EGID Express Unpublished Data

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Esophageal Biopsy Microarray (Blanchard)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

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Expression data
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Primary fibroblasts +/- IL-13 & TNFa (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Graph
Expression data
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p-value

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Primary epithelial cells +/- IL-13 & TNFa (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Graph
Expression data
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p-value

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TE-7 +/- IL-13 & TNFa Fold Change (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

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Expression data
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TE-7 scramble & STAT6 KD +/- IL-13 (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

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Expression data
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3' Biopsy EoE NL TPM RNAseq (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Experimental Design:

~30 of NL and active EoE (eos > 15/hpf, no treatment) biopsies were sequenced using 3’ RNA FWD kit from Lexogen. Data were processed by CLC genomics software and presented as TPM.

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Expression data
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EoE Transcriptome (Kottyan)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

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Expression data
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Eoe vs PPI-REE pre vs post (Shoda)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Experimental Design:

RNA sequencing was performed to quantify transcripts present in esophageal biopsy specimens obtained from patients with EoE and PPI-REE. Paired samples from 16 PPI-REE and 9 EoE subjects were included. Graphs were depicted by the RPKM for each individual.

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Expression data
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EDP - Eos & Inflammation

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Experimental Design:

RNA was isolated from distal esophageal tissue of CCHMC individuals. The RNA was subjected to EDP analysis, which quantifies 96 individual gene transcripts. Graphs depict the -deltaCt value -(ct of GAPDH – ct of gene of interest) for each individual.

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Expression data
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Silenced TSPAN12 Endothelial RNASeq

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Experimental Design:

Human Esophageal Microvascular Endothelial Cells (HEsMEC; #2700, ScienCell Research Laboratories) was transfected with either non-silencing control shRNA (HEsMEC_shCtrl) or TSPAN12 shRNA (HEsMEC_shTSPAN12). Cells were grown in monolayer culture with endothelial cell medium (ScienCell Research Laboratories). Graphs were depicted by the TPM for each sample.

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Expression data
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Eve Technologies EPC2 & Primary Cell Cytokines (Brusilovsky)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

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Expression data
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Eve Technologies TSLPTg Mouse Serum (Mario)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Experimental Design:

Values are in pg/mL

Sample: Mouse Serum

Subjects:

WT - C57BL/6 Mice, age at sacrifice: between 2 and 5 months.

Het - K14-TSLPTg / TSLPR (+/-) have an additional heterozygous knock-out for the TSLP Receptor (CRLF2)

Tg - K14-TSLPTg mice overexpress TSLP under the control of the Keratin 14 promoter

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Expression data
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Eve Technologies Esophageal Stem Cell Cytokines (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

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Bar graph: individual samples

Experimental Design:

These are esophageal stem cells sorted from the biopsy and grown in colonies on the irradiated MEFs. Cells (seeded on MEFs) and MEFs (separately as a control) were stimmed with IL-13 and TNF, and supernatants were sent to Eve Technology for multiplex.

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Expression data
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Note: blank condition excluded from t-test because it has only 1 sample

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Rochman EPC2 IL-6 RNAseq

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Experimental Design:

EPC2 cells were seeded at 500k/well in a 24-well plate in KSFM medium. The next day cells were stimulated with IL-6 at the final concentration of 50 ng/ml in fresh KSFM. After 24 hr cells were collected in Tripure for RNA isolation and sequencing

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Kendall Bulk RNAseq 2024

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

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Experimental Design:

Bulk RNA sequencing was performed to quantify transcripts present in mouse dorsal root ganglia (DRG) and nodose ganglia (NG) cells. 'Allergic' mice (n=3) were subjected to repeated intranasal Alternaria exposure compared with 'control' mice (n=3) which were given saline.

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Expression data
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Search all experiments by gene (single cell excluded)

Gene:

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Proteomics from Biopsies (Rochman)

Protein:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Experimental Design:

Protemoic analysis from 18 non-inflamed (full histological remission, not normal controls) and 18 active EoE biopsies

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Expression data
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Proteomics from EPC2 cells (Rochman)

Protein:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Experimental Design:

Normalized counts for the proteomics analysis of EPC2 cells, either WT, PADI1 KO, or OE. Cells are either a monolayer or ALI, either untreated (UT) or IL-13-treated.

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Expression data
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basal v suprabasal EoE, normal, remission RNAseq (Rochman)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

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Expression data
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Bulk-RNA Seq of Skin and Esophagus of TslpTg Mice (Mario)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Ear skin and esophagus tissues were harvested from matched adult wild-type (WT; n = 3) and TslpTg (n = 6) mice, preserved in RNAlater, and total RNA was isolated according to standard protocols. Library preparation and sequencing were performed by the Cincinnati Children's Hospital Medical Center (CCHMC) Genomics Sequencing Facility. Sequencing reads were aligned to the mouse reference genome (GRCm38/mm10), and gene expression was quantified as transcripts per million (TPM) using CLC Genomics Workbench (Qiagen, version 23.0.5).

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Expression data
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TslpTg Tissue Eve Tech (Mario)

Protein:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Cytokine and chemokine levels were measured from whole-tissue lysates of esophagus and skin from matched adult mice (3 Wt and 4 TslpTg). Tissues were homogenized in RIPA buffer (Thermo Fisher Scientific, 89900) supplemented with protease inhibitor cocktail (cOmplete™ ULTRA; Roche, 05892970001), and protein extraction was performed using a Covaris system according to the manufacturer’s instructions. Lysates were clarified by centrifugation, and total protein concentration was determined for each sample. Cytokine and chemokine profiling was performed using the Mouse Cytokine/Chemokine 32-Plex Discovery Assay (Eve Technologies Corp.) according to the manufacturer’s instructions.

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Expression data
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10XG Esophagus Biopsies (Netali)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

Esophageal biopsies were obtained from patients with active EoE (N = 6), patients with EoE in histologic remission (n =7), and control individuals with histologically normal esophageal biopsies (n = 6). These biopsies were subjected to 10X scRNA-seq. This dataset includes all esophageal cells detected by the platform.

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Sample Information

Honeycomb Peripheral Blood (Netali)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

Peripheral blood samples were obtained from patients with EoE (N= 3) and patients with EoE (n = 3). These blood samples were subjected to Honeycomb scRNA-seq. This dataset includes cells (sans erythrocytes) detected by the platform.

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Sample Information

SeqWell Esophagus Biopsies (Netali)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

A previously reported cohort of biopsies obtained for patients with active EoE (n = 6) subjected to SeqWell scRNA-seq was analyzed using its published data set (GEO: GSE175930).

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Sample Information

SeqWell Esophagus Biopsies and
Honeycomb Blood Merged (Netali)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

To facilitate joint analysis of the peripheral blood (EoE, n = 3; Control, n =3) and esophageal (active EoE, n = 6) datasets, gene names were converted to Ensembl 104 version using the biomaRt R package.

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Sample Information

Reanalysis of the Esophageal Epithelium in Allergic Inflammation (Mario)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

A previously published human single-cell esophageal epithelial dataset was re-analyzed (Rochman et al. 2022, JCI). Downstream analyses were performed using the RNA assay. Highly variable genes (2,000) were identified using the vst method, followed by data scaling, principal component analysis, UMAP dimensionality reduction (20 principal components), construction of a shared nearest-neighbor graph (dimensions 1–20), and graph-based clustering (resolution 0.1) to identify major epithelial cell states.

This UMAP projection shows clustering into seven epithelial states: Quiescent, Proliferative, Activated proliferative, Trans1, Trans2, Differentiated, and TIRE.

Graph
Sample Information

Whole Esophageal scRNAseq TslpTG vs Ctrl (Mario)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

Esophageal tissues from four TslpTg and four control mice were collected and maintained in RPMI-1640 at 4°C for no longer than 2 hours. Tissues were incubated in EDTA stripping buffer for 15 minutes at 37°C, followed by digestion with Liberase TL and DNase I for 30 minutes at 37°C. Samples were mechanically dissociated through a 19-gauge needle, filtered through a 70-µm cell strainer, labeled with sample-specific barcodes, pooled, and processed using the BD Rhapsody Single-Cell Analysis System. Whole-transcriptome libraries were sequenced on a NovaSeq 6000. After quality-control filtering, 21,599 cells were retained, including 12,802 TslpTg and 8,797 control cells.

Graph
Sample Information

Epithelial Subset TslpTg vs Ctrl (Mario)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

This dataset was derived from the whole esophageal single-cell RNA-sequencing dataset by selecting annotated epithelial cells. Principal-component analysis was performed using the SCT assay, followed by nearest-neighbor graph construction and graph-based reclustering. Small contractile mesenchymal and neural-like populations were identified by coherent lineage-associated transcriptional signatures and excluded.

Graph
Sample Information

Lymphoid Subset TslpTg vs Ctrl (Mario)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Experimental Design:

This dataset was derived from the annotated lymphoid compartment of the whole esophageal single-cell RNA-sequencing dataset using curated cell-identity annotations. Principal-component analysis was performed using the SCT assay, followed by nearest-neighbor graph construction and graph-based reclustering.

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Sample Information

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Esophageal Biopsy Microarray (Blanchard)

p-value

Primary fibroblasts +/- IL-13 & TNFa (Rochman)

p-value

Primary epithelial cells +/- IL-13 & TNFa (Rochman)

p-value

TE-7 +/- IL-13 & TNFa Fold Change (Rochman)

TE-7 scramble & STAT6 KD +/- IL-13 (Rochman)

3' Biopsy EoE NL TPM RNAseq (Rochman)

p-value

EoE Transcriptome (Kottyan)

p-value

Eoe vs PPI-REE pre vs post (Shoda)

p-value

EDP - Eos & Inflammation

p-value

Silenced TSPAN12 Endothelial RNASeq

p-value

Eve Technologies EPC2 & Primary Cell Cytokines (Brusilovsky)

p-value

Eve Technologies TSLPTg Mouse Serum (Mario)

p-value

Eve Technologies Esophageal Stem Cell Cytokines (Rochman)

p-value

Note: blank condition excluded from t-test because it has only 1 sample

Rochman EPC2 IL-6 RNAseq

p-value

Kendall Bulk RNAseq 2024

p-value

Search all experiments by gene (single cell excluded)

Proteomics from Biopsies (Rochman)

p-value

Proteomics from EPC2 cells (Rochman)

p-value

basal v suprabasal EoE, normal, remission RNAseq (Rochman)

p-value

Bulk-RNA Seq of Skin and Esophagus of TslpTg Mice (Mario)

p-value

TslpTg Tissue Eve Tech (Mario)

p-value

10XG Esophagus Biopsies (Netali)

Honeycomb Peripheral Blood (Netali)

SeqWell Esophagus Biopsies (Netali)

SeqWell Esophagus Biopsies andHoneycomb Blood Merged (Netali)

Reanalysis of the Esophageal Epithelium in Allergic Inflammation (Mario)

Whole Esophageal scRNAseq TslpTG vs Ctrl (Mario)

Epithelial Subset TslpTg vs Ctrl (Mario)

Lymphoid Subset TslpTg vs Ctrl (Mario)

SeqWell Esophagus Biopsies and
Honeycomb Blood Merged (Netali)