title: 140008

description: Gene expression data from nasal brushing of subject 140008.

value: Female

value: Former smoker

value: Cancer


title: GNAQ WT no dox, vehicle - rep 1

status: Public on Oct 25 2022

type: SRA

city: Cincinnati

first: Sandra

last: Schrenk

address: 3333 Burnet Ave.

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
RNA-seq reads in FASTQ format were subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments.   The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference human genome version hg38 with the program STAR v2.6.1e
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package
Raw counts were normalized as transcripts per million (TPM)
Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: Matrix table (tab-delimited text file) including tpm values for all genes in all samples
Supplementary files format and content: Matrix table (tab-delimited text file) including DEseq2 normalized values. GNAQ-WT vs GNAQ-Q209L cells
Supplementary files format and content: Matrix table (tab-delimited text file) including DEseq2 normalized values.  GNAQ-Q209L cells, vehicle-treated vs trametinib-treated

molecule: total RNA

organism: Homo sapiens

source_name: Cord blood

growth_protocol: Cells were grown in low-serum media (2% FBS in Endothelial growth medium) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina Stranded mRNA Prep – Ligation kit was used for library preparation

treatment_protocol: To induce gene expression prior to RNA collection, cells were treated with 1µg/mL doxycycline for 18 hours, followed by an additional 6 hours of DMSO (vehicle control) or 10nM Trametinib treatment.

tag: tissue

value: Cord blood

tag: cell line

value: Endothelial colony forming cell

tag: cell type

value: Endothelial

tag: genotype

value: GNAQ-WT

tag: treatment

value: no dox, vehicle


title: Patient 7 derived orthoxenograft (PDOX) [S22]

city: L'Hospitalet de Llobregat

first: David

last: Llobet

state: Barcelona

address: Gran Via de L'Hospitalet 199-203

department: Gynecologic cancer

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Samples from xenografts were aligned against mouse transcriptome (mm10/GRCm38), previously indexed. We used R package XenofilteR for deconvolution of mouse and human reads on xenografts samples.

data_processing:
Raw files were merged, and quality control assessed by FastQC analysis
Trimmomatic software was used to trim Illumina adaptors and bad quality reads
Trimmed reads were mapped over human reference transcriptome (hg19/GRCh38) with STAR. An annotation file in GTF format (downloaded from the UCSC Table Browser, using RefSeq genes table)   were used for the indexing step.
Aligned sequences were quantified with RSEM
Assembly: hg19/GRCh38
Supplementary files format and content: tab delimited text file of raw count data values for each Sample

source_name: Patient derived xenograft

extract_protocol:
Total RNA was isolated from primary tumors (BX) and PDOX tumors from mice using the RNeasy Micro kit (Qiagen, 74004)
NGS libraries with polyA capture were prepared according to the manual NEBNext® Ultra™ II Directional RNA  Library Prep Kit for Illumina® (New England Biolabs) (Version 1.0, 4/17)

value: Patient derived xenograft

value: Tumor


title: 90011

type: RNA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing of subject 90011.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

label: biotin

source_name: Brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

tag: Sex

tag: age

tag: smoking status

value: Current smoker

tag: fev1 % predicted

tag: cancer status

value: Benign


title: genomic DNA from glioma patient 1

type: genomic

city: Beijing

first: changlin

last: yang

address: No. 119 South Fourth Ring Road West

department: Department of Molecular Neuropathology

country: China

institute: Beijing Neurosurgical Institute, Capital Medical University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  IlluminaInfinium Methylation EPICBeadChip.These chips include more than 850,000 methylation sites across whole genome.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: DNA methylation data were analyzed using the methylation analysis module within BeadStudio software employing default parameters (Illumina, Inc., San Diego CA, USA). The raw intensity data were loaded to a biocondutor package minfi. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated). Differentially methylated CpGs were selected using an algorithm in IMA Bioconductor. In this study, we assessed the mean-difference β-value (Δβ) between the two sample groups for each CpG site. Specifically, we considered a probe as differentially methylated if the absolute Δβ was higher than 0.14 and the statistical test was significant (p value <0.05).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: glioma sample 1

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from glioma sample using OMEGA TISSUE DNA Kit according to the manufacturer’s instructions.

treatment_protocol: The specimens were frozen in liquid nitrogen within 5 min of resection.

tag: gender

value: glioma sample

value: CNS WHO Grade 3


title: 250501

description: Gene expression data from nasal brushing of subject 250501.


title: GNAQ WT no dox, vehicle - rep 2


title: 130164

description: Gene expression data from nasal brushing of subject 130164.


title: Patient 10 derived orthoxenograft (PDOX) [S25]


title: NoCFC_Sleep_HA_PELL_23

city: Ann Arbor

first: Lijing

last: Wang

state: MI

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

data_processing:
Amplified complementary DNA libraries were prepared using Takara’s SMART-seq v4 Ultra Low Input RNA Kit (Takara 634888) and sequenced on Illumina’s NovaSEq. 6000 platform.
Reads mapped to unique transcripts were counted with featureCounts.
Libraries were run with onboard cluster generation, and together comprised 40% of a NovaSeq S4 200 cycle kit (v1.5; ~16–20 billion paired-end reads per flow cell, quality score ≥ 90% of bases higher than Q30).
Sequencing reads (50 bp, paired-end) were mapped to Mus musculus using Star v2.6.1a and quality checked with Multiqc (v1.6a0). Reads mapped to unique transcripts were counted with featureCounts.
Assembly: GRCm38.p6
Supplementary files format and content: merged_counts.txt has counts for each different GeneID for all samples

organism: Mus musculus

source_name: Brain

growth_protocol: Refer to: Delorme J, Wang L, Kodoth V, Wang Y, Ma J, Jiang S, Aton SJ. Hippocampal neurons' cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2108534118. doi: 10.1073/pnas.2108534118. PMID: 34819370; PMCID: PMC8640746.

extract_protocol:
RiboTag TRAP was performed as previously described by indirect conjugation, separating MB and free-floating ribosomes. Following homogenization and centrifugation, the resulting supernatant (cytosolic fraction) was transferred to a new tube while the pellet (MB fraction) was resuspended in homogenization buffer. Both MB and cytosolic fractions were separated into Input, Camk2a+, and pS6+ fractions. For isolating ribosomes from Camk2a+ populations, fractions were incubated with 1:40 anti-HA antibody (Abcam, ab9110). To isolate ribosomes from highly active (pS6+) neurons, fractions were incubated with 1:25 anti-pS6 244-247 (ThermoFisher 44-923G). Homogenate-antibody solution was added directly to Protein G Dynabeads (ThermoFisher, 10009D) for incubation. After washing conjugated beads and removing the supernatant, RNA was eluted by vortexing the beads vigorously in 350 μL RLT (Qiagen, 79216). Eluted RNA was purified using RNeasy Micro kit (Qiagen).
Amplified complementary DNA libraries were prepared using Takara’s SMART-seq v4 Ultra Low Input RNA Kit (Takara 634888)

value: Brain

value: neuron

value: male

tag: cell population

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: membrane(PELL)

tag: treatment cfc

value: NO

tag: treatment sleep

value: Sleep


title: NoCFC_Sleep_S6_SUP_23

treatment_protocol: Refer to: Delorme J, Wang L, Kodoth V, Wang Y, Ma J, Jiang S, Aton SJ. Hippocampal neurons' cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2108534118. doi: 10.1073/pnas.2108534118. PMID: 34819370; PMCID: PMC8640746.

value: cytosolic (SUP)


title: Patient 8 derived orthoxenograft (PDOX) [S23]


title: NoCFC_Sleep_HA_SUP_23


title: CFC_SD_Input_PELL_22

value: Input

value: YES

value: SD


title: 120531

description: Gene expression data from nasal brushing of subject 120531.

value: Male

value: Former smoker

value: Cancer


title: RA-FLSs_METs_48h-rep3

city: Guangzhou

first: Weizhen

last: Weng

address: tianhe road 600

institute: the third affiliated hospital of SYSU

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tool
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by  differential expressed genes. We used clusterProfiler R package（3.8.1） to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Assembly: mm8

source_name: human synovial tissues

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard lllumia protocols.

tag: disease state

value: Rheumatoid arthritis (RA)

value: human synovial tissues

value: RA-FLS

value: METs


title: Patient 4 derived orthoxenograft (PDOX) [S19]

value: Patient derived xenograft

value: Tumor


title: CFC_SD_S6_SUP_22

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: RA-FLSs_METs_48h-rep2


title: CFC_SD_Input_SUP_22

value: cytosolic (SUP)


title: Patient 2 derived orthoxenograft (PDOX) [S17]


title: Patient 5 derived orthoxenograft (PDOX) [S20]


title: Patient 6 derived orthoxenograft (PDOX) [S21]


title: CFC_SD_S6_PELL_22

value: membrane(PELL)


title: CFC_SD_Input_PELL_21

value: Input

value: YES


title: RA-FLSs_no METs_48h-rep2


title: RA-FLSs_no METs_48h-rep3


title: 160502

description: Gene expression data from nasal brushing of subject 160502.

value: Male

value: Benign


title: 50001

description: Gene expression data from nasal brushing of subject 50001.

value: Female

value: Former smoker


title: VCM10 2972-JX-5

first: Jintao

last: Xu

address: 2215 Fuller Rd

institute: University of Michigan Hospital

description:
VCM10
10x Genomics

data_processing: none provided by the submitter

source_name: blood

extract_protocol: none provided by the submitter

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Mild

tag: time

value: day 0


title: CFC_SD_HA_PELL_22

tag: tissue

value: Brain

value: SD


title: 90015

description: Gene expression data from nasal brushing of subject 90015.

value: Current smoker


title: RA-FLSs_no METs_48h-rep1

value: Rheumatoid arthritis (RA)

value: human synovial tissues

value: RA-FLS


title: Patient 3 derived orthoxenograft (PDOX) [S18]

value: Patient derived xenograft

tag: cell line

value: Tumor


title: RA-FLSs_METs_48h-rep1

tag: cell type

value: METs


title: VCM09 2972-JX-4

description:
VCM09
10x Genomics

tag: genotype

value: day 5


title: CFC_SD_HA_SUP_22

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)

value: YES


title: 110016

description: Gene expression data from nasal brushing of subject 110016.

value: Male

value: Cancer


title: VCM08 2972-JX-3

description:
VCM08
10x Genomics

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Severe


title: CFC_SD_Input_SUP_21

value: Brain

value: Input

value: SD


title: Primary tumor Patient 13 [S13]

source_name: Endometrioid endometrial cancer

value: Endometrioid endometrial cancer

value: Tumor


title: Primary tumor Patient 14 [S14]


title: VCM09 2972-JX-2

description:
VCM09
10x Genomics

value: Mild

value: day 0


title: CFC_SD_S6_PELL_21

value: neuron

value: male

value: membrane(PELL)


title: 220515

description: Gene expression data from nasal brushing of subject 220515.

value: Female

value: Former smoker


title: 220516

description: Gene expression data from nasal brushing of subject 220516.

value: Current smoker

value: Cancer


title: Patient 1 derived orthoxenograft (PDOX) [S16]

value: Patient derived xenograft


title: Primary tumor Patient 15 [S15]


title: CFC_SD_HA_PELL_21

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: YES


title: Primary tumor Patient 12 [S12]


title: CFC_SD_S6_SUP_21

value: Brain

value: cytosolic (SUP)


title: VCM08 2972-JX-1

description:
VCM08
10x Genomics

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Severe


title: NoCFC_Sleep_HA_SUP_24

value: NO

value: Sleep


title: 120512

description: Gene expression data from nasal brushing of subject 120512.

value: Male


title: Primary tumor Patient 11 [S11]

value: Endometrioid endometrial cancer

value: Tumor


title: CFC_SD_HA_SUP_21

value: neuron

value: male

value: SD


title: VCH05 2654-JX-12

description:
VCH05
10x Genomics

value: Healthy

value: day 0


title: VCH04 2654-JX-11

description:
VCH04
10x Genomics


title: Primary tumor Patient 10 [S10]


title: CFC_SD_Input_PELL_20

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: YES


title: 120519

description: Gene expression data from nasal brushing of subject 120519.

value: Female

value: Current smoker

value: Cancer


title: 120514

description: Gene expression data from nasal brushing of subject 120514.


title: 140132

description: Gene expression data from nasal brushing of subject 140132.


title: VCH03 2654-JX-10

description:
VCH03
10x Genomics

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood


title: 10119

description: Gene expression data from nasal brushing of subject 10119.

value: Former smoker

value: Benign


title: CFC_SD_Input_SUP_20

value: Brain

value: neuron

value: cytosolic (SUP)


title: Primary tumor Patient 9 [S9]

value: Endometrioid endometrial cancer

value: Tumor


title: CFC_SD_HA_PELL_20

value: male

value: SD


title: Primary tumor Patient 7 [S7]


title: VCH02 2654-JX-9

description:
VCH02
10x Genomics

value: Healthy

value: day 0


title: Primary tumor Patient 8 [S8]


title: CFC_SD_S6_PELL_20

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: YES


title: 260517

description: Gene expression data from nasal brushing of subject 260517.

value: Male


title: VCH01 2654-JX-8

description:
VCH01
10x Genomics

value: blood

value: Not a cell line


title: Primary tumor Patient 6 [S6]


title: VSC01 2654-JX-7

description:
VSC01
10x Genomics

value: immune cells/neutrophils from fresh blood

value: Severe

value: day 20


title: Treated2_00251275_HDAC1

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

library_source: genomic

data_processing:
The 75-nt single end sequence reads were mapped to the human reference genome (GRCh37/hg19) using the BWA algorithm  with default settings.
Duplicate reads were removed and only uniquely mapped reads were used for further analysis.
Peak locations (enriched regions) for HDAC1, BRD4, H3K9Ac, H3K27ac were determined using the MACS algorithm (v1.4.2) with a cutoff p-value of 1E-7 for narrow peaks and 1E-1 for broad peaks.
Assembly: GRCh37/hg19
Supplementary files format and content: narrowPeak

source_name: CLL,1275 Abexinostat 400mM  6h

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. 15 ug of chromatin was immunoprecipitated per sample using antibodies against HDAC1 (Active Motif # 40967) and BRD4 (Active Motif # 91301, 4l), H3K9Ac (Active Motif # 39917), H3K27Ac (Active Motif # 39133), and RNA Pol II (Active Motif # 91151),
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500.

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

tag: chip antibody

value: HDAC1 (Active Motif # 40967)

tag: treatment

value: Abexinostat


title: CFC_SD_S6_SUP_20

value: Brain

value: neuron

tag: Sex

value: male

value: cytosolic (SUP)

value: SD


title: VCM06 2654-JX-6

description:
VCM06
10x Genomics

value: day 5


title: 50019

description: Gene expression data from nasal brushing of subject 50019.

value: Male

tag: age

tag: smoking status

value: Former smoker

value: Cancer


title: Primary tumor Patient 5 [S5]

value: Endometrioid endometrial cancer

value: Tumor


title: CFC_SD_HA_SUP_20

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: YES


title: Primary tumor Patient 4 [S4]


title: VCM05 2654-JX-5

description:
VCM05
10x Genomics

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Severe


title: NoCFC_Sleep_Input_PELL_2

value: Brain

value: Input

value: membrane(PELL)

value: NO

value: Sleep


title: 140113

description: Gene expression data from nasal brushing of subject 140113.

tag: fev1 % predicted

tag: cancer status


title: Primary tumor Patient 3 [S3]


title: 90009

description: Gene expression data from nasal brushing of subject 90009.


title: VCM06 2654-JX-4

description:
VCM06
10x Genomics

value: day 0


title: 110020

description: Gene expression data from nasal brushing of subject 110020.

value: Male

value: Benign


title: 10008

description: Gene expression data from nasal brushing of subject 10008.

value: Female

value: Former smoker


title: NoCFC_Sleep_S6_PELL_2

value: neuron

value: male

tag: cell population


title: VCM05 2654-JX-3

description:
VCM05
10x Genomics


title: VCM04 2654-JX-2

description:
VCM04
10x Genomics

value: day 5


title: Primary tumor Patient 1 [S1]

value: Endometrioid endometrial cancer

value: Tumor


title: NoCFC_Sleep_HA_PELL_2

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction


title: VCM04 2654-JX-1

description:
VCM04
10x Genomics

value: blood

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Severe


title: NoCFC_Sleep_S6_SUP_2

value: Brain

value: cytosolic (SUP)

tag: treatment cfc

value: NO


title: 60014

description: Gene expression data from nasal brushing of subject 60014.

value: Cancer


title: VCM03 1577-JX-7

description:
VCM03
10x Genomics

value: Mild


title: NoCFC_Sleep_HA_SUP_2

tag: treatment sleep

value: Sleep


title: LH_1925

description: Gene expression data from nasal brushing LH_1925.

library_source: transcriptomic single cell

data_processing:
Quality metrics and gene-level counts were generated for the single-cell RNA-sequencing samples using Scruff.
Cells had a median UMI of 3095, a median number of genes detected of 1277, median predicted contamination of 0.04%, and the percentage of predicted doublets of 7.5%.
Poor quality cells were identified if the cell satisfied any of the following criteria; 1) bottom quantile for a total number of genes detected, 2) bottom quantile for total library size and 3) greater than 30% of the counts mapped to the mitochondrial genome.  In total, 15787 cells were filtered and 34833 cells were kept for further analysis.
Cells were defined by examining the relative expression level of knowledge-based gene markers. Transitional cells were named based on their relative location on the UMAP plot and expression of a combination of marker genes.
In the nasal scRNA-seq data, markers included KRT5, KRT15 and KRT 17 (basal cells), SCGB1A1 (club cells), MUC5AC (goblet cells), FOXJ1 (ciliated cells), FOXI1 (ionocytes), CD3D (T cells), CD74 (neutrophils and macrophages), STATH and C15orf48 (secretory cells), CDC20B (maturing ciliated cells), SPRR3 (keratinizing epithelial cells).
Assembly: hg19
Supplementary files format and content: SU2C_nasal_single_cell_counts.tsv: Tab-separated value (TSV) file containing count matrix for 33,694 genes (rows) x 34,833 cells (columns).
Supplementary files format and content: SU2C_nasal_single_cell_labels.tsv: Tab-separated value (TSV) file containing the barcode, subject ID, and cell-type label for each of the 34,833 cells (rows).

extract_protocol:
Cells were initially dissociated from two nasal swabs obtained from the inferior turbinate. The cells were then washed with Phosphate-buffered saline (PBS, Sigma Aldrich, Burlington, MA) and dissociated to single-cell suspensions using 0.25% Trypsin/EDTA (Thermo Fisher, Waltham, MA). The red blood cells were removed after being treated in the 1X RBC Lysis Buffer (Thermo Fisher, Waltham, MA) for 2 minutes. Trypan blue (STEMCELL, Vancouver, BC, Canada) was used for measuring cell viability. The final concentration of the cells was measured using a hemocytometer under a light microscope before library preparation using the 10X Genomics Platform (Pleasanton, CA).
Samples with over 85% viability were prepared for single-cell sequencing using the 10X Genomics Platform.

value: Brushing of nasal epithelium

value: Male

value: Current

tag: race

value: White


title: LH_0951

description: Gene expression data from nasal brushing LH_0951.


title: 160597

description: Gene expression data from nasal brushing of subject 160597.

value: Female

value: Current smoker


title: 140063

description: Gene expression data from nasal brushing of subject 140063.

value: Former smoker

value: Benign


title: 110512

description: Gene expression data from nasal brushing of subject 110512.


title: 70522

description: Gene expression data from nasal brushing of subject 70522.


title: VCM02 1577-JX-6

description:
VCM02
10x Genomics

value: blood

value: Not a cell line

tag: time

value: day 5


title: CFC_SD_Input_PELL_19

tag: tissue

value: Brain

value: neuron

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: YES

value: SD


title: NoCFC_Sleep_Input_SUP_2

value: cytosolic (SUP)

value: NO

value: Sleep


title: LH_0034

description: Gene expression data from nasal brushing LH_0034.

value: Brushing of nasal epithelium

value: Male

value: Former

value: White


title: CFC_SD_Input_SUP_19


title: Primary tumor Patient 2 [S2]

value: Endometrioid endometrial cancer

tag: cell line

value: Tumor


title: LH_0012

description: Gene expression data from nasal brushing LH_0012.


title: VCM02 1577-JX-4

description:
VCM02
10x Genomics

value: blood

value: Not a cell line

tag: cell type

value: immune cells/neutrophils from fresh blood

value: Severe

value: day 0


title: 10133

description: Gene expression data from nasal brushing of subject 10133.

value: Female

value: Former smoker

value: Benign


title: 140024

description: Gene expression data from nasal brushing of subject 140024.

value: Current smoker

value: Cancer


title: CFC_SD_S6_PELL_19

value: Brain

value: neuron

value: male

tag: genotype

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: YES

value: SD


title: 130134

description: Gene expression data from nasal brushing of subject 130134.


title: UCM01 1577-JX-3

description:
UCM01
10x Genomics

value: blood

value: day 5


title: KA_left

description: Gene expression data from nasal brushing KA_left.

value: Brushing of nasal epithelium

value: Unknown

value: Asian


title: 140115

description: Gene expression data from nasal brushing of subject 140115.

value: Female


title: CFC_SD_S6_SUP_19

value: cytosolic (SUP)


title: UCM01 1577-JX-2

description:
UCM01
10x Genomics

value: Not a cell line

value: immune cells/neutrophils from fresh blood

value: Severe

value: day 0


title: BU_R1

description: Gene expression data from nasal brushing BU_R1.

value: Male

value: Never

value: White


title: CFC_SD_HA_SUP_19

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: BU_L1

description: Gene expression data from nasal brushing BU_L1.


title: VCM01 1577-JX-1

description:
VCM01
10x Genomics

value: blood

value: Mild


title: VCM03 1577-JX-5

description:
VCM03
10x Genomics


title: IDA030_S2

description: Gene expression data from bronchial brushing IDA030, replicate 2.

data_processing:
Initial sample-level demultiplexing and creation of FASTQ files was performed using BaseSpace.
Quality metrics and gene-level counts were generated for the single-cell RNA-sequencing samples using Scruff.
In the bronchial scRNA-seq data, cells had a median UMI of 4580, a median number of genes detected of 1870, median predicted contamination of 0.168 %, and the percentage of predicted doublets of 7.51%. Poor quality cells were identified if they met any of the following criteria: 1) bottom quantile for a total number of genes detected, 2) bottom quantile for total library size and 3) top quantile for the percentage of counts mapped to the mitochondrial genome. Overall, 1189 cells (including 34 empty wells) were filtered and 2075 cells were kept for further analysis.
Cells were defined by examining the relative expression level of knowledge-based gene markers. Transitional cells were named based on their relative location on the UMAP plot and expression of a combination of marker genes.
In the bronchial scRNA-seq data, markers included KRT5 (basal cells), CEACAM5 (peri-goblet cells), SCGB1A1 (club cells), MUC5AC (goblet cells), FOXJ1 (ciliated cells), FOXI1 (ionocytes), CD3D (T cells), GNLY (NK cells), KIT (mast cells), CXCR2 (neutrophil and macrophages).
Assembly: hg19
Supplementary files format and content: IDA_bronchial_single_cell_counts.tsv: Tab-separated value (TSV) file containing count matrix for 24138 features (rows) x 2075 cells (columns).
Supplementary files format and content: IDA_bronchial_single_cell_barcodes.tsv: Tab-separated value (TSV) file containing the barcode sequence for each of the 96 CEL-Seq2 wells.
Supplementary files format and content: IDA_bronchial_single_cell_labels.tsv: Tab-separated value (TSV) file containing the subject ID, barcode, and cell-type label for each of the 2075 cells (rows).

source_name: Brushing of bronchial epithelium

extract_protocol:
The tissue obtained from bronchial brushings was treated with 0.25% Trypsin/EDTA for epithelial sheet dissociation and cells were sorted using a BD FACSAria II. FACS was used to isolate singlet events based on forward scatter height vs. forward scatter area (FSH-H vs. FSH-A). Dead cells (PI+) and red blood cells (GYPA/CD235a+) are stained and excluded. For each donor, single live cells (Hoechst 33342+ Prodium Iodide- CD235a-) were sorted into 2 96-well PCR plates per patient sample.
Cells were resuspended and sorted into 96-well PCR plates before being processed using the CEL-Seq2 RNA library preparation protocol.

value: Brushing of bronchial epithelium

tag: subject

value: Former

value: Black or African American


title: CFC_SD_Input_SUP_18

value: Input

value: cytosolic (SUP)

value: YES

value: SD


title: CFC_SD_Input_PELL_18

value: membrane(PELL)


title: KA_right

description: Gene expression data from nasal brushing KA_right.

value: Brushing of nasal epithelium

value: Female

value: Unknown

value: Asian


title: IDA030_S1

description: Gene expression data from bronchial brushing IDA030, replicate 1.


title: CFC_SD_HA_PELL_19

value: Brain

value: neuron


title: LH_2077

description: Gene expression data from nasal brushing LH_2077.

value: White


title: FSCN1 KO H295R clone 1, biol. rep.2

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

description: column G

data_processing:
Quality control of fastq data by FastQC in Galaxy  (https://usegalaxy.eu).
Adapter sequences removed by Trimmomatic in Galaxy (https://usegalaxy.eu).
Reads mapping on human genome by RNA STAR in Galaxy (https://usegalaxy.eu).
Calculation of number of reads mapping to NCBI RefSeq features by featureCounts in Galaxy (https://usegalaxy.eu).
Counts normalization by DESeq2 in Galaxy (https://usegalaxy.eu).
Assembly: hg38
Supplementary files format and content: A tab-delimited text files includes normalized count values for each sample.

source_name: Adrenal cortex

growth_protocol: Cells were grown in DMEM/F12 supplemented with 2% NuSerum, % ITS+, penicillin/streptomycin, 5 ug/ml blasticidin, 100 ug/ml zeocin.

extract_protocol:
Total RNA was extracted by Trizol reagent.
Illumina TruSeq stranded Total RNA with RiboZero chemistry.

value: Adrenal cortex

value: cancer

value: FSCN1 KO

tag: treatment

value: female


title: FSCN1 KO H295R clone 2, biol. rep.2

description: column I


title: FSCN1 KO H295R clone 2, biol. rep.1

description: column H


title: CFC_SD_S6_PELL_18

tag: Sex

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: IDA028_S2

description: Gene expression data from bronchial brushing IDA028, replicate 2.

value: Brushing of bronchial epithelium

tag: age

value: Current

value: Caucasian


title: CFC_SD_HA_PELL_18

value: membrane(PELL)

value: YES

value: SD


title: 170501

description: Gene expression data from nasal brushing of subject 170501.

value: Male

tag: smoking status

value: Current smoker

value: Benign


title: FSCN1 KO H295R clone 1, biol. rep.1

description: column F


title: 120024

description: Gene expression data from nasal brushing of subject 120024.

value: Female

tag: fev1 % predicted

value: Cancer


title: 210508

description: Gene expression data from nasal brushing of subject 210508.

value: Former smoker

tag: cancer status


title: IDA028_S1

description: Gene expression data from bronchial brushing IDA028, replicate 1.


title: CFC_SD_S6_SUP_18

value: Brain

value: neuron

tag: cell population

value: cytosolic (SUP)


title: control H295R clone 2, biol. rep.2

description: column E

value: Adrenal cortex

value: cancer

value: control

value: female


title: 120005

description: Gene expression data from nasal brushing of subject 120005.


title: 10076

description: Gene expression data from nasal brushing of subject 10076.


title: 50552

description: Gene expression data from nasal brushing of subject 50552.


title: control H295R clone 2, biol. rep.1

description: column D


title: IDA027_S2

description: Gene expression data from bronchial brushing IDA027, replicate 2.

value: Brushing of bronchial epithelium

value: Former

value: Caucasian


title: 10051

description: Gene expression data from nasal brushing of subject 10051.


title: 130119

description: Gene expression data from nasal brushing of subject 130119.


title: control H295R clone 1, biol. rep.2

description: column C


title: IDA027_S1

description: Gene expression data from bronchial brushing IDA027, replicate 1.


title: CFC_Sleep_Input_PELL_17

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: membrane(PELL)

value: YES

value: Sleep


title: control H295R clone 1, biol. rep.1

description: column B


title: CFC_Sleep_Input_SUP_17

tag: treatment cfc


title: IDA026_S2

description: Gene expression data from bronchial brushing IDA026, replicate 2.

value: Female


title: 100010

description: Gene expression data from nasal brushing of subject 100010.

value: Male

value: Current smoker

value: Benign


title: Huh-7, M3

city: Changchun

first: Shui

last: Liu

state: Jilin Province

address: Ziqiang Stree No.218

department: The Second Hospital of Jilin University

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the original data was statistically analyzed, and the sequencing data quality of the samples was visually evaluated by FastQC.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, HISAT2 was used to compare the quality-controlled sequencing sequence with the reference genome, and the results were statistically compared by RSeQC.
Fragments Per Kilobase of exon transcript per Million fragments mapped reads(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: hepatocellular  carcinoma

growth_protocol: The Huh-7 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. All cells were maintained at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
The transfected cells were digested with trypsin and washed three times with PBS, and total RNA was harvested using Trizol reagent. Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (Cat#12301ES96) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Huh-7 cells were transfected with miR-27a-3p mimics or NC using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis.

value: Transfection with miR-27a-3p mimics


title: Huh-7, M2


title: 70006

description: Gene expression data from nasal brushing of subject 70006.

value: Former smoker

value: Cancer


title: CFC_Sleep_S6_PELL_17

value: Brain

value: neuron

tag: treatment sleep


title: CFC_Sleep_HA_PELL_17


title: IDA026_S1

description: Gene expression data from bronchial brushing IDA026, replicate 1.

value: Brushing of bronchial epithelium

value: Former

tag: race


title: IDA025_S2

description: Gene expression data from bronchial brushing IDA025, replicate 2.

value: Black or African American


title: CFC_Sleep_S6_SUP_17

value: male

value: cytosolic (SUP)


title: 250509

description: Gene expression data from nasal brushing of subject 250509.


title: CFC_SD_HA_SUP_18

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: SD


title: Huh-7, NC3

value: Transfection with NC


title: IDA020_S2

description: Gene expression data from bronchial brushing IDA020, replicate 2.


title: Huh-7, M1


title: CFC_Sleep_Input_PELL_16

value: Input

value: membrane(PELL)

value: YES

value: Sleep


title: 50002

description: Gene expression data from nasal brushing of subject 50002.

value: Female


title: IDA020_S1

description: Gene expression data from bronchial brushing IDA020, replicate 1.

value: Male


title: 10013

description: Gene expression data from nasal brushing of subject 10013.

value: Former smoker

value: Cancer


title: Huh-7, NC2


title: Huh-7, NC1


title: IDA025_S1

description: Gene expression data from bronchial brushing IDA025, replicate 1.


title: CFC_Sleep_HA_SUP_17

value: Brain

value: neuron


title: CFC_Sleep_Input_SUP_16


title: IDA019_S2

description: Gene expression data from bronchial brushing IDA019, replicate 2.

value: Brushing of bronchial epithelium

value: Current


title: IDA019_S1

description: Gene expression data from bronchial brushing IDA019, replicate 1.

value: Black or African American


title: CFC_Sleep_HA_PELL_16

value: male


title: IDA017_S1

description: Gene expression data from bronchial brushing IDA017, replicate 1.

value: Former

value: Caucasian


title: CFC_Sleep_S6_SUP_16

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: TOV21G_sh-Ctrl

city: Taipei

first: Wendy

middle: W

last: Hwang-Verslues

state: Not in USA

address: No. 128, Sec. 2, Academia Road, Nangang District, Genomics Research Center, Academia Sinica

country: Taiwan

institute: Academia Sinica

data_processing:
Raw reads were initially processed to quality filtering and adaptor trimming by Cutadapt (v1.12)
The trimmed reads were then aligned to the Human genome (hg38), using STAR (v2.5.3a)
The expected read counts of each gene were estimated with RSEM (v1.2.31), followed by adjusting the CPM with the effective library size  via the calcNormFactors function implemented in the R package edgeR (v.3.26.8)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include the expected read count, TPM, FPKM values for each Sample

source_name: ovarian surface epithelial cells

growth_protocol: PA-1 was maintained in EMEM with 10% heat inactivated FBS. TOV21G was maintained in 1:1 mixture of MCDB 105 medium and Medium 199 with 15% FBS.

extract_protocol:
Total RNA was extracted using Sigma TRI Reagent (Merck) following the manufacturer's instructions. RNA was treated with DNase I ((Thermo Scientific™) and quantified using the NanoDrop (Thermo Scientific™, Cat# ND 1000). All samples with OD 260/280 ratio greater than 1.8 and OD 230/260 ratio greater than 2 were sent to BIOTOOLS Company in Taiwan for sequencing. RNA quality was also measured on a Qsep100 Bio-Fragment Analyzers. RNA samples with a RQN > 6.8 were used for cDNA library construction.
A total amount of 1 ug total RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using magnetic oligo-dT beads. Captured mRNA was fragmented by incubating at a high temperature in the presence of magnesium in KAPA Fragment, Prime and Elute Buffer (1x). First strand cDNA was synthesized using random hexamer priming. Combined 2nd strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporated dUTP into the second cDNA strand, and added dAMP to the 3’ ends of the resulting dscDNA. dsDNA adapter with 3’dTMP overhangs were ligated to library insert fragments to generate the library fragments carrying the adapters. In order to select cDNA fragments of preferentially 300 to 400bp in length, the library fragments were purified with KAPA Pure Beads system (KAPA Biosystems, Roche, Basel, Switzerland). The library carrying appropriate adapter sequences at both ends was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Roche, Basel, Switzerland) along with library amplification primers. The strand marked with dUTP in not amplified, allowing strand-specific sequencing. At last, PCR products were purified using KAPA Pure Beads system and the library quality was assessed on the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina NovaSeq6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Cells were infected with sh-Ctrl (TRC2-Scramble_ASN0003), sh-MEX3A#1 (TRCN230492) or sh-MEX3A#2 (TRCN230494) lentivirus purchased from the National RNAi Core Facility (Taipei, Taiwan).

value: ovarian surface epithelial cells

value: Ovarian clear cell carcinoma

value: Scramble control


title: TOV21G_sh-MEX3A#1

value: MEX3A knockdown


title: TOV21G_sh-MEX3A#2


title: CFC_Sleep_Input_PELL_15

value: Input

value: membrane(PELL)

value: YES

value: Sleep


title: IDA015_S2

description: Gene expression data from bronchial brushing IDA015, replicate 2.

value: Female


title: CFC_Sleep_HA_SUP_16

value: Brain

value: neuron


title: IDA015_S1

description: Gene expression data from bronchial brushing IDA015, replicate 1.

value: Brushing of bronchial epithelium

value: Current


title: IDA013_S1

description: Gene expression data from bronchial brushing IDA013, replicate 1.

value: Former


title: d10_3_non_ind

city: Helsinki

first: Kirsi

middle: Tuulia

last: Sepponen

address: Haartmaninkatu 8

department: Obstetrics and Gynecology

country: Finland

institute: University of Helsinki

data_processing:
Illumina NovaSeq system using an S4 flow cell with lane divider (Illumina, San Diego, CA, USA) was used for paired-end sequencing of the sample libraries. Read length was 151+8+8+151 bp and sequencing depth 25 M read pairs. Quality control of raw sequence data was conducted with FastQC-0.11.5. Reads were trimmed and filtered with Trimmomatic-0.32 and aligned against the human genome (GRCh38 release 82) using STAR 2.3.0e. RNASeq quality was assessed with picard-tools-1.119. RNA-SeQC v1.1.8. “Gene-level” read counting using Ensembl gene-ids was generated by featureCounts software (Subread-1.4.5-p1) resulting in genome-wide quantification of reads aligning to all genetic features.
Genome_build: GRCh38

source_name: gonadal-like cells

growth_protocol: Gonadal-like cells were derived by differentiating 1.5 x 10^5 iPSCs on 0.5 µg/cm2 Human Type I collagen in DMEM/F12 + 2% B27 supplemented with 100 ng/ml Activin A + 5 µM CHIR-99021 + 2 µM dorsomorphin + 10 µM Y-27632 for 24 h, in 3 µM CHIR-99021 + 10 ng/ml BMP7 for 24 h, in 3 µM CHIR-99021 + 2 µM dorsomorphin for 48 h and finally in plain DMEM/F12 + 2% B27 for 6 days.

extract_protocol:
Cells were disrupted directly on culture wells with QlAzol Lysis Reagent (Qiagen, MD, USA). Total RNA was extracted and purified with miRNeasy Mini Kit (Qiagen, Hilden, Germany) including an additional On-Column DNase Digestion with the RNase-Free DNase Set.
RNA libraries were prepared with TruSeq Stranded Total w. Ribo-depletion.

treatment_protocol: Cells in ind-condition were treated with 10 µg/ml doxycycline and 10 µM trimethoprim at days 4 to 10 of differentiation (for 6 days in total). Cells in non-ind condition were not treated with doxycycline and trimethoprim.

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14

value: no treatment

tag: timepoint


title: d10_3_ind

value: 10 µg/ml doxycycline and 10 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: CFC_Sleep_S6_PELL_16

tag: tissue

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 140090

description: Gene expression data from nasal brushing of subject 140090.

value: Former smoker

value: Benign


title: PA-1_sh-MEX3A#2

value: ovarian surface epithelial cells

tag: cell line

value: Ovarian teratocarcinoma

value: MEX3A knockdown


title: PA-1_sh-MEX3A#1

tag: cell type


title: IDA017_S2

description: Gene expression data from bronchial brushing IDA017, replicate 2.

value: Male

value: Caucasian


title: CFC_Sleep_Input_SUP_15

value: Brain

value: neuron

value: Input

tag: genotype

value: cytosolic (SUP)

value: YES

value: Sleep


title: IDA013_S2

description: Gene expression data from bronchial brushing IDA013, replicate 2.

value: Brushing of bronchial epithelium

tag: subject

value: Female

value: Former


title: PA-1_sh-Ctrl

value: Scramble control


title: CFC_Sleep_S6_PELL_15

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)


title: 30021

description: Gene expression data from nasal brushing of subject 30021.

value: Former smoker

value: Benign


title: CFC_Sleep_S6_SUP_15


title: d10_2_non_ind

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14

tag: treatment

value: no treatment


title: 150509

description: Gene expression data from nasal brushing of subject 150509.

tag: Sex

value: Cancer


title: IDA012_S2

description: Gene expression data from bronchial brushing IDA012, replicate 2.

tag: age

value: Current

value: Black or African American


title: IDA012_S1

description: Gene expression data from bronchial brushing IDA012, replicate 1.

tag: smoking status


title: 120505

description: Gene expression data from nasal brushing of subject 120505.

value: Male

tag: fev1 % predicted


title: CFC_Sleep_HA_PELL_15

value: Brain

value: neuron

value: YES

value: Sleep


title: 160520

description: Gene expression data from nasal brushing of subject 160520.

value: Female

value: Current smoker

tag: cancer status


title: CFC_Sleep_HA_SUP_15

value: male

tag: cell population

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: 90013

description: Gene expression data from nasal brushing of subject 90013.

value: Former smoker


title: 140103

description: Gene expression data from nasal brushing of subject 140103.

value: Benign


title: d10_1_non_ind

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14


title: IDA010_S1

description: Gene expression data from bronchial brushing IDA010, replicate 1.

value: Brushing of bronchial epithelium

value: Former

value: Caucasian


title: 120047

description: Gene expression data from nasal brushing of subject 120047.

value: Cancer


title: 140095

description: Gene expression data from nasal brushing of subject 140095.


title: 220507

description: Gene expression data from nasal brushing of subject 220507.


title: 50085

description: Gene expression data from nasal brushing of subject 50085.


title: 210507

description: Gene expression data from nasal brushing of subject 210507.


title: CFC_Sleep_Input_PELL_14

value: Brain

value: Input

tag: fraction

value: membrane(PELL)


title: 140041

description: Gene expression data from nasal brushing of subject 140041.


title: 50008

description: Gene expression data from nasal brushing of subject 50008.


title: d10_1_ind

value: 10 µg/ml doxycycline and 10 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: CFC_Sleep_Input_SUP_14

value: neuron

tag: treatment cfc

value: YES

value: Sleep


title: d10_2_ind


title: 140066

description: Gene expression data from nasal brushing of subject 140066.

value: Female


title: IDA009_S2

description: Gene expression data from bronchial brushing IDA009, replicate 2.

value: Current

value: Black or African American


title: d8_3_non_ind

value: no treatment


title: CFC_Sleep_S6_PELL_14

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: treatment sleep


title: IDA008_S2

description: Gene expression data from bronchial brushing IDA008, replicate 2.

value: Brushing of bronchial epithelium

value: Male

tag: race


title: IDA009_S1

description: Gene expression data from bronchial brushing IDA009, replicate 1.


title: IDA010_S2

description: Gene expression data from bronchial brushing IDA010, replicate 2.

value: Former

value: Caucasian


title: d8_3_ind

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14

tag: timepoint


title: CFC_Sleep_HA_PELL_14

tag: tissue

value: Brain

value: membrane(PELL)


title: d8_2_non_ind

tag: cell line


title: IDA008_S1

description: Gene expression data from bronchial brushing IDA008, replicate 1.


title: CFC_Sleep_S6_SUP_14

tag: cell type

value: neuron

value: cytosolic (SUP)


title: CFC_Sleep_HA_SUP_14

tag: genotype

value: YES

value: Sleep


title: IDA007_S2

description: Gene expression data from bronchial brushing IDA007, replicate 2.

tag: subject

value: Female


title: 120504

description: Gene expression data from nasal brushing of subject 120504.

value: Former smoker

value: Benign


title: IDA007_S1

description: Gene expression data from bronchial brushing IDA007, replicate 1.

value: Black or African American


title: 50017

description: Gene expression data from nasal brushing of subject 50017.

value: Current smoker


title: d8_1_ind

tag: treatment

value: 10 µg/ml doxycycline and 10 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: 130122

description: Gene expression data from nasal brushing of subject 130122.

tag: Sex

value: Male

value: Cancer


title: CFC_Sleep_Input_PELL_13

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 70011

description: Gene expression data from nasal brushing of subject 70011.

tag: age


title: CFC_Sleep_Input_SUP_13

value: Brain


title: 140004

description: Gene expression data from nasal brushing of subject 140004.

tag: smoking status


title: IDA006_S2

description: Gene expression data from bronchial brushing IDA006, replicate 2.

value: Brushing of bronchial epithelium

value: Current


title: IDA006_S1

description: Gene expression data from bronchial brushing IDA006, replicate 1.


title: d6_3_non_ind

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14

value: no treatment


title: d6_3_ind


title: CFC_Sleep_S6_PELL_13

value: neuron

value: membrane(PELL)

value: YES

value: Sleep


title: IDA005_S1

description: Gene expression data from bronchial brushing IDA005, replicate 1.

value: Female

value: Black or African American


title: IDA005_S2

description: Gene expression data from bronchial brushing IDA005, replicate 2.


title: d8_2_ind

value: 10 µg/ml doxycycline and 10 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: CFC_Sleep_S6_SUP_13

value: cytosolic (SUP)


title: d6_2_non_ind


title: d6_2_ind


title: 40003

description: Gene expression data from nasal brushing of subject 40003.

value: Male

value: Former smoker

tag: fev1 % predicted

value: Cancer


title: d8_1_non_ind


title: 110025

description: Gene expression data from nasal brushing of subject 110025.

value: Current smoker

tag: cancer status

value: Benign


title: 160551

description: Gene expression data from nasal brushing of subject 160551.


title: CFC_Sleep_Input_PELL_12

value: Brain

value: male

tag: cell population

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 4798-027-54

description: Gene expression data from nasal brushing 4798-027-54.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_nasal_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_nasal_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

extract_protocol:
Total RNA was isolated from nasal and bronchial brushings using the miRNeasy Mini Kit [QIAGEN].
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit.

value: Brushing of nasal epithelium

tag: fev1 %_predicted


title: 4798-028-54

description: Gene expression data from nasal brushing 4798-028-54.


title: d6_1_non_ind

value: iPSC-derived gonadal-like cells

value: HEL46.11-DDdCas9Vp192-SF1 clone 14

value: no treatment


title: d6_1_ind


title: 10131

description: Gene expression data from nasal brushing of subject 10131.

value: Female


title: 140018

description: Gene expression data from nasal brushing of subject 140018.


title: CFC_Sleep_Input_SUP_12

value: neuron

tag: fraction

tag: treatment cfc

value: YES

value: Sleep


title: CFC_Sleep_HA_PELL_13

value: membrane(PELL)

tag: treatment sleep


title: 4798-021-54

description: Gene expression data from nasal brushing 4798-021-54.

value: Male

value: Former smoker


title: CFC_Sleep_S6_PELL_12


title: 90002

description: Gene expression data from nasal brushing of subject 90002.

value: Cancer


title: 4798-010-54

description: Gene expression data from nasal brushing 4798-010-54.


title: d4_3

tag: timepoint


title: 4798-023-54

description: Gene expression data from nasal brushing 4798-023-54.

tag: tissue

value: Current smoker


title: 120547

description: Gene expression data from nasal brushing of subject 120547.

value: Benign


title: CFC_Sleep_HA_SUP_13

value: Brain

value: male

value: cytosolic (SUP)


title: CFC_Sleep_HA_PELL_12

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: CFC_Sleep_S6_SUP_12


title: 4798-009-54

description: Gene expression data from nasal brushing 4798-009-54.

value: Brushing of nasal epithelium


title: d4_2

value: iPSC-derived gonadal-like cells

tag: cell line

value: HEL46.11-DDdCas9Vp192-SF1 clone 14


title: d4_1

tag: cell type

value: no treatment


title: 60029

description: Gene expression data from nasal brushing of subject 60029.

value: Female


title: 50540

description: Gene expression data from nasal brushing of subject 50540.


title: MCF7_D_5

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

data_processing:
RNA-seq data were first processed with Salmon (Patro et al., 2017). This tool was used to quantify transcript abundance by mapping the reads against a reference transcriptome (Homo sapiens GRCh38 cDNA fasta). The Salmon output was then imported in R using the Bioconductor package tximport.
Genome_build: Homo sapiens GRCh38 cDNA fasta
Supplementary_files_format_and_content: Abundance data (salmon output file)

growth_protocol: The MCF-7 cell line was grown in DMEM (Life Technologies, UK) supplemented with  2-mM glutamine (GE Healthcare Life Sciences), 10 mg/ml penicillin/streptomycin (Life Technologies, UK) and 5% fetal bovine serum (FBS). MCF-10A and MCF-12A cells were cultured in Dulbecco’s modified Eagle’s media F12 (DMEM-F12: Life Technologies, UK) supplemented with 20ng/ml Epidermal Growth Factor (EGF), 0.5 μg/ml ul hydrocortisone (Life Technologies, UK), 100ng/ml cholera toxin, 10 μg/ml insulin (Thermo Fisher scientific), 10 mg/ml penicillin/streptomycin (Life Technologies, UK), 5% horse serum. All cell cultures were grown at 37C (5% CO2) in 75cm2 flasks (Corning, Tewksbury, USA). The cells were detached using 0.05% trypsin EDTA (Life Technologies, UK) and counted using a haemocytometer.

extract_protocol:
After 48 hour exposure, RNA was extracted using the Qiagen RNeasy Mini Kit. The quality of the RNA samples was checked using a Nanodrop instrument (NanoDrop™ One Microvolume UV-Vis Spectrophotometers, Thermo Fisher Scientific, USA). All RNA samples were sent off to Genewiz (Lepizig, Germany) where they were sequenced.
RNA Library Preparation and cDNA Sequencing was performed by Genewiz (Leipzig, Germany). RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing library preparation was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

treatment_protocol: BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ, as well as pendimethalin, were purchased from Merck KGaA (Sigma Aldrich®, Gillingham, Dorset, UK). The pendimethalin formulation Stomp aqua (BasF, 455g/L Pendimethalin) was purchased from PestControl Expert S.R.L. To prepare stock solutions the test substances were individually diluted in DMSO. Then the stock solutions were further diluted using media containing self-stripped serums leading to a final volume of 0.1% of DMOS in the test solutions. For the MCF-7 cell line, the media used for diluting the bisphenols consisted of DMEM supplemented with  2-mM glutamine, 10 mg/ml penicillin-streptomycin and 5% charcoal-stripped FBS. For the MCF-10A and MCF-12A cell lines DMEM-F12 supplemented with 20ng/ml EGF, 0.5μg/ml hydrocortisone, 100ng/ml cholera toxin, 10 μg/ml insulin, 10 mg/ml penicillin-streptomycin and 2% charcoal-stripped horse serum were used.

tag: group

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM

tag: batch


title: 10111

description: Gene expression data from nasal brushing of subject 10111.


title: 4798-005-54

description: Gene expression data from nasal brushing 4798-005-54.

tag: subject


title: CFC_Sleep_HA_SUP_12

value: neuron

tag: Sex

tag: genotype

value: YES

value: Sleep


title: MCF7_C_5

value: C

tag: treatment

value: Mid dose (BPA) of 50 nM


title: 4797-048-54

description: Gene expression data from nasal brushing 4797-048-54.

value: Male

tag: age

tag: smoking status

value: Former smoker


title: 220517

description: Gene expression data from nasal brushing of subject 220517.

tag: fev1 % predicted

tag: cancer status

value: Cancer


title: 4797-044-54

description: Gene expression data from nasal brushing 4797-044-54.

tag: fev1 %_predicted


title: MCF10A_B_1

value: B

value: High dose (BPA) of 250 nM


title: MCF7_B_5


title: NoCFC_SD_Input_SUP_11

value: Brain

value: male

tag: cell population

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: cytosolic (SUP)

tag: treatment cfc

value: NO

value: SD


title: NoCFC_SD_HA_PELL_11

tag: tissue

value: neuron

value: membrane(PELL)

tag: treatment sleep


title: 4797-018-54

description: Gene expression data from nasal brushing 4797-018-54.

value: Brushing of nasal epithelium

value: Female


title: NoCFC_SD_S6_SUP_11

tag: cell type


title: MCF7_A_1

tag: cell line

tag: group

value: A

value: Negative Control


title: NoCFC_SD_S6_PELL_11


title: 4797-042-54

description: Gene expression data from nasal brushing 4797-042-54.

tag: subject

value: Male

value: Current smoker


title: MCF12A_A_3

tag: batch


title: NoCFC_SD_HA_SUP_11

tag: Sex

tag: genotype


title: MCF12A_H_3

value: H

tag: treatment

value: Stomp Aqua at 10 nM pendimethalin


title: 140131

description: Gene expression data from nasal brushing of subject 140131.

tag: age

tag: smoking status

value: Former smoker

value: Benign


title: 20018

description: Gene expression data from nasal brushing of subject 20018.

tag: fev1 % predicted

tag: cancer status

value: Cancer


title: 4796-143-54

description: Gene expression data from nasal brushing 4796-143-54.

tag: fev1 %_predicted


title: 250513

description: Gene expression data from nasal brushing of subject 250513.


title: MCF12A_G_3

value: G

value: Pendimethalin at 10 nM


title: 4796-132-54

description: Gene expression data from nasal brushing 4796-132-54.


title: NoCFC_SD_Input_PELL_11

value: Brain

value: male

tag: cell population

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: NO


title: 4797-067-54

description: Gene expression data from nasal brushing 4797-067-54.

tag: tissue

value: Brushing of nasal epithelium


title: 160600

description: Gene expression data from nasal brushing of subject 160600.

value: Female


title: NoCFC_SD_Input_PELL_10

value: neuron

value: membrane(PELL)

tag: treatment cfc

tag: treatment sleep

value: SD


title: 120013

description: Gene expression data from nasal brushing of subject 120013.

value: Current smoker


title: 10017

description: Gene expression data from nasal brushing of subject 10017.


title: 160571

description: Gene expression data from nasal brushing of subject 160571.


title: MCF7_H_1

tag: cell line

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4796-130-54

description: Gene expression data from nasal brushing 4796-130-54.

value: Former smoker


title: MCF12A_F_3

tag: group

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 4796-126-54

description: Gene expression data from nasal brushing 4796-126-54.

tag: subject

value: Male


title: NoCFC_SD_S6_PELL_10

value: Brain

tag: cell type


title: NoCFC_SD_Input_SUP_10

tag: Sex

value: male

value: cytosolic (SUP)


title: NoCFC_SD_HA_PELL_10

tag: genotype

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 110021

description: Gene expression data from nasal brushing of subject 110021.

value: Cancer


title: MCF12A_E_3

value: E

tag: treatment

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM

tag: batch


title: 4796-098-54

description: Gene expression data from nasal brushing 4796-098-54.

value: Brushing of nasal epithelium

value: Female

tag: age

tag: smoking status


title: 4796-120-54

description: Gene expression data from nasal brushing 4796-120-54.


title: NoCFC_SD_HA_SUP_10

value: neuron

value: NO

value: SD


title: MCF12A_D_3

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: MCF12A_B_3

value: B

value: High dose (BPA) of 250 nM


title: 4796-096-54

description: Gene expression data from nasal brushing 4796-096-54.

value: Male

value: Current smoker


title: NoCFC_SD_S6_SUP_10

value: Brain

value: male


title: 70519

description: Gene expression data from nasal brushing of subject 70519.

tag: fev1 % predicted

tag: cancer status

value: Benign


title: 4796-081-54

description: Gene expression data from nasal brushing 4796-081-54.

value: Former smoker

tag: fev1 %_predicted


title: NoCFC_Sleep_Input_PELL_1

tag: cell population

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: membrane(PELL)

value: Sleep


title: MCF12A_C_3

value: C

value: Mid dose (BPA) of 50 nM


title: 190508

description: Gene expression data from nasal brushing of subject 190508.

value: Female

value: Cancer


title: MCF10A_A_3

value: A

value: Negative Control


title: MCF10A_H_3

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4796-121-54

description: Gene expression data from nasal brushing 4796-121-54.

tag: tissue

value: Brushing of nasal epithelium

value: Male


title: 4796-077-54

description: Gene expression data from nasal brushing 4796-077-54.


title: 90003

description: Gene expression data from nasal brushing of subject 90003.


title: 60016

description: Gene expression data from nasal brushing of subject 60016.

value: Current smoker


title: NoCFC_Sleep_S6_PELL_1

value: Brain

value: neuron

value: male

tag: treatment cfc

value: NO

tag: treatment sleep


title: 120542

description: Gene expression data from nasal brushing of subject 120542.


title: NoCFC_Sleep_Input_SUP_1

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: 4796-075-54

description: Gene expression data from nasal brushing 4796-075-54.

value: Former smoker


title: NoCFC_Sleep_HA_PELL_1

value: membrane(PELL)

value: Sleep


title: 110029

description: Gene expression data from nasal brushing of subject 110029.

value: Cancer


title: MCF10A_G_3

tag: cell line

tag: group

value: G

value: Pendimethalin at 10 nM


title: MCF10A_F_3

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 4796-068-54

description: Gene expression data from nasal brushing 4796-068-54.

value: Brushing of nasal epithelium

tag: subject

value: Male


title: 140057

description: Gene expression data from nasal brushing of subject 140057.

tag: Sex

value: Female

value: Benign


title: 4796-006-55

description: Gene expression data from nasal brushing 4796-006-55.

value: Current smoker


title: NoCFC_Sleep_HA_SUP_1

value: Brain

tag: cell type

value: neuron

value: male

tag: genotype

value: NO


title: NoCFC_Sleep_S6_SUP_1

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: MCF10A_E_3

value: E

tag: treatment

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM

tag: batch


title: 220509

description: Gene expression data from nasal brushing of subject 220509.

tag: age

tag: smoking status

value: Cancer


title: MCF7_G_1

value: G

value: Pendimethalin at 10 nM


title: 4795-164-54

description: Gene expression data from nasal brushing 4795-164-54.


title: MCF10A_D_3

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 4795-162-54

description: Gene expression data from nasal brushing 4795-162-54.

value: Brushing of nasal epithelium

value: Former smoker


title: MCF10A_C_3

value: C

value: Mid dose (BPA) of 50 nM


title: Glomeruli, HDAC KO, rep2

city: New Haven

first: Paulina

last: Medina Rangel

state: Connecticut

address: 333 Cedar St

department: Internal Medicine

institute: Yale University

data_processing:
The raw TRAPseq fastq files were processed using fastp tool (version 0.20)
With a default setting, sequencing reads wit low-quality bases were trimmed or filtered. Alignment was performed for cleaned reads using STAR (version 2.7.9) and mouse reference genome (gencode version GRCm38.p6 with vM25 gene annotation).
Expression quantification was performed for alignment results using featureCounts (version 2.0.0)
As genes with low expression levels that represent noise to be excluded before downstream analysis, we defined low expression filtering as expressed gene should have >= 6 read counts in at least 20% of samples
The filtered read counts matrix was then normalized by transcripts per million (TPM) method. Detection of differentially expressed genes was performed using R package DESeq2 (version 1.30.1) and The Benjamin-Hochberg procedure was used for multiple test correction
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files include TPM normalized expression values for each sample

molecule: polyA RNA

source_name: Kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNAseq poly(A)

value: Kidney

value: Glomeruli

value: 3 weeks-old

value: HDAC KO

value: Podocyte-specific KO


title: 4795-161-54

description: Gene expression data from nasal brushing 4795-161-54.

value: Male


title: Glomeruli, HDAC KO, rep1


title: MCF10A_B_3

value: B

value: High dose (BPA) of 250 nM


title: Glomeruli, control, rep1

value: Control (WT)

value: No treatment


title: MCF7_A_3

value: A

value: Negative Control


title: 4795-158-54

description: Gene expression data from nasal brushing 4795-158-54.

value: Female


title: 150506

description: Gene expression data from nasal brushing of subject 150506.

tag: fev1 % predicted

tag: cancer status

value: Benign


title: MCF7_H_3

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 50509

description: Gene expression data from nasal brushing of subject 50509.

value: Former smoker

value: Cancer


title: 70532

description: Gene expression data from nasal brushing of subject 70532.


title: 4795-156-54

description: Gene expression data from nasal brushing 4795-156-54.

value: Brushing of nasal epithelium

tag: fev1 %_predicted


title: Glomeruli, control, rep2

value: Kidney

value: Glomeruli

value: 3 weeks-old


title: 120511

description: Gene expression data from nasal brushing of subject 120511.


title: 160545

description: Gene expression data from nasal brushing of subject 160545.

value: Male

value: Current smoker


title: 160544

description: Gene expression data from nasal brushing of subject 160544.


title: WT_sham2

city: Chengdu

first: Feng

middle: Zhong

last: Xue

state: Sichuan

address: No. 2222, Frontier Medical Center, Xin Chuan Road, Zhong He Street

institute: Sichuan University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each sample

source_name: bone marrow cells

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).And RNA was harvested using Trizol reagent.IIIumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 3. ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using stanard IIIumina protocols.Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: bone marrow cells

tag: strain

value: Wild type

value: sham-operated


title: 4795-154-54

description: Gene expression data from nasal brushing 4795-154-54.

tag: tissue


title: WT_sham3


title: 4795-163-54

description: Gene expression data from nasal brushing 4795-163-54.


title: WT_sham1


title: MCF7_F_3

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 4795-153-54

description: Gene expression data from nasal brushing 4795-153-54.


title: 50507

description: Gene expression data from nasal brushing of subject 50507.

value: Female


title: MCF7_E_3

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 4795-150-54

description: Gene expression data from nasal brushing 4795-150-54.


title: 20026

description: Gene expression data from nasal brushing of subject 20026.


title: 140088

description: Gene expression data from nasal brushing of subject 140088.

value: Benign


title: WT_CLP2

value: caecal ligation plus puncture ( CLP)


title: WT_CLP3


title: MCF7_D_3

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: MCF7_G_3

value: G

value: Pendimethalin at 10 nM


title: 4795-149-54

description: Gene expression data from nasal brushing 4795-149-54.

value: Brushing of nasal epithelium


title: MCF7_C_3

value: C

value: Mid dose (BPA) of 50 nM


title: WT_CLP1

value: bone marrow cells


title: KO_sham3

value: IMD knockout


title: 4795-139-54

description: Gene expression data from nasal brushing 4795-139-54.

value: Male

value: Former smoker


title: MCF7_F_1

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: MCF7_B_3

value: B

value: High dose (BPA) of 250 nM


title: 50505

description: Gene expression data from nasal brushing of subject 50505.

value: Female

value: Cancer


title: 210522

description: Gene expression data from nasal brushing of subject 210522.


title: 160574

description: Gene expression data from nasal brushing of subject 160574.


title: 50053

description: Gene expression data from nasal brushing of subject 50053.

value: Current smoker


title: MCF12A_A_2

value: A

value: Negative Control


title: KO_sham1

value: sham-operated


title: 50056

description: Gene expression data from nasal brushing of subject 50056.


title: 140092

description: Gene expression data from nasal brushing of subject 140092.

value: Benign


title: MCF12A_H_2

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4795-131-54

description: Gene expression data from nasal brushing 4795-131-54.

value: Brushing of nasal epithelium


title: 210505

description: Gene expression data from nasal brushing of subject 210505.


title: KO_CLP3

value: bone marrow cells

value: IMD knockout

value: caecal ligation plus puncture ( CLP)


title: KO_CLP2


title: 4795-130-54

description: Gene expression data from nasal brushing 4795-130-54.

value: Male


title: MCF12A_G_2

value: G

value: Pendimethalin at 10 nM


title: KO_CLP1


title: MCF12A_F_2

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: KO_sham2


title: 4795-134-54

description: Gene expression data from nasal brushing 4795-134-54.

value: Female


title: 140017

description: Gene expression data from nasal brushing of subject 140017.

value: Current smoker

value: Cancer


title: 4795-138-54

description: Gene expression data from nasal brushing 4795-138-54.


title: 4795-129-54

description: Gene expression data from nasal brushing 4795-129-54.


title: liver, HFD, ApoA4 knockdown

city: Shaanxi

first: Xiaoming

last: Li

address: Zhuque Street

institute: xian jiaotong univercity

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: liver

extract_protocol:
After anaesthesia, the primary liver cells were isolated as described previously. Briefly, the mouse liver was perfused with Hanks (ZHONGHUIHECAI, Xi'an, China) solution with 0.5 M EDTA (ZHONGHUIHECAI, Xi'an, China) through the left ventricle until the liver turned white (approximately 6 minutes). The liver tissue was minced and digested with PSCeasy (Cellapy, Beijing, China), disassociated by pipetting every 20 minutes, and then swiftly ground on a 40 µm filter (FALCON, One Riverfront Plaza, NY, USA). The filtered product was centrifuged at 50 g for 3 min to remove hepatocytes and collect the immune cells in the supernatant. The cells were lysed with red blood cell lysate (CWBIO, Beijing, China) on ice for 2 minutes and washed once with PBS. Subsequently, the liver immune cells were used for scRNA-seq analysis.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, liver immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).  Library sequencing was performed by Illumina NovaSeq using PE150 protocol.

value: liver

value: immune cell

value: ApoA4 knockdown

value: high fat diet


title: MCF12A_E_2

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 160566

description: Gene expression data from nasal brushing of subject 160566.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

value: Former smoker

value: Benign


title: 4795-128-54

description: Gene expression data from nasal brushing 4795-128-54.

value: Brushing of nasal epithelium


title: 110502

description: Gene expression data from nasal brushing of subject 110502.


title: liver, HFD, wild type

description: 10x Genomics

value: WT


title: 4795-132-54

description: Gene expression data from nasal brushing 4795-132-54.


title: MCF12A_D_2

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 4795-113-54

description: Gene expression data from nasal brushing 4795-113-54.


title: Wild-type age-matched control mouse sciatic nerves_6mos_3

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

department: Genetics

institute: Washington University School of Medicine

data_processing:
Basecalling and demultiplexing with bcl2fastq, RNA-seq mapped to reference genome using STAR v2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: mm10
Supplementary files format and content: Raw expression count matrix
Supplementary files format and content: CPM normalized expression count matrix

source_name: Sciatic nerve

extract_protocol:
RNA extracted using Trizol/Chloroform extraction and RNeasy MinElute Cleanup Kit (Qiagen 74204)
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000

value: Sciatic nerve

value: Wild type


title: MCF12A_C_2

value: C

value: Mid dose (BPA) of 50 nM


title: 70514

description: Gene expression data from nasal brushing of subject 70514.

value: Female


title: 4795-111-54

description: Gene expression data from nasal brushing 4795-111-54.


title: Wild-type age-matched control mouse sciatic nerves_6mos_2


title: MCF12A_B_2

value: B

value: High dose (BPA) of 250 nM


title: Wild-type age-matched control mouse sciatic nerves_6mos_1


title: 50538

description: Gene expression data from nasal brushing of subject 50538.

value: Male

value: Cancer


title: 4795-107-54

description: Gene expression data from nasal brushing 4795-107-54.


title: 130148

description: Gene expression data from nasal brushing of subject 130148.


title: 4795-104-54

description: Gene expression data from nasal brushing 4795-104-54.

value: Current smoker


title: Wild-type age-matched control mouse sciatic nerves_2mos_3


title: MCF7_E_1

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 4795-088-54

description: Gene expression data from nasal brushing 4795-088-54.


title: MCF10A_H_2

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: Wild-type age-matched control mouse sciatic nerves_2mos_2


title: Wild-type age-matched control mouse sciatic nerves_2mos_1


title: 140009

description: Gene expression data from nasal brushing of subject 140009.

value: Former smoker


title: MCF10A_G_2

value: G

value: Pendimethalin at 10 nM


title: 4795-084-54

description: Gene expression data from nasal brushing 4795-084-54.

value: Brushing of nasal epithelium


title: 4795-073-54

description: Gene expression data from nasal brushing 4795-073-54.


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_6mos_3

value: Sciatic nerve

value: NMNAT2 V98M/R232Q


title: MCF10A_F_2

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 50023

description: Gene expression data from nasal brushing of subject 50023.

value: Female


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_6mos_2


title: 120556

description: Gene expression data from nasal brushing of subject 120556.

value: Benign


title: MCF10A_E_2


title: 140022

description: Gene expression data from nasal brushing of subject 140022.


title: 140125

description: Gene expression data from nasal brushing of subject 140125.

value: Male


title: MCF10A_A_2

value: A

value: Negative Control


title: 4794-012-54

description: Gene expression data from nasal brushing 4794-012-54.

value: Current smoker


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_6mos_1


title: 130147

description: Gene expression data from nasal brushing of subject 130147.


title: MCF10A_D_2

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_2mos_3


title: 4794-011-54

description: Gene expression data from nasal brushing 4794-011-54.


title: 4794-010-54

description: Gene expression data from nasal brushing 4794-010-54.


title: 140099

description: Gene expression data from nasal brushing of subject 140099.

value: Cancer


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_2mos_2


title: MCF10A_B_2

value: B

value: High dose (BPA) of 250 nM


title: 4794-009-54

description: Gene expression data from nasal brushing 4794-009-54.

value: Former smoker


title: NMNAT2 V98M/R232Q transheterozygous mouse sciatic nerves_2mos_1


title: 120023

description: Gene expression data from nasal brushing of subject 120023.


title: 4795-052-54

description: Gene expression data from nasal brushing 4795-052-54.

value: Brushing of nasal epithelium


title: 120522

description: Gene expression data from nasal brushing of subject 120522.


title: MCF7_A_2


title: 4794-008-54

description: Gene expression data from nasal brushing 4794-008-54.


title: 4794-006-54

description: Gene expression data from nasal brushing 4794-006-54.


title: ATAC-seq_G7FSen_2

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

data_processing:
Read quality was assessed by FastQC 0.11.8. All adapters were removed by Fastp 0.21.0.
The clean data was then aligned to mouse genome using Bowtie2 2.2.5.
BigWig files were generated using deeptools 3.3.1. Peaks were called using Macs2 2.1.0
Union peak sets were created by Bedtools 2.29.2, reads corresponding to each region were assigned by featureCounts 2.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw read counts for each sample.

source_name: Skeletal muscles (tibialis anterior, gastrocnemius and quadriceps)

growth_protocol: Mice were housed in standard cages under 12-hour light-dark cycles and fed ad libitum with a standard chow diet.

extract_protocol:
Sorted cells were directly processed for ATAC-seq library preparation without in vitro culture.  Sorted cells were centrifuged at 500 × g for 5min at 4°C and lysed using cold ATAC-RSB (10mM Tris-HCl, pH7.4,10mM NaCl, 3mM MgCl2 supplemented in 0.1% NP40, 0.1% Tween20 and 0.1mg/ml Digitonin) on ice for 3min. Next, the lysed cells were added in 50µl of transposition mix (25 µl of 2 × TD buffer (20mM Tris-HCl, pH7.6, 10mM MgCl2, 20% Dimethyl Formamide), 1.5 µl transposase (in house, (Picelli et al., 2014)), 17.5µl of PBS, 0.5µl of 10% Digitonin, 0.5µl of 10% Tween20 and 5µl of nuclease-free water). The transposition reaction was carried out for 30 min at 37°C and placed at 10°C. The transposition sample was purified using a Qiagen MinElute kit and eluted using 21µl of EB buffer.
The transposed fragments were amplified using 50ul of PCR mix (20µl of DNA, 2.5µl of custom Nextera PCR primers 1 and 2, and 25µl of KAPA HiFi HS Ready Mix for a total of 15 cycles. The PCR amplification conditions were 72°C for 5 min and 95°C for 30 sec, followed by 15 cycles at 95 °C for 10 s, 63 °C for 30 s, and 72 °C for 60 s, with a final extension at 72 °C for 5 min. Following PCR amplification, the libraries were purified, and the size was selected from 150 to 800bp using AMPure XP beads.

treatment_protocol: Cells were isolated from skeletal muscle tissue (tibialis anterior, gastrocnemius and quadriceps).

value: Fibroadipogenic progenitors

tag: spider staining

value: SPiDER+

value: geriatric (28months old)

tag: muscle state

value: 7 days after injury (Cardiotoxin)


title: MCF7_G_2

tag: cell line

value: G

value: Pendimethalin at 10 nM


title: 210502

description: Gene expression data from nasal brushing of subject 210502.

source_name: Brushing of nasal epithelium

value: Female


title: ATAC-seq_G7FNSen_2

value: SPiDER-


title: ATAC-seq_G7FSen_1


title: MCF7_H_2

tag: group

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4794-004-54

description: Gene expression data from nasal brushing 4794-004-54.

tag: subject

value: Male


title: MCF7_D_1

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: MCF10A_C_2

value: C

value: Mid dose (BPA) of 50 nM


title: 4794-003-54

description: Gene expression data from nasal brushing 4794-003-54.

tag: Sex

value: Current smoker


title: ATAC-seq_G3FSen_2

tag: cell type

value: 3 days after injury (Cardiotoxin)


title: MCF7_F_2

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 20022

description: Gene expression data from nasal brushing of subject 20022.

value: Former smoker

value: Cancer


title: MCF7_E_2

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 10088

description: Gene expression data from nasal brushing of subject 10088.


title: ATAC-seq_G3FSen_1

value: Fibroadipogenic progenitors

value: SPiDER+

value: geriatric (28months old)


title: MCF7_D_2


title: 4793-055-54

description: Gene expression data from nasal brushing 4793-055-54.

value: Brushing of nasal epithelium


title: ATAC-seq_G3FNSen_2

value: SPiDER-


title: 4793-057-54

description: Gene expression data from nasal brushing 4793-057-54.

value: Male


title: 130150

description: Gene expression data from nasal brushing of subject 130150.

value: Female


title: 4794-005-54

description: Gene expression data from nasal brushing 4794-005-54.


title: MCF7_C_2

value: C


title: 4793-041-54

description: Gene expression data from nasal brushing 4793-041-54.


title: 210517

description: Gene expression data from nasal brushing of subject 210517.


title: ATAC-seq_G7FNSen_1

value: 7 days after injury (Cardiotoxin)


title: ATAC-seq_G3FNSen_1


title: 4793-020-55

description: Gene expression data from nasal brushing 4793-020-55.


title: ATAC-seq_G3F_2

value: non-injured contralateral muscle at 3 days post injury


title: MCF7_B_2

value: B

value: High dose (BPA) of 250 nM


title: MCF12A_A_1

value: A

value: Negative Control


title: 10077

description: Gene expression data from nasal brushing of subject 10077.

value: Current smoker

value: Cancer


title: 4792-002-55

description: Gene expression data from nasal brushing 4792-002-55.


title: 30025

description: Gene expression data from nasal brushing of subject 30025.

value: Former smoker

value: Benign


title: 110537

description: Gene expression data from nasal brushing of subject 110537.


title: ATAC-seq_G3F_1

value: Fibroadipogenic progenitors


title: 70507

description: Gene expression data from nasal brushing of subject 70507.


title: ATAC-seq_Y7FSen_2

value: SPiDER+

value: young (3-6 months old)


title: 10137

description: Gene expression data from nasal brushing of subject 10137.


title: 50058

description: Gene expression data from nasal brushing of subject 50058.


title: 4791-011-54

description: Gene expression data from nasal brushing 4791-011-54.

value: Brushing of nasal epithelium


title: MCF12A_F_1

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: MCF12A_G_1

value: G

value: Pendimethalin at 10 nM


title: 4791-008-54

description: Gene expression data from nasal brushing 4791-008-54.

value: Male


title: ATAC-seq_Y7FNSen_2

value: SPiDER-

value: 7 days after injury (Cardiotoxin)


title: 4791-007-54

description: Gene expression data from nasal brushing 4791-007-54.


title: ATAC-seq_Y7FNSen_1


title: ATAC-seq_Y3FSen_2

value: 3 days after injury (Cardiotoxin)


title: 4790-086-54

description: Gene expression data from nasal brushing 4790-086-54.


title: MCF12A_E_1

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: MCF12A_D_1

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: MCF12A_H_1

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: MCF7_C_1

value: C

value: Mid dose (BPA) of 50 nM


title: 4791-013-54

description: Gene expression data from nasal brushing 4791-013-54.

value: Brushing of nasal epithelium

value: Female

value: Former smoker


title: ATAC-seq_Y3FSen_1

value: Fibroadipogenic progenitors

value: SPiDER+

value: young (3-6 months old)


title: 4790-065-54

description: Gene expression data from nasal brushing 4790-065-54.

value: Male

value: Current smoker


title: MCF12A_C_1


title: 180505

description: Gene expression data from nasal brushing of subject 180505.

value: Cancer


title: 160539

description: Gene expression data from nasal brushing of subject 160539.

value: Benign


title: ATAC-seq_Y3FNSen_2

value: SPiDER-

value: 3 days after injury (Cardiotoxin)


title: 100004

description: Gene expression data from nasal brushing of subject 100004.


title: 250506

description: Gene expression data from nasal brushing of subject 250506.


title: ATAC-seq_Y7FSen_1

value: 7 days after injury (Cardiotoxin)


title: 50092

description: Gene expression data from nasal brushing of subject 50092.


title: 4790-062-54

description: Gene expression data from nasal brushing 4790-062-54.


title: 4790-058-54

description: Gene expression data from nasal brushing 4790-058-54.


title: MCF12A_B_1

value: B

value: High dose (BPA) of 250 nM


title: ATAC-seq_Y3F_2

value: non-injured contralateral muscle at 3 days post injury


title: 4790-108-54

description: Gene expression data from nasal brushing 4790-108-54.


title: 120028

description: Gene expression data from nasal brushing of subject 120028.


title: MCF10A_A_1

value: A

value: Negative Control


title: 140021

description: Gene expression data from nasal brushing of subject 140021.

value: Female


title: 4790-049-54

description: Gene expression data from nasal brushing 4790-049-54.

value: Brushing of nasal epithelium

value: Former smoker


title: ATAC-seq_Y3F_1

value: Fibroadipogenic progenitors


title: 70518

description: Gene expression data from nasal brushing of subject 70518.


title: MCF10A_H_1

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4790-047-54

description: Gene expression data from nasal brushing 4790-047-54.

value: Male

value: Current smoker


title: MCF12A_A_6


title: ATAC-seq_G7MSen_2

value: Myeloid cells

value: SPiDER+

value: geriatric (28months old)


title: 4790-036-54

description: Gene expression data from nasal brushing 4790-036-54.


title: MCF12A_H_6


title: 120046

description: Gene expression data from nasal brushing of subject 120046.

value: Benign


title: 160537

description: Gene expression data from nasal brushing of subject 160537.

value: Cancer


title: 10089

description: Gene expression data from nasal brushing of subject 10089.


title: MCF12A_G_6

value: G

value: Pendimethalin at 10 nM


title: ATAC-seq_G7MSen_1

value: 7 days after injury (Cardiotoxin)


title: ATAC-seq_Y3FNSen_1

value: SPiDER-

value: young (3-6 months old)

value: 3 days after injury (Cardiotoxin)


title: ATAC-seq_G7MNSen_2


title: 4714-042-54

description: Gene expression data from nasal brushing 4714-042-54.

value: Brushing of nasal epithelium


title: 10009

description: Gene expression data from nasal brushing of subject 10009.

value: Former smoker


title: 4714-038-54

description: Gene expression data from nasal brushing 4714-038-54.