title: D520_001_GEX_CZINY-0228

description:
Library name: D520_001_GEX_CZINY-0228_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 25 years

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

value: fresh

tag: death type

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: raw matrix_value_units

value: UMI

tag: assay type


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample15

status: Public on Jun 06 2025

type: SRA

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

country: USA

institute: United States Environmental Protection Agency

description:
Chem6_C_D1
Chem6_counts_matrix.txt

library_source: transcriptomic

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA).
The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene.
The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018).
Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021).
Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into separate (tab-delimited) count matrix files for each chemical treatment group where columns represented samples and rows represented genes.
Assembly: GCA_003203535.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

molecule: polyA RNA

organism: Raphidocelis subcapitata

source_name: whole body

growth_protocol: not applicable

extract_protocol:
After a series of flash freezing and homogenization, algae total RNA was extracted using the Norgen Biotek Plant/Fungi Total RNA kit (Norgen) according to the manufacturer’s protocol. Sample quantity and quality was assessed using a NanoDrop Eight spectrophotometer (Thermo Scientific) and 4200 TapeStation (Agilent Technologies).
Sample libraries were prepared using QuantSeq 3’ mRNA-Seq V2 Library Prep Kits (Lexogen, GmbH, Austria) with Unique Dual Index (UDI) and QuantSeq Unique Molecular Identifiers (UMI). Preparation followed manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays.

treatment_protocol: 800 µL of algae was loaded into each well of 4 x 96-well plates (Beckman Cat #267007) using the Biomek robot. The algae were pelleted by centrifugation at 4000 rpm for 5 min and 400 µL of the supernatant (i.e., media) was removed. Final exposure concentrations were achieved by loading 400 µL of the 2X dosing solutions to the appropriate wells. After the dosing solutions were added, the plates were covered with optical adhesive covers, vortexed briefly to disrupt the algae pellet, and pulse centrifuged making sure to the algae did not pellet. The exposure plates, each containing 700 µL algae after 100 µL was removed for Time 0 apical measurements, were incubated for 24 h at 24ºC under a constant LED 4300 lux grow light and on a timed orbital shaker (Titramax 1000, Heidolph Instruments GmbH) turning on and off every 15 min so the algae remained in suspension.

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: 4-chlorophenyl methyl sulfone


title: D520_001_GEX_CZINY-0232

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: D520_001_GEX_CZINY-0232_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

library_source: transcriptomic single cell

data_processing:
raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_background_barcodes_included:False
Assembly: GRCh38, GENCODE32
Supplementary files format and content: h5ad, count matrix

organism: Homo sapiens

extract_protocol:
Tissue was obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement via LiveOnNY, the organ procurement organization for the New York metropolitan area and through the Cambridge Biorepository for Translational Medicine. Each tissue was subjected to a tissue-specific protocol to maximize mononuclear cell (MNC) recovery and viability across a diversity of sites. A series of detailed protocols are available on protocols.io (https://dx.doi.org/10.17504/protocols.io.bwrjpd4n, https://dx.doi.org/10.17504/protocols.io.bwr9pd96, https://dx.doi.org/10.17504/protocols.io.bwsapeae, https://dx.doi.org/10.17504/protocols.io.bwq4pdyw, https://dx.doi.org/10.17504/protocols.io.bwq7pdzn, https://dx.doi.org/10.17504/protocols.io.bwr6pd9e, https://dx.doi.org/10.17504/protocols.io.bz4qp8vw). Each individual tissue single cell suspension (500,000 or 1,000,000 cells) was hash tagged to allow pooling of tissue samples. CITE-seq labeling used either a TotalSeq-C cocktail containing 137 protein targets (10x 5’ libraries) or TotalSeq-A cocktail containing 277 protein targets (10x 3’ libraries).
For scRNA-seq experiments, single cells were loaded onto the channels of a Chromium chip (10x Genomics). cDNA synthesis, amplification, and sequencing libraries were generated using either the Single Cell 5′ Reagent (v1 and v2) or 3′ Reagent (v3) Kits. TCRαβ and BCR paired VDJ libraries were prepared from samples made with the 5′ Reagent kit. All libraries were sequenced on either an Illumina NextSeq 500/550 or NovaSeq 6000 instrument.

tag: donor id

tag: age

value: adult stage

tag: Sex

value: female

tag: ethnicity

value: Middle Eastern/North African

value: LiveOnNY

tag: sample preservation_method

tag: smoking history

value: never

value: brain stem death

tag: cause of_death

value: anoxia

tag: body mass_index

value: positive

value: 120 mg/dL

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

value: scRNA-seq


title: D520_001_GEX_CZINY-0226

description:
Library name: D520_001_GEX_CZINY-0226_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 25 years

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

value: fresh

tag: death type

tag: height

tag: test results.ebv

tag: test results.cmv

tag: test results.blood_sugar

tag: raw matrix_value_units

value: UMI

tag: assay type


title: D512_001_GEX_CZINY-0176

description:
Library name: D512_001_GEX_CZINY-0176_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 27 years

value: adult stage

tag: Sex

tag: ethnicity

value: Hispanic or Latin American

tag: tissue

tag: sample preservation_method

tag: smoking history

value: current, 0.45 pack-years

tag: cause of_death

tag: body mass_index

value: 211 mg/dL

tag: library protocol


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample13

description:
Chem6_B_D6
Chem6_counts_matrix.txt

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: 4-chlorophenyl methyl sulfone


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample14

description:
Chem6_B_D7
Chem6_counts_matrix.txt


title: D520_001_GEX_CZINY-0225

description:
Library name: D520_001_GEX_CZINY-0225_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

value: female

value: Middle Eastern/North African

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: never

tag: death type

value: brain stem death

value: anoxia

tag: height

tag: test results.ebv

value: positive

value: 120 mg/dL

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type


title: D512_001_GEX_CZINY-0174

description:
Library name: D512_001_GEX_CZINY-0174_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: tissue

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

tag: cause of_death

tag: test results.cmv

tag: test results.blood_sugar

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

tag: assay type

value: scRNA-seq


title: D520_001_GEX_CZINY-0229

description:
Library name: D520_001_GEX_CZINY-0229_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 25 years

tag: dev stage

value: adult stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: death type

tag: body mass_index

tag: height

tag: test results.ebv

tag: library protocol


title: D512_001_GEX_CZINY-0175

description:
Library name: D512_001_GEX_CZINY-0175_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 27 years

tag: Sex

value: female

tag: ethnicity

value: Hispanic or Latin American

tag: tissue

tag: sample preservation_method

value: current, 0.45 pack-years

value: 211 mg/dL

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample11

description:
Chem6_B_D4
Chem6_counts_matrix.txt

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: 4-chlorophenyl methyl sulfone


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample10

description:
Chem6_B_D3
Chem6_counts_matrix.txt


title: D512_001_GEX_CZINY-0173

description:
Library name: D512_001_GEX_CZINY-0173_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

value: anoxia

value: positive

tag: test results.cmv

tag: test results.blood_sugar

tag: raw matrix_value_units

tag: assay type


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample9

description:
Chem6_B_D2
Chem6_counts_matrix.txt

tag: tissue


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample8

description:
Chem6_B_D1
Chem6_counts_matrix.txt


title: D512_001_GEX_CZINY-0170

description:
Library name: D512_001_GEX_CZINY-0170_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: sample preservation_method

value: fresh

tag: body mass_index

tag: height

tag: test results.ebv

tag: library protocol

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: D512_001_GEX_CZINY-0171

description:
Library name: D512_001_GEX_CZINY-0171_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 27 years

tag: dev stage

value: adult stage

value: female

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

tag: test results.cmv

tag: enriched cell_type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample7

description:
Chem6_A_D7
Chem6_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

tag: treatment


title: D512_001_GEX_CZINY-0168

description:
Library name: D512_001_GEX_CZINY-0168_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: Hispanic or Latin American

tag: sample preservation_method

value: current, 0.45 pack-years

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

value: 211 mg/dL

tag: library protocol

tag: raw matrix_value_units

tag: assay type


title: D520_001_GEX_CZINY-0227

description:
Library name: D520_001_GEX_CZINY-0227_lib
scRNA-seq of mononuclear cells from pooled:blood,colonic epithelium,jejunal epithelium,lung,bone marrow,mesenteric lymph node,lamina propria of mucosa of colon,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 25 years

tag: dev stage

value: Middle Eastern/North African

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: smoking history

value: never

tag: death type

tag: cause of_death

tag: test results.cmv

value: 120 mg/dL

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample5

description:
Chem6_A_D5
Chem6_counts_matrix.txt

tag: tissue

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: 4-chlorophenyl methyl sulfone


title: D512_001_GEX_CZINY-0167

description:
Library name: D512_001_GEX_CZINY-0167_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: sample preservation_method

value: fresh

value: brain stem death

value: anoxia

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell


title: D512_001_GEX_CZINY-0169

description:
Library name: D512_001_GEX_CZINY-0169_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 27 years

tag: dev stage

value: adult stage

value: female

value: Hispanic or Latin American

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

value: current, 0.45 pack-years

tag: death type

tag: cause of_death

tag: test results.cmv

value: 211 mg/dL

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample4

description:
Chem6_A_D4
Chem6_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: D512_001_GEX_CZINY-0166

description:
Library name: D512_001_GEX_CZINY-0166_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: LiveOnNY

value: FALSE

tag: sample preservation_method

value: fresh

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_value_units

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample3

description:
Chem6_A_D3
Chem6_counts_matrix.txt

value: 4-chlorophenyl methyl sulfone


title: D512_001_GEX_CZINY-0165

description:
Library name: D512_001_GEX_CZINY-0165_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

value: anoxia

value: positive

tag: test results.cmv

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample2

description:
Chem6_A_D2
Chem6_counts_matrix.txt

tag: tissue

tag: developmental stage

tag: treatment


title: D512_001_GEX_CZINY-0163

description:
Library name: D512_001_GEX_CZINY-0163_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 27 years

tag: Sex

tag: ethnicity

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_value_units

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

value: mononuclear cell

tag: assay type


title: D512_001_GEX_CZINY-0164

description:
Library name: D512_001_GEX_CZINY-0164_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

value: adult stage

value: female

value: Hispanic or Latin American

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

value: current, 0.45 pack-years

tag: death type

tag: cause of_death

tag: test results.cmv

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample12

description:
Chem6_B_D5
Chem6_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: R. subcapitata, 24 h exposure, DMSO, sample12

description:
Chem5_Chem6_C_CON
Chem5_counts_matrix.txt
Chem6_counts_matrix.txt

value: DMSO


title: D512_001_GEX_CZINY-0162

description:
Library name: D512_001_GEX_CZINY-0162_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: LiveOnNY

value: FALSE

tag: sample preservation_method

value: fresh

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

value: 211 mg/dL

tag: library protocol

tag: raw matrix_value_units

tag: enriched cell_type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, DMSO, sample11

description:
Chem5_Chem6_B_CON
Chem5_counts_matrix.txt
Chem6_counts_matrix.txt


title: D512_001_GEX_CZINY-0161

description:
Library name: D512_001_GEX_CZINY-0161_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

value: anoxia

value: positive

tag: test results.cmv

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: assay type


title: D512_001_GEX_CZINY-0172

description:
Library name: D512_001_GEX_CZINY-0172_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,inguinal lymph node,lung,mesenteric lymph node,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 27 years

tag: Sex

tag: ethnicity

tag: tissue

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: R. subcapitata, 24 h exposure, DMSO, sample10

description:
Chem5_Chem6_A_CON
Chem5_counts_matrix.txt
Chem6_counts_matrix.txt

tag: developmental stage

tag: treatment


title: D503_001_GEX_CZINY-0064

description:
Library name: D503_001_GEX_CZINY-0064_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 67 years

tag: dev stage

value: adult stage

value: female

value: European

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

value: never

tag: death type

tag: cause of_death

tag: test results.blood_sugar

value: 198 mg/dL

tag: library protocol

tag: raw matrix_value_units

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample20

description:
Chem5_C_D6
Chem5_counts_matrix.txt

tag: tissue

value: whole body

value: Exponential Growth Stage

value: Hydrochlorothiazide


title: D503_001_GEX_CZINY-0063

description:
Library name: D503_001_GEX_CZINY-0063_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: LiveOnNY

value: FALSE

tag: sample preservation_method

value: fresh

value: brain stem death

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample21

description:
Chem5_C_D7
Chem5_counts_matrix.txt

tag: developmental stage

tag: treatment


title: D503_001_GEX_CZINY-0062

description:
Library name: D503_001_GEX_CZINY-0062_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

value: anoxia

value: positive

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_value_units

value: UMI

value: gene symbol, antibody target

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample6

description:
Chem6_A_D6
Chem6_counts_matrix.txt

tag: tissue

value: 4-chlorophenyl methyl sulfone


title: D503_001_GEX_CZINY-0061

description:
Library name: D503_001_GEX_CZINY-0061_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 67 years

value: adult stage

tag: Sex

value: female

tag: ethnicity

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample17

description:
Chem5_C_D3
Chem5_counts_matrix.txt

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample18

description:
Chem5_C_D4
Chem5_counts_matrix.txt

value: Hydrochlorothiazide


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample16

description:
Chem5_C_D2
Chem5_counts_matrix.txt


title: D503_001_GEX_CZINY-0058

description:
Library name: D503_001_GEX_CZINY-0058_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

value: European

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: smoking history

value: never

tag: death type

tag: cause of_death

tag: test results.blood_sugar

value: 198 mg/dL

tag: library protocol

tag: raw matrix_value_units

tag: assay type


title: D503_001_GEX_CZINY-0059

description:
Library name: D503_001_GEX_CZINY-0059_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: tissue

tag: sample preservation_method

value: fresh

value: brain stem death

value: anoxia

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: raw matrix_genome_annotation

tag: raw matrix_assays

value: scRNA-seq


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample15

description:
Chem5_C_D1
Chem5_counts_matrix.txt

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample19

description:
Chem5_C_D5
Chem5_counts_matrix.txt


title: D503_001_GEX_CZINY-0060

description:
Library name: D503_001_GEX_CZINY-0060_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 67 years

tag: dev stage

value: adult stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

tag: test results.blood_sugar

tag: library protocol

value: UMI

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: enriched cell_type


title: D503_001_GEX_CZINY-0056

description:
Library name: D503_001_GEX_CZINY-0056_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

value: female

tag: ethnicity

tag: tissue

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

tag: raw matrix_value_units

value: snRNA-seq, CITE-seq

value: mononuclear cell

tag: assay type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample13

description:
Chem5_B_D6
Chem5_counts_matrix.txt

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: Hydrochlorothiazide


title: D503_001_GEX_CZINY-0057

description:
Library name: D503_001_GEX_CZINY-0057_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

value: European

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: smoking history

value: never

tag: death type

tag: cause of_death

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample10

description:
Chem5_B_D3
Chem5_counts_matrix.txt

tag: tissue


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample14

description:
Chem5_B_D7
Chem5_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 4-chlorophenyl methyl sulfone, sample1

description:
Chem6_A_D1
Chem6_counts_matrix.txt

value: 4-chlorophenyl methyl sulfone


title: D503_001_GEX_CZINY-0055

description:
Library name: D503_001_GEX_CZINY-0055_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: sample preservation_method

value: fresh

value: brain stem death

value: anoxia

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

value: 198 mg/dL

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: enriched cell_type


title: D503_001_GEX_CZINY-0051

description:
Library name: D503_001_GEX_CZINY-0051_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

value: 67 years

tag: dev stage

value: adult stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

tag: test results.blood_sugar

value: UMI

value: gene symbol, antibody target

tag: assay type

value: scRNA-seq


title: D503_001_GEX_CZINY-0053

description:
Library name: D503_001_GEX_CZINY-0053_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

value: female

tag: ethnicity

tag: tissue

tag: sample preservation_method

tag: body mass_index

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: mononuclear cell


title: D503_001_GEX_CZINY-0052

description:
Library name: D503_001_GEX_CZINY-0052_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

value: European

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: height

tag: test results.ebv

tag: test results.cmv

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: enriched cell_type


title: D503_001_GEX_CZINY-0054

description:
Library name: D503_001_GEX_CZINY-0054_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: living at_sample_collection

value: FALSE

tag: smoking history

value: never

tag: death type

tag: cause of_death

tag: test results.blood_sugar

tag: assay type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample8

description:
Chem5_B_D1
Chem5_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: Hydrochlorothiazide


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample7

description:
Chem5_A_D7
Chem5_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample11

description:
Chem5_B_D4
Chem5_counts_matrix.txt


title: D503_001_GEX_CZINY-0050

description:
Library name: D503_001_GEX_CZINY-0050_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

value: fresh

value: brain stem death

value: anoxia

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample6

description:
Chem5_A_D6
Chem5_counts_matrix.txt


title: D503_001_GEX_CZINY-0049

description:
Library name: D503_001_GEX_CZINY-0049_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,epithelial lining fluid,jejunum lamina propria

tag: donor id

tag: age

value: 67 years

value: adult stage

tag: Sex

tag: ethnicity

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

tag: test results.blood_sugar

value: 198 mg/dL

tag: raw matrix_value_units

value: UMI

tag: raw matrix_feature_keys

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample5

description:
Chem5_A_D5
Chem5_counts_matrix.txt

tag: tissue

tag: developmental stage

tag: treatment


title: D496_002_GEX_CZINY-0111

description:
Library name: D496_002_GEX_CZINY-0111_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: 56 years

tag: dev stage

value: male

value: Hispanic or Latin American

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

value: current, 90 pack-years

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.cmv

value: 150 mg/dL

tag: library protocol

tag: raw matrix_genome_annotation

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample4

description:
Chem5_A_D4
Chem5_counts_matrix.txt

value: whole body

value: Exponential Growth Stage

value: Hydrochlorothiazide


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample3

description:
Chem5_A_D3
Chem5_counts_matrix.txt


title: D496_002_GEX_CZINY-0110

description:
Library name: D496_002_GEX_CZINY-0110_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: LiveOnNY

tag: living at_sample_collection

value: FALSE

value: fresh

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

value: positive

tag: test results.blood_sugar

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: mononuclear cell


title: D496_002_GEX_CZINY-0109

description:
Library name: D496_002_GEX_CZINY-0109_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: 56 years

tag: dev stage

value: adult stage

value: male

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

value: UMI

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample1

description:
Chem5_A_D1
Chem5_counts_matrix.txt

tag: developmental stage

tag: treatment


title: D496_002_GEX_CZINY-0107

description:
Library name: D496_002_GEX_CZINY-0107_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: Hispanic or Latin American

tag: living at_sample_collection

tag: smoking history

value: current, 90 pack-years

tag: death type

tag: cause of_death

value: Cerebrovascular/Stroke

tag: test results.cmv

value: 150 mg/dL

tag: library protocol

tag: raw matrix_genome_annotation

tag: assay type


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample2

description:
Chem5_A_D2
Chem5_counts_matrix.txt

tag: tissue

value: whole body


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample12

description:
Chem5_B_D5
Chem5_counts_matrix.txt

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample21

description:
Chem4_C_D7
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample20

description:
Chem4_C_D6
Chem4_counts_matrix.txt


title: D496_002_GEX_CZINY-0106

description:
Library name: D496_002_GEX_CZINY-0106_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

tag: raw matrix_value_units

tag: raw matrix_feature_keys

value: gene symbol, antibody target

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

value: scRNA-seq


title: R. subcapitata, 24 h exposure, Hydrochlorothiazide, sample9

description:
Chem5_B_D2
Chem5_counts_matrix.txt

tag: developmental stage

tag: treatment

value: Hydrochlorothiazide


title: D496_002_GEX_CZINY-0105

description:
Library name: D496_002_GEX_CZINY-0105_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: LiveOnNY

tag: living at_sample_collection

value: FALSE

value: fresh

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

tag: test results.cmv

tag: library protocol

tag: raw matrix_genome_annotation

tag: enriched cell_type


title: D496_002_GEX_CZINY-0104

description:
Library name: D496_002_GEX_CZINY-0104_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

value: 56 years

tag: dev stage

value: adult stage

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.blood_sugar

tag: raw matrix_value_units

value: mononuclear cell

tag: assay type


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample18

description:
Chem4_C_D4
Chem4_counts_matrix.txt

tag: developmental stage

tag: treatment


title: D496_002_GEX_CZINY-0103

description:
Library name: D496_002_GEX_CZINY-0103_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: living at_sample_collection

tag: smoking history

value: current, 90 pack-years

tag: death type

tag: cause of_death

tag: test results.cmv

tag: library protocol

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: D496_002_GEX_CZINY-0112

description:
Library name: D496_002_GEX_CZINY-0112_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

value: Cerebrovascular/Stroke

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

value: 150 mg/dL

tag: raw matrix_genome_annotation

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample16

description:
Chem4_C_D2
Chem4_counts_matrix.txt

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment


title: D496_002_GEX_CZINY-0102

description:
Library name: D496_002_GEX_CZINY-0102_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

tag: living at_sample_collection

tag: smoking history

tag: death type

tag: cause of_death

tag: test results.cmv

tag: library protocol

tag: raw matrix_value_units

value: gene symbol, antibody target

value: snRNA-seq, CITE-seq

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample15

description:
Chem4_C_D1
Chem4_counts_matrix.txt

tag: tissue


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample14

description:
Chem4_B_D7
Chem4_counts_matrix.txt


title: D496_002_GEX_CZINY-0101

description:
Library name: D496_002_GEX_CZINY-0101_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

value: FALSE

tag: sample preservation_method

value: fresh

tag: body mass_index

tag: height

tag: test results.ebv

tag: test results.blood_sugar

tag: raw matrix_genome_annotation

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: D496_002_GEX_CZINY-0100

description:
Library name: D496_002_GEX_CZINY-0100_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

value: adult stage

tag: Sex

tag: ethnicity

tag: living at_sample_collection

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

tag: test results.cmv

tag: enriched cell_type


title: D496_002_GEX_CZINY-0099

description:
Library name: D496_002_GEX_CZINY-0099_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: dev stage

value: male

tag: tissue

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: sample preservation_method

tag: body mass_index

value: positive

tag: library protocol

tag: raw matrix_value_units

value: mononuclear cell

tag: assay type


title: D496_002_GEX_CZINY-0098

description:
Library name: D496_002_GEX_CZINY-0098_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

tag: Sex

tag: ethnicity

value: Hispanic or Latin American

value: current, 90 pack-years

tag: height

tag: test results.ebv

tag: test results.blood_sugar

tag: raw matrix_genome_annotation

value: UMI

tag: raw matrix_feature_keys

tag: raw matrix_assays


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample13

description:
Chem4_B_D6
Chem4_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

tag: treatment


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample19

description:
Chem4_C_D5
Chem4_counts_matrix.txt

value: Exponential Growth Stage


title: D496_002_GEX_CZINY-0108

description:
Library name: D496_002_GEX_CZINY-0108_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: dev stage

tag: source

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

tag: sample preservation_method

tag: smoking history

tag: death type

tag: cause of_death

value: Cerebrovascular/Stroke

tag: body mass_index

tag: test results.cmv

value: 150 mg/dL

value: gene symbol, antibody target

tag: enriched cell_type


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample10

description:
Chem4_B_D3
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample11

description:
Chem4_B_D4
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample9

description:
Chem4_B_D2
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample8

description:
Chem4_B_D1
Chem4_counts_matrix.txt


title: DOT1L knockdon RME cell, 35 mM gluocose 36 h, rep1

city: Quzhou

first: Si-wei

last: Wang

address: No.100 Minjiang Road

country: China

institute: Quzhou people's hospital

description:
Library name: DOT1L_1
null

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the homo sapiens genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

growth_protocol: The cells were cultured in endothelial cell culture medium supplemented with 10% v/v fetal bovine serum and 100 U/mL penicillin/streptomycin at 37℃ in a humidified atmosphere with 5% CO2.

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

treatment_protocol: The cells were treated with 35mM glucose siNC or 35 mM glucose siDOT1L for 36 h.

tag: cell line

value: human retinal microvascular endothelial cells

tag: cell type

value: retinal microvascular endothelial cell

tag: genotype

value: DOT1L knockdon

value: 35 mM glucose, siDOT1L

tag: batch


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample6

description:
Chem4_A_D6
Chem4_counts_matrix.txt

tag: tissue

tag: developmental stage

tag: treatment


title: DOT1L knockdon RME cell, 35 mM gluocose 36 h, rep2

description:
Library name: DOT1L_2
null


title: RME cell, 35 mM gluocose 36 h, rep3

description:
Library name: HG_3
null

value: WT

value: 35 mM glucose, siNC


title: DOT1L knockdon RME cell, 35 mM gluocose 36 h, rep3

description:
Library name: DOT1L_3
null


title: RME cell, 35 mM gluocose 36 h, rep2

description:
Library name: HG_2
null


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample7

description:
Chem4_A_D7
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample17

description:
Chem4_C_D3
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample5

description:
Chem4_A_D5
Chem4_counts_matrix.txt


title: RME cell, 35 mM gluocose 36 h, rep1

description:
Library name: HG_1
null


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample4

description:
Chem4_A_D4
Chem4_counts_matrix.txt


title: Human BE organoid line WU010 Transitional group

city: St. Louis

first: Ramon

last: Jin

address: 600 S Euclid

institute: Washington University School of Medicine

description:
Library name: WU010
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Quality control for filtering, normalization, clustering, and differential expression analysis was conducted in Seurat/R (Seurat  v4)
Assembly: GRCh38
Supplementary files format and content: Web_summary, Raw/Filtered barcodes tab-separated values file, features tab-separated values file, and matrix file

source_name: human BE

growth_protocol: Barrett’s esophagus organoids were cultured with L-WRN-conditioned media supplemented with 10 nM gastrin (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), 10 µM SB202190 (Sigma-Aldrich), 200 ng/mL FGF10 (Peprotech), 10 µM Y-27632 (Sigma-Aldrich), and 10 µM Primocin (Invivogen) in 3D Matrigel (Corning) in 24-well plates (Greiner Bio-One). Organoids were expanded and passaged every 7-10 days by mechanical dissociation from Matrigel, dispersed using TrypLE (Gibco) and manual pipetting, and transferred into new Matrigel and plated in 24-well plates.

extract_protocol:
For human Barrett’s esophagus organoid single-cell expression profiling, organoids were pelleted and digested to single cells using TrypLE (Gibco) digestion and manual pipetting dissociation, and then neutralized with Advanced DMEM/F12 (Gibco), 10% FBS (Gibco), 1X HEPES, 1X L-glutamine, 1X Pen/strep, 10 µM Y-27632 (Biogems), and 10 µM Primocin (InvivoGen). Cells were filtered using a 30 µm filter, counted, and volume adjusted before submission to the Washington University Genome Technology Access Core (GTAC).
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3’v3 instruction (10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. After passed the quality control, the next-generation sequencing of libraries was performed on NovaSeq 6000 (Illumina).

value: human BE

value: organoid

tag: chemistry

value: Single Cell 3' v3

tag: transcriptome

tag: pipeline version

tag: estimated number_of_cells

tag: mean reads_per_cell

tag: median genes_per_cell

tag: median umi_counts_per_cell

tag: sequencing saturation

tag: fraction of_reads_in_cells


title: Human BE organoid line WU012 Foregut group

description:
Library name: WU012
10x Genomics

treatment_protocol: Barrett’s esophagus organoids were cultured with L-WRN-conditioned media supplemented with 10 nM gastrin (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), 10 µM SB202190 (Sigma-Aldrich), 200 ng/mL FGF10 (Peprotech), 10 µM Y-27632 (Sigma-Aldrich), and 10 µM Primocin (Invivogen) in 3D Matrigel (Corning) in 24-well plates (Greiner Bio-One). Organoids were expanded and passaged every 7-10 days by mechanical dissociation from Matrigel, dispersed using TrypLE (Gibco) and manual pipetting, and transferred into new Matrigel and plated in 24-well plates.


title: Human BE organoid line WU002 Hindgut group

description:
Library name: WU002
10x Genomics


title: Human BE organoid line WU014 Hindgut group

description:
Library name: WU014
10x Genomics


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample3

description:
Chem4_A_D3
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample1

description:
Chem4_A_D1
Chem4_counts_matrix.txt


title: D496_002_GEX_CZINY-0097

description:
Library name: D496_002_GEX_CZINY-0097_lib
scRNA-seq of mononuclear cells from pooled:blood,jejunal epithelium,lung,spleen,bone marrow,thoracic lymph node,jejunum lamina propria

tag: donor id

tag: age

value: 56 years

tag: dev stage

value: adult stage

tag: Sex

value: male

tag: ethnicity

value: Hispanic or Latin American

tag: source

value: LiveOnNY

tag: suspension cell_depletion_factors

tag: raw matrix_cellranger_assay_chemistry

tag: living at_sample_collection

value: FALSE

tag: sample preservation_method

value: fresh

tag: smoking history

tag: death type

value: brain stem death

tag: cause of_death

tag: body mass_index

tag: height

tag: test results.ebv

value: positive

tag: test results.cmv

tag: test results.blood_sugar

tag: library protocol

tag: raw matrix_genome_annotation

tag: raw matrix_value_units

tag: raw matrix_feature_keys

tag: raw matrix_assays

value: snRNA-seq, CITE-seq

tag: enriched cell_type

value: mononuclear cell

tag: assay type

value: scRNA-seq


title: R. subcapitata, 24 h exposure, DMSO, sample9

description:
Chem3_Chem4_C_CON
Chem3_counts_matrix.txt
Chem4_counts_matrix.txt

tag: tissue

value: whole body

tag: developmental stage

value: Exponential Growth Stage

tag: treatment

value: DMSO


title: R. subcapitata, 24 h exposure, DMSO, sample8

description:
Chem3_Chem4_B_CON
Chem3_counts_matrix.txt
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, DMSO, sample7

description:
Chem3_Chem4_A_CON
Chem3_counts_matrix.txt
Chem4_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample12

description:
Chem4_B_D5
Chem4_counts_matrix.txt


title: NPC43, CUT&RUN-seq, IgG

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

country: Hong Kong

institute: the University of Hong Kong

description:
Library name: NPC43 CUT_RUN IgG
EBV+NPC, detectable EBV copies in NPC

library_source: genomic

data_processing:
Sequencing adaptors were trimmed via Trimmomatic (v0.39).
Bowtie2 was used to align reads to the human genome (hg19) and EBV genome (NC_007605) with the parameters -p 2 --dovetail --phred33.
The reads were sorted, and PCR duplicates were removed with Picard in GATK (v4.2.3.0).
Peak calling with matched control IgG was performed for each sample at -q 0.05.
The CUT&RUN RPKM signals were normalised by deeptools bamCoverage with --binsize 1.
Assembly: hg19 & EBV genome (NC_007605)
Supplementary files format and content: .bw file can be visualised in IGV browser
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: cell line

growth_protocol: Fresh cells cultured in 37oC, 5% CO2

extract_protocol:
The CUTANATM ChIC/CUT&RUN Kit (Cat# 14-1048) was used in this experiment. A total of 500,000 cells were harvested and bound to concanavalin A-coated (ConA) magnetic beads. The cell membranes were permeabilised with 5% digitonin, allowing the primary antibody to bind histones with posttranslational modifications (PTMs) or transcription factors (TFs). CUTANA™ pAG-MNase (Cat# 15-1016) at a volume of 2.5 µL was incubated with the samples for 10 minutes at room temperature to target the primary antibody heavy chain at the region of interest. A 100 mM calcium chloride solution was used to initiate DNA digestion for 2 hours at 4°C. The enriched DNA was purified and prepared for sequencing libraries. One to ten nanograms of enriched DNA was collected to generate the sequencing libraries using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Cat# E7370L).
NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Cat# E7370L)

treatment_protocol: No treatment

value: cell line

tag: cell line

tag: cell type

value: nasopharyngeal cancer cells

value: Wild-type


title: C666, CUT&RUN-seq, IgG

description:
Library name: C666 CUT_RUN IgG
EBV+NPC, detectable EBV copies in NPC


title: NP460, CUT&RUN-seq, IgG

description:
Library name: NP460 CUT_RUN IgG
Normal NPE

value: nasopharyngeal epithelial cells


title: NP460, CUT&RUN-seq, CTCF

description:
Library name: NP460 CUT_RUN CTCF
Normal NPE


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample20

description:
Chem3_C_D6
Chem3_counts_matrix.txt

value: Metribuzin-DA


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample17

description:
Chem3_C_D3
Chem3_counts_matrix.txt


title: NP460, CUT&RUN-seq, H3K4me3

description:
Library name: NP460 CUT_RUN H3K4me3
Normal NPE


title: CC-030, IPAH, scRNA-seq

city: Baltimore

first: Catherine

last: Simpson

state: Maryland

address: 1830 E. Monument St. 5th Fl

institute: Johns Hopkins University

description: Library name: CC-030

data_processing:
Normalization, PCA, UMAP, and clustering were performed using the Seurat software package.
Batch effect correction using Harmony software package.
Assembly: Hg38
Supplementary files format and content: TSV files, matrix files, and RDS file

source_name: Lung

extract_protocol:
Tissue samples were collected at the time of lung transplantation according to a standardized protocol. Explants were immediately processed, and standardized coronal sectioning was performed. All samples analyzed came from coronal slice #3 of the right lung, with three blocks cut from predefined locations, each measuring 0.5 (length) x 1 (depth) x 1 (width) cm, and immediately fixed in 10% neutral buffered formalin (NBF). Tissue was then paraffin-embedded and stored at room temperature. Twenty-five uM tissue sections were cut from banked tissue blocks. Peripheral lung samples were prioritized to capture distal pulmonary vessels. Tissue sections were rehydrated and transferred to a 1.5ml tube.  Tissues were de-paraffinized using a series of sequential xylene, ethanol, and PBS washes. Pestle dissociation was performed using a dissociation enzyme mix prepared per manufacturer’s instructions. Following dissociation, tissues were centrifugated and tissue pellet was resuspended, after which cell concentration was determined. Single cells were isolated following manufacturer’s protocols described in detail at www.10xgenomics.com/support/flex-gene-expression/documentation/steps/sample-prep, Demonstrated Protocol CG000632 RevB.
Single-cell RNA sequencing (scRNAseq) was performed using the 10X Genomics Chromium Flex platform. Library quality and quantity were assessed using the Agilent Bioanalyzer system and Qubit fluorometer before proceeding to sequencing. Sequencing was carried out on an Illumina NovaSeq platform. The sequencing data were processed and demultiplexed using the 10X Genomics Cell Ranger software.

value: Lung

tag: sample condition

value: IPAH


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample16

description:
Chem3_C_D2
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample19

description:
Chem3_C_D5
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 2-tert-butyl-4-methoxyphenol, sample2

description:
Chem4_A_D2
Chem4_counts_matrix.txt


title: BA-014, IPAH, scRNA-seq

description: Library name: BA-014


title: ST-059, SSc-PAH, scRNA-seq

description: Library name: ST-059

value: SSc-PAH


title: BA-008, IPAH, scRNA-seq

description: Library name: BA-008


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample15

description:
Chem3_C_D1
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample14

description:
Chem3_B_D7
Chem3_counts_matrix.txt


title: ST-005, SSc-PAH, scRNA-seq

description: Library name: ST-005


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample13

description:
Chem3_B_D6
Chem3_counts_matrix.txt


title: BA-024, SSc-PAH, scRNA-seq

description: Library name: BA-024


title: C17, CUT&RUN-seq, IgG

description:
Library name: C17 CUT_RUN IgG
EBV+NPC, detectable EBV copies in NPC


title: BA-025, SSc-PAH, scRNA-seq

description: Library name: BA-025


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample10

description:
Chem3_B_D3
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample12

description:
Chem3_B_D5
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample21

description:
Chem3_C_D7
Chem3_counts_matrix.txt


title: BA-058, Failed Donor, scRNA-seq

description: Library name: BA-058

value: Failed Donor


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample9

description:
Chem3_B_D2
Chem3_counts_matrix.txt


title: BA-053, Failed Donor, scRNA-seq

description: Library name: BA-053


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample8

description:
Chem3_B_D1
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample18

description:
Chem3_C_D4
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample7

description:
Chem3_A_D7
Chem3_counts_matrix.txt


title: NP69, CUT&RUN-seq, IgG

description:
Library name: NP69 CUT_RUN IgG
Normal NPE


title: ST-042, IPAH, scRNA-seq

description: Library name: ST-042


title: BA-044, Failed Donor, scRNA-seq

description: Library name: BA-044


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample5

description:
Chem3_A_D5
Chem3_counts_matrix.txt


title: PEO4 B, h3k27ac CT, Rep2

city: London

first: Marco

last: Di Antonio

address: Molecular Sciences Research Hub, 82 Wood Lane

country: United Kingdom

institute: Imperial College London

data_processing:
CUT&Tag read quality was assessed using FastQC, and technical repeats merged using cat.
CUT&Tag reads were trimmed from the 3' end using fastp, and discarding any reads < 20 bp.
Trimmed reads were then aligned to the human genome build bg38 using Bowtie2.
Samtools was used to filter any unmapped, secondary and mitochondial reads, and blacklisted regions were removed using bedtools intersect.
Duplicated reads were removed using picard Markduplicates, and the aligned file was then indexed using samtools.
Peaks were called using MACS2 using the -nolambda parameter.
Peaks in common with 2/3 of the biological replicates were identified using bedtools intersect.
Assembly: hg38
Supplementary files format and content: .bed intersected peak files from 2/3 biological repeats
Supplementary files format and content: .bigWig files for alignment
Library strategy: CUT&Tag

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 2 minutes before being quenched with glycine. The CUT&Tag protocol was then followed, using either h3k27ac antibody or BG4 to target h3k27ac or G-quadruplexes resepctively. Tagmented DNA was purified using the Zymo DNA clean and concentrator-5 kit.
Libraries were prepared using Illumina sequencing primers (i5 and i7 barcodes), and amplified on a thermocycler. Amplified DNA was extracted and cleaned using Ampure XP paramagnetic beads and the fragment size distribution was analysed using Agilent high sensitivity D1000 screentape.

value: human ovarian adenocarcinoma

tag: genotype

value: WT

tag: antibody


title: PEO4 B, h3k27ac CT, Rep3


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample4

description:
Chem3_A_D4
Chem3_counts_matrix.txt


title: PEO4 B, h3k27ac CT, Rep1


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample3

description:
Chem3_A_D3
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample2

description:
Chem3_A_D2
Chem3_counts_matrix.txt


title: PEO1 B, h3k27ac CT, Rep3


title: R. subcapitata, 24 h exposure, Gabapentin, sample21

description:
Chem2_C_D7
Chem2_counts_matrix.txt

value: Gabapentin


title: PEO1 B, h3k27ac CT, Rep1


title: PEO4 B, G4 CT, Rep3


title: R. subcapitata, 24 h exposure, Gabapentin, sample20

description:
Chem2_C_D6
Chem2_counts_matrix.txt


title: BA-048, Failed Donor, scRNA-seq

description: Library name: BA-048


title: PEO4 B, G4 CT, Rep2


title: R. subcapitata, 24 h exposure, Gabapentin, sample18

description:
Chem2_C_D4
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample19

description:
Chem2_C_D5
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample17

description:
Chem2_C_D3
Chem2_counts_matrix.txt


title: PEO4 B, G4 CT, Rep1


title: PEO1 B, G4 CT, Rep3


title: PEO1 B, G4 CT, Rep2


title: R. subcapitata, 24 h exposure, Gabapentin, sample16

description:
Chem2_C_D2
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample11

description:
Chem3_B_D4
Chem3_counts_matrix.txt


title: PEO4 B, RNA, Rep3

description:
peo4_0hr_3
fc_peo_RNA_2024.txt

data_processing:
Quality of the reads was assessed using FastQC
RNA-seq reads were trimmed from the 3' end using fastp, and discarding any reads < 20 bp.
Reads were aligned to the hg38 human genome build with STAR and sorted by coordinate.
Feature count file matrix was generate using featureCounts.
Assembly: hg38
Supplementary files format and content: .txt feature count file

extract_protocol:
RNA was extracted from 3.5 million cells per sample using Qiagen’s Rneasy mini extraction kit, using Qiagen’s QIAshedder homogenizing columns and and an on-column DNase I digestion steps. Sample quality was assessed on an Agilent TapeStation using the RNA ScreenTape.
For A cell lines, libraries were prepared by The Francis Crick Institute Advanced Sequencing Facility using NEBNext Ultra II Directional PolyA mRNA preparation kit.

treatment_protocol: For the PDS treated samples, the cells were incubated with media containing 5 µM PDS for either 2 or 6 hours before RNA extraction.

tag: treatment time


title: R. subcapitata, 24 h exposure, Gabapentin, sample15

description:
Chem2_C_D1
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample6

description:
Chem3_A_D6
Chem3_counts_matrix.txt


title: PEO1 B, G4 CT, Rep1


title: R. subcapitata, 24 h exposure, Gabapentin, sample14

description:
Chem2_B_D7
Chem2_counts_matrix.txt


title: PEO4 B, RNA, Rep2

description:
peo4_0hr_2
fc_peo_RNA_2024.txt


title: PEO1 B, RNA, Rep3

description:
peo1_0hr_3
fc_peo_RNA_2024.txt


title: PEO1 B, h3k27ac CT, Rep2


title: PEO1 B, RNA, Rep2

description:
peo1_0hr_2
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Metribuzin-DA, sample1

description:
Chem3_A_D1
Chem3_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample11

description:
Chem2_B_D4
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample12

description:
Chem2_B_D5
Chem2_counts_matrix.txt


title: PEO4 B, RNA, Rep1

description:
peo4_0hr_1
fc_peo_RNA_2024.txt


title: PEO4 B, PDS 6hr, RNA, Rep3

description:
peo4_6hr_3
fc_peo_RNA_2024.txt

value: PDS 5 µM

value: 6 hours


title: PEO4 B, PDS 6hr, RNA, Rep2

description:
peo4_6hr_2
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample8

description:
Chem2_B_D1
Chem2_counts_matrix.txt

value: whole body


title: R. subcapitata, 24 h exposure, Gabapentin, sample7

description:
Chem2_A_D7
Chem2_counts_matrix.txt

value: Exponential Growth Stage


title: R. subcapitata, 24 h exposure, Gabapentin, sample9

description:
Chem2_B_D2
Chem2_counts_matrix.txt


title: PEO1 B, RNA, Rep1

description:
peo1_0hr_1
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample10

description:
Chem2_B_D3
Chem2_counts_matrix.txt


title: PEO4 B, PDS 2hr, RNA, Rep3

description:
peo4_2hr_3
fc_peo_RNA_2024.txt

value: 2 hours


title: R. subcapitata, 24 h exposure, Gabapentin, sample5

description:
Chem2_A_D5
Chem2_counts_matrix.txt


title: PEO4 B, PDS 2hr, RNA, Rep2

description:
peo4_2hr_2
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample6

description:
Chem2_A_D6
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample4

description:
Chem2_A_D4
Chem2_counts_matrix.txt


title: PEO4 B, PDS 2hr, RNA, Rep1

description:
peo4_2hr_1
fc_peo_RNA_2024.txt


title: PEO1 B, PDS 6hr, RNA, Rep3

description:
peo1_6hr_3
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample3

description:
Chem2_A_D3
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample2

description:
Chem2_A_D2
Chem2_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample13

description:
Chem2_B_D6
Chem2_counts_matrix.txt


title: PEO1 B, PDS 6hr, RNA, Rep1

description:
peo1_6hr_1
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, Gabapentin, sample1

description:
Chem2_A_D1
Chem2_counts_matrix.txt


title: MV4-11 VEN+CSA 24H-2

city: Chongqing

first: CHENGFANG

last: ZHOU

address: No. 30, Gaotanyan Street.

department: Department of Hematology, Southwest Hospital

institute: Army Medical University

data_processing:
The raw sequencing data were subjected to quality control, aligned to the reference genome using STAR software, and gene expression was quantified using RSEM.
Differential expression analysis was performed using DESeq2, and gene set enrichment analysis (GSEA) was conducted to identify enriched biological pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: The mv411 were cultured in 100nM VEN,2.5uM CsA  or VEN+CsA with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cells or tissues using the Total RNA Extractor (Trizol) reagent according to the manufacturer's instructions. The samples were lysed, and RNA was separated by adding chloroform, followed by centrifugation.
For RNA sequencing library preparation, 1 µg of RNA was used and processed using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, USA). The libraries were sequenced using an Illumina platform with a 150-bp paired-end configuration.

value: Acute myeloid leukemia

value: gavage differenttion


title: PEO1 B, PDS 2hr, RNA, Rep3

description:
peo1_2hr_3
fc_peo_RNA_2024.txt


title: PEO1 B, PDS 2hr, RNA, Rep1

description:
peo1_2hr_1
fc_peo_RNA_2024.txt


title: MV4-11 VEN+CSA 24H-1


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample21

description:
Chem12_C_D7
Chem12_counts_matrix.txt

value: 3,4-Dichlorophenyl isocyanate


title: MV4-11 CSA 24H-2


title: PEO4 A, RNA, Rep3

description:
PEO4_3
PEO1_4_FC_2.txt


title: PEO1 B, PDS 2hr, RNA, Rep2

description:
peo1_2hr_2
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample20

description:
Chem12_C_D6
Chem12_counts_matrix.txt


title: PEO4 A, RNA, Rep2

description:
PEO4_2
PEO1_4_FC_2.txt


title: PEO4 B, PDS 6hr, RNA, Rep1

description:
peo4_6hr_1
fc_peo_RNA_2024.txt


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample19

description:
Chem12_C_D5
Chem12_counts_matrix.txt


title: PEO1 A, RNA, Rep3

description:
PEO1_3
PEO1_4_FC_2.txt


title: MV4-11 CSA 24H-1


title: PEO4 A, RNA, Rep1

description:
PEO4_1
PEO1_4_FC_2.txt


title: PEO1 A, RNA, Rep 2

description:
PEO1_2
PEO1_4_FC_2.txt


title: MV4-11 VEN 24H-2


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample18

description:
Chem12_C_D4
Chem12_counts_matrix.txt


title: PEO1 A, RNA, Rep1

description:
PEO1_1
PEO1_4_FC_2.txt


title: MV4-11 VEN 24H-1


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample17

description:
Chem12_C_D3
Chem12_counts_matrix.txt


title: PEO1 B, PDS 6hr, RNA, Rep2

description:
peo1_6hr_2
fc_peo_RNA_2024.txt


title: PEO4 A, Input, Rep3

data_processing:
ChIP-seq read quality was assessed using FastQC.
ChIP technical replicates were merges using cat.
ChIP-seq reads were trimmed from the 3' end using fastp, and discarding any reads < 20 bp.
Trimmed reads were then aligned to the human genome build bg38 using Bowtie2.
Samtools was used to filter any unmapped, secondary and mitochondial reads, and blacklisted regions were removed using bedtools intersect.
Duplicated reads were removed using picard Markduplicates, and the aligned file was then indexed using samtools.
Peaks were called using MACS2 default parameters.
Peaks in common with 2/3 of the biological replicates were identified using bedtools intersect.
Assembly: hg38
Supplementary files format and content: .bed shared peak files

extract_protocol:
Cells were fixed for 10 minutes using 1% formaldehyde before being quenched with glycine. After lysis, chromatin was sonicated using a Diagenode Pico Bioruptor sonicator to 100-500bp.
ChIP-seq libraries were prepared by The Francis Crick Institute Advanced Sequencing Facility using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

tag: chip antibody


title: PEO4 A, G4 ChIP, Rep2


title: PEO4 A, G4 ChIP, Rep3


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample16

description:
Chem12_C_D2
Chem12_counts_matrix.txt


title: ATAC_H1975_shNKX2-1

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

data_processing:
RNA seq
sequence reads were trimmed for adaptor sequence / low-quality sequence using basespace defult process
read count extraction and normalization were performed using R and EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample
ATAC-Seq
The ATAC-seq pipeline was employed for processing and analyzing sequencing data, utilizing default parameters. The raw ATAC-seq fastq reads were aligned to the hg19 reference genome using the BWA Aligner (v1.1.4) on the basespace platform. The signal intensity present in the bedgraph files was determined as the fold enrichment of the signal per million reads within a sample compared to a modeled local background, utilizing the bdgcmp function in MACS2. Differential accessible peaks were detected using the MACS2 package and annotated with the ChIPseeker package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files contain information on the distribution and enrichment of intersected peaks for both the control and shNKX2-1 samples.
Spatial Transcriptomics
The raw sequencing reads undergo processing using Space Ranger pipeline version 2.0.1. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Spaceranger count pipline output files (Tab-separated values files and matrix files) Aligned tissue images: Spatial_lung_parental.tif; Spatial_lung_shNkx2-1.tif Cytassist image: Spatial_lung_parental_cytassist.tif; Spatial_lung_shNkx2-1_cytassist.tif Scalefactors in json format: Spatial_lung_parental_alignment.json; Spatial_lung_shNkx2-1_alignment.json
scRNA-seq
The raw sequencing reads undergo processing using Cell Ranger pipeline version 6.1.2. Sequences were aligned to mm10 genome.
Assembly: mm10
Supplementary files format and content: Cellranger count pipline output files (Tab-separated values files and matrix files)

growth_protocol: H1975 cells were cultured in RPMI-1640 media supplemented with 10% Fetal Bovine Serum (FBS), 100 mg/mL streptomycin, and 100 U/mL penicillin in a humidified atmosphere at 37°C.

extract_protocol:
ATAC-seq libraries were prepared according to the ATAC-seq kit (Diagenode; #C01080001) protocol.
The ATAC-seq assay was conducted following the optimized Diagenode protocol. Initially, cells were processed by pelleting, lysing, washing, and re-pelleting using the specified lysis and wash buffers. Subsequently, a transposition mix containing Tn5 was added to the samples, and the transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer set at 1000 rpm. Following transposition, the transposed DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min, 98 °C for 30 s, and thermocycling at 98°C for 15 s, 60 °C for 30 s, and 72°C for 3 min; following by 72°C 5 min. Libraries were purified with AMPURE XP Bead-based reagent to remove contaminating primer dimers. Library quality was checked using Qubit 2.0 Fluorimeter (Invitrogen, United States). Lastly, the samples were subjected to paired-end 75-bp sequencing on an Illumina Novaseq 6000.

treatment_protocol: Puromycin dihydrochloride stock was prepared by dissolving it in water to achieve a concentration of 50 mg/mL. The solution was then filtered through a 0.22 µm filter and stored in aliquots at –20 °C. To establish stable cell lines, 2 µg/mL of the dissolved puromycin was added to fresh culture media, while the control group received fresh culture media with only water. All mixtures were thoroughly mixed

value: NKX2-1 Knockdown


title: ATAC_H1975_shCtrl


title: PEO4 A, Input, Rep2


title: PEO4 A, G4 ChIP, Rep1


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample15

description:
Chem12_C_D1
Chem12_counts_matrix.txt


title: PEO4 A, Input, Rep1


title: PEO1 A, G4 ChIP, Rep3


title: LuNE, CCS1477 3#

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, RPKM/FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt file of RPKM/FPKM values

source_name: Prostate

growth_protocol: Prostate cancer cell lines LNCaP, 22Rv1 and LuNE cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin

extract_protocol:
RNA was extracted using the nucleospin RNA kit (Takara) according to the manufacturer’s recommended protocol
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: 1.LNCaP cells were infected with FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at D0, D2, D7, D14, D21 and D28 for RNA analysis. 2.22Rv1 cells were infected with control (plv) or  FOXA2 overexpression virus and fallowed up by 28 days, cells were collected at week4 for RNA analysis. 3. LuNE cells were infected gRNAs targeting control (sgNC), NKX2-1 (sgNKX2-1), FOXA2 (sgFOXA2) and both NKX2-1/FOXA2 (sgFOXA2+NKX2-1) or shRNAs targeting control (shCtrl), P300 (shP300), CBP (shCBP) and both P300/CBP (shP300+CBP), the cells were collected for RNA analysis 5 days after infection. 4. LuNE cells were treated with DMSO or CCS1477 (250nM) for 72h and collected for RNA analysis.

value: Prostate

value: LNCaP (LuNE)

value: Prostate cancer cell


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample14

description:
Chem12_B_D7
Chem12_counts_matrix.txt


title: LuNE, CCS1477 2#


title: PEO1 A, G4 ChIP, Rep2


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample13

description:
Chem12_B_D6
Chem12_counts_matrix.txt


title: PEO1 A, Input, Rep3


title: PEO1 A, Input, Rep2


title: LuNE, CCS1477 1#


title: PEO1 A, G4 ChIP, Rep1


title: PEO1 A, Input, Rep1


title: PEO4 A, ATAC, Rep4

data_processing:
ATAC-seq read quality was assessed using FastQC.
ATAC-seq reads were trimmed from the 3' end using fastp, and discarding any reads < 20 bp.
Trimmed reads were then aligned to the human genome build bg38 using Bowtie2.
Samtools was used to filter any unmapped, secondary and mitochondial reads, and blacklisted regions were removed using bedtools intersect.
Duplicated reads were removed using picard Markduplicates, and the aligned file was then indexed using samtools.
Peaks were called using MACS2 using the -nolambda parameter.
Peaks in common with 4 of the biological replicates were identified using bedtools intersect.
Assembly: hg38
Supplementary files format and content: .bed intersected peak files
Supplementary files format and content: .bigWig alignment files

extract_protocol:
Cells were harvested and lysed to obtain nuclei. The nuclei then underwent a transposition reacrion using Tn5, and the DNA was purified after using Qiagen MinElute PCR Purification Kit.
Libraries were made using Custom Nextera PCR Primers containing barcodes, and amplified 8-10 times on a thermocycler depending on results of a qPCR to ensure minimal amplification. Library quantification and frgament distribution were analysed using an Agilent 4200 TapeStation system using the Agilent high sensitivity D1000 screentape following manufacture’s instructions.


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample11

description:
Chem12_B_D4
Chem12_counts_matrix.txt


title: LuNE, DMSO 2#

value: DMSO


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample10

description:
Chem12_B_D3
Chem12_counts_matrix.txt


title: PEO4 A, ATAC, Rep2


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample9

description:
Chem12_B_D2
Chem12_counts_matrix.txt


title: PEO1 A, ATAC, Rep4


title: PEO1 A, ATAC, Rep3


title: PEO4 A, ATAC. Rep1


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample8

description:
Chem12_B_D1
Chem12_counts_matrix.txt


title: PEO1 A, ATAC, Rep2


title: PEO1 A, ATAC, Rep1


title: 22Rv1, FOXA2-Week4 1#


title: LuNE, DMSO 1#


title: NPC43, CUT&RUN-seq, H3K27ac

source_name: EBV+NPC, detectable EBV copies in NPC

value: cell line

value: nasopharyngeal cancer cells

value: Wild-type


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample7

description:
Chem12_A_D7
Chem12_counts_matrix.txt


title: 22Rv1, plv-Week4 2#

value: WT


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample12

description:
Chem12_B_D5
Chem12_counts_matrix.txt


title: 22Rv1, plv-Week4 1#


title: NPC43, CUT&RUN-seq, CTCF

value: anti-CTCF


title: NPC43, CUT&RUN-seq, H3K4me3


title: LuNE, DMSO 3#


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample6

description:
Chem12_A_D6
Chem12_counts_matrix.txt


title: PEO4 A, ATAC, Rep3

value: human ovarian adenocarcinoma


title: C17, CUT&RUN-seq, H3K27ac


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample5

description:
Chem12_A_D5
Chem12_counts_matrix.txt

value: whole body


title: C666, CUT&RUN-seq, H3K4me3


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample4

description:
Chem12_A_D4
Chem12_counts_matrix.txt

value: Exponential Growth Stage


title: LNCaP, FOXA2-D28 2#

value: LNCaP


title: 22Rv1, FOXA2-Week4 2#


title: NP69, CUT&RUN-seq, CTCF

source_name: Normal NPE

value: nasopharyngeal epithelial cells


title: LNCaP, FOXA2-D28 3#


title: C17, CUT&RUN-seq, CTCF


title: LNCaP, FOXA2-D28 1#


title: NP69, CUT&RUN-seq, H3K4me3


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample2

description:
Chem12_A_D2
Chem12_counts_matrix.txt


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample3

description:
Chem12_A_D3
Chem12_counts_matrix.txt


title: HK1 ATAC_rep2

description: EBV-NPC, no detectable EBV copies

data_processing:
Trimmomatic was used to remove the adapter sequences and poor-quality bases and reads.
The ENCODE ATAC-Seq pipeline (v1.0) was applied for alignment, peak calling, and quality evaluation.
The peaks for differential analysis were obtained by merging the narrowPeaks files of the same condition.
The bioinformatics tool featureCounts was used for creating the count matrices. DESeq2 was used for identifying the differentially accessible regions. Only the regions with absolute log2 fold change ≥ 2 and q-value <0.01 were considered as significant. The function rlog was used for normalization.
Assembly: hg19 & EBV genome (NC_007605)
Supplementary files format and content: .bw file can be visualised in IGV browser
Supplementary files format and content: .narrowPeak files were generated by ENCODE ATAC-Seq pipeline

extract_protocol:
Briefly, 50,000 cells were lysed in a cold lysis buffer. The cell lysates were incubated with Tn5 transposase (Illumina Cat# E7645S) at 37°C for 30 min. Libraries were sequenced on the NovaSeq 6000 platform. Data analysis was performed following the ENCODE ATAC-Seq pipeline (v1.0).
Tn5 transposase (Illumina Cat# E7645S)


title: LNCaP, FOXA2-D21 3#


title: HK1 ATAC_rep1

description: EBV-NPC, no detectable EBV copies


title: C666, CUT&RUN-seq, CTCF


title: NPC38 ATAC_rep2

description: EBV-NPC, no detectable EBV copies


title: LNCaP, FOXA2-D21 2#


title: R. subcapitata, 24 h exposure, 3,4-Dichlorophenyl isocyanate, sample1

description:
Chem12_A_D1
Chem12_counts_matrix.txt


title: NPC38 ATAC_rep1

description: EBV-NPC, no detectable EBV copies


title: NPC53 ATAC_rep1

description: EBV-NPC, no detectable EBV copies


title: NPC43 ATAC_rep2

description: EBV+NPC, detectable EBV copies in NPC


title: LNCaP, FOXA2-D21 1#


title: C17, CUT&RUN-seq, H3K4me3


title: R. subcapitata, 24 h exposure, DMSO, sample6

description:
Chem11_Chem12_C_CON
Chem11_counts_matrix.txt
Chem12_counts_matrix.txt


title: R. subcapitata, 24 h exposure, DMSO, sample5

description:
Chem11_Chem12_B_CON
Chem11_counts_matrix.txt
Chem12_counts_matrix.txt


title: NPC53 ATAC_rep2

description: EBV-NPC, no detectable EBV copies


title: LNCaP, FOXA2-D14 2#


title: R. subcapitata, 24 h exposure, DMSO, sample4

description:
Chem11_Chem12_A_CON
Chem11_counts_matrix.txt
Chem12_counts_matrix.txt


title: LNCaP, FOXA2-D14 3#


title: C666 ATAC_rep2

description: EBV+NPC, detectable EBV copies in NPC


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample21

description:
Chem11_C_D7
Chem11_counts_matrix.txt

value: Metolachlor OA


title: C666 ATAC_rep1

description: EBV+NPC, detectable EBV copies in NPC


title: NPC43 ATAC_rep1

description: EBV+NPC, detectable EBV copies in NPC


title: C17 ATAC_rep1

description: EBV+NPC, detectable EBV copies in NPC


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample20

description:
Chem11_C_D6
Chem11_counts_matrix.txt


title: NP460 ATAC_rep1

description: Normal NPE


title: LNCaP, FOXA2-D14 1#


title: LNCaP, FOXA2-D7 3#


title: NP460 ATAC_rep2

description: Normal NPE


title: C17 ATAC_rep2

description: EBV+NPC, detectable EBV copies in NPC


title: NP69 ATAC_rep2

description: Normal NPE


title: LNCaP, FOXA2-D7 2#


title: NP69 ATAC_rep1

description: Normal NPE


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample19

description:
Chem11_C_D5
Chem11_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample18

description:
Chem11_C_D4
Chem11_counts_matrix.txt


title: BV-organoids,CCM3KO

city: Greifswald

first: Dariush

last: Skowronek

address: Fleischmannstraße 43

country: Germany

institute: Institut für Humangenetik

description: 10x Genomics

data_processing:
Cellranger version 7.0.1 was used to generate read data, demultiplex single cells, perform sequence alignment, and generate raw count data. Further filtering of raw data, generation of clusters, and analysis of gene expression differences were performed with Seurat 4.0.4.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated matix and value files

source_name: HiPSC-derived blood vessel organoids

growth_protocol: iPSCs were maintained on growth factor reduced matrigel (Corning) in E8 Flex medium (Thermo Fisher)

extract_protocol:
a single cell suspension was achived with an enzymatic mix containing 4 mg Liberase TH solution, 30 mg Dispase II, and 0.5 mg DNase I solution in PBS
Chromium Single Cell Next GEM 3’ Reagent Kit v3.1 (10x Genomics) on a Single Cell 3’ device

treatment_protocol: hiPSCs were differentiated to blood vessel organoids

value: HiPSC-derived blood vessel organoids

value: CCM3 KO


title: LNCaP, FOXA2-D7 1#

value: Prostate


title: LNCaP, FOXA2-D2 3#


title: BV-organoids,WT

description: 10x Genomics


title: BV-organoids, CCM2KO

description: 10x Genomics

value: CCM2 KO


title: BV-organoids,CCM1KO

description: 10x Genomics

value: CCM1 KO


title: LuNE, DMSO, p300 ChIP

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Assembly: hg19
Supplementary files format and content: bigwig generated from bam

growth_protocol: Prostate cancer cell lines LNCaP, 22Rv1 and LuNE cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin and  NCI-H660 cells were maintained in ATCC-formulated RPMI-1640 Medium (Catalog No.30-2001) with 0.005 mg/ml Insulin, 0.01 mg/ml Transferrin, 30nM Sodium selenite, 10 nM Hydrocortisone, 10 nM beta-estradiol, 5% fetal bovine serum. 2. LuCaP PDX were maintained in NOD SCID male mice which were purchased from Charles River

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde (Thermo fisher, Cat#28908)) for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions.

treatment_protocol: 1.LNCaP cells were co-infected with FOXA2 virus along with either sgNC or sgNKX2-1 virus and infected cells were collected at D7, D14, D21 and D28 for ChIP analysis  2. LuNE cells were infected gRNAs targeting control (sgNC), NKX2-1 (sgNKX2-1), FOXA2 (sgFOXA2) or shRNAs targeting control (shCtrl), P300 (shP300), CBP (shCBP), the cells were collected for ChIP analysis 5 days after infection. 3. LuNE cells were treated with DMSO or CCS1477 (500nM) for 24h and collected for ChIP analysis.

value: LuNE

value: Prostate cancer cell


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample16

description:
Chem11_C_D2
Chem11_counts_matrix.txt


title: LNCaP, FOXA2-D2 2#


title: LNCaP, CCS1477, H3K27ac ChIP

value: H3K27ac, Cst, Cat#8173S


title: Healthy control CRISPRa 2

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

data_processing:
star align 2.7a
edgeR
Assembly: hg38
Supplementary files format and content: .xlsx with raw reads per gene

source_name: neuronal

extract_protocol:
Cells were lysed using TriZol Reagent and RNA extractions were performed on with the Direct-zol RNA Miniprep kit (Zymo Research). 500ng total RNA was used to construct libraries according to Novogene sample submission guidelines.
Library construction was performed by the UC Davis DNA Technologies Core and Novogene.

value: neuronal

value: NSC


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample15

description:
Chem11_C_D1
Chem11_counts_matrix.txt

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA).
The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene.
The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018).
Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021).
Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into separate (tab-delimited) count matrix files for each chemical treatment group where columns represented samples and rows represented genes.
Assembly: GCA_003203535.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

extract_protocol:
After a series of flash freezing and homogenization, algae total RNA was extracted using the Norgen Biotek Plant/Fungi Total RNA kit (Norgen) according to the manufacturer’s protocol. Sample quantity and quality was assessed using a NanoDrop Eight spectrophotometer (Thermo Scientific) and 4200 TapeStation (Agilent Technologies).
Sample libraries were prepared using QuantSeq 3’ mRNA-Seq V2 Library Prep Kits (Lexogen, GmbH, Austria) with Unique Dual Index (UDI) and QuantSeq Unique Molecular Identifiers (UMI). Preparation followed manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays.


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample14

description:
Chem11_B_D7
Chem11_counts_matrix.txt


title: C666, CUT&RUN-seq, H3K27ac

value: cell line

value: nasopharyngeal cancer cells

value: Wild-type


title: LNCaP, DMSO, H3K27ac ChIP

value: WT

value: DMSO


title: LNCaP, FOXA2-D0 3#

value: LNCaP


title: Healthy control 2


title: LNCaP, FOXA2-D2 1#


title: LNCaP, FOXA2-D0 2#


title: Healthy control non-treated 2


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample13

description:
Chem11_B_D6
Chem11_counts_matrix.txt

value: whole body

value: Exponential Growth Stage

value: Metolachlor OA


title: Healthy control 1


title: LNCaP, FOXA2-D0 1#

value: Prostate


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample17

description:
Chem11_C_D3
Chem11_counts_matrix.txt


title: FOXG1 iso CRISPRa 2

value: patient-derived NSC, CRISPR corrected


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample11

description:
Chem11_B_D4
Chem11_counts_matrix.txt


title: Healthy control non-treated 1


title: FOXG1 iso CRISPRa 3


title: LuNE, shCBP, H3K27ac ChIP 1#

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
bigwig generated from bam
Assembly: hg19
Supplementary files format and content: bigwig

value: LNCaP (LuNE)

value: shCBP


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample10

description:
Chem11_B_D3
Chem11_counts_matrix.txt


title: FOXG1 iso control 2


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample9

description:
Chem11_B_D2
Chem11_counts_matrix.txt


title: FOXG1 iso control 3


title: FOXG1 iso control 1


title: Healthy control CRISPRa 1


title: LuNE, CCS1477, H3K27ac ChIP 1#

value: Prostate cancer cell


title: FOXG1 iso non-treated 2


title: FOXG1 iso non-treated 3


title: LuNE, shCtrl, H3K27ac ChIP 1#

value: H3K27ac, Cst, Cat#8173S

value: shCtrl


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample12

description:
Chem11_B_D5
Chem11_counts_matrix.txt


title: FOXG1 W308X non-treated 3

value: neuronal

value: NSC


title: FOXG1 iso non-treated 1


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample8

description:
Chem11_B_D1
Chem11_counts_matrix.txt


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample7

description:
Chem11_A_D7
Chem11_counts_matrix.txt


title: FOXG1 W308X non-treated 1

value: patient-derived NSC


title: FOXG1 W308X control 3


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample6

description:
Chem11_A_D6
Chem11_counts_matrix.txt


title: LuNE, DMSO, H3K27ac ChIP 1#


title: R. subcapitata, 24 h exposure, Metolachlor OA, sample5

description:
Chem11_A_D5
Chem11_counts_matrix.txt


title: LNCaP, FOXA2-D14, FOXA2 ChIP

value: FOXA2, Abcam, Cat#ab108422


title: FOXG1 W308X non-treated 2


title: FOXG1 iso CRISPRa 1