title: MSK-109, CD45+, run 2, scATACseq

description: 10x Genomics

data_processing:
Raw sequencing reads were processed using 10x Cell Ranger ATAC pipeline.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, comma-separated values files, and (h5) Hierarchical Data Format 5 Files

extract_protocol:
Tumor tissue from glioma operations was collected immediately after resection and transported in MACS storage solution (Miltenyi Biotec, Germany) within 15 min to the laboratory. Resected tissue was morselized into small pieces under sterile conditions using sterile scalpels, triturated using pipettes, then transferred to a 50 mL falcon tube (Corning, USA) for incubation with papain (37°C, 25 min) (Worthington, USA) according to manufacturer instructions. After incubation HBSS without magnesium or calcium was then added to make up to 50 ml and the sample was centrifuged (300×g, 5 min, 4°C) and supernatant aspirated before being passed through a 70um cell strainer (BD Biosciences, USA). Erythrocytes were removed by resuspending and incubating the obtained pellet in 5 ml of 1X RBC Lysis Buffer (eBioscience, USA) for 10 min, followed by centrifugation (300×g, 5 min,4°C). Residual myelin and extracellular debris were eliminated using the Debris Removal Kit (Miltenyi Biotec, Germany). Cell counts were determined using an automated cell counter (Nexcelom Bioscience, USA) after resuspending the pellet in PBS. A portion of the single-cell suspensions were then enriched for CD45+ cells by CD45-MACS enrichment (Miltenyi Biotec, Germany). The final cell suspensions were centrifuged again (350×g, 10 min, RT) and isolated unsorted, CD45+, and CD45- cells were stored in Bambanker (Wako, Japan).
For the scATACexperiment, we followed 10x single-cellATAC–seq protocol from 10x Genomics Chromium (Single CellATACReagent Kits User Guide). Briefly, cells werecentrifuged (300g, 5 min, 4 °C) and permeabilized with 100 μl chilled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL-CA630, 0.01% digitonin and 1% BSA). The samples were incubated on ice for 3-5 min and resuspended with 1 ml chilled wash buffer (10 mM Tris-HCl pH 7.4, 10 mMNaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA). After centrifugation (500g, 5 min, 4 °C), the pellets were resuspended in 100 μl chilled Nuclei buffer (10xGenomics). Nuclei were counted using a haemocytometer, and finally the nucleus concentration was adjusted to 3,000 nuclei per μl. We used 15,360 nuclei as inputfor tagmentation. Nuclei were diluted to 5 μl with 1× nuclei buffer (10x Genomics) and mixed withATACbuffer (10x Genomics) andATACenzyme (10x Genomics) fortagmentation (60 min, 37 °C). Single-cellATAC–seq libraries were generated using the Chromium Chip E Single CellATACkit (10x Genomics, 1000086) and indexes(Chromium i7 Multiplex Kit N, Set A, 10x Genomics, 1000084) following the manufacturer’s instructions. Final libraries were quantified using a Qubit fluorimeter (LifeTechnologies) and the nucleosomal pattern was verified using a BioAnalyzer (Agilent). Libraries were sequenced on a NovaqSeq6000 (Illumina) with the following readlengths: 50 + 8 + 16 + 50 (Read1 + Index1 + Index2 + Read2).


title: MSK-102, CD45+, run 2, scATACseq

status: Public on Nov 30 2025

type: SRA

city: New York

first: Kenny

last: Yu

state: NY

address: 1275 York Ave

department: Neurosurgery

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain Tumor (Glioma)

tag: tissue

value: Brain Tumor (Glioma)

tag: cell type

value: Leukocytes

tag: genotype

value: IDH-wildtype


title: MSK-108, CD45+, run 2, scATACseq

description: 10x Genomics

value: IDH-mutant


title: MSK-101, CD45+, run 2, scATACseq

description: 10x Genomics


title: MSK-115, CD45+, scATACseq

description: 10x Genomics


title: MSK-NB1, CD45+, scATACseq

description: 10x Genomics

source_name: Normal Brain (Autopsy)

value: Normal Brain (Autopsy)


title: MSK-113, CD45+, scATACseq

description: 10x Genomics


title: MSK-112, CD45+, scATACseq

description: 10x Genomics


title: MSK-111, CD45+, scATACseq

description: 10x Genomics


title: MSK-114, CD45+, scATACseq

description: 10x Genomics


title: MSK-110, CD45+, scATACseq

description: 10x Genomics


title: MSK-109, CD45+, run 1, scATACseq

description: 10x Genomics


title: MSK-108, CD45+, run 1, scATACseq

description: 10x Genomics


title: MSK-105, CD45+, scATACseq

description: 10x Genomics


title: MSK-103, CD45+, scATACseq

description: 10x Genomics


title: MSK-102, CD45+, run 1, scATACseq

description: 10x Genomics


title: MSK-104, CD45+, scATACseq

description: 10x Genomics


title: MSK-105, CD45+, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned to the GRCh38 reference genome using Cell Ranger (v7.1).
Assembly: hg38
Supplementary files format and content: comma-separated value files and matrix files

molecule: total RNA

extract_protocol:
Tumor tissue from glioma operations was collected immediately after resection and transported in MACS storage solution (Miltenyi Biotec, Germany) within 15 min to the laboratory. Resected tissue was morselized into small pieces under sterile conditions using sterile scalpels, triturated using pipettes, then transferred to a 50 mL falcon tube (Corning, USA) for incubation with papain (37°C, 25 min) (Worthington, USA) according to manufacturer instructions. After incubation HBSS without magnesium or calcium was then added to make up to 50 ml and the sample was centrifuged (300×g, 5 min, 4°C) and supernatant aspirated before being passed through a 70um cell strainer (BD Biosciences, USA). Erythrocytes were removed by resuspending and incubating the obtained pellet in 5 ml of 1X RBC Lysis Buffer (eBioscience, USA) for 10 min, followed by centrifugation (300×g, 5 min,4°C). Residual myelin and extracellular debris were eliminated using the Debris Removal Kit (Miltenyi Biotec, Germany). Cell counts were determined using an automated cell counter (Nexcelom Bioscience, USA) after resuspending the pellet in PBS. A portion of the single-cell suspensions were then enriched for CD45+ cells by CD45-MACS enrichment (Miltenyi Biotec, Germany). The final cell suspensions were centrifuged again (350×g, 10 min, RT) and isolated unsorted, CD45+, and CD45- cells were stored in Bambanker (Wako, Japan).
Cells were loaded for GEM generation using the 10x Genomics Chromium platform. 3’ RNA gene expression libraries were prepared using the Chromium Single-cell 3′ Reagent Kit v3 (10x Genomics, USA) according to the manufacturer’s guidelines.  Final libraries were quantified using a Qubit fluorimeter (Life Technologies, USA) and the nucleosomal pattern was verified using a BioAnalyzer (Agilent Technologies, USA). scRNA libraries were sequenced on a NovaSeq6000 (Illumina, USA).


title: MSK-101, CD45+, run 1, scATACseq

description: 10x Genomics


title: MSK-106, CD45+, scATACseq

description: 10x Genomics


title: MSK-150, CD45+, mGAM, input, ChIPseq

data_processing:
ChIP-seq sequencing reads were trimmed and filtered for quality (Q15) and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates of Picard Tools (v2.16.0). To ascertain enriched regions, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 and scored against matched input as the control. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/ hg38.blacklist.bed.gz)
Assembly: hg38
Supplementary files format and content: BIGWIG, narrowPeak

extract_protocol:
Freshly harvested cells were sorted, crosslinked in PBS with 1% formaldehyde for 10 min at room temperature, quenched with 0.125M glycine for 5 min and washed in PBS with protease inhibitors (Millipore Sigma, USA) three times before being snap frozen in cryotubes and sent to MSKCC’s Epigenetics Research Innovation Lab for processing. Low input ChIP-seq was performed using the Low-Cell ChIP-Seq kit (Active Motif, USA) following the manufacturer’s instructions, with the subsequent modifications. After thawing, the fixed cells were resuspended in 130uL of ChIP buffer, transferred into a microTUBE-130 (Covaris, USA) and sonicated using a Covaris E220 ultra-sonicator, with the following parameters: PIP=140, Duty Factor=5, CBP/Burst per sec=200, Time = 900s. After sonication, samples were transferred to siliconized micro-centrifuge tubes and centrifuged at 18,000g for 2 minutes at 4°C. After centrifugation, the supernatants were transferred to new labeled siliconized micro-centrifuge tubes. One percent of each sample was used as input. All samples and inputs were snap frozen and stored at -80°C. After the chromatin being processed following the manufacturer’s recommendations, all samples and inputs were de-crosslinked overnight at 65°C. DNA was finally isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research, USA) following the manufacturer’s instructions.
After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit (Takara Bio Inc., Japan) following the manufacturer’s instructions, purified with SPRIselect magnetic beads (Beckman Coulter), quantified using a Qubit Flex fluorometer (ThermoFisher Scientific, USA) and profiled using a TapeStation 2200 (Agilent Technologies, USA).

value: Myeloid cells

tag: subset

value: mGAM


title: MSK-150, CD45+, mGAM, FOSL2, ChIPseq

tag: chip antibody

value: anti-human FOSL2 (EpigenTek cat# A71553)


title: MSK-144, CD45+, non-mGAM, FOSL2, ChIPseq

value: non-mGAM


title: MSK-144, CD45+, mGAM, FOSL2, ChIPseq


title: MSK-138, CD45+, mGAM, FOSL2, ChIPseq


title: MSK-150, CD45+, non-mGAM, FOSL2, ChIPseq


title: MSK-NB2, CD45+, scATACseq

description: 10x Genomics


title: MCF-7 siMETTL3 Estrogen #3

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

library_source: transcriptomic

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

growth_protocol: MCF-7 cells were maintained at 37C and 5% CO2 in phenol red containing RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin-glutamine, 2 mM L-Glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with on-column DNase treatment
Illumina

treatment_protocol: siRNA-mediated functional depletion of METTL3 was performed in vehicle (ethanol) and estrogen treated MCF-7 breast cancer cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. ON-TARGETplus siRNA–SMART pools for Human METTL3 (L-005170-02-0005) (GE DharmaconTM) and ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.

value: Breast Cancer Cells

tag: cell line

tag: transfection

value: METTL3 depleted

tag: treatment

value: Estrogen


title: MSK-150, CD45+, non-mGAM, input, ChIPseq


title: MCF-7 siMETTL3 Vehicle #3

value: Vehicle


title: MCF-7 siMETTL3 Vehicle #2


title: MCF-7 siMETTL3 Estrogen #2


title: MCF-7 siMETTL3 Vehicle #1


title: MCF-7 siScramble non-gene targetting Estrogen #3

value: Non-gene targeting control


title: MCF-7 siScramble non-gene targetting Estrogen #2


title: MCF-7 siScramble non-gene targetting Estrogen #1


title: MCF-7 siScramble non-gene targetting Vehicle #3


title: MSK-107, CD45+, scATACseq

description: 10x Genomics


title: MCF-7 siScramble non-gene targetting Vehicle #1


title: MCF-7 siMETTL14 Estrogen #3

treatment_protocol: siRNA-mediated functional depletion of METTL14 was performed in vehicle (ethanol) and estrogen treated MCF-7 breast cancer cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. ON-TARGETplus siRNA–SMART pools for Human METTL14 (L-014169-02-0005) (GE DharmaconTM) and ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.

value: METTL14 depleted


title: MCF-7 siMETTL14 Estrogen #2


title: MCF-7 siMETTL14 Vehicle #3


title: MCF-7 siMETTL14 Estrogen #1


title: MCF-7 siMETTL14 Vehicle #1


title: MCF-7 siMETTL14 Vehicle #2


title: Healthy Sample 12

status: Public on Nov 27 2025

city: Beirut

first: Melhem

last: Bilen

address: Bliss street

department: Department of Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

description:
Library name: SH18
Zymo Extraction Kit

data_processing:
Adapters trimmed using TrimGalore.
Reads denoised and ASVs generated using DADA2 in QIIME2.
Taxonomy assigned using Greengenes 2024.09 as a reference in QIIME2.
Diversity metrics computed with QIIME2 core-metrics workflow.
Plots generated using R and GraphPad
Assembly: feces metagenome
Supplementary files format and content: CSV
Library strategy: 16S rRNA-seq

source_name: Feces/ Fecal sample

growth_protocol: Not applicable- samples are fecal and not cultured

extract_protocol:
Fecal DNA was extraced using the Qiagen PowerFecal DNA kt
16S V3–V4 region amplified and indexed using Zymo Quick-16S™ kit; sequenced on Illumina MiSeq.

treatment_protocol: No treatment administered; observational study

value: Feces/ Fecal sample


title: MCF-7 siMETTL3 Estrogen #1


title: Healthy Sample 11

description:
Library name: SH15
Zymo Extraction Kit


title: Healthy Sample 10

description:
Library name: SH14
Zymo Extraction Kit


title: Healthy Sample 8

description:
Library name: SH12
Zymo Extraction Kit


title: Healthy Sample 9

description:
Library name: SH13
Zymo Extraction Kit


title: Healthy Sample 7

description:
Library name: SH10
Zymo Extraction Kit


title: MCF-7 siScramble non-gene targetting Vehicle #2


title: Healthy Sample 5

description:
Library name: SH4
Zymo Extraction Kit


title: Healthy Sample 6

description:
Library name: SH9
Zymo Extraction Kit


title: Healthy Sample 1

description:
Library name: SH02
Illumina Extraction kit


title: Healthy Sample 4

description:
Library name: SH1
Zymo Extraction Kit


title: Healthy Sample 3

description:
Library name: SH04
Illumina Extraction kit


title: Ulcerative Colitis 12

description:
Library name: UC17
Zymo Extraction Kit


title: Ulcerative Colitis 11

description:
Library name: UC15
Zymo Extraction Kit


title: Healthy Sample 2

description:
Library name: SH03
Illumina Extraction kit


title: Ulcerative Colitis 9

description:
Library name: UC9
Illumina Extraction kit


title: Ulcerative Colitis 8

description:
Library name: UC8
Illumina Extraction kit


title: Ulcerative Colitis 6

description:
Library name: UC6
Illumina Extraction kit


title: Ulcerative Colitis 2

description:
Library name: UC2
Illumina Extraction kit


title: Ulcerative Colitis 3

description:
Library name: UC3
Illumina Extraction kit


title: Ulcerative Colitis 4

description:
Library name: UC4
Illumina Extraction kit


title: Sample P24052_1009 scATAC

status: Public on Nov 25 2025

city: Umeå

first: Johan

last: Henriksson

address: Sjukhusområdet Umeå universitet

country: Sweden

institute: Umeå University

description:
Library name: P24052_1009_scATAC
10x Multiome ATAC library

library_source: genomic single cell

data_processing:
Raw FASTQ files were processed using Cell Ranger ARC v2.0.0 with the GRCh38 10x Multiome reference.
Assembly: GRCh38 (10x Genomics refdata-cellranger-arc-GRCh38-2020-A)
Supplementary files format and content: Gene expression matrices: 10x Genomics filtered_feature_bc_matrix.h5 (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) and filtered_feature_bc_matrix.h5.h5.
Supplementary files format and content: ATAC-seq processed data: MACS2 peak file (atac_peaks.bed), transposition fragment file (atac_fragments.tsv.gz + index), and peak annotation table (atac_peak_annotation.tsv).

source_name: Buffy coat

growth_protocol: PBMCs were isolated from human buffy coat by density-gradient centrifugation. Naive CD3+ CD4+ T cells were enriched by negative magnetic selection using antibody-based depletion kits according to the manufacturer’s protocol.

extract_protocol:
Nuclei were isolated following the 10x Genomics Chromium Next GEM Multiome ATAC+GEX protocol. Cells were washed, lysed with ATAC Nuclei Isolation Buffer containing RSB, NP-40 and Tween-20, and nuclei were cleaned and resuspended in Nuclei Buffer.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression libraries were generated using 10x Genomics reagents. ATAC transposition and reverse transcription were performed in GEMs. Libraries were constructed, amplified, and indexed according to the manufacturer’s protocol.

treatment_protocol: Naive CD4+ T cells were stimulated under lineage-specific cytokine conditions to induce differentiation towards Th1, Th2, Th17, or Treg phenotypes. Differentiation was performed in parallel for each condition.

value: Buffy coat

value: Naive CD3+ CD4+ T cells enriched via negative magnetic selection

value: Differentiated toward Th1/Th2/Th17/Treg conditions


title: Sample P24052_1007 scATAC

description:
Library name: P24052_1007_scATAC
10x Multiome ATAC library


title: Ulcerative Colitis 5

description:
Library name: UC5
Illumina Extraction kit


title: Sample P24051_1008 scRNA

description:
Library name: P24051_1008_scRNA
10x Multiome GEX library

molecule: polyA RNA


title: Sample P24051_1007 scRNA

description:
Library name: P24051_1007_scRNA
10x Multiome GEX library


title: Input_CTCF-Nm_rep1

status: Public on Nov 20 2025

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description: Library name: Sample 11

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag.
Samples were deduplicated using Picard, normalized and converted to bigWig files using bamCoverage with the --CPM flag.
Assembly: mm9
Supplementary files format and content: bigWig including peak information for samples.

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
20 million cells were crosslinked in 37o prewarmed culture medium with 1% formaldehyde for 10 min at RT.  Cells were then treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4o to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin were then precleared with Dynabeads Protein A at 4o for 2 hours. 1/30 lysates were kept as input and the rest incubated with 2.5ug SMC3 antibody  or CTCF antibody overnight at 4o. IP samples were then captured by Dynabeads Protein A at 4o for at least 2 hours, followed by bead washing and elution. IP and Input DNA were then de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
Purified DNA was subjected to ChIP-Seq library preparation with the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs and sequenced via paired end 150-bp sequencing on a Illumina NovoSeq 6000 machine.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days.

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: Sample P24051_1006 scRNA

description:
Library name: P24051_1006_scRNA
10x Multiome GEX library


title: Sample P24051_1009 scRNA

description:
Library name: P24051_1009_scRNA
10x Multiome GEX library


title: Sample P24052_1006 scATAC

description:
Library name: P24052_1006_scATAC
10x Multiome ATAC library


title: Input_CTCF-Nm_rep2

description: Library name: Sample 12


title: Input_WT_rep2

description: Library name: Sample 10

value: Emu-Bcl2+, RAG1(D708A)


title: IP_CTCF_CTCF-Nm_rep1

description: Library name: Sample 7


title: IP_SMC3_CTCF-Nm_rep2

description: Library name: Sample 4


title: IP_CTCF_WT_rep2

description: Library name: Sample 6


title: IP_CTCF_WT_rep1

description: Library name: Sample 5


title: IP_SMC3_WT_rep2

description: Library name: Sample 2


title: Input_WT_rep1

description: Library name: Sample 9


title: IP_CTCF_CTCF-Nm_rep2

description: Library name: Sample 8


title: IP_SMC3_CTCF-Nm_rep1

description: Library name: Sample 3


title: IP_SMC3_WT_rep1

description: Library name: Sample 1


title: Ulcerative Colitis 7

description:
Library name: UC7
Illumina Extraction kit


title: Ulcerative Colitis 1

description:
Library name: UC1
Illumina Extraction kit


title: 3C_dCas9-blockade_rep2

description:
Library name: Sample 24
aligned to modified genome: mm9_dCas9 binding sites

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same coordinates. Additionally, we filtered reads aligned to telomeric and satellite repeat regions to avoid potential PCR artifacts. We also removed bait region reads to minimize the impact of self-ligation on quantitative analysis.
Assembly: mm9 and modified genomes as indicated
Supplementary files format and content: bedGraph including peak information for samples.

extract_protocol:
10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37 degrees celsius, 1 hour) and 1.8% Triton X-100 treatment (37 degrees celsius, 1 hour) successively, followed by overnight NalIII (700 units) digestion at 37 degrees celsius.  DpnII was inactivated at 65 degrees celsius for 20 min and samples were subjected to ligation under dilute condition with T4 DNA ligase (100 units). Ligated chromatin was de-crosslinked with Proteinase K (56 degrees celsius, ON) and treated with RNaseA (37 degrees celsius, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200ul 1XTE buffer.
4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98 degrees celsius 2min, 1cycle; 95 degrees celsius 30sec, 58 degrees celsius 30sec, 72 degrees celsius 90sec, 80 cycles; 72 degrees celsius 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25 degrees celsius 1 hour, 22 degrees celsius 3 hours, 16 degrees celsius overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95 degrees celsius 5min, 1cycle; 95 degrees celsius 30sec, 60 degrees celsius 30sec, 72 degrees celsius 60sec, 15 cycles; 72 degrees celsius 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95 degrees celsius 5min, 1cycle; 95 degrees celsius 30sec, 60 degrees celsius 30sec, 72 degrees celsius 60sec, 12 cycles; 72 degrees celsius 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to Mi-Seq machine (Illumina) with paired-end 300 bp sequencing.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest. For induction of dCas9-blockade, 2 ug/ml doxycycline was added 4 hours prior to G1 arrest.

value: Wapl-AID2, CTCF(Y226A/F228A), Igk+/-, dCas9-blockade, Emu-Bcl2+, RAG1(D708A)

value: 2 ug/ml doxycycline and 3 uM STI-571 treated for 4 days.


title: 3C_BS-only_rep1

description:
Library name: Sample 21
aligned to modified genome: mm9_dCas9 binding sites

value: Wapl-AID2, CTCF(Y226A/F228A), Igk+/-, dCas9-BS-inserted, Emu-Bcl2+, RAG1(D708A)


title: 3C_Wapl-AID2_5PhIAA_rep3

description: Library name: Sample 17

value: Wapl-AID2, Emu-Bcl2+, RAG1(D708A)

value: 1 uM 5-Ph-IAA treated for 4 hours followed by 3 uM STI-571 treated for 4 days.


title: Sample P24052_1008 scATAC

description:
Library name: P24052_1008_scATAC
10x Multiome ATAC library


title: 3C_BS-only_rep2

description:
Library name: Sample 22
aligned to modified genome: mm9_dCas9 binding sites


title: 3C_dCas9-blockade_rep1

description:
Library name: Sample 23
aligned to modified genome: mm9_dCas9 binding sites


title: 3C_Wapl-AID2_5PhIAA_rep2

description: Library name: Sample 16


title: 3C_Wapl-AID2_CTCF-Nm_5PhIAA_rep3

description: Library name: Sample 12

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)


title: 3C_Wapl-AID2_untreated_rep2

description: Library name: Sample 14


title: 3C_Wapl-AID2_CTCF-Nm_untreated_rep1

description: Library name: Sample 7


title: 3C_Wapl-AID2_CTCF-Nm_5PhIAA_rep1

description: Library name: Sample 10


title: 3C_CTCF-Nm_rep2

description: Library name: Sample 5


title: 3C_Wapl-AID2_CTCF-Nm_5PhIAA_rep2

description: Library name: Sample 11


title: 3C_CTCF-Nm_rep3

description: Library name: Sample 6


title: 3C_CTCF-Nm_rep1

description: Library name: Sample 4


title: 3C_WT_rep1

description: Library name: Sample 1


title: 3C_WT_rep3

description: Library name: Sample 3


title: CMEC_Organoids_Doxy_2

status: Public on Nov 19 2025

city: Palo Alto

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: Library name: CEO7D2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Raw read counts were counted by using FeatureCounts
Assembly: hg38
Supplementary files format and content: TPM_1stSets.csv
Supplementary files format and content: TPM_2ndSets.csv
Supplementary files format and content: TPM_3rdSets.csv

source_name: cells

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
mRNA was purified using Dynabeads Oligo(dT) (Life Technologies) and fragmented into 200-300 bp segments for preparation of index-tagged paired-end cDNA libraries. Illumina sequencing adapters were ligated to cDNA fragments during PCR amplification, and libraries were sequenced on an Illumina HiSeq platform.

value: cells

value: iPSC-CMs and iPSC-ECs

value: Cardiac Organoid

value: Doxycycline-inducible PIEZO1 overexpression (piggyBac Tet-On system)

value: Doxycycline treatment


title: CMEC_Organoids_Sunitinib_3

description: Library name: CEO6S3

value: Sunitinib treatment


title: CMEC_Organoids_Doxy_3

description: Library name: CEO7D3


title: CMEC_Organoids_Sunitinib_1

description: Library name: CEO6S1


title: CMEC_Organoids_Basal_3

description: Library name: CEO1B3

value: No treatment


title: Ulcerative Colitis 10

description:
Library name: UC14
Zymo Extraction Kit

value: Feces/ Fecal sample


title: CMEC_Organoids_Basal_2

description: Library name: CEO1B2


title: CM_Organoids_Yoda1_2

description: Library name: CTY7d2

value: iPSC-CMs

value: WT

value: Yoda1 treatment


title: 3C_Wapl-AID2_CTCF-Nm_untreated_rep2

description: Library name: Sample 8

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: CMEC_Organoids_Basal_1

description: Library name: CEO1B1


title: CM_Organoids_Sunitinib_1

description: Library name: CT7d1


title: 3C_Wapl-AID2_untreated_rep1

description: Library name: Sample 13


title: 3C_Wapl-AID2_CTCF-Nm_untreated_rep3

description: Library name: Sample 9


title: CM_Organoids_Sunitinib_2

description: Library name: CT7d2


title: 3C_WT_rep2

description: Library name: Sample 2

value: Emu-Bcl2+, RAG1(D708A)


title: CMEC_Organoids_Yoda1_1

description: Library name: CETY7d1


title: 3C_Wapl-AID2_5PhIAA_rep1

description: Library name: Sample 15

value: Wapl-AID2, Emu-Bcl2+, RAG1(D708A)


title: CMEC_Organoid_Sunitinib_2

description: Library name: CET7d2


title: CMEC_Organoids_Sunitinib_2

description: Library name: CEO6S2


title: CMEC_Organoids_Control_1

description: Library name: CECTRL1

value: Vehicle treatment


title: CMEC_Organoids_Yoda1_2

description: Library name: CETY7d2


title: CM_Organoids_Control_2

description: Library name: CCTRL2


title: CMEC_Organoid_Sunitinib_1

description: Library name: CET7d1


title: CMEC_Organoids_Control_2

description: Library name: CECTRL2


title: CM_Organoids_Control_1

description: Library name: CCTRL1


title: HCMVEC_Sunitinib_2

description: Library name: HMES2

value: human cardiac microvascular endothelial cells

value: Endothelial cell


title: CM_Organoids_Yoda1_1

description: Library name: CTY7d1

value: cells


title: HCMVEC_Sunitinib_3

description: Library name: HMES3


title: HCMVEC_Sunitinib_1

description: Library name: HMES1


title: HCMVEC_Control_2

description: Library name: HMEDM2


title: HCMVEC_Control_3

description: Library name: HMEDM3


title: HCMVEC_Control_1

description: Library name: HMEDM1


title: CMEC_Organoids_Doxy_1

description: Library name: CEO7D1

value: iPSC-CMs and iPSC-ECs

value: Cardiac Organoid


title: HAo_EC_Sunitinib_2

description: Library name: HAES2

value: Human aortic endothelial cells


title: HAo_EC_Sunitinib_3

description: Library name: HAES3

value: Sunitinib treatment


title: HAo_EC_Control_2

description: Library name: HAEDM2


title: HAo_EC_Control_1

description: Library name: HAEDM1


title: HAo_EC_Control_3

description: Library name: HAEDM3


title: iPSC_EC_Control_12

description: Library name: A2076Con

value: iPSC-ECs


title: iPSC_EC_Tet-on_Basal_1

description: Library name: iETB1

value: Doxycycline-inducible PIEZO1 overexpression (piggyBac Tet-On system)

value: No treatment


title: iPSC_EC_Tet-on_Basal_2

description: Library name: iETB2


title: iPSC_EC_Tet-on_Doxy_3

description: Library name: iETD13

value: Doxycycline treatment


title: iPSC_EC_Tet-on_Sun_3

description: Library name: iETS13


title: iPSC_EC_Tet-on_Sun_1

description: Library name: iETS11


title: HAo_EC_Sunitinib_1

description: Library name: HAES1

value: WT


title: iPSC_EC_Tet-on_Sun_2

description: Library name: iETS12


title: iPSC_EC_Sunitinib_12

description: Library name: A2076Sun


title: iPSC_EC_Control_10

description: Library name: A2119Con


title: iPSC_EC_Control_11

description: Library name: A2109Con


title: iPSC_EC_Sunitinib_11

description: Library name: A2109Sun


title: iPSC_EC_Tet-on_Doxy_1

description: Library name: iETD11


title: iPSC_EC_Control_9

description: Library name: A2122Con


title: iPSC_EC_Sunitinib_10

description: Library name: A2119Sun


title: iPSC_EC_Tet-on_Doxy_2

description: Library name: iETD12


title: iPSC_EC_Sunitinib_9

description: Library name: A2122Sun


title: iPSC_EC_Control_8

description: Library name: A2144Con


title: iPSC_EC_Sunitinib_8

description: Library name: A2144Sun


title: iPSC_EC_Control_7

description: Library name: A2154Con


title: iPSC_EC_Sunitinib_6

description: Library name: A2168Sun


title: iPSC_EC_Tet-on_Basal_3

description: Library name: iETB3


title: iPSC_EC_Control_6

description: Library name: A2168Con


title: iPSC_EC_Sunitinib_7

description: Library name: A2154Sun


title: iPSC_EC_Sunitinib_5

description: Library name: A2181Sun


title: iPSC_EC_Sunitinib_4

description: Library name: A2188Sun


title: iPSC_EC_Control_4

description: Library name: A2188Con


title: iPSC_EC_Control_5

description: Library name: A2181Con


title: iPSC_EC_Sunitinib_3

description: Library name: A2193Sun


title: iPSC_EC_Control_3

description: Library name: A2193Con


title: iPSC_EC_Control_2

description: Library name: A2225Con


title: iPSC_EC_Control_1

description: Library name: A516Con


title: iPSC_EC_Yoda1_4

description: Library name: HAESY1

value: Yoda1 treatment


title: iPSC_EC_Sunitinib_1

description: Library name: A516Sun


title: iPSC_EC_Yoda1_3

description: Library name: HMESY3


title: iPSC_EC_Yoda1_1

description: Library name: HMESY1


title: iPSC_EC_Yoda1_2

description: Library name: HMESY2


title: iPSC_EC_Yoda1_6

description: Library name: HAESY3


title: iPSC_EC_Yoda1_5

description: Library name: HAESY2


title: Primary astrocytes, LPS+shFABP5, rep5

city: Shenzhen

first: Chuantao

last: Wu

state: Guangdong

address: Gongchang Street No.66

country: China

institute: Sun Yat-sen University

description:
Library name: Seq_15
treat with mouse FABP5-targeting shRNA expression plasmids for 5 days and 1 μg/mL LPS (Sigma) for 24 hours

data_processing:
CLC Genomics Workbench v11.0.1
Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using CLC Genomics Workbench with mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8.
Gene-level read counts were calculated and normalized using CLC Genomics Workbench.
Assembly: mm10.
Supplementary files format and content: The processed data file (gene_counts.txt) contains raw gene-level counts for all samples; each column corresponds to a library name.

source_name: primary astrocyte

growth_protocol: Primary astrocytes were isolated from the cerebral cortex of postnatal day 1–2 (P1–P2) C57BL/6 mice and cultured in DMEM supplemented with 20% fetal bovine serum (FBS) and penicillin/streptomycin (50 U/mL penicillin, 50 µg/mL streptomycin) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen). Approximately 1.3 μg oftotal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit (Takara) following manufacturer's protocols.

treatment_protocol: Cells were treated with 1 μg/mL LPS (Sigma) for 24 hours, or co-treated with mouse FABP5-targeting shRNA expression plasmids for 5 days, control cells received no treatment.

value: primary astrocyte

value: LPS + shFABP5

tag: batch


title: Primary astrocytes, LPS+shFABP5, rep4

description:
Library name: Seq_14
treat with mouse FABP5-targeting shRNA expression plasmids for 5 days and 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, LPS, rep5

description:
Library name: Seq_10
treat with 1 μg/mL LPS (Sigma) for 24 hours

value: LPS


title: Primary astrocytes, LPS+shFABP5, rep2

description:
Library name: Seq_12
treat with mouse FABP5-targeting shRNA expression plasmids for 5 days and 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, LPS+shFABP5, rep3

description:
Library name: Seq_13
treat with mouse FABP5-targeting shRNA expression plasmids for 5 days and 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, LPS, rep3

description:
Library name: Seq_8
treat with 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, LPS, rep4

description:
Library name: Seq_9
treat with 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, LPS, rep2

description:
Library name: Seq_7
treat with 1 μg/mL LPS (Sigma) for 24 hours


title: Primary astrocytes, Control, rep5

description:
Library name: Seq_5
control

value: Control


title: Primary astrocytes, Control, rep4

description:
Library name: Seq_4
control


title: Primary astrocytes, Control, rep3

description:
Library name: Seq_3
control


title: Primary astrocytes, Control, rep2

description:
Library name: Seq_2
control


title: iPSC_EC_Sunitinib_2

description: Library name: A2225Sun


title: Primary astrocytes, Control, rep1

description:
Library name: Seq_1
control


title: Male, Oct4 KO, sample 1

city: Cleveland

first: Olga

last: Cherepanova

state: OH

address: 9500 Euclid Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

description: Library name: KO_M_1

data_processing:
The genome was bulit using Hisat2 V2.0.5
FeatureCounts v1.5--p3 was used to count the read numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: Comma separated value file containing raw counts for each gene

source_name: MAEC

growth_protocol: Mouse aotic endothelial cells were maintained in F-12 media with 20% fetal bovine serum (FBS), antibiotics, heparin, and endothelial cell growth factors in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Tizol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers., followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: no treatment

value: MAEC

value: Oct4 KO

tag: gender

value: male

value: no treatment


title: Male, Oct4 KO, sample 3

description: Library name: KO_M_3

value: Endothelial cell


title: Male, Oct4 KO, sample 2

description: Library name: KO_M_2


title: Female, Oct4 KO, sample 3

description: Library name: KO_F_3

value: female


title: Female, Oct4 KO, sample 2

description: Library name: KO_F_2


title: Female, Oct4 KO, sample 1

description: Library name: KO_F_1


title: HUVEC, siCTRL, rep3

status: Public on Nov 17 2025

city: Guangzhou

first: Keli

address: 7 Jinsui Road

description: Library name: SAMPLES 3

data_processing:
After removing low-quality reads, clean reads were aligned to the human reference genome using HISAT2 and assembled into gene expression matrices. Genes with low expression levels (defined as average transcripts per million, TPM<1 across all treatment groups) were filtered out. Differential expression analysis was performed using the DESeq2 package in R. Genes with an adjusted p-value<0.05 (after Benjamini-Hochberg correction) and a fold change>1.5 were identified as differentially expressed genes (DEGs)
Assembly: GRCH38
Supplementary files format and content: matrix

source_name: umbilical vein

extract_protocol:
TRIzol™ Plus RNA Purification Kit
DNBSEQ Transcriptome

value: umbilical vein

value: Primary isolated cell


title: HUVEC, siJAM3, rep4

description: Library name: SAMPLES 8


title: HUVEC, siCTRL, rep1

description: Library name: SAMPLES 1


title: HUVEC, siCTRL, rep2

description: Library name: SAMPLES 2


title: Primary astrocytes, LPS+shFABP5, rep1

description:
Library name: Seq_11
treat with mouse FABP5-targeting shRNA expression plasmids for 5 days and 1 μg/mL LPS (Sigma) for 24 hours


title: HUVEC, siJAM3, rep3

description: Library name: SAMPLES 7


title: HUVEC, siJAM3, rep1

description: Library name: SAMPLES 5


title: HUVEC, siJAM3, rep2

description: Library name: SAMPLES 6


title: HUVEC, siCTRL, rep4

description: Library name: SAMPLES 4


title: Primary astrocytes, LPS, rep1

description:
Library name: Seq_6
treat with 1 μg/mL LPS (Sigma) for 24 hours


title: 2MHF40

status: Public on Nov 15 2025

city: Lexington

first: Nirmal

last: Verma

state: Kentcuky

address: 900 S Limestone

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

description: Library name: sample49

data_processing:
The libraries was sequenced in PE150 format on HiseqX10 platform
Supplementary files format and content: text file includes processes data file

source_name: frontal cortex brain

growth_protocol: mice were put on high fat diet for 2 month(WT) and 4 month (WT, Amylin-KO, and human amylin conditional transgenic mice, conditional human amylin expressing mice were injected with either vehicle or tamoxifen and organs brain were collected after 2 months.

extract_protocol:
RNA were isoated from frontal cortex region of the brain and RNA quality was checked on nanodrop and Agilent tapestation
Illumina Truseq Stranded mRNA was used to construct RNA library

treatment_protocol: mice transgenic for human amylin were injected with vehicle or tamoxifen

value: frontal cortex brain

value: brain

value: frontal cortex


title: 2MHF39

description: Library name: sample48


title: 2MHF34

description: Library name: sample43


title: 2MHF37

description: Library name: sample46


title: 2MHF38

description: Library name: sample47


title: 2MHF35

description: Library name: sample44


title: 2MHF36

description: Library name: sample45


title: 2MHF33

description: Library name: sample42


title: 2MHF32

description: Library name: sample41


title: 4MHFA15

description: Library name: sample40


title: 4MHFA21

description: Library name: sample35


title: 4MHFA16

description: Library name: sample38


title: 4MHFA12

description: Library name: sample36


title: 4MHFA7

description: Library name: sample34


title: 4MHFA19

description: Library name: sample33


title: 4MHFW25

description: Library name: sample30


title: 4MHFA6

description: Library name: sample32


title: 4MHFA8

description: Library name: sample31


title: 4MHFW24

description: Library name: sample29


title: 4MHFW12

description: Library name: sample22


title: CreVE10

description: Library name: sample20


title: 4MHFW11

description: Library name: sample23


title: 4MHFW15

description: Library name: sample25


title: 4MHFW23

description: Library name: sample28


title: CreVE40

description: Library name: sample18


title: CreVE11

description: Library name: sample19


title: 4MHFW21

description: Library name: sample26


title: 4MHFW22

description: Library name: sample27


title: CreVE41

description: Library name: sample17


title: CreVE39

description: Library name: sample16


title: CreVE16

description: Library name: sample15


title: CreVE1

description: Library name: sample11


title: CreVE3

description: Library name: sample12


title: CreTM21

description: Library name: sample9


title: CreTM45

description: Library name: sample7


title: CreTM27

description: Library name: sample6


title: CreTM44

description: Library name: sample5


title: CreTM15

description: Library name: sample3


title: CreTM33

description: Library name: sample1


title: CreTM18

description: Library name: sample2


title: p5_distant_TCR

status: Public on Nov 13 2025

city: Paris

first: Alexandre

last: Lanau

address: 26 rue d'Ulm

department: Unité 830

country: France

institute: Institut Curie

description: Library name: p5_distant_TCR

data_processing:
The demutiplexing, barcoded processing, gene counting and aggregatation were realized using CellRanger v7.0.0
Assembly: human hg38
Supplementary files format and content: Tab-seperated values files and matrix files
Library strategy: TCR-Seq

molecule: cytoplasmic RNA

source_name: thymus

extract_protocol:
Thymus or thymoma samples were cut into 1 mm3 pieces using a scalpel. Tissues were digested enzymatically for 20-40 min at 37°C under agitation, in CO2-independent medium (Invitrogen) containing collagenase I (2 mg/ml; Sigma-Aldrich), hyaluronidase (2 mg/ml; SigmaAldrich), and deoxyribonuclease (25 mg/ml; Sigma-Aldrich). The tissue pieces were then dissociated with a 20ml syringe plunger on a 40 µm cell strainer (BD) in 1 % Fetal Calf Serum (FCS), 2 mM EDTA phosphate-buffered saline (PBS) (Invitrogen) until uniform cell suspensions were obtained. The suspended cells were subsequently centrifuged for 10 min at 400 g before either staining for flow cytometry, or CD3+ T cell enrichment followed by scRNA-seq as described below.  Thymic tissue samples were cut into ~1 cm3 pieces in PBS. The bulk of thymocytes was removed by a gentle pressure on the tissue fragment. After removing the supernatant, the remaining tissues was cut into fragments of 2-4 mm. Three sequential digestion steps were then performed. 1) 10 mL Collagenase A (2 mg/ml)/DNAseI (0.1 mg/mL) in 10 mL RPMI for 45 min at 37°C under slow rotation (190 rpm). Centrifugation at 110 g for 2 min was then performed to sediment fragment and supernatant was discarded. 2) a digestion, identic to the first one, was performed on the remaining tissue. 3) tissue remnants were incubated in 0.05% Trypsin in the collagenase/DNAse mix solution for 45min at 37° with constant agitation (190 rpm). During the last 10-15 min of the incubation, FCS (1:5) was added to neutralize Trypsin activity. After centrifugation (110 g for 2 min), the supernatant was collected before sorting the TECs. Alive CD45-EPCAM+ cells were sorted using a HP800 SONY sorter before scRNA-analysis
T cells were loaded into a Chromium Single Cell 5′ V(D)J Enrichment Kit, Human T Cell (10X Genomics), according to the manufacturer’s instructions. The thymoma TEC were analyzed using scRNAseq (3’ chromium kit) 10x genomics.

value: thymus

value: Thymocytes & T lymphocytes


title: p5_tumor_TCR

description: Library name: p5_tumor_TCR


title: p4_tumor_RNA

description: Library name: p4_tumor_RNA

data_processing:
The demutiplexing, barcoded processing, gene counting and aggregatation were realized using CellRanger v7.0.0
Assembly: human hg38
Supplementary files format and content: Tab-seperated values files and matrix files


title: p4_tumor_TCR

description: Library name: p4_tumor_TCR


title: p5_tumor_RNA

description: Library name: p5_tumor_RNA


title: p6_tumor_TCR

description: Library name: p6_tumor_TCR


title: p6_juxta_TCR

description: Library name: p6_juxta_TCR


title: CreVE5

description: Library name: sample13


title: p5_distant_RNA

description: Library name: p5_distant_RNA


title: CreVE4

description: Library name: sample14


title: p6_distant_TCR

description: Library name: p6_distant_TCR


title: p6_distant_RNA

description: Library name: p6_distant_RNA


title: p6_tumor_RNA

description: Library name: p6_tumor_RNA


title: p15_tumor_TCR

description: Library name: p15_tumor_TCR


title: p15_juxta_TCR

description: Library name: p15_juxta_TCR


title: CreTM28

description: Library name: sample10


title: p15_distant_TCR

description: Library name: p15_distant_TCR


title: CreTM9

description: Library name: sample8


title: CreTM16

description: Library name: sample4


title: p15_tumor_RNA

description: Library name: p15_tumor_RNA


title: p15_distant_RNA

description: Library name: p15_distant_RNA


title: p16_tumor_RNA

description: Library name: p16_tumor_RNA


title: p16_tumor_TCR

description: Library name: p16_tumor_TCR


title: p16_distant_TCR

description: Library name: p16_distant_TCR


title: p15_juxta_RNA

description: Library name: p15_juxta_RNA


title: p16_distant_RNA

description: Library name: p16_distant_RNA


title: p29_TEC

description: Library name: p29_TEC

value: Thymic epithelials cells


title: p6_juxta_RNA

description: Library name: p6_juxta_RNA


title: p17_TEC

description: Library name: p17_TEC


title: healthy_control_2_RNA

description: Library name: healthy_control_2_RNA


title: p19_TEC

description: Library name: p19_TEC


title: healthy_control_1_RNA

description: Library name: healthy_control_1_RNA


title: p24_tumor_TCR

description: Library name: p24_tumor_TCR


title: p24_juxta_TCR

description: Library name: p24_juxta_TCR


title: p23_tumor_TCR

description: Library name: p23_tumor_TCR


title: p23_distant_TCR

description: Library name: p23_distant_TCR


title: healthy_control_2_TCR

description: Library name: healthy_control_2_TCR


title: p23_juxta_TCR

description: Library name: p23_juxta_TCR


title: p24_juxta_RNA

description: Library name: p24_juxta_RNA


title: p24_distant_RNA

description: Library name: p24_distant_RNA


title: p24_distant_TCR

description: Library name: p24_distant_TCR


title: p24_tumor_RNA

description: Library name: p24_tumor_RNA


title: p23_distant_RNA

description: Library name: p23_distant_RNA


title: p16_juxta_TCR

description: Library name: p16_juxta_TCR


title: p23_juxta_RNA

description: Library name: p23_juxta_RNA


title: healthy_control_3_RNA

description: Library name: healthy_control_3_RNA


title: p16_juxta_RNA

description: Library name: p16_juxta_RNA


title: p25_tumor_RNA

description: Library name: p25_tumor_RNA


title: p25_juxta_RNA

description: Library name: p25_juxta_RNA


title: MASTR_FXS_2_rep2_FMR1

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

institute: Washington University in St. Louis

description:
Library name: FXS_2_rep2_FMR1 target  long read
FMR1 target nanopore data generated by MASTR-seq

data_processing:
We performed base-calling of raw nanopore fast5/pod5 using dorado (version 0.7.3), aligned the basecalled data to hg38 using dorado (version 0.7.3). We performed several quality-control steps to ensure only high-quality reads were used in downstream analysis, removing reads that did not align to the target locus and kept reads with at least three consecutive CAGs for HTT CAG STR, kept reads with at least four consecutive CCGs for FMR1 CCG STR, kept reads with at least two consecutive G4C2 for C9orf72 CGG STR. Finally, we quantified the number of repeat units in the continuous STR tract and plotted representative nanopore long-reads for visualization.
Assembly: hg38
Supplementary files format and content: txt format. The identifiers included in the *allcounts.txt files are unique nanopore long read ID
Supplementary files format and content: tsv format

growth_protocol: hESCs or hiPSCs are grown in  mTeSR Plus media (STEMCELL Technology, 05825) supplemented with 1% (v/v) penicillin-streptomycin (Thermo Fisher, 15140122) at 37 °C and 5 % CO2 on Matrigel coated plates. Cells were passaged by incubating in 5 ml of Versene Solution (Thermo Fisher, 15040066) at 37 °C for 3 min, after which Versene was inactivated by mixing with 10 ml of full growth media. Cells were passaged every 2 - 7 days. All hESC culture plates were coated with 1.2 % (v/v) Matrigel hESC-Qualified Matrix (Corning, 354277) in DMEM/F-12 (Thermo Fisher, 11320033) for at least 1 hr at 37°C.

extract_protocol:
We obtain HMW DNA from 5-10×10⁶ iPSCs or 20 mg brain tissue with commercial kits (NEB #T3050S/3060S). Use a broad range dsDNA quantitation kit to detect HMW genomic DNA concentration. Assess gDNA purity with OD260/280 by Nanodrop. Check integrity of HMW DNA on a 0.6% 1X TAE agarose gel with 1 kb Extend DNA ladder (NEB#N3239S). For unsheared high-quality HMW DNA, we expect most of the DNA to be larger than 48.5 kb.
To perform targeted sequencing of FMR1, HTT and C9orf72, we designed and synthesized CRISPR–Cas9 crRNAs targeting the genomic regions adjacent to the target STRs with the IDT CRISPR design tool. The crRNAs used are listed in Supplementary Table 1. Preparation of the Cas9 nucleoprotein complex (Cas9 RNPs) was performed as follows: lyophilized Cas9 crRNA and tracrRNA (IDT) were suspended at 100 μM in TE (pH 7.5). The 4 crRNA probes were pooled for the cleavage reaction by combining equal volumes of each crRNA probe (0.25 μl /each) and 1 μl tracrRNA (100 μM stock) in 8 μl of water. The pooled crRNAs and tracrRNA were annealed with a thermal cycler at 95º C for 5 mins, allowed to cool to room temperature, then spun down to collect any liquid in the bottom of the tube. To form Cas9 RNPs (for 10 reactions), components were assembled in a 1.5 ml Eppendorf DNA LoBind tube in the following order: annealed 10 μl crRNA•tracrRNA pool (10 μM), 10 μl 10x NEB CutSmart buffer, 79.2 μl Nuclease-free water, 0.8 μl HiFi Cas9 (62 μM, IDT). The tube was mixed thoroughly by flicking. RNPs were formed by incubating the tube at room temperature for 30 mins, then returned to ice until required. Meanwhile, dephosphorylated genomic DNA was prepared by assembling the components in a 1.5 ml Eppendorf DNA LoBind tube in the following order: 5 μg of high molecular weight (HMW) DNA in 24 μl, 3 μl NEB CutSmart Buffer (10x) and 3 μl of QuickCIP enzyme (NEBM0525S). The sample was then incubated in a thermocycler at 37º C for 20 minutes, 80º C for 2 minutes, then held at 20º C (room temperature). The reaction was mixed gently by flicking the tube and spun down. 10 μl RNPs from the previous step was incubated with 5 μg of dephosphorylated HMW DNA, 1 μl of 10 mM dATP, and 1 μl of Taq polymerase (NEB) for 60 min at 37 °C on a thermocycler followed by 5 min at 72 °C. 1 μl Proteinase K (Sigma, 20 mg/ml stock concentration) was added to each reaction, and samples were incubated at 43°C for 30 mins to remove proteins for following size selection. The reaction was then purified to remove high concentration salt as follows: Cas9-cut genomic DNA(total volume is 42 ul) was precipitated using 16 ul of 5 M ammonium acetate together with 126 ul of ice-cold ethanol (absolute) and gently inverted ten times. Precipitated DNA was spun down at 16,000g for 5 min. DNA was washed with 500 ul of 70% ethanol and centrifuged at 16,000g for 5 min, and this step was repeated two times. The supernatant was removed and the DNA pellet was dried at RT for 2-5 min. Rehydration of DNA was performed at 50 °C for 1 hour using 200 μl of 10 mM Tris-HCl (pH 8). DNA was further homogenized on a rotator at 37 °C and 20 r.p.m overnight. Size selection was then performed with the Bluepippin BLF7510 (sagescience) using the “0.75DF 3-10 kb Marker S1-Improved Recovery” cassette definition with size range at 4-15 kb. To perform barcode ligation, the following was performed: 3 μl unique barcode SQK-NBD114.24(R10.4.1 flowcell )  was added to 50 μl of Blunt/TA Ligase Master Mix (NEB) for each sample. The reactions were incubated at RT for 10 min, spun down, and then put on a magnet. The beads were washed with 200 μl of freshly-prepared 70% ethanol, without disturbing the pellet, twice, and allowed to dry for 30~60 seconds. The remaining pellet was then resuspended in 16 μl nuclease-free water and incubated for 10 minutes at room temperature. The reaction was then placed on a magnet and 16 μl of supernatant was removed into a clean 1.5 ml Eppendorf DNA LoBind tube. Samples were then quantified using a Qubit fluorometer, together with the Qubit dsDNA HS assay kit (Thermo Fisher Scientific). Adapters were then ligated by first adding 20 μl NEBNext® Quick Ligation Buffer (NEB#E6056S), 10 μl NEBNext Quick T4 DNA ligase(NEB#E6056S), and 5 μl Native Adapter (NA) for R10.4.1 flowcell  at room temperature in a separate 1.5 ml Eppendorf DNA LoBind Tube. The ligation reaction was mixed thoroughly. 20 μl of the adapter ligation reaction was mixed with the pooled native barcode-ligated samples. Immediately after mixing, the remaining 15 μl of the adapter ligation mix was added to the native barcode-ligated sample, to yield a 100 μl ligation mix. The reaction was incubated for 10 minutes at room temperature. Then 1 volume (100 μl) of TE (pH 8.0) was added to the ligation mix, followed by 0.4x volume (80 μl) of AMPure XP Beads. The sample was then incubated for 10 minutes at room temperature, placed back on the magnet, and the supernatant was removed. The beads were then washed with 250 μl Long Fragment Buffer (LFB) twice and then air-dried for ~30 seconds. The library was eluted off the beads in 14 μl Elution Buffer (EB). 13 uL of the libary was then mixed with 37.5 μl sequencing buffer (SQB) and 25.5 μl loading beads (LIB) and loaded onto the MinION flowcell.

value: iPSC

value: Expanded allele of  FMR1 CGG STR in X chromosome, male

value: single


title: p25_distant_RNA

description: Library name: p25_distant_RNA


title: MASTR_FXS_2_rep1_FMR1

description:
Library name: FXS_2_rep1_FMR1 target  long read
FMR1 target nanopore data generated by MASTR-seq


title: healthy_control_1_TCR

description: Library name: healthy_control_1_TCR


title: p25_tumor_TCR

description: Library name: p25_tumor_TCR


title: p25_juxta_TCR

description: Library name: p25_juxta_TCR


title: p23_tumor_RNA

description: Library name: p23_tumor_RNA


title: p25_distant_TCR

description: Library name: p25_distant_TCR


title: healthy_control_3_TCR

description: Library name: healthy_control_3_TCR


title: healthy_control_4_TCR

description: Library name: healthy_control_4_TCR


title: MASTR_HTT_Q20

description:
Library name: HTT_Q20 target  long read
HTT target nanopore data generated by MASTR-seq

value: hESC

value: One allele is normal length of HTT CAG STR,the other allele is gene edited normal length of HTT CAG STR


title: healthy_control_4_RNA

description: Library name: healthy_control_4_RNA


title: MASTR_HTT_Q56

description:
Library name: HTT_Q56 target  long read
HTT target nanopore data generated by MASTR-seq

value: One allele is normal length of HTT CAG STR,the other allele is expanded length of HTT CAG STR


title: MASTR_FXS_1_rep1_FMR1

description:
Library name: FXS_1_rep1_FMR1 target  long read
FMR1 target nanopore data generated by MASTR-seq


title: MASTR_HTT_parental

description:
Library name: HTT_parental target  long read
HTT target nanopore data generated by MASTR-seq

value: Normal length of HTT CAG STR


title: Myoepithelial KLF5 10356-24

status: Public on Nov 09 2025

type: other

first: Cristina

last: Antonescu

address: 1275 York Avenue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPICv2 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system and standard recommended Illumina scanner setting

data_processing:
minfi package v1.52.1 in R environment (v4.1)
processed value definition: Average Beta (bVals_myoepithelial.csv)

label: Cy3 and Cy5

source_name: formalin-fixed paraffin-embedded tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue after manual macrodissection to ensure at least 10% tumor content, followed by bisulfite converstion.

value: formalin-fixed paraffin-embedded

tag: age group [years]

tag: site

value: knee

tag: histology

value: myoepithelial tumor


title: MASTR_HTT_Q72

description:
Library name: HTT_Q72 target  long read
HTT target nanopore data generated by MASTR-seq


title: MASTR_ALS_C9orf72

description:
Library name: ALS_C9orf72 target  long read
C9orf72 target nanopore data generated by MASTR-seq

value: One allele is normal length of G4C2 STR,the other allele is expanded  G4C2 STR


title: MASTR_FXS_5006_FMR1

description:
Library name: FXS_5006_FMR1 target  long read
FMR1 target nanopore data generated by MASTR-seq

source_name: brain tissue

value: brain tissue

tag: Sex

value: male

value: Expanded allele of  FMR1 CGG STR in X chromosome


title: NFATC2 10342-24

value: radius


title: gata6_d016_rep3

status: Public on Nov 03 2025

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

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

source_name: ES cells

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

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

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

value: ES cells

value: cells carrying a doxycycline-inducible gata6 expression cassette

tag: strain

value: dox

tag: time point

tag: antibody


title: 259_T137

status: Public on Oct 30 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
Library name: lib96795
combined_counts_ALI.csv

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. Resulting bcl files were deconvoluted and converted to fastq format using Casava from Illumina. Fastq files were aligned to the Ensembl version of the human genome (GRCh38, Ensembl 91) by using STAR (version 2.4.2a). HTSeq-count (version 0.4.1) was used to generate gene counts with mode as “intersection (nonempty)” and minimum alignment quality set to 20 and otherwise set to default parameters. Quality metrics were compiled from PICARD (version 1.134), FASTQC (version 0.11.3), Samtools (version 1.2), and HTSeq-count (version 0.4.1). For quality control, samples that had human aligned counts greater than 1 million mapped reads and a median coefficient of variation coverage less than 0.7 were kept. Genes were filtered to include those that had a trimmed mean of M value normalization count of at least 0.3 in at least 10% of samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights by using voomWithQualityWeights from the limma R package (version 4.2.1).
Assembly: Human GRCh38
Supplementary files format and content: csv file voom normalized counts

source_name: Organotypic airway epithelial cell culture

extract_protocol:
Bronchial epithelial cells (BECs) from children with asthma (n=37) and healthy children (n=3)  ages 6-18 years of age were obtained from subjects while under general anesthesia for an elective surgery using 4-mm Harrell unsheathed bronchoscope cytology brushes (CONMED®) inserted through an endotracheal tube as we have previously described (8, 42). Cells were then seeded onto T-25 cell culture flasks (Corning®) precoated with type I collagen and proliferated under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) (8). BECs (passage 2 or 3) were proliferated on transwells under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) for 4-7 days then differentiated to an organotypic pseudostratified ciliated state (Supplemental Figure 1) for 21 days at ALI using PneumaCult™ALI medium (Stemcell™) as previously described (8, 43–45). We have previously demonstrated stability of gene expression in primary BEC ALI cultures between passages 1 and 3 (46).RNA was collected from BEC cultures pre-infection and at 2d, 4d, 7d, and 10d post RV infection. To collect RNA from BEC cultures, media was first removed from the basolateral chamber of transwells. 800 µL of lysis buffer (Invitrogen®, Product No. AM1912) was added to the apical surface of cultures. A pipet tip was then used to gently scratch each apical well in a crosshatch pattern to loosen BECs from the transwell membrane. RNA was extracted using the RNAqueous™ kit for total RNA isolation (Thermo Fisher Scientific). BEC cultures from SE (n=6) and NSE (n=6) donors were treated with IFN-β or CXCL10 starting 2 days prior to RV infection and continued for 2 days following RV infection. Recombinant human recombinant human IFN-β (1 ng/mL; AbcamⓇ) or CXCL10 (2 ng/mL; R&D SystemsⓇ) was added to BEC ALI medium starting 2 days prior to RV infection and refreshed with each medium change (every other day). Two days following initiation of treatment with IFN-β or CXCL10 BEC cultures were infected with human RV-A16 at an MOI of 0.5 as described above. RNA was collected from BEC cultures pre-infection and 2d following RV infection.
Total RNA was used to construct libraries by using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, San Jose, Calif), with reverse transcription followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed by using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina, San Diego, Calif) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Mass). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads with a target depth of 5 million reads per sample

tag: studygroup

value: Asthma

tag: donorid

tag: exacerbation status

value: No Severe Exacerbation

tag: infection

tag: timepoint

tag: age

value: female

tag: ethnicity

value: Black

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage

tag: total reads

tag: pct aligned


title: 256_T137

description:
Library name: lib96792
combined_counts_ALI.csv

tag: studygroup

tag: cell type

value: Organotypic airway epithelial cell culture

tag: treatment

tag: Sex

tag: batch


title: gata6_d016_rep1

tag: tissue

tag: cell line

tag: strain

tag: time point

tag: antibody


title: 250_T137

description:
Library name: lib96786
combined_counts_ALI.csv

tag: donorid

tag: exacerbation status

tag: infection

tag: timepoint

tag: age

tag: ethnicity

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)


title: 253_T137

description:
Library name: lib96789
combined_counts_ALI.csv

tag: studygroup

tag: cell type

tag: treatment

tag: Sex

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage

tag: total reads

tag: pct aligned


title: 248_T137

description:
Library name: lib96784
combined_counts_ALI.csv

tag: donorid

tag: exacerbation status

tag: infection

tag: timepoint

value: Control

tag: batch


title: MASTR_FXS_1_rep2_FMR1

description:
Library name: FXS_1_rep2_FMR1 target  long read
FMR1 target nanopore data generated by MASTR-seq

tag: tissue

value: iPSC

tag: genotype

value: Expanded allele of  FMR1 CGG STR in X chromosome, male

value: single


title: 242_T1007

description:
Library name: lib96778
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

value: American Indian/Native Alaskan

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)


title: 236_T1007

description:
Library name: lib96772
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage


title: 239_T1007

description:
Library name: lib96775
combined_counts_ALI.csv

tag: donorid

tag: exacerbation status

tag: infection

tag: timepoint

tag: total reads

tag: pct aligned

tag: batch


title: 234_T1007

description:
Library name: lib96770
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: eos absolute_(mm2)


title: 222_T1006

description:
Library name: lib96758
combined_counts_ALI.csv

tag: cell type

value: Severe Exacerbation

tag: treatment

tag: Sex

value: White

tag: feno (ppb)

tag: fev1 (%_predicted)


title: 231_T1006

description:
Library name: lib96767
combined_counts_ALI.csv

tag: donorid

value: male

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage


title: 225_T1006

description:
Library name: lib96761
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: total reads

tag: pct aligned


title: 228_T1006

description:
Library name: lib96764
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 220_T1006

description:
Library name: lib96756
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: feno (ppb)


title: 211_T176

description:
Library name: lib96747
combined_counts_ALI.csv

tag: donorid

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load


title: 203_T161

description:
Library name: lib96739
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: median cv_coverage

tag: total reads


title: 200_T161

description:
Library name: lib96736
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 217_T176

description:
Library name: lib96753
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 192_T161

description:
Library name: lib96728
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)


title: 194_T161

description:
Library name: lib96730
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: viral load

tag: median cv_coverage


title: 189_T1005

description:
Library name: lib96725
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 214_T176

description:
Library name: lib96750
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 206_T176

description:
Library name: lib96742
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 208_T176

description:
Library name: lib96744
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 178_T1005

description:
Library name: lib96714
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 175_T1004

description:
Library name: lib96711
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 180_T1005

description:
Library name: lib96716
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 183_T1005

description:
Library name: lib96719
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 172_T1004

description:
Library name: lib96708
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 169_T1004

description:
Library name: lib96705
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 166_T1004

description:
Library name: lib96702
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 245_T1007

description:
Library name: lib96781
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 164_T1004

description:
Library name: lib96700
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 161_T1003

description:
Library name: lib96697
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 155_T1003

description:
Library name: lib96691
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 158_T1003

description:
Library name: lib96694
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 150_T1003

description:
Library name: lib96686
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 197_T161

description:
Library name: lib96733
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 152_T1003

description:
Library name: lib96688
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 186_T1005

description:
Library name: lib96722
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 144_T175

description:
Library name: lib96680
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 138_T175

description:
Library name: lib96674
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 147_T175

description:
Library name: lib96683
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 141_T175

description:
Library name: lib96677
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 133_T173

description:
Library name: lib96669
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 136_T175

description:
Library name: lib96672
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 127_T173

description:
Library name: lib96663
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 105_T1001

description:
Library name: lib96641
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 102_T1001

description:
Library name: lib96638
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 91_T3030

description:
Library name: lib96627
combined_counts_ALI.csv

value: Healthy

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 99_T1001

description:
Library name: lib96635
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 96_T1001

description:
Library name: lib96632
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 124_T173

description:
Library name: lib96660
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 122_T173

description:
Library name: lib96658
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 130_T173

description:
Library name: lib96666
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 110_T1002

description:
Library name: lib96646
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 119_T1002

description:
Library name: lib96655
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 108_T1002

description:
Library name: lib96644
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 88_T3030

description:
Library name: lib96624
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 113_T1002

description:
Library name: lib96649
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 94_T1001

description:
Library name: lib96630
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 85_T3030

description:
Library name: lib96621
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 82_T3030

description:
Library name: lib96618
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 77_T183

description:
Library name: lib96613
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 80_T3030

description:
Library name: lib96616
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 74_T183

description:
Library name: lib96610
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 68_T183

description:
Library name: lib96604
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 60_T3027

description:
Library name: lib96596
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 63_T3027

description:
Library name: lib96599
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 54_T3027

description:
Library name: lib96590
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 52_T3027

description:
Library name: lib96588
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 116_T1002

description:
Library name: lib96652
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 57_T3027

description:
Library name: lib96593
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 38_T184

description:
Library name: lib96574
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 40_T184

description:
Library name: lib96576
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 35_T163

description:
Library name: lib96571
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 20_T199

description:
Library name: lib96556
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

value: Hispanic

tag: allergic sensitization

tag: pct aligned


title: 46_T184

description:
Library name: lib96582
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 11_T198

description:
Library name: lib96547
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 43_T184

description:
Library name: lib96579
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 17_T199

description:
Library name: lib96553
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 13_T198

description:
Library name: lib96549
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 18_T199

description:
Library name: lib96554
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 8_T198

description:
Library name: lib96544
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 6_T198

description:
Library name: lib96542
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 29_T163

description:
Library name: lib96565
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 32_T163

description:
Library name: lib96568
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 26_T163

description:
Library name: lib96562
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 24_T163

description:
Library name: lib96560
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 9_T198

description:
Library name: lib96545
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 15_T199

description:
Library name: lib96551
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 4_T383

description:
Library name: lib96540
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 66_T183

description:
Library name: lib96602
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 5_T383

description:
Library name: lib96541
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 49_T184

description:
Library name: lib96585
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 174_T197

description:
Library name: lib90736
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

value: No

tag: total reads


title: 3_T383

description:
Library name: lib96539
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 1_T383

description:
Library name: lib96537
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 2_T383

description:
Library name: lib96538
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 177_T197

description:
Library name: lib90739
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 176_T197

description:
Library name: lib90738
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 179_T197

description:
Library name: lib90741
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 22_T199

description:
Library name: lib96558
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 172_T197

description:
Library name: lib90734
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 168_T196

description:
Library name: lib90730
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 167_T196

description:
Library name: lib90729
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 163_T196

description:
Library name: lib90725
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 159_T195

description:
Library name: lib90721
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 158_T195

description:
Library name: lib90720
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 149_T179

description:
Library name: lib90711
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 150_T179

description:
Library name: lib90712
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 152_T179

description:
Library name: lib90714
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 141_T177

description:
Library name: lib90703
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

value: Yes

tag: batch


title: 140_T177

description:
Library name: lib90702
combined_counts_ALI.csv

value: Asthma

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 145_T179

description:
Library name: lib90707
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 143_T177

description:
Library name: lib90705
combined_counts_ALI.csv

tag: exacerbation status

value: No Severe Exacerbation

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 138_T177

description:
Library name: lib90700
combined_counts_ALI.csv

tag: studygroup

tag: age

value: female

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 132_T187

description:
Library name: lib90694
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 136_T177

description:
Library name: lib90698
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 134_T187

description:
Library name: lib90696
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 131_T187

description:
Library name: lib90693
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 129_T187

description:
Library name: lib90691
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 122_T174

description:
Library name: lib90684
combined_counts_ALI.csv

tag: donorid

value: Native Hawaiian/PI

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 123_T174

description:
Library name: lib90685
combined_counts_ALI.csv

value: Organotypic airway epithelial cell culture

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 127_T187

description:
Library name: lib90689
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 120_T174

description:
Library name: lib90682
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 118_T174

description:
Library name: lib90680
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 147_T179

description:
Library name: lib90709
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 161_T195

description:
Library name: lib90723
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 156_T195

description:
Library name: lib90718
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 114_T186

description:
Library name: lib90676
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 113_T186

description:
Library name: lib90675
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

value: Control

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 154_T195

description:
Library name: lib90716
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 104_T185

description:
Library name: lib90666
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 109_T186

description:
Library name: lib90671
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 105_T185

description:
Library name: lib90667
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 170_T196

description:
Library name: lib90732
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 111_T186

description:
Library name: lib90673
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 102_T185

description:
Library name: lib90664
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 100_T185

description:
Library name: lib90662
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 107_T185

description:
Library name: lib90669
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 96_T181

description:
Library name: lib90658
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

value: Black

tag: eos absolute_(mm2)

tag: pct aligned


title: 98_T181

description:
Library name: lib90660
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 125_T174

description:
Library name: lib90687
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 165_T196

description:
Library name: lib90727
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 95_T181

description:
Library name: lib90657
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 89_T126

description:
Library name: lib90651
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 87_T126

description:
Library name: lib90649
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 86_T126

description:
Library name: lib90648
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 116_T186

description:
Library name: lib90678
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 82_T126

description:
Library name: lib90644
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 84_T126

description:
Library name: lib90646
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 93_T181

description:
Library name: lib90655
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 78_T170

description:
Library name: lib90640
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 77_T170

description:
Library name: lib90639
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 75_T170

description:
Library name: lib90637
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 73_T170

description:
Library name: lib90635
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 71_T194

description:
Library name: lib90633
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 69_T194

description:
Library name: lib90631
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load


title: 68_T194

description:
Library name: lib90630
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: median cv_coverage


title: 66_T194

description:
Library name: lib90628
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: total reads


title: 60_T190

description:
Library name: lib90622
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: pct aligned


title: 57_T190

description:
Library name: lib90619
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: batch


title: 59_T190

description:
Library name: lib90621
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: viral load


title: 53_T191

description:
Library name: lib90615
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: median cv_coverage


title: 91_T181

description:
Library name: lib90653
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: total reads


title: 48_T191

description:
Library name: lib90610
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: pct aligned


title: 62_T190

description:
Library name: lib90624
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: batch


title: 50_T191

description:
Library name: lib90612
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: viral load


title: 42_T193

description:
Library name: lib90604
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: median cv_coverage


title: 55_T190

description:
Library name: lib90617
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: total reads


title: 44_T193

description:
Library name: lib90606
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: pct aligned


title: 35_T182

description:
Library name: lib90597
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: batch


title: 39_T193

description:
Library name: lib90601
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: viral load


title: 51_T191

description:
Library name: lib90613
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: median cv_coverage


title: 80_T170

description:
Library name: lib90642
combined_counts_ALI.csv

tag: exacerbation status

tag: infection

tag: timepoint

tag: fef25-75 (%_predicted)

tag: total reads


title: 46_T191

description:
Library name: lib90608
combined_counts_ALI.csv

tag: studygroup

tag: age

tag: ethnicity

tag: allergic sensitization

tag: pct aligned


title: 32_T182

description:
Library name: lib90594
combined_counts_ALI.csv

tag: cell type

tag: treatment

tag: Sex

tag: eos absolute_(mm2)

tag: batch


title: 37_T193

description:
Library name: lib90599
combined_counts_ALI.csv

tag: donorid

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: viral load