ, d43, rep3

description:
Library name: EK-Hamst-NT-LacZ-43-3_R1_001
Hamst_NT_LacZd43_rep3

value: Nasal turbinates

tag: time point

value: Female

value: Adeno-LacZ intra-nasal

tag: batch


title: pfesa_bp2_EC10_48_rep1

description: Library name: SF_110

value: nM


title: Control patient 8 Visit 3 cfDNA Input Control

description: Library name: C3-8 cfDNA IC

data_processing:
To analyze the MeDIP-seq data, high-quality reads from MeDIP-seq were aligned to the human reference genome (GRCH38/hg38) using bwa-mem2. Mapped reads were processed using MEDIPS R package58 to compute genome-wide methylation signals in every 300bp sliding window. The resulting count data were normalized using the trimmed mean of M-values (TMM) methods to account for differences in library size across samples. Peaks whose midpoint was located from 2000bp upstream to 500bp downstream of transcription start sites (TSS) were defined as promoter peaks. The promoter methylation level was quantified by averaging the Relative Methylation Score (RMS) across all windows covering promoter region. RMS is a normalized metric that adjusts for sequencing read coverage and CpG density, enabling cross-sample and locus-level comparisons. For differential methylation analysis, DMRs in both tissue and cfDNA were first identified separately within the exercise and control groups by comparing pre- and post-intervention using a generalized linear model (GLM)-based approach in MEDIPS package, which utilizes the edgeR framework to model over-dispersed count data via a negative binomial distribution73. FDR correction was performed using Benjamini–Hochberg (BH). However, no windows met the adjusted p-value threshold of 0.05 during DMR detection from tissue-derived DNA. Therefore, in this study, DMRs were defined as regions with a minimum coverage of 5 reads per window, an absolute log2 fold change (|log2FC|) ≥2, and an unadjusted p-value < 0.01for both cfDNA- and tissue-derived datasets. Exercise-induced DMRs (eDMRs) were identified based on two criteria: (1) DMRs that appeared exclusively in the exercise group but not in the control group, and (2) DMRs that were detected in both groups but exhibited opposite methylation changes between pre- and post-intervention. Therefore, the identified eDMRs not only capture the time-dependent methylation changes but also reflect exercise intervention.
Assembly: hg38
Supplementary files format and content: Each .rds file contains the corresponding MEDIP R object.

extract_protocol:
Genome-wide DNA methylation profiling was performed using MeDIP-seq on both colonic biopsy tissue DNA and cfDNA, following the published methods
genomic DNA was sheared to 200-600bp fragments, denatured to single strands, and immunoprecipitated with a monoclonal antibody against 5-methylcytosine. The enriched methylated DNA fragments were then subjected to high-throughput sequencing using Illumina HiSeq platform

value: Serum


title: Nasal turbinate, d0, rep1

description:
Library name: EK-Hamst-NT-d0-1_R1_001
Hamst_NT_noXd0_rep1

value: Non


title: LongDD_24_3

city: Tsukuba

first: Shuhei

last: Suzuki

address: 1-1-1 Tennodai, Tsukuba, Ibaraki

institute: University of Tsukuba

description: Library name: Sample 36

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 22.0.1; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: CSV files were generated usingCLC Genomics Workbench (Version 22.0.1; Qiagen, Redwood City, CA).

source_name: whole bladder

growth_protocol: Central nervous Bmal1 cKO mice were kept in constant darkness (DD) for 2 days or 8 weeks.

extract_protocol:
RNA was extracted from mouse samples using NucleoSpin® RNA (Takara Bio, Shiga, Japan)
Total RNA (500 ng) was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's protocol. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

value: whole bladder

value: female

value: CaMKII-Cre; Bmal1fx/fx

value: LongDD


title: Saline_GFP_2

description:
Library name: Sample 41
mRNA expression in mouse striatum

tag: age


title: LongDD_24_2

description: Library name: Sample 35


title: pfesa_bp2_EC10_24_rep3

description: Library name: SF_34

tag: cell line

value: macrophage


title: LongDD_24_1

description: Library name: Sample 34


title: LongDD_20_3

description: Library name: Sample 33


title: pfesa_bp2_EC10_24_rep2

description: Library name: SF_30

tag: cell type

value: WT


title: L_DOPA_GFP_4

description:
Library name: Sample 39
mRNA expression in mouse striatum

value: striatum

value: lesioned L-DOPA-treated GFP-injected


title: pfesa_bp2_EC10_24_rep1

description: Library name: SF_26

tag: time


title: Saline_GFP_1

description:
Library name: Sample 40
mRNA expression in mouse striatum

value: Male


title: LongDD_20_2

description: Library name: Sample 32


title: LongDD_20_1

description: Library name: Sample 31


title: pfesa_bp2_control_72_rep3

description: Library name: SF_204

tag: replicate


title: L_DOPA_GFP_2

description:
Library name: Sample 37
mRNA expression in mouse striatum


title: LongDD_16_1

description: Library name: Sample 28


title: L_DOPA_GFP_1

description:
Library name: Sample 36
mRNA expression in mouse striatum


title: LongDD_12_3

description: Library name: Sample 27


title: LongDD_12_2

description: Library name: Sample 26


title: LongDD_16_3

description: Library name: Sample 30


title: pfesa_bp2_control_72_rep2

description: Library name: SF_200

tag: concentration


title: L_DOPA_GFP_3

description:
Library name: Sample 38
mRNA expression in mouse striatum


title: LongDD_16_2

description: Library name: Sample 29


title: LongDD_12_1

description: Library name: Sample 25


title: pfesa_bp2_control_72_rep1

description: Library name: SF_196

tag: concentration unit


title: LongDD_08_2

description: Library name: Sample 23

tag: tissue


title: L-dopa_x1_Ctrl_3

description:
Library name: Sample 35
mRNA expression in mouse striatum

value: lesioned acute L-DOPA treatment


title: LongDD_08_3

description: Library name: Sample 24


title: LongDD_04_3

description: Library name: Sample 21


title: L-dopa_x1_Ctrl_2

description:
Library name: Sample 34
mRNA expression in mouse striatum


title: LongDD_08_1

description: Library name: Sample 22


title: LongDD_04_2

description: Library name: Sample 20


title: LongDD_04_1

description: Library name: Sample 19


title: pfesa_bp2_control_48_rep1

description: Library name: SF_112


title: pfesa_bp2_control_48_rep3

description: Library name: SF_120


title: ShortDD_24_2

description: Library name: Sample 17

value: ShortDD


title: L-dopa_x1_Ctrl_1

description:
Library name: Sample 33
mRNA expression in mouse striatum


title: Control patient 5 Visit 3 Tissue Input Control

first: Eduardo

last: Vilar-Sanchez

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: C3-5 Tissue IC

value: colonic tissues


title: pfesa_bp2_control_48_rep2

description: Library name: SF_116


title: ShortDD_24_3

description: Library name: Sample 18


title: L-dopa_PLXrev_2

description:
Library name: Sample 31
mRNA expression in mouse striatum

value: lesioned L-DOPA-treated PLX reversal diet


title: ShortDD_24_1

description: Library name: Sample 16


title: pfesa_bp2_control_24_rep2

description: Library name: SF_32


title: ShortDD_20_2

description: Library name: Sample 14


title: pfesa_bp2_control_24_rep3

description: Library name: SF_36


title: ShortDD_20_3

description: Library name: Sample 15


title: L-dopa_PLXrev_1

description:
Library name: Sample 30
mRNA expression in mouse striatum


title: L-dopa_PLXrev_3

description:
Library name: Sample 32
mRNA expression in mouse striatum


title: ShortDD_16_3

description: Library name: Sample 12


title: ShortDD_20_1

description: Library name: Sample 13


title: pfesa_bp2_control_24_rep1

description: Library name: SF_28


title: L-dopa_PLX_3

description:
Library name: Sample 29
mRNA expression in mouse striatum

value: lesioned L-DOPA-treated PLX diet


title: ShortDD_16_2

description: Library name: Sample 11


title: pfos_EC5_72_rep3

description: Library name: SF_191

value: PFOS

value: nM


title: ShortDD_16_1

description: Library name: Sample 10


title: L-dopa_PLX_2

description:
Library name: Sample 28
mRNA expression in mouse striatum


title: ShortDD_12_3

description: Library name: Sample 9


title: L-dopa_PLX_1

description:
Library name: Sample 27
mRNA expression in mouse striatum


title: pfos_EC5_72_rep2

description: Library name: SF_187


title: pfos_EC5_72_rep1

description: Library name: SF_183


title: ShortDD_12_2

description: Library name: Sample 8


title: ShortDD_08_3

description: Library name: Sample 6