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

source_name: NB4 cells, 48 hr DMSO treatment


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

status: Public on Oct 31 2020

type: SRA

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

country: USA

institute: The University of Chicago

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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 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: subject status

tag: treatment

value: Vehicle-PBS

tag: age

tag: gender

value: M

tag: cell type

value: Primary Human Bronchial Epithelial Cells (BEC)

tag: library prep technician

tag: cdna concentration

tag: library concentration

tag: cdna prep date

tag: culture plate orientation

value: A


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

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

library_source: genomic

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

molecule: genomic DNA

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


title: CUT&RUN, WBP11 rep 1

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


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


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


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

value: Asthma

value: F

value: B


title: DMSO-treated NB4 iDAPT-seq, genomic DNA, Rep 3


title: Differentiated cells - COPD [C15_D]

type: RNA

city: Philadelphia

first: Umadevi

last: Sajjan

state: PA

address: 3500 N Broad Street

department: Department of Thoracic Medicine and Surgery

institute: Temple University

description: Microarray data of mucociliary-differentiated cell cultures from end-stage COPD patient

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on the Human Gene 2.1 ST arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) using default analysis settings and Gene Level RMA as normalization method.

label: Biotin

source_name: Differentiated cells from COPD patient

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Basal cells were cultured in collagen coated 10 cm dishes in Bronchial Life medium (LifeLine Cell Technologies, Frederick, MD) until 80% confluent. Cells were harvested, flow sorted based on the expression of basal cell marker nerve growth factor receptor and seeded in transwells at a density of 1 x 10^5/well. Cells were grown under submerged conditions in Bronchial Life medium until confluent (5 to 7 days) and then maintained at air/liquid interface (ALI) for another 4 weeks to promote mucociliary differentiation. Cells were harvested either at subconfluent stage that is 3-4 days after seeding (basal cells) or after 4 weeks of culturing at ALI.

extract_protocol: Cells were washed once with PBS, lysed in TRIZOL and total RNA was isolated by using miRNeasy kit (Qiagen, Valencia, CA) involving DNAse treatment step.

value: end-stage COPD patient


title: Differentiated cells - COPD [C18_D]


title: Differentiated cells - COPD [C19_D]


title: Differentiated cells - COPD [C10_D]


title: Basal cells - COPD [C19]

description: Microarray data of airway basal cells obtained from end-stage COPD patient

source_name: Airway basal cells from COPD patient

value: Basal cells


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


title: Differentiated cells - COPD [C14_D]


title: Basal cells - COPD [C18]


title: DMSO-treated NB4 iDAPT-seq, genomic DNA, Rep 2


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


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


title: DMSO-treated NB4 iDAPT-seq, genomic DNA, Rep 1


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


title: K562 iDAPT-seq, genomic DNA, Rep 3


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


title: K562 iDAPT-seq, genomic DNA, Rep 2


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


title: K562 iDAPT-seq, genomic DNA, Rep 1


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

value: C


title: K562 iDAPT-seq, nuclei, Rep 3


title: K562 iDAPT-seq, nuclei, Rep 2


title: Asthma.BEC4.RV.rep2.raw [BEC4-5_RNA-seq]


title: Differentiated cells - COPD [C6_D]


title: Basal cells - COPD [C14]


title: Basal cells - COPD [C11]


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


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


title: Basal cells - COPD [C15]


title: Basal cells - COPD [C12]


title: GM12878 iDAPT-seq, TP5, Rep 2

source_name: GM12878 cells


title: Basal cells - COPD [C10]


title: K562 iDAPT-seq, nuclei, Rep 1


title: Basal cells - COPD [C6]


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


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


title: GM12878 iDAPT-seq, TP5, Rep 1


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


title: GM12878 iDAPT-seq, TP3, Rep 2


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


title: GM12878 iDAPT-seq, TP3, Rep 1


title: Differentiated cells - Normal [N27_D]

description: Microarray data of mucociliary-differentiated cell cultures from healthy non-smoker subject

source_name: Differentiated cells from normal subject

value: healthy non-smoker subject


title: Differentiated cells - Normal [N22_D]


title: Differentiated cells - Normal [N20_D]


title: Differentiated cells - Normal [N4_D]


title: Differentiated cells - Normal [N24_D]


title: Differentiated cells - Normal [N19_D]


title: GM12878 ATAC-seq, Tn5-FLAG, Rep 1


title: Basal cells - Normal [N27]

description: Microarray data of airway basal cells obtained from healthy non-smoker subject

source_name: Airway basal cells from normal subject


title: GM12878 ATAC-seq, Nextera Tn5, Rep 2

value: Nextera Tn5


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


title: GM12878 ATAC-seq, Tn5-FLAG, Rep 2


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


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


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


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


title: GM12878 ATAC-seq, Nextera Tn5, Rep 1


title: OA_hip_NW

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Basecalls performed using cellranger mkfastq (cellranger version 3.0.1)- based on Illumina's bcl2fastq (v2.20)
cellranger count used to perform alignment and barcode and UMI counting. This generates feature-barcode matrices.
Genome_build: hg38
Supplementary_files_format_and_content: h5 matrix produced by the Cell Ranger software.Includes the barcodes/UMI and data.

source_name: normal-weight hip OA patient_Synovial fibroblasts

growth_protocol: Synovial fibroblasts were cultured from diced synovial tissue in RMPI 1640 supplemented with 10% FSC, 5% non-essential amino acids, 5% L-glutamine, 5% sodium pyruvate and 1% penicillin/ streptomycin.

extract_protocol:
Passaged fibroblasts from P2 to P4 where harvested for single-cell RNA sequencing at 70-80% confluence.
3' cDNA libraries were prepared as per 10X Chromium Single Cell 3' Library Kit v2. Cells were pooled from each condition (normal-weight n=4; obese = n=4), isolalated from a total of 2666 cells (roughly 333 cells/patient). Libraries were pooled and sequenced across 4 lanes.

tag: disease state

value: Hip osteoarthritis

tag: weight

value: Normal weight

tag: tissue

value: Synovial tissue

value: Synovial fibroblasts


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


title: OA_hip_obese

source_name: obese hip OA patients_Synovial fibroblasts

value: Obese


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

value: Vehicle-PBS


title: EV_miRNA_uninfected_72hpi_3

city: Bonn

first: Denna

last: Tabari

address: Kurt-Georg-Kiesinger Allee 3

country: Germany

institute: Federal Institute for Drugs and Medical Devices

description: microRNA

data_processing:
Basecalls performed using Illumina Miseq system software
Adapter trimming was performed with the program cutadapt.
Reads were aligned to the whole human genome using bowtie2.
DESeq2 was used to calculate the fold change, p-value (Wald test) and adjusted p-value (Benjamini Hochberg Adjustment)
Genome_build: hg19
Supplementary_files_format_and_content: xls file containing miRNA calls

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

extract_protocol:
For the analysis of intracellular miRNAs, total RNA was extracted from infected and uninfected lt-NES® cells at 24, 48 and 72 hpi using miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer’s instructions. For the analysis of EV-derived miRNAs, cell culture supernatants were collected at the indicated time points and EV-associated miRNAs were extracted using exoRNeasy Serum/Plasma Kit (Qiagen, 77064) as described by the manufacturer.
RNA sequencing libraries were generated using the NEBNext Mulitplex Small RNA Library Prep Set for Illumina (NEB E7300S) following size selection by running the samples on a 10 % polyacrylamide gel and isolating the 147 bp. Samples were purified using the QIAquick PCR Purification Kit (Qiagen, 28104). Libraries were validated on a High Sensitivity DNA chip using the 2100 Bioanalyzer (Agilent).

value: uninfected

tag: timepoint

value: EVs derived from lt-NES® cells


title: Basal cells - Normal [N20]


title: Basal cells - Normal [N24]


title: EV_miRNA_uninfected_72hpi_2

description: microRNA


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

value: Primary Human Bronchial Epithelial Cells (BEC)

value: A


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

value: Asthma

value: F


title: Basal cells - Normal [N17]


title: Basal cells - Normal [N22]


title: Basal cells - Normal [N19]


title: Basal cells - Normal [N4]


title: EV_miRNA_Polynesia_72hpi_3

description: microRNA

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

value: ZIKV French Polynesia infection


title: Basal cells - Normal [N18]

value: Basal cells


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


title: EV_miRNA_uninfected_72hpi_1

description: microRNA


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

value: M


title: EV_miRNA_Uganda_72hpi_3

description: microRNA

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

value: ZIKV Uganda infection


title: EV_miRNA_Uganda_72hpi_1

description: microRNA


title: EV_miRNA_Polynesia_72hpi_2

description: microRNA


title: left ventricle, mDia1KO, TAC

city: Yufu

first: Ichitaro

last: Abe

state: Oita

address: 1-1 Idaigaoka, Hasama

department: Department of Cardiology and Clinical Examination

country: Japan

institute: Oita University

description: The left ventricle of mDia1KO mice 3 days after TAC

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: left ventricle, knockdown

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: FVB

tag: genotype

value: left ventricle


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

tag: subject status

tag: treatment


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

tag: age

tag: gender


title: EV_miRNA_Polynesia_72hpi_1

description: microRNA


title: left ventricle, WT, TAC

description: The left ventricle of WT mice 3 days after TAC

source_name: left ventricle, wild-type

value: WT


title: AuditoryNerve-AgedAdult-1

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: cRNA recommended amounts were hybridized overnight at 45oC on GeneChip Mouse 430 2.0 Array. Hybridized GeneChips were washed and stained in an Affymetrix Fluidics Station 450. Microarrays were scanned using an Affymetrix 7G Scanner.

scan_protocol: CEL files were imported into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

data_processing: Signal is log2 RMA signal

label: biotin

source_name: Auditory nerve

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME). All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle. All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.

extract_protocol: Microdissected cochlear tissues underwent total RNA preparation using the RNeasy Minikit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

value: Auditory nerve


title: AuditoryNerve-YoungAdult-3

value: Young adult


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

tag: cell type

tag: library prep technician


title: AuditoryNerve-YoungAdult-2


title: EV_miRNA_Uganda_72hpi_2

description: microRNA


title: AuditoryNerve-AgedAdult-3


title: AuditoryNerve-AgedAdult-2


title: AuditoryNerve-YoungAdult-1


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

tag: cdna concentration

tag: library concentration


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

tag: cdna prep date

tag: culture plate orientation


title: EV_miRNA_uninfected_48hpi_3

description: microRNA

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


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


title: EV_miRNA_uninfected_48hpi_1

description: microRNA


title: EV_miRNA_uninfected_48hpi_2

description: microRNA


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

value: B


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

value: Vehicle-PBS


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


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


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


title: EV_miRNA_Uganda_48hpi_2

description: microRNA

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


title: EV_miRNA_Uganda_48hpi_3

description: microRNA


title: EV_miRNA_Polynesia_48hpi_3

description: microRNA

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


title: EV_miRNA_Polynesia_48hpi_2

description: microRNA


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

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


title: EV_miRNA_Polynesia_48hpi_1

description: microRNA


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


title: BBB Male rep 1

city: Northbrook

first: Michael

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Gene Expression of quick frozen blood brain barrier cells, male

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Drosophila melanogaster

source_name: SPG cells of the BBB

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample.  Briefly, Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

growth_protocol: Flies were grown on standard fly food under 12h:12h light dark cycles

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Blood brain barrier cells were marked by expression of UAS-dsRed driven by SNG-GAl4. Marked cells were hand-isolated.

value: male

value: SPG cells of the BBB


title: EV_miRNA_Uganda_48hpi_1

description: microRNA

value: EVs derived from lt-NES® cells


title: BBB Male rep 3


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

value: Primary Human Bronchial Epithelial Cells (BEC)


title: EV_miRNA_uninfected_24hpi_3

description: microRNA

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

value: uninfected


title: EV_miRNA_uninfected_24hpi_2

description: microRNA


title: BBB Female rep 3

description: Gene Expression of quick frozen blood brain barrier cells, female

value: female


title: BBB Male rep 2


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

value: Asthma


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


title: EV_miRNA_uninfected_24hpi_1

description: microRNA


title: EV_miRNA_Uganda_24hpi_3

description: microRNA

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


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

value: F

value: C


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


title: EV_miRNA_Uganda_24hpi_2

description: microRNA

value: ZIKV Uganda infection


title: EV_miRNA_Uganda_24hpi_1

description: microRNA


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


title: EV_miRNA_Polynesia_24hpi_1

description: microRNA

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

value: ZIKV French Polynesia infection


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


title: miRNA_uninfected_72hpi_3

description: microRNA

value: lt-NES® cells


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


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


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

value: M


title: miRNA_uninfected_72hpi_1

description: microRNA


title: EV_miRNA_Polynesia_24hpi_3

description: microRNA


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


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

value: A


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


title: EV_miRNA_Polynesia_24hpi_2

description: microRNA


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


title: miRNA_uninfected_72hpi_2

description: microRNA


title: miRNA_Uganda_72hpi_1

description: microRNA


title: R4KD: 4T1_cellline-ID1_ID3_KD_dox-rep3

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

hyb_protocol: cDNA probes were then hybridized to the Affymetrix mouse GeneChip ST 2.0 array as per the manufacturer’s instructions (Affymetrix Ca, USA) at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia).

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using the AffymetrixPowerTools apt-probeset-summarize software (version 1.15.0) (using the -a rma option)

source_name: mouse breast cancer 4T1 cell-line,  dox, ID1/3 KD

label_protocol: Total RNA was converted to cDNA. The cDNA was biotin labeled at the Ramaciotti Centre for Genomics at the University of New South Wales (UNSW, Sydney, Australia), following manufacturers instructions.

growth_protocol: 3.5x10^4 4T1 K1 cells were seeded in 6-well plates in 4T1 media (RPMI 1640 (Gibco) supplemented with 10% (v/v) FBS (Thermo Fisher Scientific), 20mM HEPES (Gibco), 1mM sodium pyruvate (Gibco), and 0.25% (v/v) glucose (Gibco).

extract_protocol: Total RNA was extracted from 1-3 million fresh frozen cells using the Qiagen RNeasy minikit according to manufacturer’s protocol.

treatment_protocol: Dox (1 µg/mL) was added to the wells as indicated in the SAMPLES section above at the time of seeding. Cells were then cultured for 48 hours and then cells pellets were frozen for RNA extraction.

value: breast cancer cel line

tag: cell line

tag: genotype/variation

value: Id1/3 knockdown

value: 4T1 K1 cell line with dox-inducible shRNA targeting Id1 and Id3

tag: +/- dox treatment

tag: id1/3 knockkdown

value: Yes

tag: replicate


title: R5KD: 4T1_cellline-ID1_ID3_KD_dox-rep4

tag: tissue


title: BBB Female rep 2

value: SPG cells of the BBB


title: R3C: 4T1_cellline-control_no_dox-rep3

source_name: mouse breast cancer 4T1 cell-line,  no-dox, control

value: Control

value: 4T1 K1 cell line with Dox-inducible shRNA targeting Id1 and Id3

value: No


title: R4C: 4T1_cellline-control_no_dox-rep4


title: BBB Female rep 1

value: female


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

value: Vehicle-PBS

value: Primary Human Bronchial Epithelial Cells (BEC)


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

value: F


title: R3KD: 4T1_cellline-ID1_ID3_KD_dox-rep2


title: miRNA_Polynesia_72hpi_2

description: microRNA

tag: timepoint


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

tag: subject status


title: miRNA_Polynesia_72hpi_3

description: microRNA

tag: treatment


title: miRNA_Polynesia_72hpi_1

description: microRNA


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

tag: age

value: C


title: miRNA_Uganda_72hpi_3

description: microRNA

value: ZIKV Uganda infection


title: miRNA_uninfected_48hpi_3

description: microRNA

value: uninfected

value: lt-NES® cells


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

tag: gender


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

tag: cell type


title: miRNA_uninfected_48hpi_2

description: microRNA


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

tag: library prep technician


title: miRNA_uninfected_48hpi_1

description: microRNA


title: miRNA_Uganda_72hpi_2

description: microRNA


title: R1C: 4T1_cellline-control_no_dox-rep1


title: R1KD: 4T1_cellline-ID1_ID3_KD_dox-rep1


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

tag: cdna concentration


title: miRNA_Uganda_48hpi_3

description: microRNA


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

tag: library concentration


title: R2C: 4T1_cellline-control_no_dox-rep2


title: miRNA_Uganda_48hpi_2

description: microRNA


title: miRNA_Uganda_48hpi_1

description: microRNA


title: miRNA_Polynesia_48hpi_1

description: microRNA

value: ZIKV French Polynesia infection


title: miRNA_Polynesia_48hpi_2

description: microRNA


title: miRNA_Polynesia_48hpi_3

description: microRNA


title: miRNA_uninfected_24hpi_3

description: microRNA


title: miRNA_uninfected_24hpi_2

description: microRNA


title: miRNA_uninfected_24hpi_1

description: microRNA


title: miRNA_Uganda_24hpi_2

description: microRNA


title: miRNA_Uganda_24hpi_3

description: microRNA


title: miRNA_Polynesia_24hpi_1

description: microRNA


title: miRNA_Polynesia_24hpi_2

description: microRNA


title: miRNA_Polynesia_24hpi_3

description: microRNA


title: KO5

city: Seoul

first: Koeul

last: Choi

address: 84, Heukseok-ro

country: South Korea

institute: Chung-Ang university

data_processing:
The raw RNA sequences were preprocessed with cutadapt (v.1.11) to remove the sequencing adapters.
Quality control checks on raw sequence data was performed using Fast QC (v0.11.5). Low-quality bases below Q20 were trimmed from 3’ ends of each read and the short reads shorter than 17 nucleotides were discarded.
The remaining high-quality reads were then mapped onto mouse reference genome (Ensembl 77) using BowTie (v.1.1.2) with only 1 mismatch (-n 1), max 80 mismatch quals across alignment, 30 seed length and the suppression of the reads showing > 5 alignments.
The reads mapped to each gene for each sample were counted using HTseq (v0.6.1p1).
Differentially expressed genes were identified using edgeR in R (v.3.10.2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include COUNT values for each Sample

source_name: Fkbp5 Knockout_PFC

extract_protocol:
Brains were removed and sectioned PFC (prefrontal cortex) region. RNA extraction was performed using miRNeasy mini kit (Qiagen, Hilden, Germany). Flow-through solution was purified using RNeasy minElute cleanup kit (Qiagen, Hilden, Germany) for miRNA enrichment. Small RNA samples were used for library preparation using a NEXTflex small RNA-seq Library Prep Kit V3 (Bioo Scientific, Austin, TX, USA).
The adapters are directly, and specifically, ligated to the miRNA molecules and adapter ligated RNA was reverse transcribed to create single stranded cDNA. The cDNA is then PCR amplified. The amplified cDNA constructs were separated on a 6% TBE gel and the 140-160bp bands were excised. After gel purification, the library was sequenced using Illumina HiSeq2500 platform in 100PE mode (Illumina, San Diego, CA, USA).

tag: strain background

tag: genotype

value: Fkbp5 Knockout

value: brain; prefrontal cortex

tag: molecule subtype

value: miRNA


title: WT3

source_name: wild type_PFC

value: wild type


title: WT2


title: miRNA_Uganda_24hpi_1

description: microRNA


title: KO1


title: WT1


title: KO4


title: KO2


title: WT4


title: TC01_N2

city: Halle

first: Tomasz

last: Chilczuk

address: Hoher Weg 8

institute: University of Halle-Wittenberg

data_processing:
Primary sequencing data was produced by Illumina NovaSeq 6000.
Raw sequenced reads were subjected to quality control (FastQC), then mapped to Serratia sp. ATCC 39006 whole genome using HISAT (version 2.1.0).
Aligned sequences were quantified using FeatureCounts (version 1.6.4).
Differential expression analysis was done using the default parameters in DeSeq2 (version 1.22.1) and a significance cut-off of an adjusted p value < 0.05.
Genome_build: GenBank CP025084.1
Supplementary_files_format_and_content: .txt files include the raw count values for each sample.

organism: Prodigiosinella confusarubida

source_name: bacterial cells

extract_protocol:
To analyze the influence of ambigols on the transcriptome of Serratia, six S39006 cultures were grown for 7 h in 6-well microtiter plates. Three cultures were incubated with 15.6 μM ambigol C in DMSO, whereas the other three were incubated with DMSO. 0.1 mL of each culture was mixed with two volumes of RNAprotect Bacteria Reagent (QIAGEN). The RNeasy Mini Kit (QIAGEN) was used for total RNA extraction, using the manufacturer’s instructions (protocol 4 from the RNAprotect Bacteria Reagent Handbook), followed with two treatments of DNase (QIAGEN). RNA concentrations and quality were evaluated using an Agilent Bioanalyzer (Agilent Technologies).
RNA sequencing was performed at the genomics service company GENEWIZ (Leipzig, Germany). RNA was depleted from rRNA using a NEBNext rRNA Depletion Kit (New England Biolabs GmbH), and a sequencing library was constructed using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs GmbH).

tag: strain

value: incubated for 10 h with DMSO


title: TC01_A3

value: incubated for 10 h with 15.6 µM ambigol C


title: TC01_N3


title: TC01_N1


title: TC01_A1


title: TC01_A2


title: A0002 Islet RNA

status: Public on Oct 28 2020

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description:
processed data file:
Islet.fpkm.tsv
JY211

data_processing:
ChIP-seq: Reads were aligned using BWA MEM with either single-end or pair-end model to the hg19 reference genome. Reads with low mapping quality (mapq<10) were filtered out, and PCR duplicates were removed using Picard tool. MACS2 were then applied to call peaks and generate signals to view in the genome browser.
STARR-seq:STARR-seq reads were aligned to the oligo libraries using BWA with default parameters. Read counts for each oligos were then counted using custom scripts. Counts for technical replicates were merged. Oligos were filtered to keep only oligos covered by more than 25 reads in the input library and more than five reads in at least three libraries.
Hi-C:Briefly, each end of read pairs were aligned separately using BWA MEM to the hg19 reference genome with default parameters. Chimeric read ends were further processed to keep only the five-prime alignment. Read ends with low mapping quality (mapq<10) were removed, and remaining read ends were paired using custom scripts. PCR duplicates were removed using Picard tool (http://broadinstitute.github.io/picard). Aligned reads were further transformed to the juicer format and processed into hic format using juicebox tool. Chromatin loops were called using Hiccups with default parameters.
WGS:Reads from whole genome sequencing (WGS) were aligned using BWA MEM in pair-end model with default parameters. PCR duplicates were removed using Picard tools (http://broadinstitute.github.io/picard). Variants were then called according to the GATK best practice pipeline using GATK 3.6-0.
RNA-seq:Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters in pair-end model. Only uniquely aligned reads were kept for further analysis. Cufflinks 2.2.1 was used to compute FPKM for each gene.
SELEX:Sequencing data of each HT-SELEX cycle was aligned to the oligo library using BWA. More specific details to identify pbSNPs can be found in methods of associated manuscript.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: Peak files in narrowPeak format and signal files in bigWig format for each samples were provided.
STARR-seq:Counts for each STARR-seq experiments were provided.
Hi-C:Juicebox hic format contains contact matrices in multiple resolutions and list of loops in text format were provided.
WGS:VCF file for all variants and phased variants in HepG2 cells were provided.
RNA-seq:Text files including FPKM values for all genes in each sample were provided.
SELEX:Text file summarizing measurements of allelic TF binding to all SNPs tested was included.

molecule: polyA RNA

source_name: A0002 Islet

growth_protocol: The HEK293T cells (ATCC, CRL-3216) and HepG2 (ATCC, HB-8065) cells were cultured under normal condition with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq:   Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65°C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit. STARR-seq:  The plasmid pool was transfected into HEK293T or HepG2 cell lines using Fugene HD and continued culturing for 48 hours before harvest. Total RNA was extracted with RNeasy kit (Qiagen, 74104) and mRNA was enriched with poly(dT)25 Dynabeads (Invitrogen, 61002). First strand cDNA was synthesized using a specific primer (5’-CAAACTCATCAATGTATCTTATCATG) with high High-Capacity cDNA Reverse Transcription kit (ThermoFisher Scientific, 4368814). The nested PCR was used to amplify the SNP specific fragments from cDNA, first using two reporter-specific PCR primers (5’-GGGCCAGCTGTTGGGGTGTCCAC & 5’-CTTATCATGTCTGCTCGAAGC) and then generic primers used in HT-SELEX. DNA was purified with AMPure beads.   Hi-C:  Briefly, the human islets were washed with cold PBS and cut into small pieces. For HepG2 cells, the cells were trypsinized and washed with PBS. The chromatin was cross-linked with 1% formaldehyde (Sigma) at ambient temperature for 10 min and quenched with 125mM glycine for 5 min. PBS washed tissue was homogenized with loose fitting douncer for 30 strokes before centrifugation to isolate the nuclei. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. The single strand overhang was filled with biotinylated-14-ATP (Life Tech.) using Klenow DNA polymerase (NEB). Different from tradition Hi-C, with in situ protocol the ligation was performed when the nuclear membrane was still intact. DNA was ligated for 4h at 16 °C using T4 ligase (NEB). Protein was degraded by proteinase K (NEB) treatment at 55 °C for 30 min. The crosslinking was reversed with 500 mM of NaCl and heated at 68 °C o/n. DNA was purified and sonicated to 300-700 bp small fragments. Biotinylated DNA was selected with Dynabeads My One T1 Streptavidin beads (Life Tech.). Sequencing library was prepared on beads and intensive wash was performed between different reactions.  Whole genome sequencing:  The genomic DNA was extracted using Qiagen kit (cat. no. 69506). The DNA was then fragmented with Covaris S220 ultrasonicator to 300-500 bp long.  RNA-seq:  The total RNA was isolated using Qiagen RNeasy mini kit. The sequencing library was prepared using Truseq illumine RNA Library Prep Kit v2 (cat. #RS-122-2001).  SELEX:  Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).
ChIP-seq:
Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65°C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit. STARR-seq:
The plasmid pool was transfected into HEK293T or HepG2 cell lines using Fugene HD and continued culturing for 48 hours before harvest. Total RNA was extracted with RNeasy kit (Qiagen, 74104) and mRNA was enriched with poly(dT)25 Dynabeads (Invitrogen, 61002). First strand cDNA was synthesized using a specific primer (5’-CAAACTCATCAATGTATCTTATCATG) with high High-Capacity cDNA Reverse Transcription kit (ThermoFisher Scientific, 4368814). The nested PCR was used to amplify the SNP specific fragments from cDNA, first using two reporter-specific PCR primers (5’-GGGCCAGCTGTTGGGGTGTCCAC & 5’-CTTATCATGTCTGCTCGAAGC) and then generic primers used in HT-SELEX. DNA was purified with AMPure beads.
Hi-C:
Briefly, the human islets were washed with cold PBS and cut into small pieces. For HepG2 cells, the cells were trypsinized and washed with PBS. The chromatin was cross-linked with 1% formaldehyde (Sigma) at ambient temperature for 10 min and quenched with 125mM glycine for 5 min. PBS washed tissue was homogenized with loose fitting douncer for 30 strokes before centrifugation to isolate the nuclei. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. The single strand overhang was filled with biotinylated-14-ATP (Life Tech.) using Klenow DNA polymerase (NEB). Different from tradition Hi-C, with in situ protocol the ligation was performed when the nuclear membrane was still intact. DNA was ligated for 4h at 16 °C using T4 ligase (NEB). Protein was degraded by proteinase K (NEB) treatment at 55 °C for 30 min. The crosslinking was reversed with 500 mM of NaCl and heated at 68 °C o/n. DNA was purified and sonicated to 300-700 bp small fragments. Biotinylated DNA was selected with Dynabeads My One T1 Streptavidin beads (Life Tech.). Sequencing library was prepared on beads and intensive wash was performed between different reactions.
Whole genome sequencing:
The genomic DNA was extracted using Qiagen kit (cat. no. 69506). The DNA was then fragmented with Covaris S220 ultrasonicator to 300-500 bp long.
RNA-seq:
The total RNA was isolated using Qiagen RNeasy mini kit. The sequencing library was prepared using Truseq illumine RNA Library Prep Kit v2 (cat. #RS-122-2001).
SELEX:
Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).

treatment_protocol: Fugene HD (Promega, E2311) was used for plasmid transfection. Specifically, 2 µg of STARR-seq plasmids were mixed with 5 µl of transfection reagents for transfection into 300,000 cells cultured in a single well of 6-well plate. For siRNA transfection, HiPerfect transfection was used following the manufacture guidance. For each experiment, 50 nM of siRNA was used with 5 ul of HiPerfect reagent to make the transfection complex for 1-3×104 cells. Cells were continued to be cultured for 72 hours. The siRNAs targeting human HLF (cat. #GS3131) and MAFG (cat. #GS4097) were commercially available from Qiagen. Silencer negative control siRNA was commercially manufactured and order from Thermo Fisher (cat. #AM4635).

tag: library strategy

value: RNA-seq

tag: cell line/type

value: Islet

value: polyA RNA


title: A0003 Islet RNA

description:
processed data file:
Islet.fpkm.tsv
JY212

source_name: A0003 Islet


title: A0001 Islet RNA

description:
processed data file:
Islet.fpkm.tsv
JY210

source_name: A0001 Islet


title: A0004 Islet RNA

description:
processed data file:
Islet.fpkm.tsv
JY213

source_name: A0004 Islet


title: 2_H9

description:
processed data file:
pbs.obs_pval05.tsv
2_H9-1

organism: synthetic construct

source_name: Synthesized DNA

value: SELEX

tag: cycle

tag: plate

value: Synthesized DNA


title: 2_H8

description:
processed data file:
pbs.obs_pval05.tsv
2_H8-1


title: 2_H6

description:
processed data file:
pbs.obs_pval05.tsv
2_H6-1


title: 2_H7

description:
processed data file:
pbs.obs_pval05.tsv
2_H7-1


title: 2_H5

description:
processed data file:
pbs.obs_pval05.tsv
2_H5-1


title: HepG2 RNA

description:
processed data file:
HepG2.fpkm.tsv
RZY791-1


title: 2_H4

description:
processed data file:
pbs.obs_pval05.tsv
2_H4-1


title: 2_H2

description:
processed data file:
pbs.obs_pval05.tsv
2_H2-1


title: 2_H3

description:
processed data file:
pbs.obs_pval05.tsv
2_H3-1


title: 2_G9

description:
processed data file:
pbs.obs_pval05.tsv
2_G9-1


title: 2_H1

description:
processed data file:
pbs.obs_pval05.tsv
2_H1-1


title: 2_H11

description:
processed data file:
pbs.obs_pval05.tsv
2_H11-1


title: iPS-RGCs_RNA

city: Kobe

first: Ayaka

last: Edo

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Laboratory for Retinal Regeneration

institute: RIKEN Center for Biosystems Dynamics Research

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

source_name: Retinal ganglion cells (RGCs) derived from human iPSCs

extract_protocol: We used High Pure RNA Isolation Kit (Roche, Product No. 11828665001).

tag: cell line

value: RGCs derived from human iPSCs (TLHD2 line)

tag: source

value: human healthy donor


title: 2_H12

description:
processed data file:
pbs.obs_pval05.tsv
2_H12-1


title: 2_G7

description:
processed data file:
pbs.obs_pval05.tsv
2_G7-1


title: 2_G8

description:
processed data file:
pbs.obs_pval05.tsv
2_G8-1


title: hStrS_d80-83_aggr

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

data_processing:
Quality control, UMI counting of Ensemble genes and aggregation of samples were performed by count and aggr functions in the Cell Ranger software (version 3.1.0 with default settings)
Genome_build: Human: GRCh38
Supplementary_files_format_and_content: Count matrices, barcodes, and features

source_name: Human induced pluripotent stem cells

extract_protocol:
Cells were loaded onto a Chromium Single cell 3’ chip (Chromium Chip B Single Cell Kit, 10x Genomics, PN-1000154) with Chromium Single Cell 3’ Library & Gel Bead kit v3 (10x Genomics, PN-1000075) and proceeded according to manufacturer’s instructions.
cDNA library was generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead kit v3 (10x Genomics, PN-1000078) according to manufacturer’s instructions.

tag: hips cell line

tag: age (day)


title: 2_H10

description:
processed data file:
pbs.obs_pval05.tsv
2_H10-1


title: 2_G6

description:
processed data file:
pbs.obs_pval05.tsv
2_G6-1


title: 2_G5

description:
processed data file:
pbs.obs_pval05.tsv
2_G5-1


title: 2_G4

description:
processed data file:
pbs.obs_pval05.tsv
2_G4-1


title: iPSCs_RNA

source_name: human induced pluripotent stem cells (iPSCs)

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

value: iPSCs


title: 2_G3

description:
processed data file:
pbs.obs_pval05.tsv
2_G3-1


title: 2_G12

description:
processed data file:
pbs.obs_pval05.tsv
2_G12-1


title: 2_G2

description:
processed data file:
pbs.obs_pval05.tsv
2_G2-1


title: PBMCs_RNA

source_name: Peripheral blood mononuclear cells from TLHD2 line donor

value: PBMCs


title: 2_F8

description:
processed data file:
pbs.obs_pval05.tsv
2_F8-1


title: 2_F9

description:
processed data file:
pbs.obs_pval05.tsv
2_F9-1


title: 2_F5

description:
processed data file:
pbs.obs_pval05.tsv
2_F5-1


title: 2_F6

description:
processed data file:
pbs.obs_pval05.tsv
2_F6-1


title: 2_G10

description:
processed data file:
pbs.obs_pval05.tsv
2_G10-1


title: 2_F7

description:
processed data file:
pbs.obs_pval05.tsv
2_F7-1


title: 2_F3

description:
processed data file:
pbs.obs_pval05.tsv
2_F3-1


title: 2_E9

description:
processed data file:
pbs.obs_pval05.tsv
2_E9-1


title: 2_E8

description:
processed data file:
pbs.obs_pval05.tsv
2_E8-1


title: 2_F11

description:
processed data file:
pbs.obs_pval05.tsv
2_F11-1


title: 2_F10

description:
processed data file:
pbs.obs_pval05.tsv
2_F10-1


title: 2_F1

description:
processed data file:
pbs.obs_pval05.tsv
2_F1-1


title: 2_E4

description:
processed data file:
pbs.obs_pval05.tsv
2_E4-1


title: 2_E5

description:
processed data file:
pbs.obs_pval05.tsv
2_E5-1


title: 2_E3

description:
processed data file:
pbs.obs_pval05.tsv
2_E3-1


title: 2_F2

description:
processed data file:
pbs.obs_pval05.tsv
2_F2-1


title: 2_E11

description:
processed data file:
pbs.obs_pval05.tsv
2_E11-1


title: 2_E2

description:
processed data file:
pbs.obs_pval05.tsv
2_E2-1


title: 2_E7

description:
processed data file:
pbs.obs_pval05.tsv
2_E7-1


title: 2_F12

description:
processed data file:
pbs.obs_pval05.tsv
2_F12-1


title: 2_E6

description:
processed data file:
pbs.obs_pval05.tsv
2_E6-1


title: 2_E10

description:
processed data file:
pbs.obs_pval05.tsv
2_E10-1


title: 2_E12

description:
processed data file:
pbs.obs_pval05.tsv
2_E12-1


title: 2_G11

description:
processed data file:
pbs.obs_pval05.tsv
2_G11-1


title: 2_G1

description:
processed data file:
pbs.obs_pval05.tsv
2_G1-1


title: 2_D9

description:
processed data file:
pbs.obs_pval05.tsv
2_D9-1


title: 2_E1

description:
processed data file:
pbs.obs_pval05.tsv
2_E1-1


title: 2_D8

description:
processed data file:
pbs.obs_pval05.tsv
2_D8-1


title: 2_F4

description:
processed data file:
pbs.obs_pval05.tsv
2_F4-1


title: 2_D7

description:
processed data file:
pbs.obs_pval05.tsv
2_D7-1


title: 2_D2

description:
processed data file:
pbs.obs_pval05.tsv
2_D2-1


title: 2_D12

description:
processed data file:
pbs.obs_pval05.tsv
2_D12-1


title: 2_D6

description:
processed data file:
pbs.obs_pval05.tsv
2_D6-1


title: 2_D4

description:
processed data file:
pbs.obs_pval05.tsv
2_D4-1


title: 2_D3

description:
processed data file:
pbs.obs_pval05.tsv
2_D3-1


title: 2_D5

description:
processed data file:
pbs.obs_pval05.tsv
2_D5-1


title: 2_D10

description:
processed data file:
pbs.obs_pval05.tsv
2_D10-1


title: 2_C9

description:
processed data file:
pbs.obs_pval05.tsv
2_C9-1


title: 2_C4

description:
processed data file:
pbs.obs_pval05.tsv
2_C4-1


title: 2_C6

description:
processed data file:
pbs.obs_pval05.tsv
2_C6-1


title: 2_C5

description:
processed data file:
pbs.obs_pval05.tsv
2_C5-1


title: 2_D1

description:
processed data file:
pbs.obs_pval05.tsv
2_D1-1


title: 2_C2

description:
processed data file:
pbs.obs_pval05.tsv
2_C2-1


title: 2_C8

description:
processed data file:
pbs.obs_pval05.tsv
2_C8-1


title: 2_C7

description:
processed data file:
pbs.obs_pval05.tsv
2_C7-1


title: 2_C3

description:
processed data file:
pbs.obs_pval05.tsv
2_C3-1


title: 2_C1

description:
processed data file:
pbs.obs_pval05.tsv
2_C1-1


title: 2_C12

description:
processed data file:
pbs.obs_pval05.tsv
2_C12-1


title: 2_C10

description:
processed data file:
pbs.obs_pval05.tsv
2_C10-1


title: 2_B9

description:
processed data file:
pbs.obs_pval05.tsv
2_B9-1


title: 2_C11

description:
processed data file:
pbs.obs_pval05.tsv
2_C11-1


title: 2_B8

description:
processed data file:
pbs.obs_pval05.tsv
2_B8-1


title: 2_B7

description:
processed data file:
pbs.obs_pval05.tsv
2_B7-1


title: 2_B6

description:
processed data file:
pbs.obs_pval05.tsv
2_B6-1


title: 2_B5

description:
processed data file:
pbs.obs_pval05.tsv
2_B5-1


title: 2_B4

description:
processed data file:
pbs.obs_pval05.tsv
2_B4-1


title: 2_B2

description:
processed data file:
pbs.obs_pval05.tsv
2_B2-1


title: 2_B12

description:
processed data file:
pbs.obs_pval05.tsv
2_B12-1


title: 2_D11

description:
processed data file:
pbs.obs_pval05.tsv
2_D11-1


title: 2_B1

description:
processed data file:
pbs.obs_pval05.tsv
2_B1-1


title: 2_A9

description:
processed data file:
pbs.obs_pval05.tsv
2_A9-1


title: 2_B11

description:
processed data file:
pbs.obs_pval05.tsv
2_B11-1


title: 2_B10

description:
processed data file:
pbs.obs_pval05.tsv
2_B10-1


title: 2_A8

description:
processed data file:
pbs.obs_pval05.tsv
2_A8-1


title: 2_A7

description:
processed data file:
pbs.obs_pval05.tsv
2_A7-1


title: 2_A4

description:
processed data file:
pbs.obs_pval05.tsv
2_A4-1


title: 2_A3

description:
processed data file:
pbs.obs_pval05.tsv
2_A3-1


title: 2_B3

description:
processed data file:
pbs.obs_pval05.tsv
2_B3-1


title: 2_A2

description:
processed data file:
pbs.obs_pval05.tsv
2_A2-1


title: 1_H9

description:
processed data file:
pbs.obs_pval05.tsv
1_H9-1


title: 1_H3

description:
processed data file:
pbs.obs_pval05.tsv
1_H3-1


title: 1_H5

description:
processed data file:
pbs.obs_pval05.tsv
1_H5-1


title: 2_A1

description:
processed data file:
pbs.obs_pval05.tsv
2_A1-1


title: 2_A11

description:
processed data file:
pbs.obs_pval05.tsv
2_A11-1


title: 2_A10

description:
processed data file:
pbs.obs_pval05.tsv
2_A10-1


title: 2_A12

description:
processed data file:
pbs.obs_pval05.tsv
2_A12-1


title: 1_H12

description:
processed data file:
pbs.obs_pval05.tsv
1_H12-1


title: 1_H11

description:
processed data file:
pbs.obs_pval05.tsv
1_H11-1


title: 1_H2

description:
processed data file:
pbs.obs_pval05.tsv
1_H2-1


title: 1_H10

description:
processed data file:
pbs.obs_pval05.tsv
1_H10-1


title: 1_H1

description:
processed data file:
pbs.obs_pval05.tsv
1_H1-1


title: 2_A6

description:
processed data file:
pbs.obs_pval05.tsv
2_A6-1


title: 1_G8

description:
processed data file:
pbs.obs_pval05.tsv
1_G8-1


title: 1_G6

description:
processed data file:
pbs.obs_pval05.tsv
1_G6-1


title: 1_G5

description:
processed data file:
pbs.obs_pval05.tsv
1_G5-1


title: 1_G9

description:
processed data file:
pbs.obs_pval05.tsv
1_G9-1


title: 1_G7

description:
processed data file:
pbs.obs_pval05.tsv
1_G7-1


title: 2_A5

description:
processed data file:
pbs.obs_pval05.tsv
2_A5-1


title: 1_H8

description:
processed data file:
pbs.obs_pval05.tsv
1_H8-1


title: 1_G3

description:
processed data file:
pbs.obs_pval05.tsv
1_G3-1


title: 1_G2

description:
processed data file:
pbs.obs_pval05.tsv
1_G2-1


title: 1_H4

description:
processed data file:
pbs.obs_pval05.tsv
1_H4-1


title: 1_H6

description:
processed data file:
pbs.obs_pval05.tsv
1_H6-1


title: 1_G12

description:
processed data file:
pbs.obs_pval05.tsv
1_G12-1


title: 1_G11

description:
processed data file:
pbs.obs_pval05.tsv
1_G11-1


title: 1_F9

description:
processed data file:
pbs.obs_pval05.tsv
1_F9-1


title: 1_F8

description:
processed data file:
pbs.obs_pval05.tsv
1_F8-1


title: 1_H7

description:
processed data file:
pbs.obs_pval05.tsv
1_H7-1


title: 1_F6

description:
processed data file:
pbs.obs_pval05.tsv
1_F6-1


title: 1_F7

description:
processed data file:
pbs.obs_pval05.tsv
1_F7-1


title: 1_G1

description:
processed data file:
pbs.obs_pval05.tsv
1_G1-1


title: 1_F3

description:
processed data file:
pbs.obs_pval05.tsv
1_F3-1


title: 1_F11

description:
processed data file:
pbs.obs_pval05.tsv
1_F11-1


title: 1_F4

description:
processed data file:
pbs.obs_pval05.tsv
1_F4-1


title: 1_G4

description:
processed data file:
pbs.obs_pval05.tsv
1_G4-1


title: 1_F10

description:
processed data file:
pbs.obs_pval05.tsv
1_F10-1


title: 1_G10

description:
processed data file:
pbs.obs_pval05.tsv
1_G10-1


title: 1_F1

description:
processed data file:
pbs.obs_pval05.tsv
1_F1-1


title: 1_F2

description:
processed data file:
pbs.obs_pval05.tsv
1_F2-1


title: 1_E9

description:
processed data file:
pbs.obs_pval05.tsv
1_E9-1


title: 1_F5

description:
processed data file:
pbs.obs_pval05.tsv
1_F5-1


title: 1_E5

description:
processed data file:
pbs.obs_pval05.tsv
1_E5-1


title: 1_E7

description:
processed data file:
pbs.obs_pval05.tsv
1_E7-1


title: 1_E6

description:
processed data file:
pbs.obs_pval05.tsv
1_E6-1


title: 1_E4

description:
processed data file:
pbs.obs_pval05.tsv
1_E4-1


title: 1_E3

description:
processed data file:
pbs.obs_pval05.tsv
1_E3-1


title: 1_E8

description:
processed data file:
pbs.obs_pval05.tsv
1_E8-1


title: 1_E2

description:
processed data file:
pbs.obs_pval05.tsv
1_E2-1


title: 1_E12

description:
processed data file:
pbs.obs_pval05.tsv
1_E12-1


title: 1_E10

description:
processed data file:
pbs.obs_pval05.tsv
1_E10-1


title: 1_E1

description:
processed data file:
pbs.obs_pval05.tsv
1_E1-1


title: 1_F12

description:
processed data file:
pbs.obs_pval05.tsv
1_F12-1


title: 1_D8

description:
processed data file:
pbs.obs_pval05.tsv
1_D8-1


title: 1_D9

description:
processed data file:
pbs.obs_pval05.tsv
1_D9-1


title: 1_D5

description:
processed data file:
pbs.obs_pval05.tsv
1_D5-1


title: 1_D2

description:
processed data file:
pbs.obs_pval05.tsv
1_D2-1


title: 1_D4

description:
processed data file:
pbs.obs_pval05.tsv
1_D4-1


title: 1_D12

description:
processed data file:
pbs.obs_pval05.tsv
1_D12-1


title: 1_D11

description:
processed data file:
pbs.obs_pval05.tsv
1_D11-1


title: 1_D1

description:
processed data file:
pbs.obs_pval05.tsv
1_D1-1


title: 1_D6

description:
processed data file:
pbs.obs_pval05.tsv
1_D6-1


title: 1_D7

description:
processed data file:
pbs.obs_pval05.tsv
1_D7-1


title: 1_C8

description:
processed data file:
pbs.obs_pval05.tsv
1_C8-1


title: 1_C6

description:
processed data file:
pbs.obs_pval05.tsv
1_C6-1


title: 1_C7

description:
processed data file:
pbs.obs_pval05.tsv
1_C7-1


title: 1_D10

description:
processed data file:
pbs.obs_pval05.tsv
1_D10-1


title: 1_C5

description:
processed data file:
pbs.obs_pval05.tsv
1_C5-1


title: 1_C3

description:
processed data file:
pbs.obs_pval05.tsv
1_C3-1


title: 1_C4

description:
processed data file:
pbs.obs_pval05.tsv
1_C4-1


title: 1_C12

description:
processed data file:
pbs.obs_pval05.tsv
1_C12-1


title: 1_C10

description:
processed data file:
pbs.obs_pval05.tsv
1_C10-1


title: 1_C1

description:
processed data file:
pbs.obs_pval05.tsv
1_C1-1


title: 1_B9

description:
processed data file:
pbs.obs_pval05.tsv
1_B9-1


title: 1_D3

description:
processed data file:
pbs.obs_pval05.tsv
1_D3-1


title: 1_B7

description:
processed data file:
pbs.obs_pval05.tsv
1_B7-1


title: 1_C9

description:
processed data file:
pbs.obs_pval05.tsv
1_C9-1


title: 1_B5

description:
processed data file:
pbs.obs_pval05.tsv
1_B5-1


title: 1_B6

description:
processed data file:
pbs.obs_pval05.tsv
1_B6-1


title: 1_B4

description:
processed data file:
pbs.obs_pval05.tsv
1_B4-1


title: 1_E11

description:
processed data file:
pbs.obs_pval05.tsv
1_E11-1


title: 1_A8

description:
processed data file:
pbs.obs_pval05.tsv
1_A8-1


title: 1_A9

description:
processed data file:
pbs.obs_pval05.tsv
1_A9-1


title: 1_B1

description:
processed data file:
pbs.obs_pval05.tsv
1_B1-1


title: 1_B2

description:
processed data file:
pbs.obs_pval05.tsv
1_B2-1


title: 1_B12

description:
processed data file:
pbs.obs_pval05.tsv
1_B12-1


title: 1_A6

description:
processed data file:
pbs.obs_pval05.tsv
1_A6-1


title: 1_C2

description:
processed data file:
pbs.obs_pval05.tsv
1_C2-1


title: 1_A7

description:
processed data file:
pbs.obs_pval05.tsv
1_A7-1


title: 1_A4

description:
processed data file:
pbs.obs_pval05.tsv
1_A4-1


title: 1_A5

description:
processed data file:
pbs.obs_pval05.tsv
1_A5-1


title: 1_A3

description:
processed data file:
pbs.obs_pval05.tsv
1_A3-1


title: 1_C11

description:
processed data file:
pbs.obs_pval05.tsv
1_C11-1


title: 1_A2

description:
processed data file:
pbs.obs_pval05.tsv
1_A2-1


title: 1_A12

description:
processed data file:
pbs.obs_pval05.tsv
1_A12-1


title: 1_B8

description:
processed data file:
pbs.obs_pval05.tsv
1_B8-1


title: 1_A11

description:
processed data file:
pbs.obs_pval05.tsv
1_A11-1


title: HSF1.FL.6.0.E5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HSF1_FL_cycle2_Protein6_E5

tag: tf

tag: tf type

value: FL (Full Length)


title: NR4A2.DBD.8.0.C12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR4A2_DBD_cycle2_Protein8_C12

value: DBD (DNA binding domain)


title: FOXP3.FL.8.0.E11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXP3_FL_cycle2_Protein8_E11


title: 1_A1

description:
processed data file:
pbs.obs_pval05.tsv
1_A1-1


title: 1_A10

description:
processed data file:
pbs.obs_pval05.tsv
1_A10-1


title: ETV1.FL.7.1.H6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ETV1_FL_cycle6_Protein7_H6


title: IRF6.FL.8.0.D10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
IRF6_FL_cycle6_Protein8_D10


title: MLX.FL.7.1.B2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MLX_FL_cycle6_Protein7_B2

value: MLX


title: 1_B11

description:
processed data file:
pbs.obs_pval05.tsv
1_B11-1


title: 1_B10

description:
processed data file:
pbs.obs_pval05.tsv
1_B10-1


title: NoProtein.NA.8.0.H7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H7

value: NoProtein


title: FOXM1.FL.8.0.H2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXM1_FL_cycle2_Protein8_H2


title: No_Protein.FL.8.0.F12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
No_Protein_FL_cycle6_Protein8_F12


title: RHOXF1.FL.7.1.E7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RHOXF1_FL_cycle2_Protein7_E7


title: MIXL1.FL.7.1.F5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MIXL1_FL_cycle2_Protein7_F5


title: HMX2.FL.6.0.C6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HMX2_FL_cycle2_Protein6_C6


title: GFI1B.DBD.8.0.A6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
GFI1B_DBD_cycle6_Protein8_A6


title: PRRX1.DBD.8.0.A9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
PRRX1_DBD_cycle6_Protein8_A9


title: ZFP161.FL.8.0.F10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZFP161_FL_cycle2_Protein8_F10


title: ZNF597.FL.6.0.D7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF597_FL_cycle2_Protein6_D7


title: ZBTB26.FL.6.0.F7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZBTB26_FL_cycle2_Protein6_F7


title: ZNF501.FL.5.1.E9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF501_FL_cycle2_Protein5_E9


title: ZNF396.FL.7.1.D9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF396_FL_cycle6_Protein7_D9


title: ZNF323.FL.7.1.G10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF323_FL_cycle6_Protein7_G10


title: TEAD1.FL.8.0.D5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TEAD1_FL_cycle2_Protein8_D5


title: ZNF580.FL.7.1.C1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF580_FL_cycle6_Protein7_C1


title: HLF.FL.7.1.A2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HLF_FL_cycle2_Protein7_A2

value: HLF


title: SOX14.FL.7.1.G5.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
SOX14_FL_cycle6_Protein7_G5


title: HOXC4.FL.7.1.G6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXC4_FL_cycle2_Protein7_G6


title: TCF7L2.FL.8.0.G9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TCF7L2_FL_cycle2_Protein8_G9


title: HOXB7.DBD.8.0.C2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXB7_DBD_cycle2_Protein8_C2


title: RHOXF1.FL.5.1.H8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RHOXF1_FL_cycle2_Protein5_H8


title: NoProtein.NA.8.0.H6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H6


title: DLX5.FL.6.0.G6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DLX5_FL_cycle2_Protein6_G6


title: ELK3.FL.5.1.E4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELK3_FL_cycle2_Protein5_E4


title: FOSL1.FL.7.1.B9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOSL1_FL_cycle2_Protein7_B9


title: DLX2.FL.7.1.C5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DLX2_FL_cycle2_Protein7_C5


title: MYOG.FL.7.1.D7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MYOG_FL_cycle2_Protein7_D7

value: MYOG


title: IRF2.FL.7.1.A5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF2_FL_cycle2_Protein7_A5


title: ASCL2.FL.8.0.E7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ASCL2_FL_cycle6_Protein8_E7


title: NoProtein.NA.8.0.H10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H10


title: KLF13.FL.5.1.D9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
KLF13_FL_cycle2_Protein5_D9


title: HSFY1.DBD.8.0.A3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HSFY1_DBD_cycle6_Protein8_A3


title: ARNT2.DBD.8.0.C3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ARNT2_DBD_cycle6_Protein8_C3


title: BARX2.FL.7.1.F10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
BARX2_FL_cycle2_Protein7_F10


title: DMRTC2.FL.7.1.A7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
DMRTC2_FL_cycle6_Protein7_A7


title: XBP1.FL.5.1.B12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
XBP1_FL_cycle2_Protein5_B12


title: MAFG.FL.5.1.E8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MAFG_FL_cycle2_Protein5_E8

value: MAFG


title: IRF8.FL.5.1.G8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF8_FL_cycle2_Protein5_G8


title: SNAI3.FL.8.0.F8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
SNAI3_FL_cycle6_Protein8_F8


title: ZNF597.FL.6.0.C2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF597_FL_cycle2_Protein6_C2


title: HOXD9.FL.6.0.A7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXD9_FL_cycle2_Protein6_A7


title: GLI2.DBD.8.0.A1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
GLI2_DBD_cycle2_Protein8_A1


title: EMX1.FL.5.1.F1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
EMX1_FL_cycle2_Protein5_F1


title: FOXR2.FL.8.0.D9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXR2_FL_cycle2_Protein8_D9


title: FOXR2.FL.7.1.E2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXR2_FL_cycle2_Protein7_E2


title: BATF.FL.7.1.C10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
BATF_FL_cycle6_Protein7_C10

value: BATF


title: RHOXF1.FL.7.1.E7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
RHOXF1_FL_cycle6_Protein7_E7


title: ESRRG.FL.6.0.B10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ESRRG_FL_cycle2_Protein6_B10

value: ESRRG


title: BARX2.FL.7.1.F10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
BARX2_FL_cycle6_Protein7_F10


title: NEUROG2.FL.5.1.B7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NEUROG2_FL_cycle2_Protein5_B7


title: POU5F1.FL.8.0.F3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
POU5F1_FL_cycle6_Protein8_F3


title: VENTX.FL.8.0.D2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
VENTX_FL_cycle2_Protein8_D2

value: VENTX


title: ETV7.FL.7.1.D2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ETV7_FL_cycle2_Protein7_D2


title: NKX2_3.FL.5.1.A4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NKX2_3_FL_cycle2_Protein5_A4


title: SNAI1.FL.7.1.A12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
SNAI1_FL_cycle6_Protein7_A12


title: HOXB4.FL.5.1.A9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXB4_FL_cycle2_Protein5_A9


title: NR5A1.FL.6.0.D6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR5A1_FL_cycle2_Protein6_D6


title: DLX3.FL.6.0.F9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DLX3_FL_cycle2_Protein6_F9


title: ETS2.FL.7.1.H1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ETS2_FL_cycle6_Protein7_H1


title: TFAP2E.FL.5.1.G1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TFAP2E_FL_cycle2_Protein5_G1


title: PROP1.DBD.8.0.A10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
PROP1_DBD_cycle6_Protein8_A10


title: NHLH1.FL.7.1.C4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NHLH1_FL_cycle6_Protein7_C4


title: ETV4.FL.7.1.B12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ETV4_FL_cycle6_Protein7_B12


title: JUN.FL.7.1.C9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
JUN_FL_cycle2_Protein7_C9

value: JUN


title: ZBTB46.DBD.8.0.B4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZBTB46_DBD_cycle6_Protein8_B4

value: SELEX


title: NoProtein.NA.8.0.H7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle6_Protein8_H7

value: Synthesized DNA


title: MBNL2.FL.7.1.G4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MBNL2_FL_cycle2_Protein7_G4


title: OVOL1.FL.7.1.E5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
OVOL1_FL_cycle2_Protein7_E5


title: ZNF77.DBD.8.0.G4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF77_DBD_cycle2_Protein8_G4


title: ZNF323.FL.5.1.D8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF323_FL_cycle2_Protein5_D8


title: ISX.FL.5.1.F5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ISX_FL_cycle2_Protein5_F5

value: ISX


title: BATF.FL.8.0.E8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
BATF_FL_cycle2_Protein8_E8


title: ATF2.FL.7.1.H2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ATF2_FL_cycle6_Protein7_H2


title: NoProtein.NA.8.0.H9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H9


title: RXRG.FL.6.0.D1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RXRG_FL_cycle2_Protein6_D1

value: RXRG


title: ZNF32.FL.7.1.F4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF32_FL_cycle2_Protein7_F4


title: MEF2B.FL.5.1.G9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MEF2B_FL_cycle2_Protein5_G9


title: HLF.FL.7.1.A2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HLF_FL_cycle6_Protein7_A2


title: HOXB5.FL.8.0.D12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXB5_FL_cycle2_Protein8_D12


title: RFX6.FL.8.0.G12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
RFX6_FL_cycle6_Protein8_G12


title: NHLH2.FL.5.1.F11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NHLH2_FL_cycle2_Protein5_F11


title: NoProtein.NA.8.0.H11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H11


title: ETV1.FL.7.1.H6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ETV1_FL_cycle2_Protein7_H6


title: CREB1.FL.7.1.A1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
CREB1_FL_cycle6_Protein7_A1


title: MAX.FL.7.1.B6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MAX_FL_cycle2_Protein7_B6

value: MAX


title: 1_B3

description:
processed data file:
pbs.obs_pval05.tsv
1_B3-1


title: OVOL2.FL.7.1.C3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
OVOL2_FL_cycle6_Protein7_C3


title: ZNF660.FL.5.1.D6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF660_FL_cycle2_Protein5_D6


title: NFIB.FL.6.0.E10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NFIB_FL_cycle2_Protein6_E10

value: NFIB


title: THRB.FL.7.1.E12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
THRB_FL_cycle2_Protein7_E12

value: THRB

value: FL (Full Length)


title: MYOG.FL.7.1.D7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MYOG_FL_cycle6_Protein7_D7


title: DLX3.FL.6.0.A4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DLX3_FL_cycle2_Protein6_A4


title: GLI2.DBD.8.0.A1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
GLI2_DBD_cycle6_Protein8_A1

value: DBD (DNA binding domain)


title: PRRX2.FL.5.1.B1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PRRX2_FL_cycle2_Protein5_B1


title: HES6.FL.8.0.E6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HES6_FL_cycle2_Protein8_E6


title: BARHL2.FL.7.1.F9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
BARHL2_FL_cycle6_Protein7_F9


title: HOXD4.FL.5.1.A7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXD4_FL_cycle2_Protein5_A7


title: ELK3.FL.6.0.D12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELK3_FL_cycle2_Protein6_D12


title: GATA3.FL.5.1.E6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
GATA3_FL_cycle2_Protein5_E6


title: HSF2.FL.7.1.E10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HSF2_FL_cycle2_Protein7_E10


title: ELF2.FL.6.0.E1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELF2_FL_cycle2_Protein6_E1


title: ELF3.FL.6.0.B4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELF3_FL_cycle2_Protein6_B4


title: FOXR2.FL.8.0.D9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
FOXR2_FL_cycle6_Protein8_D9


title: FERD3L.FL.7.1.F7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FERD3L_FL_cycle2_Protein7_F7


title: ONECUT2.FL.7.1.G2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ONECUT2_FL_cycle6_Protein7_G2


title: ZNF821.FL.7.1.A6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF821_FL_cycle2_Protein7_A6


title: HOXA2.FL.7.1.F12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXA2_FL_cycle2_Protein7_F12


title: FLI1.FL.5.1.C6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FLI1_FL_cycle2_Protein5_C6


title: HIC1.DBD.8.0.A4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HIC1_DBD_cycle6_Protein8_A4


title: DLX1.FL.5.1.E7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DLX1_FL_cycle2_Protein5_E7


title: HOXA13.FL.5.1.F3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXA13_FL_cycle2_Protein5_F3


title: NR2C1.DBD.8.0.B1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR2C1_DBD_cycle2_Protein8_B1


title: OLIG3.FL.7.1.E1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
OLIG3_FL_cycle2_Protein7_E1


title: LMX1B.FL.5.1.F8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LMX1B_FL_cycle2_Protein5_F8


title: MYOD1.FL.6.0.A11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MYOD1_FL_cycle2_Protein6_A11


title: FOXA3.FL.7.1.A4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
FOXA3_FL_cycle6_Protein7_A4


title: VENTX.FL.5.1.F2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
VENTX_FL_cycle2_Protein5_F2


title: ZNF57.FL.8.0.G1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF57_FL_cycle6_Protein8_G1


title: ZNF684.FL.8.0.D1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF684_FL_cycle6_Protein8_D1


title: BCL11B.DBD.8.0.B5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
BCL11B_DBD_cycle2_Protein8_B5


title: NoProtein.NA.8.0.H6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle6_Protein8_H6

value: NoProtein


title: MAFF.FL.6.0.B3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MAFF_FL_cycle2_Protein6_B3

value: MAFF


title: MEIS2.DBD.8.0.B6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MEIS2_DBD_cycle6_Protein8_B6


title: ZNF524.FL.7.1.E3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF524_FL_cycle6_Protein7_E3


title: HOXD10.DBD.8.0.B2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HOXD10_DBD_cycle6_Protein8_B2


title: NoProtein.NA.8.0.H11.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle6_Protein8_H11


title: PPARG.FL.8.0.H3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PPARG_FL_cycle2_Protein8_H3

value: PPARG


title: NEUROD2.FL.5.1.B8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NEUROD2_FL_cycle2_Protein5_B8


title: FOXA2.DBD.8.0.B10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
FOXA2_DBD_cycle6_Protein8_B10


title: RFXDC2.DBD.8.0.B3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
RFXDC2_DBD_cycle6_Protein8_B3


title: CDX4.FL.8.0.E1.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
CDX4_FL_cycle6_Protein8_E1


title: TEAD2.FL.7.1.C7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TEAD2_FL_cycle2_Protein7_C7


title: HIC1.DBD.8.0.A4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HIC1_DBD_cycle2_Protein8_A4


title: TFAP4.FL.6.0.H12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TFAP4_FL_cycle2_Protein6_H12


title: NKX2_8.FL.5.1.E12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NKX2_8_FL_cycle2_Protein5_E12


title: HOXC9.FL.7.1.G7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXC9_FL_cycle2_Protein7_G7


title: PITX1.FL.6.0.H5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PITX1_FL_cycle2_Protein6_H5


title: ERG.FL.7.1.H5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ERG_FL_cycle2_Protein7_H5

value: ERG


title: LHX9.FL.8.0.D3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LHX9_FL_cycle2_Protein8_D3


title: MEIS2.DBD.8.0.B6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MEIS2_DBD_cycle2_Protein8_B6


title: VSX2.FL.8.0.E2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
VSX2_FL_cycle6_Protein8_E2


title: ELK1.FL.7.1.C12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELK1_FL_cycle2_Protein7_C12


title: IRF5.FL.6.0.E7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF5_FL_cycle2_Protein6_E7


title: DMRT1.FL.7.1.G9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DMRT1_FL_cycle2_Protein7_G9


title: NHLH1.FL.7.1.C4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NHLH1_FL_cycle2_Protein7_C4


title: ATF4.FL.6.0.B2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ATF4_FL_cycle2_Protein6_B2


title: NoProtein.NA.8.0.H5.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle6_Protein8_H5


title: RHOXF2.FL.6.0.F11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RHOXF2_FL_cycle2_Protein6_F11


title: GBX2.FL.5.1.A2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
GBX2_FL_cycle2_Protein5_A2


title: PRRX1.DBD.8.0.A9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PRRX1_DBD_cycle2_Protein8_A9


title: RXRG.FL.5.1.C12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RXRG_FL_cycle2_Protein5_C12


title: HOXC9.FL.5.1.A11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXC9_FL_cycle2_Protein5_A11


title: SNAI3.FL.8.0.F8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SNAI3_FL_cycle2_Protein8_F8


title: ZNF501.FL.7.1.C2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF501_FL_cycle6_Protein7_C2


title: CREB3.FL.6.0.F12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
CREB3_FL_cycle2_Protein6_F12


title: HOXC8.FL.5.1.A10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXC8_FL_cycle2_Protein5_A10


title: IRF3.FL.5.1.C8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF3_FL_cycle2_Protein5_C8


title: SNAI1.FL.7.1.A12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SNAI1_FL_cycle2_Protein7_A12


title: IRF9.FL.5.1.C9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF9_FL_cycle2_Protein5_C9


title: NR2E1.FL.6.0.F8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR2E1_FL_cycle2_Protein6_F8


title: LMX1B.FL.7.1.G12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LMX1B_FL_cycle2_Protein7_G12


title: XPA.FL.7.1.E4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
XPA_FL_cycle6_Protein7_E4

value: XPA


title: ETS2.FL.7.1.H1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ETS2_FL_cycle2_Protein7_H1


title: E2F1.FL.5.1.G3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
E2F1_FL_cycle2_Protein5_G3


title: VENTX.FL.8.0.D2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
VENTX_FL_cycle6_Protein8_D2


title: ATF4.FL.6.0.G3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ATF4_FL_cycle2_Protein6_G3


title: DMRTC2.FL.7.1.A7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DMRTC2_FL_cycle2_Protein7_A7


title: NoProtein.NA.8.0.H5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H5


title: CREB3.FL.6.0.B1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
CREB3_FL_cycle2_Protein6_B1


title: TGIF2LY.DBD.8.0.C10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TGIF2LY_DBD_cycle2_Protein8_C10


title: ZFP161.FL.8.0.F10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZFP161_FL_cycle6_Protein8_F10


title: HOXD10.FL.7.1.C8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HOXD10_FL_cycle6_Protein7_C8


title: ZNF580.FL.7.1.C1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF580_FL_cycle2_Protein7_C1


title: TBX3.DBD.8.0.B8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TBX3_DBD_cycle2_Protein8_B8


title: SHOX.DBD.8.0.A12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SHOX_DBD_cycle2_Protein8_A12

value: SHOX


title: TGIF2LX.FL.5.1.G10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TGIF2LX_FL_cycle2_Protein5_G10


title: INSM1.DBD.8.0.G7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
INSM1_DBD_cycle2_Protein8_G7


title: RARB.FL.5.1.E10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RARB_FL_cycle2_Protein5_E10

value: RARB


title: XPA.FL.7.1.E4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
XPA_FL_cycle2_Protein7_E4


title: KLF3.FL.7.1.H12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
KLF3_FL_cycle6_Protein7_H12


title: EGR3.FL.8.0.D6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
EGR3_FL_cycle6_Protein8_D6


title: DLX4.FL.7.1.A8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
DLX4_FL_cycle6_Protein7_A8


title: NoProtein.NA.8.0.H8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle2_Protein8_H8


title: TGIF2LY.DBD.8.0.C10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
TGIF2LY_DBD_cycle6_Protein8_C10


title: PITX1.FL.6.0.H6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PITX1_FL_cycle2_Protein6_H6


title: GMEB1.FL.6.0.F1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
GMEB1_FL_cycle2_Protein6_F1


title: ZIC1.FL.5.1.H6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZIC1_FL_cycle2_Protein5_H6


title: NoProtein.NA.8.0.H10.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle6_Protein8_H10


title: SNAI1.FL.5.1.D11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SNAI1_FL_cycle2_Protein5_D11


title: PITX2.DBD.8.0.A7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
PITX2_DBD_cycle6_Protein8_A7


title: RARG.FL.5.1.G12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RARG_FL_cycle2_Protein5_G12

value: RARG


title: No_Protein.FL.8.0.F12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
No_Protein_FL_cycle2_Protein8_F12

value: SELEX


title: ZNF580.FL.6.0.C9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF580_FL_cycle2_Protein6_C9

value: Synthesized DNA


title: ESRRA.FL.8.0.F2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ESRRA_FL_cycle2_Protein8_F2

value: ESRRA


title: LHX4.FL.8.0.D8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
LHX4_FL_cycle6_Protein8_D8


title: TLX3.FL.7.1.D10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TLX3_FL_cycle2_Protein7_D10


title: MBNL2.FL.7.1.G4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MBNL2_FL_cycle6_Protein7_G4


title: MAX.FL.7.1.B6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MAX_FL_cycle6_Protein7_B6


title: ZNF32.FL.8.0.F6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ZNF32_FL_cycle6_Protein8_F6


title: YY1.FL.8.0.D11.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
YY1_FL_cycle6_Protein8_D11


title: CREB3L1.FL.6.0.D9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
CREB3L1_FL_cycle2_Protein6_D9


title: POU4F3.FL.7.1.G3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
POU4F3_FL_cycle6_Protein7_G3


title: DMRTA1.FL.7.1.E9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
DMRTA1_FL_cycle6_Protein7_E9


title: HOXA2.FL.7.1.F12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HOXA2_FL_cycle6_Protein7_F12


title: FOXM1.FL.8.0.H1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXM1_FL_cycle2_Protein8_H1


title: TBX20.FL.8.0.F5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TBX20_FL_cycle2_Protein8_F5


title: DMRTC2.FL.8.0.E10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DMRTC2_FL_cycle2_Protein8_E10


title: NR6A1.DBD.8.0.C9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
NR6A1_DBD_cycle6_Protein8_C9


title: PAX7.FL.7.1.H11.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
PAX7_FL_cycle6_Protein7_H11


title: ELF1.FL.6.0.D4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELF1_FL_cycle2_Protein6_D4


title: DLX1.FL.7.1.B4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
DLX1_FL_cycle6_Protein7_B4


title: DMRT1.FL.7.1.G9.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
DMRT1_FL_cycle6_Protein7_G9


title: IRF6.FL.6.0.E6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF6_FL_cycle2_Protein6_E6


title: PPARG.FL.8.0.G8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PPARG_FL_cycle2_Protein8_G8


title: ZSCAN16.FL.6.0.G5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZSCAN16_FL_cycle2_Protein6_G5


title: CREB1.FL.7.1.A1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
CREB1_FL_cycle2_Protein7_A1


title: BATF.FL.8.0.E8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
BATF_FL_cycle6_Protein8_E8

value: BATF


title: TEAD2.FL.7.1.C7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
TEAD2_FL_cycle6_Protein7_C7


title: EGR3.FL.8.0.D6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
EGR3_FL_cycle2_Protein8_D6


title: NR5A1.FL.6.0.B9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR5A1_FL_cycle2_Protein6_B9


title: ZFP161.FL.8.0.F9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZFP161_FL_cycle2_Protein8_F9


title: NHLH1.FL.5.1.B10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NHLH1_FL_cycle2_Protein5_B10


title: DBP.FL.5.1.F12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DBP_FL_cycle2_Protein5_F12

value: DBP


title: MAFG.FL.7.1.B11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MAFG_FL_cycle2_Protein7_B11

value: MAFG


title: ASCL2.FL.8.0.E7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ASCL2_FL_cycle2_Protein8_E7


title: ALX1.FL.6.0.G12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ALX1_FL_cycle2_Protein6_G12


title: ELK1.FL.7.1.C12.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ELK1_FL_cycle6_Protein7_C12


title: ELF5.FL.7.1.B3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ELF5_FL_cycle2_Protein7_B3


title: ZNF771.FL.5.1.D3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF771_FL_cycle2_Protein5_D3


title: HOXD3.FL.6.0.A6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXD3_FL_cycle2_Protein6_A6


title: PITX2.DBD.8.0.A7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PITX2_DBD_cycle2_Protein8_A7


title: FLI1.FL.6.0.C11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FLI1_FL_cycle2_Protein6_C11


title: MSC.FL.5.1.B9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MSC_FL_cycle2_Protein5_B9

value: MSC


title: ISX.FL.7.1.F6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ISX_FL_cycle6_Protein7_F6

value: ISX

value: FL (Full Length)


title: SPIB.FL.5.1.C5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SPIB_FL_cycle2_Protein5_C5

value: SPIB


title: ETV1.FL.8.0.F11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ETV1_FL_cycle2_Protein8_F11


title: RHOXF2.FL.6.0.A8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
RHOXF2_FL_cycle2_Protein6_A8


title: HOXA5.FL.7.1.B5.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HOXA5_FL_cycle6_Protein7_B5


title: NR6A1.DBD.8.0.C9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR6A1_DBD_cycle2_Protein8_C9

value: DBD (DNA binding domain)


title: GCM2.FL.7.1.H7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
GCM2_FL_cycle6_Protein7_H7


title: NKX6_1.DBD.8.0.G5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NKX6_1_DBD_cycle2_Protein8_G5


title: MEF2B.FL.7.1.C6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MEF2B_FL_cycle6_Protein7_C6


title: NR2F6.FL.5.1.C11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NR2F6_FL_cycle2_Protein5_C11


title: ZFP41.FL.5.1.D2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZFP41_FL_cycle2_Protein5_D2


title: LHX4.FL.6.0.D8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LHX4_FL_cycle2_Protein6_D8


title: FOXA3.FL.7.1.A4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
FOXA3_FL_cycle2_Protein7_A4


title: IRF8.FL.8.0.D4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
IRF8_FL_cycle2_Protein8_D4


title: ASCL2.FL.5.1.H12.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ASCL2_FL_cycle2_Protein5_H12


title: NEUROD1.FL.6.0.H11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NEUROD1_FL_cycle2_Protein6_H11


title: INSM1.DBD.8.0.G7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
INSM1_DBD_cycle6_Protein8_G7


title: ZIC3.FL.5.1.H11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZIC3_FL_cycle2_Protein5_H11


title: T.DBD.8.0.A5.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
T_DBD_cycle2_Protein8_A5

value: T


title: PBX1.FL.6.0.A10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PBX1_FL_cycle2_Protein6_A10


title: ESX1.FL.8.0.E4.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
ESX1_FL_cycle6_Protein8_E4


title: SNAI2.FL.7.1.B1.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
SNAI2_FL_cycle2_Protein7_B1


title: MAFB.DBD.8.0.G6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
MAFB_DBD_cycle2_Protein8_G6

value: MAFB


title: USF1.FL.7.1.D6.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
USF1_FL_cycle6_Protein7_D6


title: LHX9.FL.8.0.D3.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
LHX9_FL_cycle6_Protein8_D3


title: FOXM1.FL.8.0.H2.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
FOXM1_FL_cycle6_Protein8_H2


title: NFATC3.DBD.8.0.B7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NFATC3_DBD_cycle2_Protein8_B7


title: POU6F1.FL.8.0.F4.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
POU6F1_FL_cycle2_Protein8_F4


title: ATF2.FL.7.1.H2.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ATF2_FL_cycle2_Protein7_H2


title: FOXP3.FL.8.0.E11.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
FOXP3_FL_cycle6_Protein8_E11


title: BARHL1.DBD.8.0.A11.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
BARHL1_DBD_cycle6_Protein8_A11


title: LHX9.FL.5.1.F7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LHX9_FL_cycle2_Protein5_F7


title: NEUROG1.FL.7.1.B8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
NEUROG1_FL_cycle2_Protein7_B8


title: MAX.FL.7.1.B7.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
MAX_FL_cycle6_Protein7_B7

value: MAX


title: LIN28B.FL.5.1.D10.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
LIN28B_FL_cycle2_Protein5_D10


title: ZNF524.FL.7.1.E3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
ZNF524_FL_cycle2_Protein7_E3


title: PAX7.FL.7.1.H11.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
PAX7_FL_cycle2_Protein7_H11


title: VAX2.FL.6.0.G7.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
VAX2_FL_cycle2_Protein6_G7


title: POU5F1.FL.8.0.F3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
POU5F1_FL_cycle2_Protein8_F3


title: DMRTA1.FL.7.1.E9.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
DMRTA1_FL_cycle2_Protein7_E9


title: HOXD10.FL.7.1.C8.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXD10_FL_cycle2_Protein7_C8


title: HOXA10.FL.7.1.E6.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
HOXA10_FL_cycle2_Protein7_E6


title: TFCP2.FL.6.0.E3.cycle2

description:
processed data file:
pbs.obs_pval05.tsv
TFCP2_FL_cycle2_Protein6_E3


title: HESX1.FL.7.1.D8.cycle6

description:
processed data file:
pbs.obs_pval05.tsv
HESX1_FL_cycle6_Protein7_D8