title: Lung sci-ATAC-seq3

source_name: Lung

value: Lung


title: a-ama 2-cell input rep1

status: Public on Nov 01 2020

type: SRA

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
input_ama2C_rep1_S7
processed data file: ama2C_H33_bin100.bw

library_source: genomic

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin.
RNA-seq reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore!.
After the reads were aligned, the reads correspond to rRNA were removed. featureCounts was then used to assign the mapped reads to a transcriptional model file.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: a-ama 2-cell input

growth_protocol: Early embryos were cultured in KSOM. Male mouse embryonic stem cells were cultured with the medium that consists of GMEM (Sigma-Aldrich) containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates.

extract_protocol:
MNase-digested chromatin was used for ULI-N-ChIP-seq. Total RNA in cell lysates was directly used for RNA-seq sample preparation according to the manufacturer's  instructions (SMART-seq stranded kit, TAKARA).
ULI-N-ChIP-seq protocol was used for ChIP-seq. For RNA-seq, SMART-seq stranded kit was used.

tag: strain

value: hybrid C57BL/6/JF-1

tag: tissue/cell type

value: Embryo


title: Aphi 2-cell H3.3 ChIP-seq rep2

description:
H33_aphi2C_rep2_S2
processed data file: aphi2C_H33_bin100.bw

source_name: Aphi 2-cell H3.3 ChIP-seq

tag: chip antibody


title: Liver sci-ATAC-seq3

city: Seattle

first: Silvia

last: Domcke

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

data_processing:
Please see associated publication for details on data processing.
Seurat object with both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses
Genome_build: hg19
Supplementary_files_format_and_content:
tissue_filtered.seurat.RDS files: Seurat object for each tissue, containing only high-quality cells remaining after all filtering steps, including peak module-based filtering of doublets as described in the Cicero part of the methods section of the associated publication. Contain both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses. Include the following metadata information for each cell: number of reads in gene bodies + 2kb upstream of TSS (nCountRNA), number of gene bodies + 2 kb upstream of TSS that contain at least one read (nFeature_RNA), cell barcode, sample name, donor ID, estimated gestational age based on foot length (day_of_pregnancy), sex, tissue, experimental batch, total number of reads, total number of deduplicated reads, total number of deduplicated reads that fall into peaks, total number of deduplicated reads that fall into a 2 kb window centered on TSS, fraction of reads in peaks (frip), fraction of reads in 2 kb window centered on TSS (frit), number of 5 kb windows of the X, Y and autosomal chromosomes respectively containing reads, fraction of unique reads falling in ENCODE blacklist regions, Louvain cluster ID (resolution = 0.3), number of reads in peaks (nCount_peaks), number of peaks that contain at least one read (nFeature_peaks), tissue UMAP coordinates based on the peaks assay, assigned cell type.
File_S1.Master_list_of_sites.txt.gz: Chromosomal location, width, read number in the object evenly subsampled across cell types, and indication of whether this site was z-score filtered for downstream analyses, for each site within a merged set of 1.05 M peaks of accessibility.
File_S2.Metadata_of_high_quality_cells.txt.gz: Cell metadata for all high-quality cells remaining after all filtering steps, including peak module-based filtering of doublets as described in the Cicero part of the methods section of the associated publication cells. Includes tissue of origin, donor ID, estimated gestational age, sex, experimental batch, total number of reads, total number of deduplicated reads, total number of deduplicated reads that fall into peaks, total number of deduplicated reads that fall into a 2 kb window centered on TSS, fraction of reads in peaks (frip), fraction of reads in 2 kb window centered on TSS (frit), number of peaks that contain at least one read (nFeature_peaks), Louvain cluster ID and UMAP coordinates of per tissue (not combined) UMAP visualizations and cell type annotation.
File_S3.Motif_enrichments_across_cell_types.txt.gz: For each of the 579 motifs from the JASPAR vertebrate database, the enrichment in accessible sites in each of the main 54 cell types was determined using a linear regression model. Fold-change of the mean motif occurrence in sites of a given cell type relative to the rest of the dataset and matching Benjamini Hochberg-adjusted p-values are reported for each motif-cell type pair.
File_S4.Specificity_scores_for_top_10000_sites_per_cell_type.txt.gz: The top 10,000 specific sites for each of the 54 cell types were calculated for each site/cell type pair using Jensen-Shannon divergence. A higher score indicates a peak that is more specific to a given cell type.
File_S5.Cicero_coaccessibility_scores_by_cell_type.csv.gz: Comma-separated table of Cicero co-accessibility scores greater than 0.1, generated for each of 101 cell type/tissue pairs. The first two columns are the coordinates in hg19 of the two tested sites. Each of the remaining columns represents the co-accessibility scores for each of the cell types. NA values indicate that the pair of sites was not tested because of insufficient depth or that the co-accessibility value was less than 0.1.
File_S6.Cicero_gene_activity_scores_by_cell_type.csv.gz: Comma-separated combined triplet sparse matrix table of Cicero gene activity scores for each of 101 cell type/tissue pairs. The first column is gene symbols, the second column is cell IDs with cell type and tissue, and the third column is the associated gene activity score. NA values indicate that there was insufficient accessibility to calculate a gene activity score.
File_S7.Motif_enrichment_across_clusters_in_UMAP_of_sites.txt.gz: For each of the 579 motifs from the JASPAR vertebrate database, the enrichment in each of the 15 Louvain clusters in the UMAP of sites was determined using a linear regression model. Fold-change of the mean motif occurrence in a given cluster relative to the rest of the dataset and matching Benjamini Hochberg-adjusted p-values are reported for each motif-cluster pair.

organism: Homo sapiens

source_name: Liver

extract_protocol:
Nuclei were extracted directly from cryopreserved tissues (please see associated publication for more details). A detailed version of the full sci-ATAC-seq3 workflow is also available on protocols.io.
Please see associated publication for details on library construction. A detailed version of the full sci-ATAC-seq3 workflow is also available on protocols.io.

tag: developmental stage

value: estimated gestational age 89-125d

tag: tissue

value: Liver


title: ChIP_EoV5_B_IP

city: Oxford

first: Luke

middle: Thomas Gilbert

last: Harland

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: Oxford University

data_processing:
Paired-end reads were aligned to the mouse genome assembly mm10 using Bowtie2(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools 1.9(Li et al., 2009).
Peaks were called against input DNA using MACS 2.1.2(Zhang et al., 2008) and were considered significant if they had a fold enrichment > 2 and FDR < 0.05. Bedtools 2.27.1(Quinlan and Hall, 2010) was used to intersect the peak files from both EomesV5/V5 clones amd subtract peaks called in the WT control and genomic intervals located in mm10 blacklist regions (https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz), generating a peak file containing 338 genomic intervals (Supplementary Table 6) used for downstream analyses.
Bigwig files were generated using Deeptools2 (Ramirez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] bigWig represent genome coverage (subtract input control) generated using Deeptools2.

source_name: Day 4 EBs

growth_protocol: WT (CCE) and EomesV5/V5 (clones A and B) ESC lines were maintained in feeder free culture conditions in serum + LIF as previously described(Costello et al., 2011). 48-72 hrs prior to induction of hematopoietic differentiation cells were washed with PBS and cultured in serum free ES media containing 50% Neurobasal Media (Gibco, Cat # 21103049), 50% DMEM/F12 (Gibco, Cat # 11320033), supplemented with 0.5X of both N2 (Gibco, Cat#17502048) and B27 (Gibco, Cat# 17504044), 1%Pen/Strep, 1% glutamine, 0.05% BSA (Gibco, Cat# 15260037), 1 uM PD0325091, 3 uM CHIR99021 and 1000 U/ml LIF. At D0 cells were dissociated using Trypsin-LE (Gibco) and seeded at a density of 1×10^5 cells ml in serum-free differentiation (SF-D) media(Nostro et al., 2008) and cultured on an orbital shaker at 70 rpm for ~18 hrs in the absence of growth factors to form EBs. At D2, EBs were split 1:3 in SF-D media containing recombinant human (rh) VEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 48 hr.

extract_protocol:
Day 4 EomesV5/V5 (CCE) and WT (CCE) D4 EBs were dissociated using Trypsin-LE (Gibco) and ~3-4x107 cells were cross-linked for 10 min at RT with 1% (v/v) formaldehyde, followed by quenching with 125mM glycine. Nuclei were recovered and lysed to obtain chromatin, which was then sonicated to 200–500 bp, pre-cleared with protein G Dynabeads (Thermofisher Scientific) and ~175 ug of chromatin was immunoprecipitated with 10μg of anti-V5 (Abcam cat# ab9116, lot# GR: 322448-4) bound to protein G Dynabeads overnight on a rotator at 4ºC. Dynabeads were washed and immune complexes were eluted in IP elution buffer (1% SDS, 0.1M NaHCO3), reverse crosslinked overnight at 65ºC, RNaseA treated for 1.5hrs at 42ºC, proteinase K treated for 2hrs at 45ºC and DNA was recovered using a Zymo column kit.
DNA was multiplexed and paired end sequencing was performed on a single lane of an Illumina HiSeq4000 platform.

value: mixed mesoderm

tag: genotype


title: ME14-E3M1R

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The quality control of the rna-seq reads were done by AfterQC, Trimmomatic , MultiQC and FastQC
The ribosomal rRNA were filtered out using SortMeRna
The reads where aligned to mouse genome using STAR (1.5) with default parameters (GRCm38/mm10/Ensembl release 79 - March 2015) )
The gene expression was measured by counting the corresponding reads of the exons. This step was performed by htseq-count with parameters (-s reverse -t exon -i gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene expression count values of each samples

molecule: total RNA

source_name: Molar 1

growth_protocol: Tooth germs were dissected carefully under microscope from E13.5, E14.5 or E16.5 C57BL/6JOlaHsd mice.

extract_protocol:
The tooth germ was homogenised into TRI Reagent (Merck, Darmstadt, Germany) using Precellys 24 -homogenizer (Bertin Instruments, Montigny-le-Bretonneux, France). The RNA was extracted by guanidium thiocyanate-phenol-chloroform method and then further purified by RNeasy Plus micro kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's instructions.
The cDNA libraries were prepared with Ovation Mouse Universal RNAseq System (Tecan, Zürich, Schwitzerland).

tag: embryonic day

value: Molar 1 tooth germ


title: Kidney sci-ATAC-seq3

description: Seurat object with both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses

source_name: Kidney

value: Kidney


title: ChIP_EoV5_B_input


title: ME14-E2M1R


title: ChIP_EoV5_A_IP


title: ChIP_EoV5_A_input


title: ME14-E6M1L


title: Intestine sci-ATAC-seq3

source_name: Intestine

value: Intestine


title: Aphi 2-cell input rep1

description:
input_aphi2C_rep1_S3
processed data file: aphi2C_H33_bin100.bw

source_name: Aphi 2-cell input


title: Aphi 2-cell input rep2

description:
input_aphi2C_rep2_S4
processed data file: aphi2C_H33_bin100.bw


title: ME14-E1M1R


title: ME16-E8M1L


title: ChIP_WT_IP

value: wildtype


title: Heart sci-ATAC-seq3

source_name: Heart

value: Heart


title: ME16-E8M1R


title: 8-cell H3.3 ChIP-seq rep2

description:
H33_8C_rep2_S5
processed data file: 8C_H33_bin100.bw

source_name: 8-cell H3.3 ChIP-seq


title: Eye sci-ATAC-seq3

source_name: Eye

value: Eye


title: RNA_WT_rep_1

data_processing:
Paired-end reads were aligned against the mm10 genome using the STAR RNA-seq aligner with default parameters outputting bam files using --outSAMtype BAM SortedByCoordinate (Dobin et al., 2013).
BAM file primary alignments with a mapping quality of > 254 were treated as RNA-Seq data and imported into Seqmonk 1.45.4.  (https://www.bioinformatics.babraham.ac.uk/projects/download.html#seqmonk).
The RNA-Seq quantitation pipeline (p<0.05 and multiple testing correction applied) in SeqMonk utilizing DESeq2 (Love et al., 2014) was performed to identify significantly differentially expressed genes (p<0.05, fold change > 1.5 and FPKM >1).
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] Read Counts and DESeq2 Results from SeqMonk

source_name: Day 4 Flk-1hi/PdgfRa- EB cells

growth_protocol: WT (CCE) and Eomes-null (CCE, clone 6A6) ESC lines were maintained in feeder free culture conditions in serum + LIF as previously described(Costello et al., 2011). 48-72 hrs prior to induction of hematopoietic differentiation cells were washed with PBS and cultured in serum free ES media containing 50% Neurobasal Media (Gibco, Cat # 21103049), 50% DMEM/F12 (Gibco, Cat # 11320033), supplemented with 0.5X of both N2 (Gibco, Cat#17502048) and B27 (Gibco, Cat# 17504044), 1%Pen/Strep, 1% glutamine, 0.05% BSA (Gibco, Cat# 15260037), 1 uM PD0325091, 3 uM CHIR99021 and 1000 U/ml LIF. At D0 cells were dissociated using Trypsin-LE (Gibco) and seeded at a density of 1×10^5 cells ml in serum-free differentiation (SF-D) media(Nostro et al., 2008) and cultured on an orbital shaker at 70 rpm for ~18 hrs in the absence of growth factors to form EBs. At D2, EBs were split 1:3 in SF-D media containing recombinant human (rh) VEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 48 hr. At D4, EBs were dissociated, stained with Flk-1-APC (Cat# 17-5821-81) and PdgfRa-PECy7 (Cat# 25-1401-82) antibodies and FACS sorted.

extract_protocol:
RNA was isolated from Flk-1hi/PdgfRa- single cell suspensions (1.5x105 cells) from three independent hematopoietic differentiations of WT (CCE) and Eomes-null (clone 6A6, CCE) cells using the RNeasy Micro Kit (QIAGEN, Cat#74004). These cell samples were taken from the same cells that were also used for ATAC-seq (see below).
Total RNA was normalized to 800ng per sample, depleted of cytoplasmic and mitochondrial ribosomal RNA sequences (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324) and library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep (H/M/R) (Cat: #20020597), followed by sequencing (75-cycle paired end) on the Illumina HiSeq4000 platform.

value: hematovascular mesoderm


title: ChIP_WT_input


title: 8-cell input rep2

description:
input_8C_rep2_S7
processed data file: 8C_H33_bin100.bw

source_name: 8-cell input


title: ME16-E7M1R


title: MII oocyte H3.3 ChIP-seq rep2

description:
H33_MII_rep2_S4
processed data file: MII_H33_bin100.bw

source_name: MII oocyte H3.3 ChIP-seq


title: Cerebrum sci-ATAC-seq3

source_name: Cerebrum

value: Cerebrum


title: ATAC_Tn5_Control

data_processing:
Paired-end reads were aligned to the mouse genome assembly mm10 using Bowtie2(Langmead and Salzberg, 2012) with the very-sensitive option, sorted and mitochondrial reads discarded using Samtools(Li et al., 2009) and duplicates removed using Picard (https://broadinstitute.github.io/picard/). Bigwig files were generated using deepTools2(Ramirez et al., 2016).
Biological replicates were randomly downsampled to contain the same number of reads for each individual sample and peaks in each sample called using MACS2(Zhang et al., 2008) using the Tn5 control as a control.
MACS2 called peaks with a p-value < 10-3 were used in downstream analyses. Significant changes in ATAC-Seq datasets were identified using the DiffBind package (http://bioconductor.org/packages/release/bioc/html/DiffBind.html) using bam files and an integrative bed file of all identified peaks in each sample with the following filters: FDR < 0.05, fold change > 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] bigWig represent genome coverage generated using Deeptools2.

source_name: CCE ESC

extract_protocol:
Tagmentation and indexing of single cell suspensions (6x104 cells) from three independent differentiations of WT (CCE) and Eomes-null (clone 6A6, CCE) day 4 Flk-1hi/PdgfRa- cells was performed as previously described(Buenrostro et al., 2013), using cells from equivalent samples to those used for the RNA-seq experiments described above. To control for sequence bias of the Tn5 transposase, 100ng genomic DNA of WT (CCE) ESCs was also tagmented and indexed.
Libraries were purified with two rounds of Agencourt AMPure XP bead cleanup (Agencourt, 1.5× bead:sample ratio). Library size and concentration were determined using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent). Samples were sequenced using a 75-cycle paired end Nextera kit with custom Nextera index primers taken from Table S1 in Buenrostro et al. 2013(Buenrostro et al., 2013) on the Illumina HiSeq4000 platform.

value: CCE

value: embryonic stem cells


title: ME16-E6M1L


title: Cerebellum sci-ATAC-seq3

source_name: Cerebellum

value: Cerebellum


title: MII oocyte input rep2

description:
input_MII_rep2_S6
processed data file: MII_H33_bin100.bw

source_name: MII oocyte input


title: ATAC_Eomes_null_rep_3

value: Eomes-null


title: ME16-E6M1R


title: Adrenal gland sci-ATAC-seq3

source_name: Adrenal gland

value: Adrenal gland


title: MII oocyte H3.3 ChIP-seq rep1

description:
H33_MII_rep1_S3
processed data file: MII_H33_bin100.bw

value: Oocyte


title: Aphi 2-cell H3.3 ChIP-seq rep1

description:
H33_aphi2C_rep1_S1
processed data file: aphi2C_H33_bin100.bw

source_name: Aphi 2-cell H3.3 ChIP-seq

value: hybrid C57BL/6/JF-1

value: Embryo


title: ATAC_Eomes_null_rep_2


title: ME16-E5M1L


title: ATAC_Eomes_null_rep_1


title: MII oocyte input rep1

description:
input_MII_rep1_S5
processed data file: MII_H33_bin100.bw


title: ME16-E3M1L


title: TM5614_Rep5

city: Chicago

first: Douglas

last: Vaughan

state: IL

address: Arkes Pavilion, Suite 2330, 676 N. St. Clair Street

department: Medicine

institute: Northwestern University Feinberg School of Medicine

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Quantification of gene expression: gene expression at exons was quantified as integer counts using HOMER
Differenial expression analysis: differentially expressed exonic RNAs were identified using DESeq2 (FDR-adjusted p-value <0.05 and |LFC| > 2).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differential expression and individual replicate normalized rlog values

molecule: polyA RNA

source_name: Male WT ad lib fed +TM5614 (20 mg/kg/day for 10 days) liver mRNA

extract_protocol:
Liver was flash frozen with liquid nitrogen.  RNA harvested from frozen liver using Qiagen RNA Easy Mini Kit (Cat#: 74104, Qiagen)
mRNA libraries were constructed using KAPA mRNA HyperPrep kits (Cat#kk8580, KAPA)

treatment_protocol: TM5614 was mixed into the chow at a dose of 20/mg/kg/day for continous feeding for 10 days

tag: mouse number

value: liver

tag: age

value: 21 Weeks

tag: Sex

value: male


title: ATAC_WT_rep_3


title: NUC treated HBV LDB_57

type: RNA

city: Bethesda

first: Barbara

last: Rehermann

state: Maryland

address: 10 Center Drive

department: Liver Diseases Branch

institute: National Institutes of Health

description: nothing special

hyb_protocol: Hybridization was performed according to hybridization protocol for nCounter XT CodeSet Gene Expression Assays Including Panels. Briefly, hybridization buffer and reporter codeset were mixed first, and this mastermix was added to samples (total RNA), finally hybridization reaction was completed by adding capture probeset.

scan_protocol: The cartridge was read with maximum sensitivity (280 FOV).

data_processing: Data from all runs were imported into nSolver version 4.0 (NanoString Technologies), matched to corresponding Reporter Library File (RLF), and subjected to quality control using the software quality metrics with default cutoff criteria

source_name: peripheral blood mononucler cells

extract_protocol: Total RNA was extracted from PBMC using QIAshredder and RNeasy Mini Kit (Qiagen, Germantown, MD), and 100 ng of total RNA was used for hybridization.

treatment_protocol: Frozen PBMCs were thawed and total RNA was extracted.

tag: diseases

value: chronic HBV

tag: hbeag (+/-)

value: HBeAg-

tag: therapy that the patient received

value: long term NUC

tag: time point relative to the first pegifna injection

value: Pt1 0h

tag: nk cell response after the first  pegifna injection

value: without NK cell response


title: TM5614_Rep4


title: ATAC_WT_rep_2

value: hematovascular mesoderm

value: wildtype


title: NUC treated HBV LDB_56

description: nothing special

value: Pt1 6h


title: TM5614_Rep3


title: ATAC_WT_rep_1

value: CCE


title: NUC treated HBV LDB_55

description: nothing special

value: Pt4 0h


title: TM5614_Rep2


title: C4 cns_lag3ko_cd45

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
The Cell Ranger analysis pipeline v3.1 was used for sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier counting and aggregation of sequencing runs
Downstream analysis such as shared nearest neighbor graph-based clustering, differential expression analysis and visualization—were performed using the R package Seurat
A filtered gene barcode matrix of all samples was integrated with Seurat. Normalization of the gene barcode matrix was done using LogNormalize method with default parameters, the FindVariableFeatures function in Seurat was used to identify top 2000 variable genes, PCA was performed using the top variable genes and tSNE and UMAP was performed on the top principal components for visualizing the cells in two dimensional space,Graph-based clustering was performed for clustering analysis in Seurat
Differential expression analysis of scRNAseq data was performed using wilcox rank sum test in Seurat (FindMarkers function) to identify gene markers for a cluster/group. A gene was considered significant with adjusted P<0.05
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Filtered gene-barcode matrices containing only cellular barcodes

source_name: CD45 cells

growth_protocol: EAE was induced in aged and sex matched control (Lag3WT) or LAG3 deficient (Lag3Flox) mice groups (5 mice per group). At the peak of disease, mice with matching disease scores in each group were sacrificed and CNS cells isolated

extract_protocol:
Single cell suspensions were resuspended in RPMI plus 2% FBS at a concentration of 1x106 cells/mL and barcoded with a 10x Chromium Controller (10x Genomics) according to the manufacturer’s instructions. For each sample, we loaded 8.7µl with goal recovery of 5000 cells.
RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell 3′ v2 reagent kit (10x Genomics) according to the manufacturer’s instructions. Libraries were quantified and assessed for quality by Tape Station. Sequencing was performed with Illumina NextSeq according to the manufacturer’s instructions (Illumina).

treatment_protocol: CD45+ or CD4+ lymphocytes were enriched by positive bead selection (Miltenyi Biotec).

tag: background strain

tag: treatment

value: MOG35-55 peptide

tag: genotype/variation


title: C2 cns_wt_cd45


title: TM5614_Rep1

tag: strain


title: NUC treated HBV LDB_53

description: nothing special

value: Pt5 0h


title: M12_3I-F4

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina iScan Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Microenvironment

label_protocol: 300 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: 25,000 B16 cells, obtained from in vitro culture, were inoculated subcutaneously in the right flank and harvested when tumors reached 100-400 mm3 in size. Tumors from 3 mice per replicated were disaggregated by enzyme digestion, pooled, and sorted by flow cytometry on the basis of tdTomato. fluorescence.

extract_protocol: Total RNA was isolated from harvested cells with RNA mini isolation kits (Qiagen) with subsequent RNA quality assessment using an Agilent 2100 Bioanalyzer.

treatment_protocol: 3 injections of checkpoint inhibitors (CI) were given along with Fvax, consisting of B16 cells expressing Flt3 ligand (http://www.pnas.org/content/107/9/4275). F0- and F4-inoculated mice received the same treatment.

value: Acquired resistance to prior CI therapy; under CI treatment

tag: cell type

value: TdTomato-negative cells

tag: replicate

value: F4 cells, replicate D


title: M10_3I-F4

value: F4 cells, replicate B


title: M9_3I-F4

value: F4 cells, replicate A


title: M11_3I-F4

value: F4 cells, replicate C


title: NUC treated HBV LDB_52

description: nothing special

value: chronic HBV

value: HBeAg-

value: Pt5 6h


title: C1 cns_wt_cd45


title: NUC treated HBV LDB_54

description: nothing special

value: long term NUC

value: Pt4 6h

value: without NK cell response


title: Chow_Rep5

source_name: Male WT ad lib fed liver mRNA

tag: tissue

value: liver

value: 21 Weeks

value: male


title: 9 cns_lag3ko_cd4

source_name: CD4 T cells

value: MOG35-55 peptide


title: NUC treated HBV LDB_51

description: nothing special

value: Pt2 0h


title: M7_F0B2

value: No prior or current treatment with checkpoint inhibitors (CI)

value: F0 cells, replicate B2


title: Chow_Rep4


title: Chow_Rep3


title: M8_F0B3

value: TdTomato-negative cells

value: F0 cells, replicate B3


title: 8 cns_lag3ko_cd4


title: 7 cns_wt_cd4


title: Chow_Rep2


title: NUC treated HBV LDB_49

description: nothing special

value: Pt12 0h


title: NUC treated HBV LDB_48

description: nothing special

value: Pt12 6h


title: Chow_Rep1


title: M5_3I-F4

source_name: Tumor

value: Acquired resistance to prior CI therapy; under CI treatment

value: TdTomato-positive cells

value: F4 cells, replicate C


title: M6_3I-F4

value: F4 cells, replicate D


title: 56 cns_wt_cd4


title: NUC treated HBV LDB_47

description: nothing special

value: chronic HBV

value: HBeAg+

value: long term NUC

value: Pt6 0h

value: with NK cell response


title: M4_3I-F4

value: F4 cells, replicate B


title: scRNA_Eomes_null_D5

data_processing:
Sequencing data was demultiplexed in the binary base call (BCL) format, FASTQ files were aligned to the mm10 genome using 10X Genomics Cell Ranger software (version 2.0.0) and unique molecular identifier (UMI) counts were determined.
The Seurat v3 software package(Butler et al., 2018; Stuart et al., 2019) was used in R Studio to perform scRNA-Seq analysis.
Pre-processing was performed and cells with > 2000 RNA features and < 8 % mitochondrial RNA were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: [.tsv] barcode and feature files [.mtx] matrix files

source_name: Day 5 Flk-1hi/PdgfRa- EB cells

growth_protocol: WT (CCE) and Eomes-null (CCE, clone 6A6) ESC lines were maintained in feeder free culture conditions in serum + LIF as previously described(Costello et al., 2011). 48-72 hrs prior to induction of hematopoietic differentiation cells were washed with PBS and cultured in serum free ES media containing 50% Neurobasal Media (Gibco, Cat # 21103049), 50% DMEM/F12 (Gibco, Cat # 11320033), supplemented with 0.5X of both N2 (Gibco, Cat#17502048) and B27 (Gibco, Cat# 17504044), 1%Pen/Strep, 1% glutamine, 0.05% BSA (Gibco, Cat# 15260037), 1 uM PD0325091, 3 uM CHIR99021 and 1000 U/ml LIF. At D0 cells were dissociated using Trypsin-LE (Gibco) and seeded at a density of 1×10^5 cells ml in serum-free differentiation (SF-D) media(Nostro et al., 2008) and cultured on an orbital shaker at 70 rpm for ~18 hrs in the absence of growth factors to form EBs. At D2, EBs were split 1:3 in SF-D media containing recombinant human (rh) VEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 48 hr. At D4, EBs were split 1:2 in SF-D media containing rhVEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 24 hr.

extract_protocol:
Processing of samples was performed according to the 10x protocol using the Chromium Single Cell 3’ library & Gel Bead Kit v3 (10x Genomics).
Barcoded cell cDNAs were pooled and converted to sequence ready libraries. Multiplexed libraries were then sequenced on Illumina Nextseq using a high output 150bp Nextseq V2.5 kit.

value: hematovascular mesoderm

tag: genotype

value: Eomes-null


title: M3_3I-F4

value: F4 cells, replicate A


title: ZT18B

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description:
ZT18B
10x

data_processing:
sample demultiplexing was done by cellranger mkfastq sample specific reads in three fastq files (read 1 (R1) read 2 (R2) and index1 (I1))
Pooled data of scRNAseq were demultiplexed using cellranger count
Genome_build: refdata-cellranger-hg19-and-mm10-1.2.0
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Liver-Hepatocytes-single-cells

growth_protocol: C57bl6 male mice were fed regular chow ad libitum

extract_protocol:
Primary mouse hepatocytes were isolated from adult mice as described previously by collagenase perfusion and percoll gradient purification
library was constructed by the 10x chromium single cell 3' kit v2

treatment_protocol: mouse were anesthetize with an intraperitoneal injection of 100µl of 50mg/kg ketamine-HCl and 5 mg/kg Xylszine-Hcl in a PBS solution

value: post natal three months

tag: 10x genomics barcode


title: NUC treated HBV LDB_46

description: nothing special

value: Pt6 6h


title: ZT18A

description:
ZT18A
10x


title: ZT12C

description:
ZT12C
10x


title: NUC treated HBV LDB_45

description: nothing special

value: HBeAg-

value: Pt10 0h


title: M2_F0B3

value: No prior or current treatment with checkpoint inhibitors (CI)

value: F0 cells, replicate B3


title: NUC treated HBV LDB_50

description: nothing special

value: Pt2 6h

value: without NK cell response


title: scRNA_WT_D5

value: wildtype


title: ZT12B

description:
ZT12B
10x


title: scRNA_WT_D4

source_name: Day 4 Flk-1hi/PdgfRa- EB cells


title: NUC treated HBV LDB_43

description: nothing special

value: chronic HBV

value: Pt9 0h


title: ZT12A

description:
ZT12A
10x


title: Wildtype Sample 1561

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

description:
Exposed to 4-NQO
ReverseStrandedCounts-withNames-proteinCoding.txt

data_processing:
RNASik Pipeline 1.4.7
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Genome_build: GRCm38
Supplementary_files_format_and_content: Count Table from featureCounts quantification

source_name: Oesophageal Tissue

extract_protocol:
Qiagen Rneasy Micro Kit
TruSeq stranded mRNA as per manufacturer's protocol

treatment_protocol: Mice were treated with 4-NQO to induce tumour formation

value: Oesophageal Tissue

tag: grhl3 status

value: Wildtype


title: NUC treated HBV LDB_42

description: nothing special

value: long term NUC

value: Pt9 6h

value: with NK cell response


title: NUC treated HBV LDB_41

description: nothing special

value: Pt13 0h


title: ZT6B

description:
ZT6B
10x

tag: age

value: post natal three months


title: Wildtype Sample 1555


title: ZT6A

description:
ZT6A
10x


title: Wildtype Sample 1528


title: scRNA_Eomes_null_D4

value: hematovascular mesoderm

value: Eomes-null


title: ZT0C

description:
ZT0C
10x


title: NUC treated HBV LDB_40

description: nothing special

value: HBeAg-

value: Pt13 6h


title: NUC treated HBV LDB_44

description: nothing special

value: Pt10 6h


title: Wildtype Sample 1048


title: Wildtype Sample 1028


title: ZT0B

description:
ZT0B
10x


title: NUC treated HBV LDB_39

description: nothing special

value: Pt8 0h


title: NUC treated HBV LDB_38

description: nothing special

value: Pt8 6h

value: without NK cell response


title: GRHL3-KO-Sample 1043

source_name: Oesophageal Tumour Tissue

value: Oesophageal Tumour Tissue

value: Knock Out


title: NUC treated HBV LDB_37

description: nothing special

value: chronic HBV

value: Pt11 0h


title: NUC treated HBV LDB_36

description: nothing special

value: long term NUC

value: Pt11 6h


title: GRHL3-KO-Sample 1036


title: GRHL3-KO-Sample 1035


title: M1_F0B2

value: No prior or current treatment with checkpoint inhibitors (CI)

value: TdTomato-positive cells

value: F0 cells, replicate B2


title: GRHL3-KO-Sample 1027


title: ZT0A

description:
ZT0A
10x sequencing protocol

value: post natal three months


title: NUC treated HBV LDB_35

description: nothing special

value: Pt3 0h

value: with NK cell response


title: GRHL3-KO-Sample 1026


title: TAC(7Weeks)3

status: Public on Oct 31 2020

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

institute: University of Helsinki and Wihuri Research Institute

description: Cardiac endothelial cell RNA

data_processing:
The following software packages embedded in the Chipster analysis platform (v3.12.2; https://chipster.csc.fi) were used for analysis
The Fastq files generated in each lane of the flow cell for each sample were merged, the quality of the reads were anaysed using fastqc.
Trimmomatic tool was used to trim Illumina single end reads with the following parameters
HISAT2 package was employed to align the reads to mouse genome GRCm38.90
HTSeq count tool to quantify the aligned reads per gene
Genome_build: GRCm38.90
Supplementary_files_format_and_content: tab-delimited text files include count aligned reads per genes performed with HTSeq tool for each sample

source_name: Heart

growth_protocol: Not applicable

extract_protocol:
FACS sorted cardiac endothelial cells were homogenized in QIAshredder (#79654, Qiagen) and the RNA was purified using RNeasy Plus Micro Kit (#74034, Qiagen) according to the manufacturer’s instruction
cDNA library was synthesized using SMARTer Stranded Total RNA-Seq Kit V2 – Pico Input Mammalian (Takara Bio, USA) kit according to the manufacturer’s instructions. The library quality was determined using bioanalyzer, and sequenced using illumina NextSeq 550 System with the following specifications: 1 X 75bp, 50M single end reads were sequenced using NextSeq 500/550 High-Output v2.5 kit.

treatment_protocol: Not applicable

tag: gender

value: Male

value: Trans-aortic contriction (27G needle; 7 weeks)


title: TAC(2Weeks)4

value: Trans-aortic contriction (27G needle; 2 weeks)

value: Cardiac endothelial cell


title: NUC treated HBV LDB_32

description: nothing special

tag: diseases

value: HBeAg-

value: Pt7 6h


title: YOUNG4

value: Young (2 months old)


title: TAC(7Weeks)4


title: SHAM4

value: Sham Operated


title: TAC(7Weeks)2

description: Cardiac endothelial cell RNA


title: TAC(2Weeks)3

description: Cardiac endothelial cell RNA


title: TAC(2Weeks)2

description: Cardiac endothelial cell RNA


title: NUC treated HBV LDB_34

description: nothing special

value: chronic HBV

tag: hbeag (+/-)

value: Pt3 6h


title: NUC treated HBV LDB_33

description: nothing special

tag: therapy that the patient received

value: long term NUC

value: Pt7 0h


title: EGI-1 CM272, biological rep1

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

hyb_protocol: Following fragmentation, 2.3 mg of ss-cDNA were included in the hybridization mix, using the GeneChip® Hybridization, Wash and Stain kit (Affymetrix ThermoFisher Scientific, P/N 900720) according to recommendations of manufacturer. The resulting preparations were hybridized to Human Clariom S Arrays ( Affymetrix ThermoFisher Scientific, P/N 902926).

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Affymetrix Expression Command Console (Affymetrix ThermoFisher Scientific). Data analysis were then performed with RMA (Robust Multiarray Average) allowing that raw intensity values were background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probeset. Partek Genomics Suite and Partek Pathways softwares (Partek Incorporated, St. Louis, USA) were used for the statistical analysis and an ANOVA test was applied with a restrictive threshold at p-value ≤ 0.05.

label: biotin

source_name: EGI-1 CM272, biological rep1

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the GeneChip WT Plus Reagent kit (Affymetrix ThermoFisher Scientific, P/N 902280).

growth_protocol: EGI-1 cells were seeded in 6-well plates using DMEM supplemented with 10% FBS and antibiotics, all from Gibco Thermo-Fisher (Waltham, MA).

extract_protocol: RNA extraction was realized using Maxwell RSC SimplyRNA Tissue Kit (AS1340) according to the instructions from manufacturer and amount and quality of the RNA checked by Bioanalyzer (Agilent Technologies).

treatment_protocol: EGI-1 cells were treated with CM272 (200nM) or vehicle (0.01% DMSO) for 48 hours.

value: CM272 (200nM) for 48 hours


title: EGI-1 vehicle, biological rep2

source_name: EGI-1 vehicle, biological rep2

value: vehicle (0.01% DMSO) for 48 hours


title: TAC(2Weeks)1

description: Cardiac endothelial cell RNA


title: EGI-1 CM272, biological rep2

source_name: EGI-1 CM272, biological rep2


title: SHAM2

description: Cardiac endothelial cell RNA


title: SHAM3

description: Cardiac endothelial cell RNA


title: SHAM1

description: Cardiac endothelial cell RNA


title: TAC(7Weeks)1

description: Cardiac endothelial cell RNA


title: HFD3

description: Cardiac endothelial cell RNA

value: High fat diet feeding


title: CHOW3

description: Cardiac endothelial cell RNA

value: Standard chow diet


title: EGI-1 vehicle, biological rep1

source_name: EGI-1 vehicle, biological rep1


title: AGED3

description: Cardiac endothelial cell RNA

value: Aged (18 months old)


title: HFD2

description: Cardiac endothelial cell RNA

value: Male


title: HFD1

description: Cardiac endothelial cell RNA


title: CHOW2

description: Cardiac endothelial cell RNA


title: CHOW1

description: Cardiac endothelial cell RNA


title: AGED1

description: Cardiac endothelial cell RNA


title: Urinary Bladder Cancer Tissue #PG139

type: genomic

city: KOLKATA

first: CHINMAY

middle: KUMAR

last: PANDA

state: WEST BENGAL

address: 37, SP MUKHERJEE ROAD, KOLKATA

department: ONCOGENE REGULATION UNIT

country: India

institute: CHITTARANJAN NATIONAL CANCER INSTITUTE, INDIA

hyb_protocol: Equal amount of labeled Test & Control DNA sample was added into a fresh tube containing 25 µl of Human Cot-1 DNA (1mg/ml),  26ul of Agilent 10X blocking agent and 130ul Agilent 2X hybridization buffer. The total hybridization volume was 45ul. The above hybridization mix was denatured at 95°C for 3 minutes and incubated the microfuge tubes at 37°C for 30 minutes.  The samples were hybridized at 65°C for 40 hours in the hybridization chamber. After hybridization, the slides were washed using aCGH Wash Buffer1 (Agilent Technologies, Part Number 5188-5221) at room temperature for 5 minutes and aCGH Wash Buffer 2 (Agilent Technologies, Part Number 5188-5222) at 37°C for 1 minutes. The slides were then washed with Acetonitrile for 10 seconds.

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images were quantified using Agilent Feature Extraction Software. Feature extracted raw data was normalized using Lowes normalization and analyzed Agilent CytoGenomics 2.9 Software.

source_name: Urinary Bladder Carcinoma tissue

label_protocol: Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that,  the  control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.

extract_protocol: DNA isolation from peripheral blood lymphocytes (N) and cancer tissues (T),   using standrad Phenol/ Chloroform method. Tumor tissue were microdissected   for tumor cell enrichment before DNA extraction.

treatment_protocol: tumor tissues vs normal peripheral blood lymphocytes

tag: Stage

value: Stage T3

tag: grade

value: Grade low

tag: smoking history

value: YES

tag: alcohol ingestion

tag: drinking water source

value: surface

value: M

tag: arsenic in tumor tissue

tag: occupation of the subject

value: farmer

source_name: Peripheral Blood lymphocytes

tag: reference

value: matched normal blood


title: YOUNG3

description: Cardiac endothelial cell RNA

tag: strain

tag: treatment

value: Young (2 months old)


title: Urinary Bladder Cancer Tissue #S54

value: Stage T1

value: Grade High

value: NO

value: underground

value: F

value: housewife


title: YOUNG2

description: Cardiac endothelial cell RNA


title: YOUNG1

description: Cardiac endothelial cell RNA


title: EXE3

description: Cardiac endothelial cell RNA

value: Exercise training


title: EXE2

description: Cardiac endothelial cell RNA


title: Urinary Bladder Cancer Tissue #S57

value: Stage T2

value: Grade Low

value: gov employee


title: EXE1

description: Cardiac endothelial cell RNA

value: Male


title: Urinary Bladder Cancer Tissue #S59

value: export


title: SED1

description: Cardiac endothelial cell RNA

value: Sedentary


title: SED3

description: Cardiac endothelial cell RNA


title: YFP+_W3_scRNA-seq

first: Ben

middle: Z.

last: Stanger

address: 421 Curie Boulevard

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Library strategy: scRNA-Seq
10X Genomics CellRanger pipeline
Genome_build: mm10 with the added YFP sequence
Supplementary_files_format_and_content: UMI counts in h5 file

source_name: RosaYFP mice (injected with AAV8-TBG-Cre to lineage label hepatocytes) treated with DDC

growth_protocol: Male RosaYFP/YFP mice (Srinivas et al., 2001) were injected retro-orbitally at four weeks of age with 2.5x10^11 viral particles of AAV8-TBG-Cre virus obtained from the Penn Vector Core. One week following Cre injection, mice were treated with 0.1% DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine, Sigma-Aldrich) chow diet (Envigo) for 2-6 weeks.

extract_protocol:
Livers of control and DDC-treated mice were perfused with first 1X HBSS, followed by HBSS+ 1 mM EGTA, and HBSS + 5 mM CaCl2 with liberase. Following perfusion, livers were mechanically dissociated and incubated for 15 minutes in HBSS with CaCl2 and liberase at 37 degrees. Digests were filtered and cells isolated by FACS. After removing CD31, CD45, and CD11b cells, living cells were then sorted from the remaining cells (Bulk samples) or further sorted for YFP+ cells (YFP samples)
Following isolation of sorted cells, single cell libraries were generated by the Center for Applied Genomics at the Children’s Hospital of Philadelphia on a 10x Genomics chromium platform

treatment_protocol: AAV8-TBG-Cre labeled RosaYFP mice were treated with 0.1% DDC chow for 2, 3, 4, and 6 weeks to induce reprogramming. Following treatment, mice were sacrificed and cell isolated from the liver then sorted by FACS.

value: RosaYFP/YFP

tag: Sex

value: male

tag: timepoint

value: Week 3

tag: tissue

value: Liver

tag: cell population

value: YFP+ cells


title: Bulk_W4_scRNA-seq

value: Week 4

value: bulk (including YFP+ and YFP- cells)


title: Bulk_W2_scRNA-seq

value: Week 2


title: YFP+_W2_scRNA-seq


title: AGED2

description: Cardiac endothelial cell RNA

tag: gender

value: Aged (18 months old)


title: Urinary Bladder Cancer Tissue #S51

tag: age

value: Stage T1

value: Grade High

value: NO

value: underground

value: M

value: fish business

value: matched normal blood


title: YFP+_W6_scRNA-seq

value: Week 6


title: Urinary Bladder Cancer Tissue #PG134

value: YES

value: surface

value: PRIEST


title: YFP+_W4_scRNA-seq

value: RosaYFP/YFP

value: male

value: Liver


title: Urinary Bladder Cancer Tissue #PG71

value: Stage Ta

value: Grade high

value: F

value: HOUSEWIFE


title: Bulk_W3_scRNA-seq

value: Week 3

value: bulk (including YFP+ and YFP- cells)


title: Urinary Bladder Cancer Tissue #S53

value: Stage T2

value: Grade High

value: underground

value: gov employee


title: Bulk_W6_scRNA-seq

value: Week 6


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic White Rep 1

city: Pozuelo de Alarcon

first: Emilia

last: López Solanilla

state: Madrid

address: Parque Científico y Tecnológico UPM, Campus de Montegancedo, Ctra. M-40, km 38

institute: CBGP-Universidad Politécnica de Madrid (UPM)

description: Gene expression after 10 min white light treatment in epiphytic populations over tomato leaves

hyb_protocol: 600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent and Nuclease free water in a 25 μl reaction. Then, we added 25 μl from 2x GExHybridization buffer and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65 ºC for 17 h and then washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37 ºC (1 min).

scan_protocol: Images from Cy3 channel were equilibrated and captured with a High resolution Scanner (Agilent) and spots quantified using Feature Extraction software (Agilent).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively. log-ratio values were scaled using as scale estimator the median-absolute-value. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamani and Hochberg, 1995. The expected false discovery rate (FDR) was controlled to be less than 1 %.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Wild type epi 10 min under White light Rep 1

label_protocol: cDNA was labeled with Cy3 by using the SuperScript III indirect cDNA labeling system (invitrogen) as described in the instruction manual (One-Color Microarray Based Gene Expression Analysis Manual).

growth_protocol: Transcriptomic analyses were done with Pseudomonas syringae pv. tomato DC3000 epiphytic populations over tomato leaves. Total RNA was extracted from epiphytic cells collected after a 10 min treatment with etither white, blue or red light performed on the leaves suface.

extract_protocol: Total RNA from four biological replicates from each treatment was extracted with TRI Reagent (Ambion) as recommended by the manufacturer. The purification was accomplished by using the High Pure RNA Isolation Kit from Roche, following the manufacturer’s recommendations.

tag: pathovar

value: tomato DC3000

tag: population

value: Epiphytic


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic White Rep 2

source_name: Wild type epi 10 min under White light Rep 2


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Red Rep 4

description: Gene expression after 10 min red light treatment in epiphytic populations over tomato leaves

source_name: Wild type epi 10 min under Red light Rep 4


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Red Rep 3

source_name: Wild type epi 10 min under Red light Rep 3


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Red Rep 2

source_name: Wild type epi 10 min under Red light Rep 2


title: Urinary Bladder Cancer Tissue #S16

tag: Stage

tag: grade

value: YES

value: M

value: farmer

value: matched normal blood


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Blue Rep 1

description: Gene expression after 10 min blue light treatment in epiphytic populations over tomato leaves

source_name: Wild type epi 10 min under Blue light Rep 1


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic White Rep 3

source_name: Wild type epi 10 min under White light Rep 3


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Blue Rep 2

source_name: Wild type epi 10 min under Blue light Rep 2


title: Asthma.BEC9.RV.rep3.raw [BEC9-6_ATAC-seq]

first: Carole

last: Ober

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

data_processing:
raw fastq combined across re-sequencing files and mapped via bowtie2
Peaks called using MACS2; a Peak library (union of peaks across all samples) was generated and read counts were pulled for each peak from each sample
Total Read counts per peak are annotated in processed data
Genome_build: GRCh37(hg19)
Supplementary_files_format_and_content: standard bed file format

source_name: Primary Human Bronchial Epithelial Cells from Gift of Hope Regional Organ Bank of Illinois

growth_protocol: BECs from the 18 donors were cultured on collagen coated flasks in F-media (Everman et al., 2018) until 80-90% confluency before being transferred to 12-well collagen coated transwell membranes. Cell culture experiments were conducted in basal cells, a subset of BECs that express ICAM1, the main receptor for RV-A.

extract_protocol:
At harvest, cells were disassociated from the culture surface using Accutase (Sigma-Aldrich) and quantified using a hemocytometer and trypan blue to differentiate live and dead cells. All cultures had greater than 90% viability at the time of the harvest. After quantification, 5,000 cells from each culture well were immediately processed for ATAC-seq and the remaining cells
For each sample, 5,000 cells were processed immediately after collection using a standard ATAC-seq protocol (Buenrostro et al., 2013) with the following modifications: the transposition reaction was incubated on a heated shaker at 37°C for 30 minutes at 1,000 rpm and the Qiagen MinElute PCR Purification kit was used to clean up the transposition reaction. Samples were indexed, pooled, and sequenced on the Illumina Hi-Seq 4000 with 50bp single-end reads. Sample pools were re-sequenced until each sample had a minimum of 50 million mapped reads. Of the 108 samples sequenced, two samples from different donors failed QC. Two RV-treated samples from asthmatics were excluded (ID numbers: 7, 4); one was an outlier in several PCs including in PC1 and one did not have sufficient DNA concentrations for library prep (undetectable levels by bioanalyzer). Sequencing data that passed QC was mapped onto hg19 using bowtie2 version 2.3.2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). ATAC-seq peak calls were determined using MACS2 (Liu, 2014). Peak calls from all samples were pooled across all samples and overlapping or duplicate peaks were consolidated into a single peak that ranged from the 3’ most base to the 5’ most base in all overlapping peaks to create a peak-library or collection of all of the regions of accessible chromatin (n = 142,120 regions on autosomes) (raw data available upon request).  Next, the number of reads aligned to each peak were determined for each sample and normalized to counts per million peak-library mapped reads. PCA was used to identify potential confounding of biological and technical covariates; number of additional PCR cycles and cell culture plate location were significant and adjusted for in the model. Each sample was part of a biological triplicate (except the two samples in which one replicate each did not meet QC criteria, discussed above). Replicate samples were adjusted in analyses using duplicateCorrelation as implemented in Limma. Peaks that were associated with asthma or RV infection in cases or controls were identified using Limma with a threshold of significance set at an FDR adjusted p-value of 0.05, using the method of Benjamini and Hochberg(Hochberg and Benjamini, 1990)

treatment_protocol: After reaching confluency (3-5 days), cells were treated with either 10.2 x 10^6 plaque forming units of RV-A16 in 5.1 ul of PBS or 5.1 ul of PBS (vehicle control). The RV was propagated and purified at the University of Wisconsin, Madison as previously described (Hasegawa et al., 2019)

tag: subject status

value: Asthma

tag: cell type

value: Primary Human Bronchial Epithelial Cells (BEC)

tag: pcr cycles

tag: cell culture well location

tag: molecule subtype

value: Crosslinkined DNA-Protein


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Blue Rep 3

source_name: Wild type epi 10 min under Blue light Rep 3


title: SED2

description: Cardiac endothelial cell RNA

source_name: Heart

tag: strain

value: Male

value: Sedentary


title: Asthma.BEC9.RV.rep1.raw [BEC9-4_ATAC-seq]

tag: treatment

value: F


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Blue Rep 4

source_name: Wild type epi 10 min under Blue light Rep 4


title: Asthma.BEC9.RV.rep2.raw [BEC9-5_ATAC-seq]


title: Asthma.BEC8.RV.rep3.raw [BEC8-6_ATAC-seq]


title: Asthma.BEC9.Veh.rep3.raw [BEC9-3_ATAC-seq]

value: Vehicle-PBS


title: Asthma.BEC9.Veh.rep1.raw [BEC9-1_ATAC-seq]


title: Asthma.BEC9.Veh.rep2.raw [BEC9-2_ATAC-seq]


title: Asthma.BEC8.RV.rep2.raw [BEC8-5_ATAC-seq]


title: Asthma.BEC8.RV.rep1.raw [BEC8-4_ATAC-seq]


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Dark Rep1

description: Gene expression after 10 min darkness treatment in epiphytic populations over tomato leaves

source_name: Wild type epi 10 min Dark Rep 1


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Dark Rep2

source_name: Wild type epi 10 min Dark Rep 2


title: SW620_DMSO

city: Kyoto

first: Madhu

last: Malinee

state: Kyoto

address: Kitashirakawa-Oiwakecho,

department: Graduate School of Science

institute: Kyoto University

description: Gene expression after hr in SW620 treated with DMSO

hyb_protocol: 0.6  μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume   of 25  μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following   the manufacturer’s instructions. On completion of the fragmentation reaction, 25  μl of 2x   Agilent  hybridization  buffer  was  added  to  the  fragmentation  mixture  and  hybridized  to   SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at   65°C  in  a  rotating  Agilent  hybridization  oven.    After  hybridization,  microarrays  were   washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and   1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides  were  scanned  immediately  after  washing  on  the  Agilent  SureScan  Microarray   Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6   mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The  scanned  images  were  analyzed  with  Feature  Extraction  Software  (Agilent   Technologies)  using  default  parameters  to  obtain  background  subtracted  and  spatially   detrended Processed Signal intensities.      Processed signal intensities were normalized by the global scaling method.   A trimmed mean probe intensity was determined by removing 2% of the lower and the   higher end of the probe intensities in order to calculate the scaling factor. Normalized signal   intensities were then calculated from the target intensity on each array using the scaling   factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: SW620, DMSO, 48 hours

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1  μg Total RNA using the Low Input   Quick  Amp  Labeling  Kit  (Agilent  Technologies)  according  to  the  manufacturer's   instructions, followed by RNeasy column purification (QIAGEN).    Dye incorporation and   cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: SW620 cell medium in DMEM medium, fetal bovine serum (Sigma FBS) to a final concentration of 10%, at 37°C, 5% CO2

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations.

treatment_protocol: After 24 hs from plating, the cells were treated with DMSO or 2 μM SOX2i and RNA was extracted after 48 hours.

tag: cell line

value: DMSO


title: Asthma.BEC7.RV.rep3.raw [BEC7-6_ATAC-seq]


title: Asthma.BEC8.Veh.rep3.raw [BEC8-3_ATAC-seq]


title: Asthma.BEC8.Veh.rep2.raw [BEC8-2_ATAC-seq]


title: Asthma.BEC7.Veh.rep3.raw [BEC7-3_ATAC-seq]


title: Asthma.BEC8.Veh.rep1.raw [BEC8-1_ATAC-seq]


title: Asthma.BEC7.RV.rep1.raw [BEC7-4_ATAC-seq]


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Dark Rep3

source_name: Wild type epi 10 min Dark Rep 3


title: Asthma.BEC7.Veh.rep2.raw [BEC7-2_ATAC-seq]


title: Asthma.BEC6.RV.rep2.raw [BEC6-5_ATAC-seq]


title: Asthma.BEC6.RV.rep1.raw [BEC6-4_ATAC-seq]


title: Asthma.BEC6.RV.rep3.raw [BEC6-6_ATAC-seq]


title: Asthma.BEC6.Veh.rep3.raw [BEC6-3_ATAC-seq]


title: Asthma.BEC7.Veh.rep1.raw [BEC7-1_ATAC-seq]


title: Asthma.BEC6.Veh.rep2.raw [BEC6-2_ATAC-seq]


title: Urinary Bladder Cancer Tissue #S2

source_name: Urinary Bladder Carcinoma tissue

value: Stage T3

value: Grade Low

tag: smoking history

tag: alcohol ingestion

tag: drinking water source

value: surface

tag: arsenic in tumor tissue

tag: occupation of the subject

value: business

source_name: Peripheral Blood lymphocytes

tag: reference


title: Asthma.BEC5.RV.rep2.raw [BEC5-5_ATAC-seq]

tag: age

tag: gender


title: Asthma.BEC5.Veh.rep3.raw [BEC5-3_ATAC-seq]


title: Asthma.BEC6.Veh.rep1.raw [BEC6-1_ATAC-seq]


title: Asthma.BEC5.RV.rep1.raw [BEC5-4_ATAC-seq]


title: SW620_SOX2i

description: Gene expression after hr in SW620 treated with SOX2i

source_name: SW620, SOX2i, 48 hours


title: Asthma.BEC4.RV.rep1.raw [BEC4-4_ATAC-seq]


title: Asthma.BEC4.RV.rep3.raw [BEC4-6_ATAC-seq]


title: Asthma.BEC4.Veh.rep3.raw [BEC4-3_ATAC-seq]


title: Asthma.BEC5.Veh.rep1.raw [BEC5-1_ATAC-seq]


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic White Rep 4

source_name: Wild type epi 10 min under White light Rep 4

tag: pathovar

value: tomato DC3000

tag: population

value: Epiphytic


title: Asthma.BEC3.Veh.rep2.raw [BEC3-2_ATAC-seq]

tag: subject status

tag: cell type


title: Asthma.BEC4.Veh.rep1.raw [BEC4-1_ATAC-seq]

tag: pcr cycles

tag: cell culture well location


title: Asthma.BEC3.RV.rep2.raw [BEC3-5_ATAC-seq]

tag: molecule subtype


title: Asthma.BEC3.RV.rep3.raw [BEC3-6_ATAC-seq]

tag: treatment


title: Asthma.BEC5.RV.rep3.raw [BEC5-6_ATAC-seq]


title: Asthma.BEC3.RV.rep1.raw [BEC3-4_ATAC-seq]


title: Asthma.BEC3.Veh.rep1.raw [BEC3-1_ATAC-seq]


title: Asthma.BEC2.RV.rep2.raw [BEC2-5_ATAC-seq]

value: M


title: Asthma.BEC2.RV.rep3.raw [BEC2-6_ATAC-seq]


title: Asthma.BEC2.Veh.rep2.raw [BEC2-2_ATAC-seq]


title: Non_Asthma.BEC18.RV.rep3.raw [BEC18-6_ATAC-seq]


title: Asthma.BEC2.RV.rep1.raw [BEC2-4_ATAC-seq]


title: Non_Asthma.BEC18.RV.rep2.raw [BEC18-5_ATAC-seq]


title: Asthma.BEC5.Veh.rep2.raw [BEC5-2_ATAC-seq]


title: Asthma.BEC2.Veh.rep1.raw [BEC2-1_ATAC-seq]


title: Non_Asthma.BEC18.RV.rep1.raw [BEC18-4_ATAC-seq]


title: Asthma.BEC4.Veh.rep2.raw [BEC4-2_ATAC-seq]


title: Non_Asthma.BEC18.Veh.rep2.raw [BEC18-2_ATAC-seq]


title: Non_Asthma.BEC18.Veh.rep1.raw [BEC18-1_ATAC-seq]


title: Asthma.BEC3.Veh.rep3.raw [BEC3-3_ATAC-seq]


title: Non_Asthma.BEC17.RV.rep3.raw [BEC17-6_ATAC-seq]


title: Asthma.BEC2.Veh.rep3.raw [BEC2-3_ATAC-seq]


title: Non_Asthma.BEC17.RV.rep2.raw [BEC17-5_ATAC-seq]


title: Non_Asthma.BEC17.RV.rep1.raw [BEC17-4_ATAC-seq]


title: Non_Asthma.BEC18.Veh.rep3.raw [BEC18-3_ATAC-seq]


title: Non_Asthma.BEC17.Veh.rep3.raw [BEC17-3_ATAC-seq]


title: Non_Asthma.BEC17.Veh.rep2.raw [BEC17-2_ATAC-seq]


title: Non_Asthma.BEC17.Veh.rep1.raw [BEC17-1_ATAC-seq]


title: uninfected_72hpi_1

city: Bonn

first: Denna

last: Tabari

address: Kurt-Georg-Kiesinger Allee 3

country: Germany

institute: Federal Institute for Drugs and Medical Devices

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting for 8x60k array slides. Dye channel was set to Green.

data_processing: The scanned images were analyzed with GeneSpring Software (v.14.1.9, Agilent). Signal quality was maintained by filtering probes with compromised flags out. Signal intensities below 50 were removed from the datasets. 2way ANOVA test was used as statistical analysis and p-values were adjusted for multiple test correction using Benjamini Hochberg algorithm. Differential gene expression was calculated in fold-change (FC), whereby infected vs. uninfected cells were compared at the same time points.

source_name: uninfected lt-NES® cells at timepoint 72 hpi

label_protocol: RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies) according to the kit manual. Briefly, 100 ng RNA were reversely transcribed to cDNA, from which Cy3-labeled cRNA was transcribed, purified and hybridized to the expression microarray.

growth_protocol: Lt-NES® cells were generated from the retrovirally reprogrammed iPS cell line iLB-C-31f [32]. The cells were maintained on plastic 6-well cell culture dishes coated with 1x poly-L-ornithine and 10 mg/ml laminin (Merck, Darmstadt, Germany) in Dulbecco’s modified Eagle’s/ F12 medium (DMEM-F12) (Thermo Fisher Scientific, MA, USA) supplemented with N2 Supplement (PAA Laboratories, Pasching, Austria) and containing 10 ng/mL basic fibroblast growth factor 2 (FGF2), 10 ng/mL epidermal growth factor (EGF) (both from R&D Systems, Minneapolis, MN) and 1:1000 B-27 Supplement (Thermo Fisher Scientific, MA, USA). Passaging was performed every 2-3 days by splitting at a 1:2 ratio. In short, cells were detached using incubation with 0.125% Trypsin (Thermo Fisher Scientific, MA, USA) for 5-10 min at room temperature. Trypsin was deactivated with trypsin inhibitor (Thermo Fisher Scientific, MA, USA) and the cells were spun down at 300g for 3 min. Supernatant was aspirated and the cell pellet was resuspended in maintenance medium and plated onto poly-L-ornithine/laminin pre-coated cell culture dishes.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer’s instructions.

treatment_protocol: Two ZIKV strains were used in the study: ZIKV Uganda 976  (provided by the European Virus Archive) and ZIKV PF13/251013-18 from French Polynesia (provided by Professor Musso from the Institute Louis Marladé in Tahiti). The lt-NES® cells were seeded into 6-well plates and infected with a multiplicity of infection (MOI) of 0.1 or 1 using serum free virus stocks. Serum free virus stocks were generated by infection of Vero cells with the respective virus strain in Dulbecco’s Modified Eagle’s medium (DMEM) High Glucose (BioWest, Nuaillé, France) supplemented with 10% Fetal Bovine Serum Superior (Biochrom GmbH, Berlin, Germany), 2 mM L-Glutamine (Biochrom GmbH, Berlin, Germany), 100 U/mL penicillin and 100 μg/mL streptomycin (Paul-Ehrlich-Institut facilities, Langen, Germany). On day 3 post infection, cells were washed once with phosphate-buffered saline (PBS) followed by a medium change to DMEM supplemented with 10% KnockOutTM Serum Replacement (Thermo Fisher Scientific, MA, USA). On day 7 post infection the supernatant was harvested, centrifuged for 5 min at 1000 g and stored at -80°C until infection of lt-NES® cells. Uninfected and infected lt-NES® cells were harvested at 24, 48 and 72 hours post infection.

value: uninfected

tag: tissue

value: lt-NES® cells

tag: timepoint


title: uninfected_72hpi_3


title: uninfected_48hpi_1

source_name: uninfected lt-NES® cells at timepoint 48 hpi


title: Non_Asthma.BEC16.RV.rep3.raw [BEC16-6_ATAC-seq]


title: uninfected_72hpi_2


title: Non_Asthma.BEC16.RV.rep2.raw [BEC16-5_ATAC-seq]


title: Uganda_72hpi_2

source_name: lt-NES® cells infected with ZIKV Uganda strain for 72 h

value: ZIKV Uganda infection


title: uninfected_24hpi_2

source_name: uninfected lt-NES® cells at timepoint 24 hpi


title: Non_Asthma.BEC16.RV.rep1.raw [BEC16-4_ATAC-seq]

value: Primary Human Bronchial Epithelial Cells (BEC)


title: Uganda_72hpi_1


title: uninfected_24hpi_3


title: Polynesia_72hpi_3

source_name: lt-NES® cells infected with ZIKV French Polynesia strain for 72 h

value: ZIKV French Polynesia infection


title: Non_Asthma.BEC16.Veh.rep3.raw [BEC16-3_ATAC-seq]

source_name: Primary Human Bronchial Epithelial Cells from Gift of Hope Regional Organ Bank of Illinois

value: Crosslinkined DNA-Protein


title: uninfected_48hpi_2


title: Uganda_24hpi_1

source_name: lt-NES® cells infected with ZIKV Uganda strain for 24 h


title: Uganda_48hpi_1

source_name: lt-NES® cells infected with ZIKV Uganda strain for 48 h


title: uninfected_48hpi_3


title: Uganda_72hpi_3


title: Uganda_48hpi_3


title: Uganda_24hpi_2


title: uninfected_24hpi_1


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Red Rep 1

source_name: Wild type epi 10 min under Red light Rep 1


title: Uganda_24hpi_3


title: Non_Asthma.BEC16.Veh.rep2.raw [BEC16-2_ATAC-seq]


title: Uganda_48hpi_2


title: Polynesia_72hpi_1


title: Polynesia_72hpi_2


title: Polynesia_48hpi_3

source_name: lt-NES® cells infected with ZIKV French Polynesia strain for 48 h


title: Polynesia_48hpi_1


title: Polynesia_24hpi_3

source_name: lt-NES® cells infected with ZIKV French Polynesia strain for 24 h


title: Polynesia_48hpi_2


title: Non_Asthma.BEC15.RV.rep3.raw [BEC15-6_ATAC-seq]


title: Polynesia_24hpi_2


title: Non_Asthma.BEC15.Veh.rep2.raw [BEC15-2_ATAC-seq]


title: Non_Asthma.BEC15.Veh.rep1.raw [BEC15-1_ATAC-seq]


title: Non_Asthma.BEC14.RV.rep3.raw [BEC14-6_ATAC-seq]


title: Non_Asthma.BEC15.Veh.rep3.raw [BEC15-3_ATAC-seq]


title: Non_Asthma.BEC14.RV.rep2.raw [BEC14-5_ATAC-seq]


title: Non_Asthma.BEC15.RV.rep1.raw [BEC15-4_ATAC-seq]


title: Non_Asthma.BEC15.RV.rep2.raw [BEC15-5_ATAC-seq]


title: Non_Asthma.BEC13.RV.rep3.raw [BEC13-6_ATAC-seq]


title: Non_Asthma.BEC14.Veh.rep1.raw [BEC14-1_ATAC-seq]


title: Non_Asthma.BEC13.RV.rep1.raw [BEC13-4_ATAC-seq]


title: Non_Asthma.BEC14.RV.rep1.raw [BEC14-4_ATAC-seq]


title: Non_Asthma.BEC14.Veh.rep3.raw [BEC14-3_ATAC-seq]


title: Non_Asthma.BEC13.RV.rep2.raw [BEC13-5_ATAC-seq]


title: Non_Asthma.BEC14.Veh.rep2.raw [BEC14-2_ATAC-seq]


title: Non_Asthma.BEC13.Veh.rep3.raw [BEC13-3_ATAC-seq]


title: Non_Asthma.BEC16.Veh.rep1.raw [BEC16-1_ATAC-seq]


title: Pseudomonas syringae pv. tomato DC3000 Wild type epiphytic Dark Rep4

source_name: Wild type epi 10 min Dark Rep 4


title: Non_Asthma.BEC13.Veh.rep2.raw [BEC13-2_ATAC-seq]


title: Polynesia_24hpi_1


title: Non_Asthma.BEC13.Veh.rep1.raw [BEC13-1_ATAC-seq]


title: ROF1_induction_sampleB_20min

city: South San Francisco

first: Rebecca

middle: Y

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Science LLC

hyb_protocol: 8x15k Microarray hybridization: Set up 60°C heat block; Prepare 10x Blocking Agent: Add 1250 µL of nuclease-free water to vial containing 10x lyophilized Gene Expression Blocking Agent (part #5188-5281); Vortex and spin down; Prepare hybridization samples; For 8x15k (8-pack) microarrays, mix the following components: 450 ng Cy3-amplified cRNA, 450 ng Cy5-amplified cRNA, 7.5 µL 10X Gene Expression Blocking Agent, bring volume to 36 µL with water, and then add 1.5 µL 25x fragmentation buffer; Incubate at 60°C for 30 minutes to fragment the RNA; Add 37.5 µL of 2x Hi-RPM Hybridization Buffer to strip tube and leave on ice; Add fragmented RNA directly to Hi-RPM Buffer to stop the reaction; Mix well by pipetting up and down (avoid bubbles and do not vortex); Put sample on ice and load onto array as soon as possible; Put clean gasket onto metal hybridization chamber; Add 45 µL of hybridization onto gasket; Place array (Agilent facing down) onto gasket and close the hybridization chamber; Incubate on rotisserie at 65°C for 17 hr

scan_protocol: Labeled RNA was hybridized to Agilent 8x15k microarrays, which were then washed, scanned, and processed using the Agilent Feature Extraction software with default settings and loess dye bias correction.

data_processing:
Extracted using Agilent Feature Extractor. Raw intensity values were floored to a value of 50.
log2 ratio (sample/reference)

organism: Saccharomyces cerevisiae

label_protocol: Crude RNA was purified using RNAClean Ampure XP beads. 200 ng of cleaned RNA was used as an input to generate dye-labeled cRNA using the Agilent Quick-Amp Labeling Kit. 1) Prepare labeling reaction: Get clean PCR strip tubes ready; Dilute RNA to 57.2 ng/µL; Add 3.5 µl of RNA (200 ng total) to PCR tube; Make T7 Primer Mix (0.8 µL T7, 1 µL water);Add 1.8 µl of T7 Primer Mix to each tube. Each tube now has 5.3 µl; Denature the template and primer by incubating at 65°C for 10 min; Put reactions on ice for 5 min; 2) cDNA synthesis: Heat 5x First Strand Buffer 80°C for 3-4 minutes, vortex, do a quick spin, and keep at room temperature; Make cDNA master mix (2µL 5x First Strand Buffer, 1 µL 0.1M DTT, 0.5 µL 10 mM dNTP mix, 1.2 µL Affinity Script RNase Block Mix); Briefly spin sample and master mix tubes; Add 4.7 µL of cDNA Master Mix to sample tubes and mix by pipetting up and down. Each tube now has 10 µL; Incubate at 40°C for 2 hours; Incubate at 70°C for 15 minutes (inactivates the AffinityScript enzyme); If you don’t continue to next step, freeze samples -80°C; Ice for 5 min. 3) Labeled cRNA synthesis: Keep T7 RNA polymerase (red cap) on ice. Master Mix = 0.75 µL Water, 3.2 µL 5x Transcription Buffer, 0.6 µL 0.1M DTT, 1 µL NTP Mix, .21µL T7 RNA polymerase Blend; 0.24 µL Cy3-CTP or C5-CTP; Add 6 µL of Transcrption Master Mix with Dye to the cDNA. Each tube now contains a total volume of 16 µL; Incubate samples at 40°C for 2 hours. 4) SPRI cleanup of cRNA: Before beginning: Bring RNAClean XP to RT, Make up enough 80% ethanol for >2 200 µL washes per reaction, Set 96 well thermomixer to 37°C; Add 48 µL (3X) of RNAClean XP beads to each reaction and incubate for 10 minutes; Place plate on magnet and allow supernatant to clear (~5 minutes); Remove supernatant carefully, avoiding beads, and discard; Add 200 µL of 80% ethanol to each well and incubate for 30 seconds; Remove ethanol and repeat for a total of two washes; Remove ethanol, cover plate, and spin down for ~1 minute; Place plate back on magnet and use a p20 to remove residual ethanol; Dry beads at 37°C until beads no longer move around when placed on magnet (~4 minutes); Add 42.5 of RNAse-free water and resuspend beads, then incubate for 2-3 minutes; Place plate on magnet and transfer 40 µL to a new well before placing on ice

growth_protocol: All experiments were performed in chemostats (continuous cultures). We chose chemostats, in part, because the steady-state condition of chemostat cultures is a particularly useful feature for mathematical modeling. Under steady-state conditions, the levels of molecules and activities of process are not changing at a culture-wide level. Cells were grown under continuous culturing conditions in 500 mL vessels as previously described with minor adjustments (Saldanha AJ, Brauer MJ, Botstein D. Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. 2004;15: 4089–4104). Cultures were aerated with 6 L/min of humidified air at 30C, maintained at 300 mL, and stirred with a magnetic impeller at 400 RPM. For the majority of experiments, cultures were maintained with minimal medium under phosphate limitation (20 mg/L). Nitrogen-limited cultures were maintained at 40 mg/L ammonium sulfate. Methionine-limited cultures (McIsaac et al, 2012) were maintained at 7.5 mg/L methionine. Growth rates were maintained from 0.15-0.17 vol/hour.  Batch growth in the chemostat vessels was initiated from a 1:60 dilution of a saturated overnight culture prior to turning on the chemostat pumps. Cells were grown to steady state, as determined by culture density, prior to the addition of 1 micromolar beta-estradiol to the culture and subsequent sampling. Chemostat experiments were performed with either the Infors Sixfors or Multifors systems.

extract_protocol: RNA was prepared using a standard acid phenol extraction. Lysis buffer: 600 µL of 0.5M EDTA, 1.5 mL of 10% SDS, 300 µL 1M Tris, 27.6 mL Rnase-free water. 1) Prepare labeling reaction: Get clean PCR strip tubes ready; Dilute RNA to 57.2 ng/µL; Add 3.5 µl of RNA (200 ng total) to PCR tube; Make T7 Primer Mix (0.8 µL T7, 1 µL water);Add 1.8 µl of T7 Primer Mix to each tube. Each tube now has 5.3 µl; Denature the template and primer by incubating at 65°C for 10 min; Put reactions on ice for 5 min; 2) cDNA synthesis: Heat 5x First Strand Buffer 80°C for 3-4 minutes, vortex, do a quick spin, and keep at room temperature; Make cDNA master mix (2µL 5x First Strand Buffer, 1 µL 0.1M DTT, 0.5 µL 10 mM dNTP mix, 1.2 µL Affinity Script RNase Block Mix); Briefly spin sample and master mix tubes; Add 4.7 µL of cDNA Master Mix to sample tubes and mix by pipetting up and down. Each tube now has 10 µL; Incubate at 40°C for 2 hours; Incubate at 70°C for 15 minutes (inactivates the AffinityScript enzyme); If you don’t continue to next step, freeze samples -80°C; Ice for 5 min. 3) Labeled cRNA synthesis: Keep T7 RNA polymerase (red cap) on ice. Master Mix = 0.75 µL Water, 3.2 µL 5x Transcription Buffer, 0.6 µL 0.1M DTT, 1 µL NTP Mix, .21µL T7 RNA polymerase Blend; 0.24 µL Cy3-CTP or C5-CTP; Add 6 µL of Transcrption Master Mix with Dye to the cDNA. Each tube now contains a total volume of 16 µL; Incubate samples at 40°C for 2 hours. 4) SPRI cleanup of cRNA: Before beginning: Bring RNAClean XP to RT, Make up enough 80% ethanol for >2 200 µL washes per reaction, Set 96 well thermomixer to 37°C; Add 48 µL (3X) of RNAClean XP beads to each reaction and incubate for 10 minutes; Place plate on magnet and allow supernatant to clear (~5 minutes); Remove supernatant carefully, avoiding beads, and discard; Add 200 µL of 80% ethanol to each well and incubate for 30 seconds; Remove ethanol and repeat for a total of two washes; Remove ethanol, cover plate, and spin down for ~1 minute; Place plate back on magnet and use a p20 to remove residual ethanol; Dry beads at 37°C until beads no longer move around when placed on magnet (~4 minutes); Add 42.5 of RNAse-free water and resuspend beads, then incubate for 2-3 minutes; Place plate on magnet and transfer 40 µL to a new well before placing on ice

treatment_protocol: The t = 0 was taken (between 3 mL) and vacuum filtered. Estradiol was then added the continuous culture and sampled at various timepoints.

tag: background


title: Non_Asthma.BEC12.RV.rep3.raw [BEC12-6_ATAC-seq]


title: ROF1_induction_sampleB_0min


title: ROF1_induction_sampleB_45min


title: Non_Asthma.BEC12.RV.rep2.raw [BEC12-5_ATAC-seq]


title: ROF1_induction_sampleB_10min


title: ROF1_induction_sampleB_15min


title: Non_Asthma.BEC12.RV.rep1.raw [BEC12-4_ATAC-seq]


title: Non_Asthma.BEC12.Veh.rep3.raw [BEC12-3_ATAC-seq]


title: Non_Asthma.BEC12.Veh.rep2.raw [BEC12-2_ATAC-seq]


title: ROF1_induction_sampleA_30min


title: ROF1_induction_sampleA_20min


title: ROF1_induction_sampleA_45min


title: Non_Asthma.BEC12.Veh.rep1.raw [BEC12-1_ATAC-seq]


title: CTRL_biopsy_dermis_Healthy (139)

city: Hellerup

first: Julie

middle: Breinholt Kjær

last: Sølberg

state: Danmark

address: Gentofte Hospitalsvej 20A

department: Department of dermatology and allergy, Gentofte Hospital

country: Denmark

institute: The national allergy research centre

data_processing:
BCL files were converted to FASTQ files with the bcl2fastq software (Illumina, California, USA)
Adapters as well as consecutive stretches of low-quality bases (Q<30) from the 5’ and 3’ termini were removed using AdapterRemoval version 2.1.3.  A length threshold of 20 bp was used for read removal.
Reads were aligned using STAR (Spliced Transcripts Alignment to a Reference) version 2.5.3a with default settings  where reads with multiple alignment were discarded.
Genome_build: For alignment, the Gene transfer format (GTF) annotation file for the hg38 reference genome (from the GENCODE consortium release 27) were used.
Supplementary_files_format_and_content: One processed .txt matrix containing Deseq2 normalized abundance data for all samples. One non-lesional tape sample was excluded due to low number of reads (<0.5M), and another lesional and non-lesional tape sample were excluded due to contamination of the samples.  The excluded samples are: 31, 35, 81 (not included in this GEO study).

source_name: Skin layer

extract_protocol:
Total RNA was extracted using the Exiqon miRCURY™ RNA Isolation Kit - Cell and Plant (Exiqon, now Qiagen Denmark, Copenhagen, Denmark) following the manufacturer’s recommendation, with additional heating of the lysis buffer to 56°C for 5 min before adding 70% ethanol (Qiagen Denmark, Copenhagen, Denmark).
Library preparation was performed with the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio Europe, Saint-Germain-en-Laye, France) following the manufacturer’s recommendation without fragmentation. To capture all RNA transcripts, the kit uses random hexamer primers for amplification. The protocol included removal of ribosomal RNA. For comparability, the same protocol was used for all sample types.
Single-end sequencing (75 bp) was performed with a NextSeq 500 (Illumina Denmark, Copenhagen, Denmark)

tag: individual

value: patient number 13

tag: localization

tag: easi

tag: disease state

value: Healthy subject

value: Dermis

tag: skin site

value: Healthy

tag: sample type

value: biopsy


title: Non_Asthma.BEC11.RV.rep1.raw [BEC11-4_ATAC-seq]

tag: age

tag: gender


title: Non_Asthma.BEC11.RV.rep3.raw [BEC11-6_ATAC-seq]

tag: subject status


title: ROF1_induction_sampleA_0min


title: ROF1_induction_sampleB_30min


title: ROF1_induction_sampleA_15min


title: ROF1_induction_sampleA_5min


title: CTRL_tape_Healthy (131)

value: Stratum corneum

value: tape


title: ROF1_induction_sampleB_90min


title: CTRL_biopsy_epidermis_Healthy (1310)

value: Epidermis


title: ROF1_induction_sampleA_10min


title: CTRL_biopsy_epidermis_Healthy (1210)

value: patient number 12


title: Non_Asthma.BEC11.Veh.rep3.raw [BEC11-3_ATAC-seq]

value: Vehicle-PBS

tag: cell type


title: Non_Asthma.BEC11.RV.rep2.raw [BEC11-5_ATAC-seq]

value: M

tag: pcr cycles


title: ROF1_induction_sampleB_5min


title: Non_Asthma.BEC11.Veh.rep2.raw [BEC11-2_ATAC-seq]

tag: cell culture well location


title: Non_Asthma.BEC11.Veh.rep1.raw [BEC11-1_ATAC-seq]

tag: molecule subtype


title: CTRL_biopsy_dermis_Healthy (129)


title: CTRL_tape_Healthy (121)


title: CTRL_biopsy_dermis_Healthy (119)

value: patient number 11

value: F


title: ROF1_induction_sampleA_90min


title: Non_Asthma.BEC10.RV.rep2.raw [BEC10-5_ATAC-seq]

tag: treatment


title: CTRL_tape_Healthy (111)

tag: tissue


title: Non_Asthma.BEC10.RV.rep1.raw [BEC10-4_ATAC-seq]


title: Dermatitis_biopsy_epidermis_L (109)

value: patient number 10

value: hand

value: Atopic dermatitis

value: L


title: Dermatitis_tape_L (105)


title: Non_Asthma.BEC10.Veh.rep3.raw [BEC10-3_ATAC-seq]

value: Primary Human Bronchial Epithelial Cells (BEC)

value: Crosslinkined DNA-Protein


title: Dermatitis_biopsy_dermis_L (1010)

value: Dermis


title: Non_Asthma.BEC10.Veh.rep1.raw [BEC10-1_ATAC-seq]


title: Non_Asthma.BEC10.Veh.rep2.raw [BEC10-2_ATAC-seq]


title: Dermatitis_biopsy_epidermis_L (89)

value: patient number 8

value: body


title: Asthma.BEC1.RV.rep2.raw [BEC1-5_ATAC-seq]

value: Asthma


title: Asthma.BEC1.Veh.rep3.raw [BEC1-3_ATAC-seq]


title: Asthma.BEC1.RV.rep3.raw [BEC1-6_ATAC-seq]


title: Asthma.BEC1.Veh.rep2.raw [BEC1-2_ATAC-seq]


title: Asthma.BEC1.Veh.rep1.raw [BEC1-1_ATAC-seq]


title: Dermatitis_biopsy_epidermis_L (79)

value: patient number 7

value: biopsy


title: Dermatitis_biopsy_dermis_L (810)


title: Dermatitis_biopsy_dermis_L (710)


title: Asthma.BEC1.RV.rep3.raw [BEC1-6_RNA-seq]

data_processing:
All samples were high quality by FastQC; repeat sequencing lanes for individual samples were concatenated prior to mapping or gene calls
Reads mapped to hg19 (GRCh37) using STAR and standard settings; Reads per gene were called using STAR
Genome_build: hg19
Supplementary_files_format_and_content: chr, start, end, numbers of reads per sample

extract_protocol:
At harvest, cells were disassociated from the culture surface using Accutase (Sigma-Aldrich) and quantified using a hemocytometer and trypan blue to differentiate live and dead cells. All cultures had greater than 90% viability at the time of the harvest. After quantification, 5,000 cells from each culture well were immediately processed for ATAC-seq and the remaining cells were extracted using the Qiagen AllPrep mini kit for RNA and DNA
Standard library preparation was completed using the Illumina Nextera XT DNA Library Preparation Kit and library quality and concentration were assessed using an Agilent 2100 bioanalyzer. Indexed samples were pooled and sequenced on the Illumina HiSeq 4000 with 100 base-pair, paired-end sequencing to a minimum of 10 million mapped reads per sample and a mean of 14 million reads per sample.

treatment_protocol: After reaching confluency (3-5 days), cells were treated with either 10.2 x 106 plaque forming units of RV-A16 in 5.1 ul of PBS or 5.1 ul of PBS (vehicle control). The RV was propagated and purified at the University of Wisconsin, Madison as previously described (Hasegawa et al., 2019)

tag: library prep technician

tag: cdna concentration

tag: library concentration

tag: cdna prep date

tag: culture plate orientation

value: A


title: Dermatitis_tape_NL (71)

tag: individual

tag: localization

tag: easi

tag: disease state

value: Stratum corneum

value: NL

value: tape


title: Dermatitis_tape_L (75)

tag: gender

value: M

tag: age

tag: skin site

tag: sample type


title: Asthma.BEC1.RV.rep1.raw [BEC1-4_RNA-seq]

tag: subject status

tag: cell type


title: Asthma.BEC1.RV.rep1.raw [BEC1-4_ATAC-seq]

tag: treatment

tag: pcr cycles

tag: cell culture well location

tag: molecule subtype


title: Dermatitis_biopsy_epidermis_L (69)

value: patient number 6

value: F

tag: tissue

value: Epidermis


title: Asthma.BEC1.RV.rep2.raw [BEC1-5_RNA-seq]

tag: library prep technician

tag: cdna concentration

tag: library concentration

tag: cdna prep date


title: CTRL_biopsy_epidermis_Healthy (1110)

tag: individual

value: patient number 11

tag: localization

tag: easi

value: Healthy subject

value: Healthy


title: Non_Asthma.BEC10.RV.rep3.raw [BEC10-6_ATAC-seq]

tag: age

tag: gender

value: Primary Human Bronchial Epithelial Cells (BEC)

value: Crosslinkined DNA-Protein


title: Asthma.BEC1.Veh.rep3.raw [BEC1-3_RNA-seq]

value: Vehicle-PBS

tag: culture plate orientation


title: Asthma.BEC1.Veh.rep2.raw [BEC1-2_RNA-seq]

tag: subject status

value: Asthma


title: Asthma.BEC1.Veh.rep1.raw [BEC1-1_RNA-seq]

tag: cell type


title: Dermatitis_tape_L (65)

value: hand

tag: disease state

value: Atopic dermatitis

tag: skin site

value: L

tag: sample type


title: Dermatitis_biopsy_dermis_L (610)

value: Dermis

value: biopsy


title: Dermatitis_tape_NL (61)

value: Stratum corneum

value: NL

value: tape


title: Dermatitis_tape_L (85)

value: patient number 8

value: M

value: body


title: Dermatitis_tape_NL (101)

value: patient number 10

value: F


title: Asthma.BEC6.RV.rep2.raw [BEC6-5_RNA-seq]

tag: treatment

value: Primary Human Bronchial Epithelial Cells (BEC)

value: C


title: Asthma.BEC6.RV.rep3.raw [BEC6-6_RNA-seq]


title: Dermatitis_tape_L (55)

value: patient number 5

tag: tissue


title: Dermatitis_biopsy_dermis_L (510)


title: Asthma.BEC6.RV.rep1.raw [BEC6-4_RNA-seq]

value: Asthma

tag: library prep technician


title: Asthma.BEC6.Veh.rep2.raw [BEC6-2_RNA-seq]

value: Vehicle-PBS

tag: cdna concentration


title: Asthma.BEC6.Veh.rep3.raw [BEC6-3_RNA-seq]

tag: library concentration


title: Asthma.BEC6.Veh.rep1.raw [BEC6-1_RNA-seq]

tag: cdna prep date


title: Dermatitis_biopsy_epidermis_L (49)

tag: individual

value: patient number 4

value: Atopic dermatitis

value: Epidermis


title: Dermatitis_tape_NL (51)

tag: localization


title: Asthma.BEC3.RV.rep3.raw [BEC3-6_RNA-seq]

value: B


title: Dermatitis_tape_L (45)

tag: easi

value: Stratum corneum

value: L


title: Dermatitis_tape_NL (41)

tag: age

value: NL

value: tape


title: Asthma.BEC3.RV.rep2.raw [BEC3-5_RNA-seq]

tag: gender


title: Dermatitis_biopsy_epidermis_L (39)

value: patient number 3

value: hand

value: biopsy


title: Asthma.BEC3.RV.rep1.raw [BEC3-4_RNA-seq]

value: F

tag: culture plate orientation


title: Dermatitis_biopsy_dermis_L (410)

value: body

value: Dermis


title: Asthma.BEC3.Veh.rep3.raw [BEC3-3_RNA-seq]

tag: subject status

value: Primary Human Bronchial Epithelial Cells (BEC)


title: Dermatitis_biopsy_dermis_L (310)


title: Asthma.BEC3.Veh.rep2.raw [BEC3-2_RNA-seq]

value: Asthma

tag: cell type


title: Dermatitis_biopsy_epidermis_L (29)

value: patient number 2

value: M

tag: disease state


title: Dermatitis_biopsy_epidermis_L (59)

value: patient number 5

value: Atopic dermatitis

tag: skin site


title: Dermatitis_tape_L (25)

tag: sample type


title: Asthma.BEC3.Veh.rep1.raw [BEC3-1_RNA-seq]

tag: treatment

value: Vehicle-PBS

value: B


title: Asthma.BEC8.RV.rep2.raw [BEC8-5_RNA-seq]

value: C


title: Asthma.BEC8.RV.rep3.raw [BEC8-6_RNA-seq]


title: Asthma.BEC8.RV.rep1.raw [BEC8-4_RNA-seq]


title: Asthma.BEC8.Veh.rep2.raw [BEC8-2_RNA-seq]


title: Dermatitis_biopsy_epidermis_L (19)

value: patient number 1

tag: tissue

value: Epidermis

value: L


title: Dermatitis_tape_NL (21)

value: hand

value: Stratum corneum

value: NL

value: tape


title: Asthma.BEC8.Veh.rep3.raw [BEC8-3_RNA-seq]

tag: library prep technician


title: Dermatitis_tape_L (15)


title: Asthma.BEC8.Veh.rep1.raw [BEC8-1_RNA-seq]

tag: cdna concentration


title: Dermatitis_biopsy_dermis_L (110)

value: Dermis

value: biopsy


title: Non_Asthma.BEC18.RV.rep3.raw [BEC18-6_RNA-seq]

value: Primary Human Bronchial Epithelial Cells (BEC)

tag: library concentration


title: Dermatitis_tape_NL (11)


title: Non_Asthma.BEC18.RV.rep2.raw [BEC18-5_RNA-seq]

tag: cdna prep date


title: Non_Asthma.BEC18.RV.rep1.raw [BEC18-4_RNA-seq]


title: Non_Asthma.BEC18.Veh.rep1.raw [BEC18-1_RNA-seq]


title: Non_Asthma.BEC18.Veh.rep3.raw [BEC18-3_RNA-seq]


title: Asthma.BEC7.RV.rep3.raw [BEC7-6_RNA-seq]

value: Asthma


title: Asthma.BEC7.RV.rep2.raw [BEC7-5_RNA-seq]

value: M


title: Asthma.BEC7.RV.rep1.raw [BEC7-4_RNA-seq]


title: Non_Asthma.BEC12.RV.rep3.raw [BEC12-6_RNA-seq]

value: A


title: Asthma.BEC7.Veh.rep2.raw [BEC7-2_RNA-seq]


title: Asthma.BEC7.Veh.rep1.raw [BEC7-1_RNA-seq]


title: Dermatitis_biopsy_dermis_L (210)

tag: individual

value: patient number 2

value: Atopic dermatitis


title: CUT&RUN, IgG rep 2

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
FASTQ files from an Illumina NextSeq with 2x42 cycles were obtained from the Biopolymers Core at Harvard Medical School.
Paired-end sequencing reads were trimmed with TrimGalore v0.4.5 to remove adaptor sequence GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT with additional removal of fragments smaller than 25 bp. Reads were aligned to the hg38 reference genome using bowtie2 v2.2.9 with options “--no-unal --no-discordant --no-mixed --dovetail -I 25 -X 700”. Reads mapping to the mitochondrial genome were subsequently removed, and duplicate reads were removed with Picard v2.8.0. Reads smaller than 120 bp were retained for subsequent analysis.
Visualization was performed by mapping insertions to a genome-wide sliding 150 bp window with 20 bp offsets with bedops v2.4.30, followed by conversion to bigwig format with wigToBigWig from UCSC tools v363.
CUT&RUN peaks were called by MACS2 v2.1.1 using options “callpeak -q 0.01 --keep-dup all”.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig (.bw) file of read pileups mapping to a 150 bp genomic window with 20 bp offsets for visualization
Supplementary_files_format_and_content: narrowPeak file of peaks called with MACS2 relative to normal rabbit IgG control

source_name: K562 cells

growth_protocol: K562 (ATCC) cells were cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
500,000 K562 cells per assay were washed three times (room temperature, 3 min, 600 x g) in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and 1x cOmplete EDTA-free protease inhibitor cocktail [Roche]). Concavalin A beads were activated by washing beads in binding buffer (20 μM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 10 μL activated Concavalin A beads were added to 100 μL cell suspension and incubated with rotation for 10 min at room temperature. Supernatant was removed, and 100 μL wash buffer containing 0.01% digitonin (dig-wash buffer) was added. Antibodies were added at 1:50 concentration, and tubes were incubated with rotation overnight at 4 °C. Beads were washed with dig-wash buffer, pAG/MNase was added at a final concentration of 2 μg/mL, and suspensions were incubated for 1 h at 4 °C. Beads were further washed with wash buffer, resuspended in 100 μL wash buffer, and chilled to 0 °C in an ice-water bath. 2 μL 0.1 M CaCl2 was added to each tube, and tubes were incubated for 1 h at 0 °C. 100 μL stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 μg/mL RNase A, 50 μg/mL GlycoBlue) was added, and tubes were incubated for 15 min 37 °C to release DNA fragments. Supernatant was collected, SDS (0.1% final) and proteinase K (250 μg/mL final) were added to each 200 μL sample, and tubes were incubated for 1 h at 50 °C. DNA was isolated by phenol/chloroform extraction.
Libraries were constructed using the NEBNext Ultra kit (NEB)
CUT&RUN

tag: cut&run antibody

value: normal rabbit IgG (EMD Millipore, #12-370; 1:50)


title: Non_Asthma.BEC12.RV.rep2.raw [BEC12-5_RNA-seq]


title: CUT&RUN, IgG rep 1


title: Non_Asthma.BEC12.RV.rep1.raw [BEC12-4_RNA-seq]


title: Non_Asthma.BEC12.Veh.rep3.raw [BEC12-3_RNA-seq]

value: Vehicle-PBS


title: CUT&RUN, WBP11 rep 2


title: Non_Asthma.BEC12.Veh.rep1.raw [BEC12-1_RNA-seq]


title: CUT&RUN, ERH rep 1


title: Non_Asthma.BEC18.Veh.rep2.raw [BEC18-2_RNA-seq]

value: B


title: Non_Asthma.BEC11.RV.rep3.raw [BEC11-6_RNA-seq]


title: CUT&RUN, ERH rep 2


title: Asthma.BEC7.Veh.rep3.raw [BEC7-3_RNA-seq]


title: Non_Asthma.BEC11.RV.rep2.raw [BEC11-5_RNA-seq]


title: ATRA-treated NB4 iDAPT-seq, nuclei, Rep 2

data_processing:
FASTQ files from an Illumina NextSeq with 2x75 cycles were obtained from the Biopolymers Core at Harvard Medical School.
Paired-end sequencing reads were trimmed with TrimGalore v0.4.5 to remove adaptor sequence CTGTCTCTTATACACATCT, which arises at the 3’ end due to sequenced DNA fragments being shorter than the sequencing length (75 bp).
Reads were aligned to the hg38 reference genome using bowtie2 v2.2.9 with options “--no-unal --no-discordant --no-mixed -X 2000”. Reads mapping to the mitochondrial genome were subsequently removed, and duplicate reads were removed with Picard v2.8.0.
Reads were downsampled to approximately 5 million paired-end fragments. Visualization was performed by mapping insertions to a genome-wide sliding 150 bp window with 20 bp offsets with bedops v2.4.30, followed by conversion to bigwig format with wigToBigWig from UCSC tools v363.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig (.bw) file of read pileups mapping to a 150 bp genomic window with 20 bp offsets for visualization

source_name: NB4 cells, 48 hr ATRA treatment (1 uM)

growth_protocol: GM12878 cells (Coriell) were cultured in RPMI-1640 supplemented with L-glutamine (Gibco), 15% heat-inactivated fetal bovine serum (FBS) (Gibco), and 1% penicillin/streptomycin (Thermo Fisher Scientific). K562 (ATCC) cells were cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin. NB4 cells (DSMZ) were cultured in RPMI-1640 supplemented with 10% charcoal-stripped FBS (Gibco) and 1% penicillin/streptomycin. All-trans retinoic acid (ATRA, Sigma) was dissolved in DMSO at a concentration of 10 mM. Cells were incubated at 37 °C and 5% CO2. Genomic DNA was extracted from K562 and NB4 cells using the Quick-DNA MiniPrep kit (Zymo).

extract_protocol:
10 pmol enzyme (2 μL in 2xDB) was mixed with 12.5 pmol MEDS-A/B (1.25 μL in water) and incubated at room temperature for 1 h. In the meantime, 50,000 cells were centrifuged at 500 x g for 5 min at 4°C. Cells were resuspended in 50 μL lysis buffer 1 (LB1: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.01% digitonin, 0.1% Tween-20, and 0.1% NP-40) with trituration, incubated on ice for 3 min, and then further supplemented with 1 mL lysis buffer 2 (LB2: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Nuclei were pelleted (500 x g, 10 min, 4 °C), resuspended with 50 μL tagmentation reaction mixture (20% dimethylformamide, 10 mM MgCl2, 20 mM Tris-HCl pH 7.5, 33% 1xPBS, 0.01% digitonin, 0.1% Tween-20, and either 10 pmol enzyme equivalent of enzyme:DNA complex or 2.5 μL Nextera Tn5 [Illumina, TDE1 from FC-121-1030] in 50 μL total volume), and incubated at 37 °C for 30 min with agitation on a thermomixer (1,000 rpm). For iDAPT-seq libraries generated from K562 or NB4 cells or genomic DNA, bovine serum albumin (BSA) was added at a final concentration of 1% to lysis (LB1 and LB2) and tagmentation buffers. Tagmentation with naked genomic DNA was performed using 50 ng genomic DNA as substrate. After tagmentation, DNA libraries were extracted with DNA Clean and Concentrator-5 (Zymo) and eluted with 21 μL water.
To determine optimal PCR cycle number for library amplification, 2 μL of each ATAC-seq or iDAPT-seq library was added to 2x NEBNext Master Mix (NEB) and 0.4x SYBR Green (Thermo Fisher) with 1.25 μM of each primer (Primer 1: 5’-AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG-3’; Primer 2.1: 5’-CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCT CGTGGGCTCGGAGATGT-3’) in a final volume of 15 μL, and quantification was assessed using the following conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Optimal PCR cycle number was determined as the qPCR cycle yielding fluorescence between 1/4 and 1/3 of the maximum fluorescence. The remaining DNA library was then amplified accordingly by PCR using previously reported barcoded primers for library multiplexing, purified with DNA Clean and Concentrator-5 (Zymo), and eluted into 20 μL final volume with water.

tag: enzyme


title: ATRA-treated NB4 iDAPT-seq, nuclei, Rep 3


title: ATRA-treated NB4 iDAPT-seq, nuclei, Rep 1