title: Brca1-Day6-R1

tag: genotype

value: transfected with Brca1 siRNA


title: SA71

status: Public on Mar 14 2019

type: RNA

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

country: USA

institute: UT MD Anderson Cancer Center

description:
SAMPLE 115
Cystectomy
Bladder

data_processing:
Applied Biosystem's Sequence Detection System (SDS 2.2) software was used to compute Ct values using the default threshold and baseline parameters.
Delta Ct values were generated by subtracting experimental genes from endogenous control gene (RNU48-001006).
Fold-change values were created by subtracting the Target sample delta Ct from the control Sample delta Ct (Sample1 was used as control), then evaluated in the expression 2^-(delta-deltaCt).

label: TaqMan

molecule: total RNA

organism: Homo sapiens

source_name: Sarcomatoid carcinoma

label_protocol: Human Pool A v2.1.

extract_protocol: MasterPure Complete from Epicenter Biotechnologies.

tag: tissue

value: Sarcomatoid carcinoma


title: PMA 2_H3K4me1 _ChIP-seq

type: SRA

city: La Jolla

first: Matthew

last: Denholtz

state: California

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

description: ChIP-seq

library_source: genomic

data_processing:
Raw fastq files were aligned to the human genome build hg38 using bowtie [Langmead/Salzberg, Genome Biology, 2009] with the following parameters: -m1 --best --strata.
Sequencing data was reorganized as a HOMER (Heinz et al Mol. Cell 2010)-formatted tag directory for each data set and multiple reads mapping to the same base pair were collapsed to a single hit using the makeTagDirectory command in HOMER with the following parameters: -tbp 1
ChIP peaks were called using the findPeaks command in HOMER with default parameters
Unique reads from individual high quality biological replicates were pooled and ChIP peaks were re-called on pooled data as above using pooled inputs, conclusions were drawn from pooled ChIPseq data
Genome_build: hg38
Supplementary_files_format_and_content: ChIP peaks from pooled ChIPseq experiments are included, as are HOMER-formated tsv files for pooled input data sets. Tsv file scores represent reads per base pair.

molecule: genomic DNA

source_name: Peripheral blood neutrophils

growth_protocol: Human blood collected into heperinized syringes via venupuncture , granulocytes were purified from whole blood via density centrifugation with PolymorphPrep reagent (Accurate Chemical Scientific Corp., cat# AN1114683), purified granulocytes were cultured in HBSS +Ca +Mg -Phenol red (Life Technologies, cat# 14025092) + 0.5% endotoxin free BSA (Akron Biotech cat# Ak8917-0100) at 37degC, 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA end repair was performed using an Epicenter End-It kit (Lucigen ER0720), according to manufacturer’s instructions and column purified in a Zymo Minelute column (Zymo D4013). A-tails were added by incubating DNA in 1x NEB buffer 2 (New England Biolabs B7002S) with the addition of 200uM dATP and 7.5 units Klenow (exo-) (New England Biolabs M0212L) at 37 degrees for 45 minutes. NEB Next adaptors (New England Biolabs E7337A) were ligated using an NEB quick ligation kit (New England Biolabs M2200L) at benchtop temperature for 30 minutes followed by treatment with 2uL USER enzyme (New England Biolabs M5505L) for 15 minutes at 37°C. DNA was purified using a two-step SPRI bead protocol (from Rohland/Reich; Genome Research), resulting in purification of DNA fragments between 200-800 bp.

treatment_protocol: Human neutrophils were stimulated for three hours with either 25nM PMA (Promega, cat# V1171) or via co-culture with E. coli strain K1 at an MOI of 5 in culture conditions mirroring those in the growth protocol above

tag: chip antibody


title: genomic DNA from sample 26

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
Processed data in Series matrix table: Funnorm normalized

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: education level

tag: history of myocardial infarction

tag: age

tag: Sex

value: F

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran

value: whole blood


title: SA66

description:
SAMPLE 113
Cystectomy
Bladder


title: Bard1-Day6-R2

city: Nijmegen

first: Georgina

last: Peñalosa Ruiz

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

description: tet-OSKM lentiviral cassette was induced with doxycycline

library_source: transcriptomic

data_processing:
RNA-seq reads from mouse cells were mapped to genome mm10 using STAR version 2.5.2b with --quantMode geneCounts
Low-count gene filtering and normalization by log-cpm (log2-counts per million reads) were done with R package edgeR  version 3.20.9
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab delimited text files (.txt) containing normalized values in log counts per million reads

organism: Mus musculus

source_name: primary Mouse Embryonic Fibroblasts transduced with tet-STEMCCA lentiviruses containing Oct4, Sox2, Klf4 and c-Myc transgenes.

growth_protocol: Passage 1 MEFs were plated on gelatin-coated plates at a density of 10 000 cells per cm2. Next day they were incubated for 24 hours with inducible tet-OSKM (STEMCCA) and rtTA  lentiviruses at an MOI of 1. Reprogramming medium was composed of DMEM, 10 % FBS, 2ug/mL doxycycline, 3uM chiron, 0.25 uM Alk5i (TGFb-inhibitor), 50 ug/mL ascorbic acid and LIF.

extract_protocol:
RNA was isolated with the kit Quick-RNA microprep from Zymo Research (Cat# R1051), according to the manufacturer's instructions
200 ng total RNA were used to start the double-strand cDNA sysnthesis and library preparation with the Kapa RNA Hyper Prep Kit with Ribo Erase (Roche, #KK8561)  following standard Illumina protocols

treatment_protocol: After OSKM-rtTA transduction, cells were reverse transfected with 40 nM pooled siRNAs and RNAiMAX lipofectamine. 24 hours post-transfection, cells were re-plated on gelatin-coated wells, and induced for reprogramming with doxycycline and reprogramming medium.

tag: time when rna was collected

value: Day 6 of reprogramming

tag: strain

value: Wild-type

tag: passages

value: Reprogrammed at passage 2

tag: sirna

value: transfected with Bard1 siRNA


title: genomic DNA from sample 465

description: whole blood case sample

tag: tissue


title: SA69

description:
SAMPLE 114
Cystectomy
Bladder


title: genomic DNA from sample 85

description: whole blood case sample


title: Bard1-Day6-R1

tag: genotype


title: genomic DNA from sample 311

description: whole blood case sample

tag: diagnosis

value: M


title: genomic DNA from sample 252

description: whole blood case sample

tag: education level


title: genomic DNA from sample 203

description: whole blood control sample

value: control

tag: history of myocardial infarction


title: SA64

description:
SAMPLE 112
Cystectomy
Bladder


title: nt-Day6-R2

value: transfected with non-targeting siRNA


title: SA62

description:
SAMPLE 111
Cystectomy
Bladder


title: genomic DNA from sample 285

description: whole blood control sample

tag: age


title: genomic DNA from sample 225

description: whole blood control sample

tag: Sex


title: genomic DNA from sample 127

description: whole blood case sample

tag: snp based principle component 1


title: nt-Day6-R1


title: genomic DNA from sample 398

description: whole blood case sample

tag: snp based principle component 2


title: SA60

description:
SAMPLE 110
Cystectomy
Bladder


title: genomic DNA from sample 3

description: whole blood case sample

tag: cellcount-nk


title: Wdr5-Day3-R1

value: Day 3 of reprogramming

value: transfected with Wdr5 siRNA


title: genomic DNA from sample 414

description: whole blood case sample

tag: cellcount-bcell


title: genomic DNA from sample 156

description: whole blood control sample

tag: cellcount-mono


title: SA56

description:
SAMPLE 108
Cystectomy
Bladder


title: Brca1-Day6-R2


title: genomic DNA from sample 364

description: whole blood control sample

tag: cellcount-gran


title: SA54

description:
SAMPLE 107
Cystectomy
Bladder


title: Bard1-Day3-R2

tag: time when rna was collected


title: SA53

description:
SAMPLE 106
Cystectomy
Bladder


title: genomic DNA from sample 50

description: whole blood case sample


title: genomic DNA from sample 29

description: whole blood case sample


title: Brca1-Day3-R1

tag: strain


title: Bard1-Day3-R1

tag: passages


title: genomic DNA from sample 273

description: whole blood control sample


title: Brca1-Day3-R2

tag: sirna


title: genomic DNA from sample 215

description: whole blood control sample

tag: tissue


title: SA50

description:
SAMPLE 105
Cystectomy
Bladder


title: nt-Day3-R2

tag: genotype


title: SA58

description:
SAMPLE 109
Cystectomy
Bladder


title: SA49

description:
SAMPLE 104
Cystectomy
Bladder


title: genomic DNA from sample 417

description: whole blood case sample

tag: diagnosis


title: genomic DNA from sample 206

description: whole blood control sample

tag: education level


title: genomic DNA from sample 400

description: whole blood case sample

tag: history of myocardial infarction


title: genomic DNA from sample 379

description: whole blood control sample

tag: age


title: genomic DNA from sample 433

description: whole blood control sample

tag: Sex


title: genomic DNA from sample 368

description: whole blood case sample

tag: snp based principle component 1


title: nt-Day3-R1


title: SA47

description:
SAMPLE 103
Cystectomy
Bladder


title: Wdr5-Day3-R2


title: genomic DNA from sample 418

description: whole blood case sample

tag: snp based principle component 2


title: genomic DNA from sample 358

description: whole blood case sample

tag: cellcount-nk


title: SA44

description:
SAMPLE 102
Cystectomy
Bladder


title: Eed KO Day9 Adult Intestine Foxa1 ChIP Rep2

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Eed KO Day9 Adult Intestine Foxa1 ChIP Biological Replicate 2

data_processing:
Alignment: ATAC-seq and ChIP-seq:bowtie2 version 2.1.0, RNA-seq: STAR aligner version 2.5.3a, WGBS: Bismark version 0.13.1
ATAC-seq and ChIP-seq peak calling: MACS, version 1.4
WGBS determination of individual CpG methylation: Bismark version 0.13.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
Supplementary_files_format_and_content: WGBS: Table with individual CpG methylation status

source_name: mouse intestinal villus cells

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 1:1.5 combination of Foxa1 (Abcam 23738) and Foxa1 (Abcam 5089) overnight for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 5 consecutive days and every alternate day after that to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: mouse intestinal villus cells

value: B6;129 mixed background

tag: cell type

value: Adult Epitheial cells; proximal 1/3 of intestine

value: Eed F/F; Villin-CRE


title: SA43

description:
SAMPLE 101
Cystectomy
Bladder

value: Sarcomatoid carcinoma


title: genomic DNA from sample 236

description: whole blood case sample

value: case

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 369

description: whole blood case sample

value: F

tag: cellcount-gran


title: genomic DNA from sample 535

description: whole blood case sample

value: whole blood


title: E16.5 Intestine H3K4me1 ChIP Rep2

description: E16.5 Intestine H3K4me1 ChIP Biological Replicate 2

source_name: mouse midgut epithelial cells

extract_protocol:
E16.5 midguts were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K4me1 antibody overnight (C15410194, Diagenode) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: No treatment

value: mouse midgut epithelial cells

tag: strain

value: Embryonic epithelial cells from the midgut

value: Wild-Type


title: genomic DNA from sample 443

description: whole blood case sample


title: Eed KO Day14 Adult Intestine H3K4me1 ChIP Rep2

description: Eed KO Day14 Adult Intestine H3K4me1 ChIP Biological Replicate 2

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K4me1 antibody overnight (C15410194, Diagenode) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: SA42

description:
SAMPLE 100
Cystectomy
Bladder


title: genomic DNA from sample 297

description: whole blood control sample


title: SA40

description:
SAMPLE 99
Cystectomy
Bladder


title: genomic DNA from sample 102

description: whole blood case sample


title: SA38

description:
SAMPLE 98
Cystectomy
Bladder


title: genomic DNA from sample 98

description: whole blood case sample


title: SA35

description:
SAMPLE 97
Cystectomy
Bladder


description:
Eed_KO_Day14_Adult_Intestine_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Epithelium was frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 50 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: antibody

value: Adult Epithelial cells; proximal 1/3 of intestine

tag: developmental stage

value: adult


title: genomic DNA from sample 470

description: whole blood control sample

value: control

value: M

tag: tissue


title: genomic DNA from sample 513

description: whole blood control sample


title: genomic DNA from sample 520

description: whole blood case sample


title: genomic DNA from sample 108

description: whole blood case sample


title: genomic DNA from sample 205

description: whole blood control sample


title: SA34

description:
SAMPLE 96
Cystectomy
Bladder


title: genomic DNA from sample 434

description: whole blood case sample


title: genomic DNA from sample 150

description: whole blood control sample


title: genomic DNA from sample 314

description: whole blood control sample


description:
Eed_KO_Day11_Adult_Intestine_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt

tag: genotype


description:
Eed_KO_Day11_Adult_Intestine_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt


title: SA32

description:
SAMPLE 95
Cystectomy
Bladder


title: genomic DNA from sample 200

description: whole blood control sample

tag: diagnosis


title: SA29

description:
SAMPLE 94
Cystectomy
Bladder


title: SA27

description:
SAMPLE 93
Cystectomy
Bladder


title: genomic DNA from sample 235

description: whole blood control sample

tag: education level


title: genomic DNA from sample 183

description: whole blood case sample

tag: history of myocardial infarction


title: genomic DNA from sample 286

description: whole blood case sample

tag: age


title: Eed KO Day9 Adult Intestine H3K4me1 ChIP Rep2

description: Eed KO Day9 Adult Intestine H3K4me1 ChIP Biological Replicate 2


description:
E11.5_Intestine_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt

extract_protocol:
E11.5 midguts were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cells were immediately used for RNA extraction.
Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


description:
Eed_KO_Day14_Adult_Intestine_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt


title: SA26

description:
SAMPLE 92
Cystectomy
Bladder


title: WT Macrophage WGBS

description: WT Macrophage WGBS

extract_protocol:
C-Kit+ cells were purified from mouse bone marrow using CD117 microbead and cultured. Cellular DNA was isolated and used for subsequent WGBS.
Genomic DNA was extracted using MasterPure DNA Purification kit (Epicenter MCD85201) and used for bisulfite conversion.
EpiGenome Methyl-Seq Kit (Epicenter EGMK81312) was used to prepare WGBS libraries, 150 bp paired-end reads were sequecned on an Illumina NextSeq 500 instrument.

value: Eed F/F; RosaFlox-STOP-Flox-EYFP


title: genomic DNA from sample 179

description: whole blood control sample

tag: Sex


title: genomic DNA from sample 383

description: whole blood case sample

tag: snp based principle component 1


title: WT Adult Intestinal Epithelium WGBS

description: WT Adult Intestinal Epithelium WGBS

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cellular DNA was isolated and used for subsequent WGBS.
Genomic DNA was extracted using MasterPure DNA Purification kit (Epicenter MCD85201) and used for bisulfite conversion.
EpiGenome Methyl-Seq Kit (Epicenter EGMK81312) was used to prepare WGBS libraries, 150 bp paired-end reads were sequecned on an Illumina NextSeq 500 instrument.

value: Eed +/+; Villin-CRE


title: genomic DNA from sample 406

description: whole blood case sample

tag: snp based principle component 2


title: genomic DNA from sample 371

description: whole blood case sample

tag: cellcount-nk


title: SA20

description:
SAMPLE 90
Cystectomy
Bladder


title: SA22

description:
SAMPLE 91
Cystectomy
Bladder


title: genomic DNA from sample 507

description: whole blood control sample


title: SA19

description:
SAMPLE 89
Cystectomy
Bladder


title: genomic DNA from sample 482

description: whole blood case sample


title: genomic DNA from sample 424

description: whole blood case sample


title: E16.5 Intestinal Epithelium WGBS

description: E16.5 Intestinal Epithelium WGBS

extract_protocol:
E16.5 midguts were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cellular DNA was isolated and used for subsequent WGBS.
Genomic DNA was extracted using MasterPure DNA Purification kit (Epicenter MCD85201) and used for bisulfite conversion.
EpiGenome Methyl-Seq Kit (Epicenter EGMK81312) was used to prepare WGBS libraries, 150 bp paired-end reads were sequecned on an Illumina NextSeq 500 instrument.

tag: cell type


title: E12.5 Intestinal Epithelium WGBS

description: E12.5 Intestinal Epithelium WGBS

extract_protocol:
E12.5 midguts were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS and Epcam + cells were sorted by flowcytometry. Cellular DNA was isolated and used for subsequent WGBS.
Genomic DNA was extracted using MasterPure DNA Purification kit (Epicenter MCD85201) and used for bisulfite conversion.
EpiGenome Methyl-Seq Kit (Epicenter EGMK81312) was used to prepare WGBS libraries, 150 bp paired-end reads were sequecned on an Illumina NextSeq 500 instrument.


title: genomic DNA from sample 221

description: whole blood control sample

tag: cellcount-bcell


title: Eed KO Day11 Adult Intestine Foxg1 ChIP Rep1

description: Eed KO Day11 Adult Intestine Foxg1 ChIP Biological Replicate 1

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with Foxg1 (Active Motif 61211) overnight for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: mouse intestinal villus cells


title: genomic DNA from sample 2

description: whole blood case sample

tag: cellcount-mono


title: genomic DNA from sample 527

description: whole blood case sample

tag: cellcount-gran


title: SA16

description:
SAMPLE 88
Cystectomy
Bladder


description:
E11.5_Intestine_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt

tag: strain


title: SA15

description:
SAMPLE 87
Cystectomy
Bladder


title: genomic DNA from sample 456

description: whole blood control sample


title: Eed KO Day9 Adult Intestine Foxg1 ChIP Rep1

description: Eed KO Day9 Adult Intestine Foxg1 ChIP Biological Replicate 1

tag: antibody

value: B6;129 mixed background


title: genomic DNA from sample 139

description: whole blood control sample


title: genomic DNA from sample 307

description: whole blood case sample


title: WT Adult Intestine Foxg1 ChIP Rep1

description: WT Adult Intestine Foxg1 ChIP Biological Replicate 1

tag: developmental stage


title: SA14

description:
SAMPLE 86
Cystectomy
Bladder

tag: tissue


title: genomic DNA from sample 453

description: whole blood case sample


title: Eed KO Day11 Adult Intestine Foxa1 ChIP Rep2

description: Eed KO Day11 Adult Intestine Foxa1 ChIP Biological Replicate 2

tag: genotype


title: SA10

description:
SAMPLE 85
Cystectomy
Bladder


title: genomic DNA from sample 395

description: whole blood case sample

tag: diagnosis


title: genomic DNA from sample 519

description: whole blood case sample

tag: education level


title: genomic DNA from sample 104

description: whole blood case sample

tag: history of myocardial infarction


title: genomic DNA from sample 118

description: whole blood case sample

tag: age


title: SA08

description:
SAMPLE 84
Cystectomy
Bladder


title: genomic DNA from sample 193

description: whole blood case sample

tag: Sex


title: SA04

description:
SAMPLE 83
Cystectomy
Bladder


title: SA03

description:
SAMPLE 82
Cystectomy
Bladder


title: Eed KO Day9 Adult Intestine Foxa1 ChIP Rep1

description: Eed KO Day9 Adult Intestine Foxa1 ChIP Biological Replicate 1


title: WT Adult Intestine Foxa1 ChIP Rep2

description: WT Adult Intestine Foxa1 ChIP Biological Replicate 2


title: genomic DNA from sample 241

description: whole blood control sample

tag: snp based principle component 1


title: genomic DNA from sample 184

description: whole blood control sample

tag: snp based principle component 2


title: genomic DNA from sample 132

description: whole blood case sample

tag: cellcount-nk


title: genomic DNA from sample 517

description: whole blood case sample


title: SA01

description:
SAMPLE 81
Cystectomy
Bladder


title: genomic DNA from sample 351

description: whole blood case sample


title: WT Adult Intestine Foxa1 ChIP Rep1

description: WT Adult Intestine Foxa1 ChIP Biological Replicate 1

tag: cell type


title: genomic DNA from sample 222

description: whole blood case sample

tag: cellcount-bcell


title: WT Adult Intestine Suz12 ChIP Rep2

description: WT Adult Intestine Suz12 ChIP Biological Replicate 2

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with Suz12 antibody overnight (Cell Signaling D39F6) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.


title: genomic DNA from sample 486

description: whole blood case sample

tag: cellcount-mono


title: genomic DNA from sample 301

description: whole blood control sample

tag: cellcount-gran


title: WT Adult Intestine Suz12 ChIP Rep1

description: WT Adult Intestine Suz12 ChIP Biological Replicate 1

tag: strain


title: genomic DNA from sample 243

description: whole blood control sample


title: genomic DNA from sample 533

description: whole blood case sample


title: Eed KO Day11 Adult Intestine Foxa1 ChIP Rep1

description: Eed KO Day11 Adult Intestine Foxa1 ChIP Biological Replicate 1

tag: antibody


title: genomic DNA from sample 233

description: whole blood case sample


title: CV-43

description:
SAMPLE 79
Cystectomy
Bladder

source_name: Conventional urothelial carcinoma

value: Conventional urothelial carcinoma


title: genomic DNA from sample 353

description: whole blood control sample


title: WT Adult Intestine H3K27me2 ChIP Rep1

description: WT Adult Intestine H3K27me2 ChIP Biological Replicate 1

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K27me2 antibody overnight (Cell Signaling D18C8) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: developmental stage


title: CV-41

description:
SAMPLE 78
Cystectomy
Bladder

tag: tissue


title: WT Adult Intestine H3K27me1 ChIP Rep2

description: WT Adult Intestine H3K27me1 ChIP Biological Replicate 2

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K27me1 antibody overnight (Active Motif 61015) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: genotype


title: CV-35

description:
SAMPLE 77
Cystectomy
Bladder

extract_protocol: MasterPure Complete from Epicenter Biotechnologies.


title: genomic DNA from sample 190

description: whole blood control sample

tag: diagnosis


title: CV-34

description:
SAMPLE 76
Cystectomy
Bladder


title: CV-32

description:
SAMPLE 75
Cystectomy
Bladder


title: genomic DNA from sample 373

description: whole blood case sample

tag: education level


title: genomic DNA from sample 346

description: whole blood case sample

tag: history of myocardial infarction


title: Eed KO Day14 Adult Intestine H3K4me3 ChIP Rep2

description: Eed KO Day14 Adult Intestine H3K4me3 ChIP Biological Replicate 2

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K4me3 antibody overnight (Diagenode C15410003 ) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Eed F/F; Villin-CRE


title: CV-30

description:
SAMPLE 74
Cystectomy
Bladder


title: genomic DNA from sample 100

description: whole blood case sample

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: age


title: CV-44

description:
SAMPLE 80
Cystectomy
Bladder


title: genomic DNA from sample 198

description: whole blood control sample

tag: Sex


title: genomic DNA from sample 207

description: whole blood control sample

tag: snp based principle component 1


title: CV-26

description:
SAMPLE 73
Cystectomy
Bladder


title: genomic DNA from sample 334

description: whole blood case sample

tag: snp based principle component 2


title: genomic DNA from sample 389

description: whole blood case sample

tag: cellcount-nk


title: Eed KO Day9 Adult Intestine H3K4me3 ChIP Rep2

description: Eed KO Day9 Adult Intestine H3K4me3 ChIP Biological Replicate 2

tag: cell type


title: genomic DNA from sample 56

description: whole blood case sample

tag: cellcount-bcell


title: genomic DNA from sample 79

description: whole blood case sample

tag: cellcount-mono


title: Eed KO Day14 Adult Intestine H3K4me3 ChIP Rep1

description: Eed KO Day14 Adult Intestine H3K4me3 ChIP Biological Replicate 1


title: genomic DNA from sample 525

description: whole blood case sample

tag: cellcount-gran


title: E16.5 Intestine H3K4me1 ChIP Rep1

description: E16.5 Intestine H3K4me1 ChIP Biological Replicate 1

tag: strain


title: genomic DNA from sample 435

description: whole blood case sample


title: Eed KO Day9 Adult Intestine H3K4me3 ChIP Rep1

description: Eed KO Day9 Adult Intestine H3K4me3 ChIP Biological Replicate 1

tag: antibody


title: CV-21

description:
SAMPLE 72
Cystectomy
Bladder


title: WT Adult Intestine H3K27me2 ChIP Rep2

description: WT Adult Intestine H3K27me2 ChIP Biological Replicate 2

tag: developmental stage


title: CV-20

description:
SAMPLE 71
Cystectomy
Bladder

tag: tissue


title: CV-19

description:
SAMPLE 70
Cystectomy
Bladder


title: Eed KO Day14 Adult Intestine H3K4me1 ChIP Rep1

description: Eed KO Day14 Adult Intestine H3K4me1 ChIP Biological Replicate 1

tag: genotype


title: genomic DNA from sample 89

description: whole blood case sample

tag: diagnosis


title: genomic DNA from sample 154

description: whole blood control sample

tag: education level


title: genomic DNA from sample 410

description: whole blood case sample

tag: history of myocardial infarction


title: Eed KO Day9 Adult Intestine H3K4me1 ChIP Rep1

description: Eed KO Day9 Adult Intestine H3K4me1 ChIP Biological Replicate 1


title: genomic DNA from sample 160

description: whole blood control sample

tag: age


title: CV-18

description:
SAMPLE 69
Cystectomy
Bladder


title: genomic DNA from sample 182

description: whole blood case sample

tag: Sex


title: genomic DNA from sample 304

description: whole blood case sample

tag: snp based principle component 1


title: genomic DNA from sample 148

description: whole blood control sample

tag: snp based principle component 2


title: WT Adult Intestine H3K4me1 ChIP Rep2

description: WT Adult Intestine H3K4me1 ChIP Biological Replicate 2


title: CV-17

description:
SAMPLE 68
Cystectomy
Bladder


title: genomic DNA from sample 348

description: whole blood case sample

tag: cellcount-nk


title: WT Adult Intestine H3K4me1 ChIP Rep1

description: WT Adult Intestine H3K4me1 ChIP Biological Replicate 1

treatment_protocol: Not injected with tamoxifen.

tag: cell type


title: genomic DNA from sample 463

description: whole blood control sample

tag: cellcount-bcell


title: CV-16

description:
SAMPLE 67
Cystectomy
Bladder


title: CV-15

description:
SAMPLE 66
Cystectomy
Bladder


title: genomic DNA from sample 230

description: whole blood case sample

tag: cellcount-mono


title: TGA4_pChx_Rep3

city: Urbana

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

description: PolyA RNA

data_processing:
Raw reads were trimmed to remove low quality bases (q<10) and adapter contamination.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the TopHat (v2) package and estimating read counts by the GenomicFeatures/Alignments package.
Genes responding significantly (FDR adjusted p-val <0.05) to TGA4 relative to the empty vector control were identified using DESeq2 using a ~TF+treatment model. Genes that responded to nitrogen treatment vs. the KCl control were identified for the protoplasts and whole roots using DESeq2 (FDR adjusted p-val <0.05) to compare the nitrogen response in protoplasts vs. whole roots.
Genome_build: TAIR10
Supplementary_files_format_and_content: *.csv: Read counts output from GenomicFeatures/Alignments package.

organism: Arabidopsis thaliana

source_name: root protoplasts

growth_protocol: Arabidopsis seedlings grown in MS basal media w/o C or N + 1% sucrose and 1mM KNO3. For protoplast isolation, plants were grown on vertical plates and for whole root N-response plants were grown in liquid media in Phytatrays.

extract_protocol:
For protoplast samples, approximately 10,000-20,000 cells were FACS sorted into RLT buffer and frozen. For whole tissue, roots were transferred into microfuge tubes and flash frozen in liquid nitrogen, pulverized with a bead beater and RLT buffer was added. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Final quantity was determined using the DNA TapeStation and KAPA Library Quant qPCR.

treatment_protocol: Protoplasts were isolated from root tissue and transfected with expression vector. The following morning protoplasts were treated with the indicated N supply (0N = 20 mM KCL, 5N = 5 mM KNO3, and 60N = 20 mM KNO3 + 20 mM NH4NO3), +/- 35 uM cycloheximide and 10 uM dexamethasone. Whole roots were treated with 20 mM KCl or 20 mM KNO3 + 20 mM NH4NO3.

tag: ecotype

value: root protoplasts

tag: expression vector

tag: treatments

value: Nitrogen, plus Cycloheximide, Dexamethasone

value: 10 days


title: genomic DNA from sample 423

description: whole blood case sample

value: case

tag: cellcount-gran

value: whole blood


title: TGA4_pChx_Rep1

description: PolyA RNA

tag: tissue


title: TGA4_pChx_Rep2

description: PolyA RNA


title: Eed KO Macrophage H3K27ac ChIP Rep2

description: Eed KO Macrophage H3K27ac ChIP Biological Replicate 2

extract_protocol:
C-Kit+ cells were purified from mouse bone marrow using CD117 microbead and cultured. Cells were harvested, snap-frozen in liquid nitrogen, and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K27ac antibody overnight (Active Motif 39135) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Cells were infected with MSCV-Cre virus to activate tamoxifen-inducible Cre and recombine conditional alleles.

tag: antibody

tag: strain

tag: developmental stage

tag: genotype


title: Eed KO Macrophage H3K27ac ChIP Rep1

description: Eed KO Macrophage H3K27ac ChIP Biological Replicate 1


title: CV-14

description:
SAMPLE 65
Cystectomy
Bladder


title: TGA4_mChx_Rep3

description: PolyA RNA

value: Nitrogen, minus Cycloheximide, Dexamethasone

tag: age


title: CV-13

description:
SAMPLE 64
Cystectomy
Bladder


title: genomic DNA from sample 367

description: whole blood NA sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: Sex

value: F


title: WT Macrophage H3K27ac ChIP Rep2

description: WT Macrophage H3K27ac ChIP Biological Replicate 2

tag: cell type

value: Adult Epithelial cells; proximal 1/3 of intestine


title: genomic DNA from sample 227

description: whole blood control sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell


title: WT Macrophage H3K27ac ChIP Rep1

description: WT Macrophage H3K27ac ChIP Biological Replicate 1

value: adult


title: TGA4_mChx_Rep2

description: PolyA RNA

tag: ecotype

tag: expression vector

tag: treatments


title: genomic DNA from sample 229

description: whole blood control sample

value: control

tag: cellcount-mono

tag: cellcount-gran

tag: tissue


title: Eed KO Day14 Adult Intestine H3K27ac ChIP Rep2

description: Eed KO Day14 Adult Intestine H3K27ac ChIP Biological Replicate 2

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K27ac antibody overnight (Active Motif 39135) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: antibody

tag: strain

tag: developmental stage

tag: genotype


title: CV-12

description:
SAMPLE 63
Cystectomy
Bladder


title: CV-10

description:
SAMPLE 61
Cystectomy
Bladder


title: Eed KO Day14 Adult Intestine H3K27ac ChIP Rep1

description: Eed KO Day14 Adult Intestine H3K27ac ChIP Biological Replicate 1


title: genomic DNA from sample 442

description: whole blood control sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: age


title: genomic DNA from sample 47

description: whole blood case sample

tag: Sex

tag: snp based principle component 1

tag: snp based principle component 2


title: Eed KO Day9 Adult Intestine H3K27ac ChIP Rep3

description: Eed KO Day9 Adult Intestine H3K27ac ChIP Biological Replicate 3

tag: cell type


title: CV-08

description:
SAMPLE 59
Cystectomy
Bladder


title: genomic DNA from sample 516

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-bcell


title: TGA4_60N_Rep3

description: PolyA RNA

tag: ecotype

tag: expression vector

tag: treatments

value: 60N, Cycloheximide, Dexamethasone


title: TGA4_mChx_Rep1

description: PolyA RNA

tag: tissue


title: Eed KO Day9 Adult Intestine H3K27ac ChIP Rep2

description: Eed KO Day9 Adult Intestine H3K27ac ChIP Biological Replicate 2

tag: antibody

tag: strain


title: TGA4_60N_Rep1

description: PolyA RNA


title: TGA4_60N_Rep2

description: PolyA RNA


title: Eed KO Day9 Adult Intestine H3K27ac ChIP Rep1

description: Eed KO Day9 Adult Intestine H3K27ac ChIP Biological Replicate 1

tag: developmental stage

tag: genotype


title: genomic DNA from sample 450

description: whole blood control sample

tag: diagnosis

tag: education level

tag: cellcount-mono

tag: cellcount-gran


title: TGA4_5N_Rep3

description: PolyA RNA

value: 5N, Cycloheximide, Dexamethasone

tag: age


title: CV-06

description:
SAMPLE 57
Cystectomy
Bladder


title: WT Adult Intestine H3K27ac ChIP Rep3

description: WT Adult Intestine H3K27ac ChIP Biological Replicate 3

value: Eed +/+; Villin-CRE


title: TGA4_5N_Rep2

description: PolyA RNA


title: genomic DNA from sample 439

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

value: M

tag: snp based principle component 1

tag: snp based principle component 2


title: CV-05

description:
SAMPLE 56
Cystectomy
Bladder


title: CV-11

description:
SAMPLE 62
Cystectomy
Bladder


title: genomic DNA from sample 521

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-bcell


title: WT Adult Intestine H3K27ac ChIP Rep2

description: WT Adult Intestine H3K27ac ChIP Biological Replicate 2

value: mouse intestinal villus cells

value: B6;129 mixed background

tag: cell type


title: genomic DNA from sample 347

description: whole blood case sample

tag: tissue


title: TGA4_5N_Rep1

description: PolyA RNA

tag: ecotype

tag: expression vector

tag: treatments


title: WT Adult Intestine H3K27ac ChIP Rep1

description: WT Adult Intestine H3K27ac ChIP Biological Replicate 1

tag: antibody

tag: strain

tag: developmental stage

tag: genotype


title: CV-04

description:
SAMPLE 55
Cystectomy
Bladder

value: Conventional urothelial carcinoma


title: TGA4_0N_Rep3

description: PolyA RNA

value: root protoplasts

value: 0N, Cycloheximide, Dexamethasone


title: CV-09

description:
SAMPLE 60
Cystectomy
Bladder


title: genomic DNA from sample 191

description: whole blood control sample

tag: diagnosis

tag: education level

tag: cellcount-mono

tag: cellcount-gran


title: Eed KO Day9 Intestine ChIP INPUT

description: Eed KO Day9 Intestine ChIP INPUT

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and used for library preparation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: input

value: Eed F/F; Villin-CRE


title: CV-03

description:
SAMPLE 54
Cystectomy
Bladder


title: TGA4_0N_Rep2

description: PolyA RNA

tag: age

value: 10 days


title: genomic DNA from sample 497

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1

tag: snp based principle component 2

value: whole blood


title: CV-07

description:
SAMPLE 58
Cystectomy
Bladder

tag: tissue


title: CV-02

description:
SAMPLE 53
Cystectomy
Bladder


title: WT Adult Intestine ChIP INPUT

description: WT Adult Intestine ChIP INPUT

tag: cell type


title: genomic DNA from sample 409

description: whole blood case sample

value: case

value: F

tag: cellcount-nk

tag: cellcount-bcell


title: CV-01

description:
SAMPLE 52
Cystectomy
Bladder


title: Root_60N_Rep4

description: PolyA RNA

source_name: whole roots

tag: ecotype

value: whole roots

tag: treatments


title: genomic DNA from sample 374

description: whole blood case sample


title: WT Adult Intestine ATAC Rep1

description:
WT Adult Intestine ATAC Biological Replicate 1
processed data file: WT_Adult_Intestine_ATAC.bw

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Epithlium was disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and cells were immediately used for chromatin transposition.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
Transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: antibody

tag: strain

value: Adult Epithelial cells; proximal 1/3 of intestine

tag: developmental stage

value: adult


title: CV-95

description:
SAMPLE 51
Cystectomy
Bladder


title: WT Adult Intestine ATAC Rep2

description:
WT Adult Intestine ATAC Biological Replicate 2
processed data file: WT_Adult_Intestine_ATAC.bw

tag: genotype


title: Root_60N_Rep3

description: PolyA RNA


title: CV-94

description:
SAMPLE 50
Cystectomy
Bladder


title: Root_60N_Rep2

description: PolyA RNA


title: genomic DNA from sample 365

description: whole blood case sample

tag: diagnosis

tag: education level

tag: cellcount-mono


title: Root_0N_Rep4

description: PolyA RNA

tag: age


title: genomic DNA from sample 321

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-gran


title: CV-93

description:
SAMPLE 49
Cystectomy
Bladder

tag: tissue


title: genomic DNA from sample 392

description: whole blood control sample

value: control

tag: snp based principle component 1

tag: snp based principle component 2


title: Root_60N_Rep1

description: PolyA RNA


title: CV-92

description:
SAMPLE 48
Cystectomy
Bladder


title: CV-91

description:
SAMPLE 47
Cystectomy
Bladder


title: ATACseq_HUDEP2_CRISPR_115edit_cloneD3

first: Stuart

last: Orkin

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Children's Hospital

data_processing:
In processing ATAC-seq data, paired-end reads were trimmed and aligned to hg19 using Trimmomatic and Bowtie2 respectively. For promoter-edited samples, these were aligned to a custom hg19 genome where there is a 1 bp deletion in HBG1 promoter and a 13 bp deletion in the HBG2 promoter (exact locations shown in Figure S6A). Reads were piled-up using MACS2 --SPMR -B parameters and visualized with IGV.
Note that reads are aligned to custom hg19 where there is 1-bp deletion at chr11:5271199 and 13-bp deletion at chr11:5276109, corresponding to distal TGACCA motif deletion of HBG1/2.
Genome_build: hg19 custom
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: broadPeak – peaks generated with MACS v2 (callpeak--broad --broad-cutoff 0.1 --nomodel --nolambda -B) for ATAC-seq data
Supplementary_files_format_and_content: gappedPeak – generated by broad peak calling from MACS v2 for ATAC-seq data

source_name: human umbilical cord blood-derived erythroid progenitor (HUDEP)

extract_protocol:
ATAC-seq was performed with Illumina Nextera DNA Preparation kit   (Illumina, FC-121-1030) as previously described (Buenrostro et al.,   2015). 50,000 cells of expansion phase HUDEP-2 or derived cell lines   were collected, and permeabilized with 50 mL ice cold lysis buffer (10   mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360) for 10   minutes. The transposition reaction was carried out at 37 degrees for 60   minutes in 50 mL volume containing 25 mL 2x TD buffer and 2.5 mL   transpose enzyme (contained in Illumina Nextera DNA Preparation kit).   DNA was purified with QIAGEN MinElute PCR purification kit.
Library amplification was  done with NEBNext Ultra II Q5 Master Mix   (contained in NEBNext Ultra II DNA Library Prep Kit). PCR amplification   was carried out as follow: 72 degrees 5 min, 98 degrees 30 s, 98 degrees   10 s, 63 degrees 30 s, 72 degrees 1 min, repeat steps 3-5 for another 7   cycles, hold at 4 degrees. The resulting libraries were purified using   QIAGEN MinElute PCR purification kit, and quantified with Qubit   fluorometer and bioanalyzer, and then sequenced in NextSeq 500 platform.   Sequencing parameter was paired end 2x41 bp reads, 8 bp index.

value: erythroid

tag: cell line

value: Crispr edited HUDEP2 clone D3

tag: differentiation days

tag: replicate


title: ATACseq_HUDEP2

data_processing:
In processing ATAC-seq data, paired-end reads were trimmed and aligned to hg19 using Trimmomatic and Bowtie2 respectively. For promoter-edited samples, these were aligned to a custom hg19 genome where there is a 1 bp deletion in HBG1 promoter and a 13 bp deletion in the HBG2 promoter (exact locations shown in Figure S6A). Reads were piled-up using MACS2 --SPMR -B parameters and visualized with IGV.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: broadPeak – peaks generated with MACS v2 (callpeak--broad --broad-cutoff 0.1 --nomodel --nolambda -B) for ATAC-seq data
Supplementary_files_format_and_content: gappedPeak – generated by broad peak calling from MACS v2 for ATAC-seq data

value: HUDEP2 cells


title: ATACseq_HUDEP2_CRISPR_115edit_bulk

value: Crispr edited HUDEP2 bulk


title: Root_0N_Rep3

description: PolyA RNA

tag: ecotype

tag: treatments


title: TGA4_0N_Rep1

description: PolyA RNA

tag: expression vector


title: CTCF_HUDEP2_ChIP

data_processing:
Paired-end reads were trimmed and aligned to hg19 using Trimmomatic and  Bowtie2 respectively. MACS (Zhang et al., 2008) version 2.1 was used to call peaks from the BAM file with narrowPeak setting, p value cutoff of 1e-5, and with --SPMR which normalizes the signal intensity to facilitate comparison between tracks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: narrowPeak – peaks generated with MACS v2 (callpeak -g hs -f BAMPE -q 0.01)".

extract_protocol:
10^7 expansion phase HUDEP-2 cells were collected and fixed with 1%   formaldehyde for 5 minutes at room temperature. Fixation was quenched   with 125 mM glycine. Cells were washed with ice cold PBS twice and   resuspended in 0.13 mL lysis buffer (50 mM Tris-HCl 8.0, 10 mM EDTA,   0.5% SDS) and sonicated in a microtube (Covaris, 520045) with Covaris   E220 ultrasonicator (Covaris). 0.12 mL sonicated chromatin was mixed   with 1 mL ChIP dilution buffer (20 mM Tris-HCl 8.0, 2 mM EDTA, 1% Triton   X-100, 300 mM NaCl, protease inhibitor), 20 mL Dynabeads protein G   (Thermo Fisher Scientific) and 3 mg antibody (CTCF, 07-729, Millipore).   After overnight rotating, the beads were washed with the following   buffers: twice with RIPA150, twice with RIPA500, 500 mM NaCl, 0.1%   Sodium Deoxycholate, 0.1% SDS), twice with LiCl buffer (10 mM Tris-HCl   8.0, 1 mM EDTA, 0.5% NP-40, 250 mM LiCl, 0.5% Sodium Deoxycholate),   twice with TE buffer (10 mM Tris-HCl 8.0, 1 mM EDTA). To elute and   decrosslink, 300 mL Elution buffer (50 mM Tris-HCl 8.0, 10 mM EDTA, 1%   SDS, 150 mM NaCl, 0.1 mg/mL Proteinase K) was added to the beads and   incubated at 65 degrees overnight. The eluted material was extracted   with phenol-chloroform, and DNA was precipitated by adding 750 mL   absolute ethanol. DNA was pelleted by centrifuging at 14000 rpm for 15   minutes, washed once with 75% ethanol, then dried and dissolved with 50   mL TE buffer. The quality of ChIP was verified by real-time PCR.
To construct ChIP-seq library, we used NEBNext Ultra II DNA Library Prep   Kit (NEB) according to manufacturer   s protocol. Quality check of library   was carried out with Qubit and bioanalyzer. The library was sequenced in   the NextSeq 500 platform with NextSeq 500/550 High Output Kit v2 (75   cycles). Paired-end sequencing was performed (2x42 bp, 6 bp index).

tag: antibody

value: CTCF


title: genomic DNA from sample 393

description: whole blood control sample

tag: diagnosis

value: M

tag: cellcount-nk

tag: cellcount-bcell


title: Root_0N_Rep2

description: PolyA RNA

tag: age


title: CV-90

description:
SAMPLE 46
Cystectomy
Bladder

value: Conventional urothelial carcinoma


title: genomic DNA from sample 168

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: cellcount-mono


title: genomic DNA from sample 515

description: whole blood case sample

tag: Sex

tag: cellcount-gran

tag: tissue


title: CV-88

description:
SAMPLE 44
Cystectomy
Bladder


title: genomic DNA from sample 1

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2


title: CV-89

description:
SAMPLE 45
Cystectomy
Bladder


title: genomic DNA from sample 454

description: whole blood control sample


title: Protoplast_60N_Rep4

description: PolyA RNA

value: root protoplasts


title: CV-87

description:
SAMPLE 43
Cystectomy
Bladder


title: scRNA data of skin cells from healthy donor_sample_SC125

city: Pittsburgh

first: Zhe

last: Sun

state: PA

address: 130 DeSoto Street

institute: University of Pittsburgh

data_processing:
Standard 10X Genomics CellRanger pipeline; R1 read is technical (16bp Chromium barcode and 10bp UMI), R2 is biological and I1 is 8bp sample index
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

tag: subject status

value: healthy

value: dorsal mid-forearm

tag: cell type

value: skin cells


title: scRNA data of skin cells from healthy donor_sample_SC68


title: scRNA data of skin cells from healthy donor_sample_SC124


title: ATACseq_BCL11AKO_HUDEP2

tag: cell line

value: BCL11A KO HUDEP-2 cells

tag: differentiation days

tag: replicate


title: CV-86

description:
SAMPLE 42
Cystectomy
Bladder


title: Protoplast_60N_Rep3

description: PolyA RNA

tag: ecotype

tag: treatments

value: 10 days


title: Root_0N_Rep1

description: PolyA RNA

value: whole roots


title: Protoplast_60N_Rep2

description: PolyA RNA


title: Protoplast_60N_Rep1

description: PolyA RNA


title: genomic DNA from sample 109

description: whole blood case sample

tag: diagnosis

value: case

tag: cellcount-nk

tag: cellcount-bcell

value: whole blood


title: P4936_WCE_MS2_4HR_TC1

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Input control background in P493-6 cells

data_processing:
Reads were aligned to the HG19 NCBI Refseq (GRCh37) reference using bowtie2 with default parameters.
Enriched regions were determined using MACS1.4.2 (Zhang et al., 2008) using a p-value threshold of 1e-9
Genome_build: HG19 (GRCh37)
Supplementary_files_format_and_content: .wig files of read density

growth_protocol: P493-6 was a gift from D. Eick. Cell lines were not authenticated in our hands. Cell lines were tested intermittently throughout studies using MycoAlert Mycoplasma Detection Kit (Lonza, Cat#LT07-418), generally a few days after thawing and immediately before significant studies (e.g. RNA-seq experiment). Cells were cultured in a humidified incubator at 37.0 ̊ C and 5.0% CO2. P493-6 cells were cultured in RPMI Medium 1640 (gibco, 11875-093) supplemented with 10% Tet-approved FBS (Takara, Cat#631106) and penicillin-streptomycin (Corning, 30-002-CI).

extract_protocol:
Chromatin immunoprecipitation sequencing. ChIP-seq for c-Myc, Max, and H3K27ac was performed as in (Lin et al., 2012) with minor changes. P493-6 cells were grown to a density of 1 × 10^6 cells / mL prior to the start of time course. At each time point, pellets of 50 million cells were isolated and cross-linked with 1% formaldehyde (10 min) followed by quenching (125 mM glycine). Cells were washed in cold PBS and harvested by cell scraper in cold PBS with protease inhibitors (Roche). Cells were centrifuged at 1,650g for 5 min and flash frozen and stored at –80°C at 5 × 106 cells per pellet. Pellets were resuspended in cytosolic and then nuclear lysis buffer, and DNA was sheared at 4 °C using a water-bath sonicator (Bioruptor, Diagenode) for 25 min at high output (30 s on, 30 s off) in 1 ml of sonication buffer supplemented with 0.5% SDS. Sonicated lysates were cleared by centrifuging at 20,000g for 10 min and incubated overnight end over end at 4 °C with magnetic beads prebound with antibody. Beads were washed three times with sonication buffer, one time with sonication buffer with 500 mM NaCl added, once with LiCl wash buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE. DNA was eluted in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg/ml RNase A for 2 h followed by 0.2 mg/ml proteinase K for 1 hour. DNA was purified with phenol chloroform extraction and ethanol precipitation.
Libraries for sequencing were prepared using the Rubicon Thruplex DNA-seq/FD library preparation kit. An input of 50 ng of DNA or less was used, and following ligation, libraries were amplified per the manufacturer’s instructions. Amplified libraries were then size selected using AMPure beads (Agencourt AMPure XP) according to the manufacturer’s instructions. Further size selection was performed using a 2% gel cassette in the Pippin Prep (SAGE Sciences) set to capture fragments of 200–700 bp in size.
Libraries were multiplexed at equimolar ratios and run on a NextSeq 500 instrument (75-bp, single-end reads).

treatment_protocol: Cells were treated with 1uM KI-MS2-008 for duration indicated for each sample

tag: treatment

tag: timepoint

value: 4 hour

tag: epitope


title: genomic DNA from sample 261

description: whole blood control sample

value: control

tag: education level

tag: history of myocardial infarction

tag: age

tag: Sex

value: F

tag: cellcount-mono

tag: cellcount-gran


title: CV-85

description:
SAMPLE 41
Cystectomy
Bladder

tag: tissue


title: Protoplast_0N_Rep4

description: PolyA RNA


title: P4936_WCE_MS2_24HR_TC1

value: 24 hour


title: genomic DNA from sample 350

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2


title: CV-84

description:
SAMPLE 40
Cystectomy
Bladder


title: Protoplast_0N_Rep3

description: PolyA RNA

tag: ecotype


title: CV-83

description:
SAMPLE 39
Cystectomy
Bladder


title: Protoplast_0N_Rep2

description: PolyA RNA

tag: treatments


title: genomic DNA from sample 53

description: whole blood case sample

tag: diagnosis


title: P4936_WCE_MS2_0HR_TC2

value: 0 hour


title: P4936_WCE_MS2_0HR_TC1


title: CV-81

description:
SAMPLE 37
Cystectomy
Bladder


title: genomic DNA from sample 445

description: whole blood case sample

tag: cellcount-nk


title: P4936_WCE_MS2_4HR_TC2


title: genomic DNA from sample 514

description: whole blood control sample

tag: cellcount-bcell


title: CV-82

description:
SAMPLE 38
Cystectomy
Bladder


title: P4936_MYC_MS2_4HR_TC1

description: ChIP-seq for MYC in P493-6 cells

tag: treatment

tag: antibody manufacturer

value: abcam

tag: antibody catalog

value: MYC

tag: background


title: EV_pChx_Rep3

description: PolyA RNA

tag: expression vector

value: empty

value: Nitrogen, plus Cycloheximide, Dexamethasone


title: CV-80

description:
SAMPLE 36
Cystectomy
Bladder

value: Conventional urothelial carcinoma


title: EV_pChx_Rep2

description: PolyA RNA

value: root protoplasts

tag: age


title: genomic DNA from sample 14

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: Sex


title: CV-79

description:
SAMPLE 35
Cystectomy
Bladder

tag: tissue


title: P4936_MYC_MS2_0HR_TC1

description: ChIP-seq for MYC in P493-6 cells

tag: timepoint

tag: epitope


title: genomic DNA from sample 240

description: whole blood control sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-mono

tag: cellcount-gran


title: EV_pChx_Rep1

description: PolyA RNA

tag: ecotype

tag: treatments


title: P4936_MAX_MS2_4HR_TC2

description: ChIP-seq for MAX in P493-6 cells

tag: treatment

tag: antibody manufacturer

value: santa cruz

value: MAX


title: CV-77

description:
SAMPLE 33
Cystectomy
Bladder


title: genomic DNA from sample 257

description: whole blood control sample

tag: diagnosis

tag: cellcount-nk

tag: cellcount-bcell


title: EV_mChx_Rep3

description: PolyA RNA

tag: expression vector

value: Nitrogen, minus Cycloheximide, Dexamethasone

tag: age

value: 10 days


title: P4936_MAX_MS2_24HR_TC1

description: ChIP-seq for MAX in P493-6 cells

tag: antibody catalog

tag: background


title: genomic DNA from sample 9

description: whole blood case sample

value: case

tag: education level

tag: history of myocardial infarction

tag: Sex

value: M

tag: tissue


title: P4936_MAX_MS2_0HR_TC2

description: ChIP-seq for MAX in P493-6 cells

tag: timepoint

tag: epitope


title: CV-76

description:
SAMPLE 32
Cystectomy
Bladder


title: EV_mChx_Rep2

description: PolyA RNA

tag: ecotype


title: P4936_MYC_MS2_24HR_TC1

description: ChIP-seq for MYC in P493-6 cells


title: genomic DNA from sample 510

description: whole blood control sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-mono

tag: cellcount-gran

value: whole blood


title: genomic DNA from sample 323

description: whole blood case sample

tag: diagnosis

tag: cellcount-nk


title: P4936_H3K27AC_MS2_4HR_TC1

description: ChIP-seq for H3K27ac in P493-6 cells

tag: treatment

value: 4 hour

tag: antibody manufacturer


title: CV-75

description:
SAMPLE 31
Cystectomy
Bladder


title: EV_mChx_Rep1

description: PolyA RNA

tag: expression vector

tag: treatments

tag: age


title: P4936_H3K27AC_MS2_24HR_TC1

description: ChIP-seq for H3K27ac in P493-6 cells

tag: antibody catalog

tag: background


title: EV_60N_Rep2

description: PolyA RNA

tag: tissue

value: 60N, Cycloheximide, Dexamethasone


title: CV-74

description:
SAMPLE 30
Cystectomy
Bladder


title: EV_60N_Rep3

description: PolyA RNA


title: genomic DNA from sample 444

description: whole blood control sample

value: control

tag: education level

tag: history of myocardial infarction

tag: Sex

value: F

tag: cellcount-bcell


title: genomic DNA from sample 306

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2


title: CV-73

description:
SAMPLE 29
Cystectomy
Bladder


title: CV-78

description:
SAMPLE 34
Cystectomy
Bladder


title: genomic DNA from sample 281

description: whole blood control sample

tag: cellcount-mono

tag: cellcount-gran


title: CV-72

description:
SAMPLE 28
Cystectomy
Bladder


title: CV-71

description:
SAMPLE 27
Cystectomy
Bladder


title: G401_LacZ_Day5_rep2

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters (--outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000
Reads Per Kilobase of exon per Megabase of library size (RPKM) and ranscripts Per Kilobase Million (TPM) were calculated by using RSEM (Li et al, BMC bioinformatics, 2011)
Differential analysis was performed by DESeq2 (Love et al, Genome biology, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample

growth_protocol: G401 cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA is extracted using TriZol
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: cell line

tag: cell type

value: kidney rhabdoid tumor derived cell line

tag: genotype/variation

tag: timepoint


title: G401_LacZ_Day5_rep1


title: EV_5N_Rep3

description: PolyA RNA

tag: ecotype

tag: expression vector

tag: treatments

value: 5N, Cycloheximide, Dexamethasone


title: genomic DNA from sample 125

description: whole blood case sample

tag: diagnosis

tag: age

tag: cellcount-nk


title: CV-70

description:
SAMPLE 26
Cystectomy
Bladder

tag: tissue


title: EV_5N_Rep2

description: PolyA RNA

value: empty


title: G401_BRD9KO_Day5_rep2

value: BRD9 KO


title: genomic DNA from sample 289

description: whole blood control sample

tag: education level

tag: history of myocardial infarction

tag: Sex


title: EV_0N_Rep3

description: PolyA RNA

value: 0N, Cycloheximide, Dexamethasone


title: G401_BRD9KO_Day5_rep1


title: genomic DNA from sample 15

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-bcell


title: EV_5N_Rep1

description: PolyA RNA

value: root protoplasts


title: G401_LacZ_Day3_rep2

tag: cell line


title: CV-68

description:
SAMPLE 24
Cystectomy
Bladder

value: Conventional urothelial carcinoma


title: P4936_H3K27AC_MS2_0HR_TC1

description: ChIP-seq for H3K27ac in P493-6 cells

tag: treatment

value: 0 hour

tag: antibody manufacturer

value: abcam

tag: antibody catalog

tag: epitope

tag: background


title: CV-67

description:
SAMPLE 23
Cystectomy
Bladder


title: CV-69

description:
SAMPLE 25
Cystectomy
Bladder


title: G401_LacZ_Day3_rep1

tag: cell type

tag: genotype/variation

tag: timepoint


title: genomic DNA from sample 204

description: whole blood case sample

tag: diagnosis

tag: age

tag: cellcount-nk

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 25

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1

tag: tissue


title: EV_0N_Rep1

description: PolyA RNA

tag: ecotype

tag: expression vector

tag: treatments

value: 10 days


title: CV-66

description:
SAMPLE 22
Cystectomy
Bladder


title: EV_60N_Rep1

description: PolyA RNA


title: genomic DNA from sample 447

description: whole blood control sample

tag: snp based principle component 2

tag: cellcount-bcell


title: genomic DNA from sample 128

description: whole blood case sample

value: case


title: G401_BRD9KO_Day3_rep2

tag: cell line

tag: cell type

tag: genotype/variation


title: G401_BRD9KO_Day3_rep1

tag: timepoint


title: CV-64

description:
SAMPLE 20
Cystectomy
Bladder


title: Protoplast_0N_Rep1

description: PolyA RNA

tag: age


title: CV-65

description:
SAMPLE 21
Cystectomy
Bladder


title: genomic DNA from sample 377

description: whole blood case sample

tag: diagnosis

value: M

tag: cellcount-nk

tag: cellcount-mono


title: G401_LacZ_Day2_rep2


title: genomic DNA from sample 188

description: whole blood control sample

tag: education level

tag: history of myocardial infarction

tag: cellcount-gran

value: whole blood


title: G401_LacZ_Day2_rep1


title: CV-63

description:
SAMPLE 19
Cystectomy
Bladder

tag: tissue


title: EV_0N_Rep2

description: PolyA RNA

tag: ecotype


title: genomic DNA from sample 226

description: whole blood control sample

tag: Sex

tag: snp based principle component 1


title: HB6_B3_Rep3

data_processing:
Raw reads were trimmed to remove low quality bases (q<10) and adapter contamination.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the TopHat (v2) package and estimating read counts by the GenomicFeatures/Alignments package.
Genes responding significantly (FDR adjusted p-val <0.05) to each of the N-early response TFs  relative to the empty vector control were identified using DESeq2 with a ~TF+Batch model.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts output from GenomicFeatures/Alignments package

molecule: polyA RNA

growth_protocol: Arabidopsis seedlings grown on vertical plates containing MS basal media w/o C or N, 1% sucrose and 1mM KNO3

extract_protocol:
Approximately 10,000-20,000 cells were FACS sorted into RLT buffer and frozen. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Final quantity was determined using the DNA TapeStation and KAPA Library Quant qPCR.

treatment_protocol: Protoplasts were isolated from root tissue and transfected with expression vector. The following morning protoplasts were treated with 60 mM nitrogen (20 mM KNO3 + 20 mM NH4NO3), 35 uM cycloheximide and 10uM dexamethasone

tag: organ

value: root

tag: treatments

value: Nitrogen, Cycloheximide, Dexamethasone

tag: transfection


title: HB6_B3_Rep1


title: HB6_B3_Rep2


title: LBD37_B6_Rep3


title: G401_BRD9KO_Day2_rep2

tag: cell line

tag: cell type


title: CV-61

description:
SAMPLE 17
Cystectomy
Bladder


title: G401_BRD9KO_Day2_rep1

tag: genotype/variation

tag: timepoint


title: CV-60

description:
SAMPLE 16
Cystectomy
Bladder


title: genomic DNA from sample 292

description: whole blood case sample

tag: diagnosis

tag: age

tag: snp based principle component 2

tag: cellcount-bcell


title: DIV1_B6_Rep3


title: G401_LacZ_Day1_rep2

value: control


title: CV-59

description:
SAMPLE 15
Cystectomy
Bladder


title: G401_LacZ_Day1_rep1


title: genomic DNA from sample 51

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

value: F

tag: cellcount-nk

tag: cellcount-mono


title: LBD37_B6_Rep2

tag: ecotype


title: genomic DNA from sample 255

description: whole blood control sample

tag: Sex

tag: snp based principle component 1

tag: cellcount-gran

tag: tissue


title: genomic DNA from sample 146

description: whole blood control sample


title: G401_BRD9KO_Day1_rep1

tag: cell line

value: kidney rhabdoid tumor derived cell line


title: WRKY54_B6_Rep2

tag: organ

tag: treatments

tag: transfection


title: CV-57

description:
SAMPLE 13
Cystectomy
Bladder


title: CV-62

description:
SAMPLE 18
Cystectomy
Bladder


title: genomic DNA from sample 263

description: whole blood control sample

tag: diagnosis


title: CV-56

description:
SAMPLE 12
Cystectomy
Bladder


title: G401_control_H3K4me3_rep1

data_processing:
The sequenced reads were aligned to the hg19 genome assembly using Bowtie, allowing up to 10 matches (‘-m 1 --best’ options).
Reads on the 24 assembled chromosomes excluding the encode blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "1read")
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: hg19
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

extract_protocol:
Chromatin was fragmented the adaptive focused acoustics (AFA) technology developed by Covaris for the cell lines.
5-10ng of ChIP DNA is used for library prep using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

treatment_protocol: Cells were incubated with 1% formaldehyde for 10 min and subsequently quenched with glycine for 5 min. Cells were washed with PBS three times prior to nuclear extraction.

tag: cell type

tag: genotype/variation

value: wildtype tumor derived cell line

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology:9751)


title: genomic DNA from sample 428

description: whole blood case sample

tag: education level

tag: age

tag: snp based principle component 2

tag: cellcount-bcell


title: G401_control_Input_rep1


title: G401_BRD9KO_Day1_rep2

value: BRD9 KO

tag: timepoint


title: genomic DNA from sample 101

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-nk

tag: cellcount-mono


title: CV-55

description:
SAMPLE 11
Cystectomy
Bladder

tag: tissue


title: genomic DNA from sample 7

description: whole blood case sample

tag: snp based principle component 1

tag: cellcount-gran


title: LBD37_B6_Rep1

tag: organ

tag: ecotype

tag: treatments

tag: transfection


title: G401_control_H3K27Ac_rep2

tag: cell line

tag: cell type

tag: genotype/variation

tag: chip antibody

value: H3K27Ac (Cell Signaling Technology:8173)


title: CV-53

description:
SAMPLE 9
Cystectomy
Bladder


title: G401_control_H3K27Ac_rep1


title: VRN1_B6_Rep3

tag: age


title: genomic DNA from sample 22

description: whole blood case sample

tag: diagnosis

tag: education level

tag: snp based principle component 2

tag: cellcount-bcell


title: DIV1_B6_Rep1


title: genomic DNA from sample 161

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-nk

tag: cellcount-mono


title: RAV1_B6_Rep3

tag: organ


title: DIV1_B6_Rep2

tag: ecotype


title: G401_BRD9KO_Input_rep1


title: CV-58

description:
SAMPLE 14
Cystectomy
Bladder

tag: tissue


title: CV-52

description:
SAMPLE 8
Cystectomy
Bladder


title: G401_BRD9KO_H3K4me3_rep1


title: CV-51

description:
SAMPLE 7
Cystectomy
Bladder


title: ERF5_B6_Rep3

tag: treatments

tag: transfection


title: genomic DNA from sample 391

description: whole blood control sample

tag: snp based principle component 1

tag: cellcount-gran


title: G401_BRD9KO_H3K27Ac_rep2

tag: cell line

tag: cell type

tag: genotype/variation

tag: chip antibody


title: WRKY54_B6_Rep1

tag: age


title: CV-50

description:
SAMPLE 6
Cystectomy
Bladder


title: CV-54

description:
SAMPLE 10
Cystectomy
Bladder


title: genomic DNA from sample 479

description: whole blood case sample

tag: diagnosis

tag: education level

tag: snp based principle component 2

tag: cellcount-bcell


title: EV_B6_Rep3

value: empty vector


title: genomic DNA from sample 10

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-nk

tag: cellcount-mono


title: VRN1_B6_Rep2

tag: organ

tag: ecotype

tag: treatments


title: CV-48

description:
SAMPLE 4
Cystectomy
Bladder

tag: tissue

value: Conventional urothelial carcinoma


title: CV-49

description:
SAMPLE 5
Cystectomy
Bladder


title: G401_BRD9KO_H3K27Ac_rep1

tag: cell line


title: RAV1_B6_Rep2

tag: transfection


title: G401_HAIP_BRD9_rep2

tag: cell type

tag: genotype/variation

value: HA-tag (Cell Signaling Technology:3724)


title: CV-47

description:
SAMPLE 3
Cystectomy
Bladder


title: G401_HAIP_Input_rep1

tag: chip antibody


title: genomic DNA from sample 474

description: whole blood control sample

tag: diagnosis

tag: age

tag: snp based principle component 1

tag: cellcount-gran


title: genomic DNA from sample 404

description: whole blood control sample

tag: education level

tag: history of myocardial infarction

tag: snp based principle component 2

tag: cellcount-bcell


title: ERF5_B6_Rep2

tag: organ


title: CV-46

description:
SAMPLE 2
Cystectomy
Bladder


title: WRKY54_B6_Rep3

tag: ecotype


title: genomic DNA from sample 298

description: whole blood case sample

tag: Sex

tag: cellcount-nk

tag: cellcount-mono


title: genomic DNA from sample 129

description: whole blood case sample

tag: tissue


title: G401_LacZ_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters (--outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000
Reads Per Kilobase of exon per Megabase of library size (RPKM) and transcripts Per Kilobase Million (TPM) were calculated by using RSEM (Li et al, BMC bioinformatics, 2011)
Differential analysis was performed by DESeq2 (Love et al, Genome biology, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample.

extract_protocol:
Total RNA is extracted using Direct-zol RNA Kits (Zymo Research)
1ug of RNA is used to make the library using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: cell line

tag: cell type


title: G401_HAIP_BRD9_rep1

tag: genotype/variation

tag: chip antibody


title: genomic DNA from sample 483

description: whole blood case sample

tag: diagnosis

tag: age


title: G401_LacZ_rep1


title: GRH165

city: Paris

first: Antoine

last: Boivin

address: 9 Quai St Bernard

department: Institut Biologie Paris-Seine

country: France

institute: Sorbonne Universite

description: total small RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to Drosophila melanogaster Jan. 2013 (Flybase r5.49) whole genome and again subset libraries (such as miRNA, tRNA, introns, exons, etc..) using bowtie v2.0.3 with parameters -v 1 -k 1 --best -p 2
The number of reads matching the miRNA sequences reported in rpm was used as a standardization factor
Small RNA sequences from each experimental condition were then matched against P(lacW) or 42AB piRNA-cluster sequences using bowtie v2.0.3 with parameters -v1 -m 1 -p 12 --suppress 6,7,8.
Readmap and histograms from alignment files from sRbowtie aligment (Galaxy Version 1.2.7.3) were generated taking into account miRNA-rpm-based nomalization factor previously calculated
Genome_build: Drosophila melanogaster r5.49
Supplementary_files_format_and_content: tab-delimited text files
Galaxy29_Readmap_dataframe_42AB_norm2.txt: 42AB Readmap (GRH77, 78 and 49)
Galaxy30_Size_distribution_dataframe.txt: 42AB Size distribution  (GRH77, 78 and 49)
Galaxy39_Readmap_dataframe_placw_norm2.txt: P(lacW) Readmap  (GRH77, 78 and 49)
Galaxy40_Size_distribution_dataframe.txt: P(lacW) Size distribution  (GRH77, 78 and 49)
Galaxy36_Readmap_dataframe_23_29_placw.txt:  P(lacW) 23-29 Readmap (GRH160-165)
Galaxy37_Size_distribution_dataframe.txt: P(lacW) Size distribution (GRH160-165)

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Ovaries were hand dissected, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. A small RNA fraction of 18nt to 30nt in length was obtained by separating it on a denaturing polyacrylamide gel from total RNA extracted from dissected ovaries.
This fraction was used to generate multiplexed libraries with Illumina TruSeq Small RNA library preparation kits (RS-200-0012, RS200-0024, RS-200-036 or RS-200-048) at Fasteris (http://www.fasteris.com).  A house protocol based on TruSeq, which reduces 2S RNA (30nt) contamination in the final library, was performed. Libraries were sequenced using Illumina HiSeq 2500.

value: ovary

tag: genotype

tag: temperature


title: RAV1_B6_Rep1

tag: treatments

value: 10 days

tag: transfection


title: GRH164

description: total small RNA


title: G401_BRD9KO_rep1


title: genomic DNA from sample 478

description: whole blood case sample

value: case

tag: education level

tag: history of myocardial infarction

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-gran


title: ERF5_B6_Rep1

tag: organ

tag: ecotype


title: HMGA1 binding in vector control cells

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: HMGA1 binding in control Grosing cells

data_processing:
Chip-seq data was aligned using bowtie version 0.12.9 to human genome hg19
Peak calling in RAS-induced senescent cells was done with HOMER software using empty vector sample as a control with -style factor -fdr 0.1 parameters
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains HOMER peak calling output for RAS-induced senescent cells as compared to vector control

growth_protocol: IMR90 human diploid fibroblasts were cultured according to ATCC under low oxygen tension (2%) in Dulbecco’s Modified Eagle medium (DMEM, 4.5 g/L glucose) supplemented with 10% FBS, L-glutamine, sodium pyruvate, nonessential amino acids, and sodium bicarbonate. All experiments were performed on IMR90 fibroblasts between population doublings #25 and 35 unless indicated otherwise. IMR90 fibroblasts cultured to the population doublings of 30 and 90 were considered early and late passage, respectively.

extract_protocol:
ChIP DNAs were extracted for ChIP-seq using 5 ug of anti-HMGA1 antibody (Abcam, Cat. No. 129153, lot GR211599-2).
Preparation of the ChIP-seq libraries for next-generation sequencing was performed using the NEB Next Ultra DNA Library Prep kit for Illumina (New England Biolabs) from 10 nanograms of ChIP DNA. Q5 high-fidelity DNA polymerase (New England Biolabs) was used to amplify the ChIP-seq libraries (12 cycles)

treatment_protocol: IMR90 cells were infected with RAS or vector retrovirus on day 1. On day 2, the same cells were infected with another round of retrovirus (vector or RAS). On day 3, the cells were selected using 1 ug/ml of puromycin. The cells were then cultured an additional 9 days - and harvested for ChIP analysis (12 day total experiment).

tag: cell line

tag: cell type

value: human diploid fibroblasts

tag: infected with

value: vector


title: GRH163

description: total small RNA

tag: tissue


title: genomic DNA from sample 96

description: whole blood case sample

tag: diagnosis

tag: age

tag: Sex

value: M

tag: cellcount-nk

tag: cellcount-mono

value: whole blood


title: GRH162

description: total small RNA

tag: genotype

tag: temperature


title: TCP23_B5_Rep3

value: root

tag: treatments

value: Nitrogen, Cycloheximide, Dexamethasone

tag: transfection


title: genomic DNA from sample 134

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

value: F

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-bcell


title: genomic DNA from sample 249

description: whole blood control sample

value: control

tag: cellcount-gran


title: VRN1_B6_Rep1

tag: organ

tag: ecotype


title: FBH4_B5_Rep3


title: CV-45

description:
SAMPLE 1
Cystectomy
Bladder

data_processing:
Applied Biosystem's Sequence Detection System (SDS 2.2) software was used to compute Ct values using the default threshold and baseline parameters.
Delta Ct values were generated by subtracting experimental genes from endogenous control gene (RNU48-001006).
Fold-change values were created by subtracting the Target sample delta Ct from the control Sample delta Ct (Sample1 was used as control), then evaluated in the expression 2^-(delta-deltaCt).

extract_protocol: MasterPure Complete from Epicenter Biotechnologies.

tag: tissue


title: genomic DNA from sample 438

description: whole blood control sample

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

tag: age


title: GRH161

description: total small RNA


title: MYB61_B5_Rep3


title: HMGA1 binding in RAS-induced senescent cells

tag: cell line

tag: cell type

tag: infected with

value: RAS

tag: chip antibody

value: anti-HMGA1 antibody (Abcam, Cat. No. 129153, lot GR211599-2)


title: TCP23_B5_Rep2

tag: treatments


title: GRH49

description: total small RNA

tag: genotype

tag: temperature


title: MYB61_B5_Rep2

tag: transfection


title: genomic DNA from sample 36

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1

tag: cellcount-nk

tag: cellcount-mono


title: G401_BRD9KO_rep2

value: kidney rhabdoid tumor derived cell line

tag: genotype/variation

value: BRD9 KO


title: GRH78

description: total small RNA

tag: tissue

value: BX2theta, P(TARGET)


title: genomic DNA from sample 122

description: whole blood case sample

tag: diagnosis

tag: age

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-gran


title: TCP23_B5_Rep1

tag: organ

tag: ecotype

tag: treatments


title: EV_B6_Rep1

tag: transfection

value: empty vector


title: genomic DNA from sample 270

description: whole blood control sample

tag: education level


title: genomic DNA from sample 430

description: whole blood case sample

tag: history of myocardial infarction


title: FBH4_B5_Rep1


title: MYB61_B5_Rep1


title: genomic DNA from sample 322

description: whole blood case sample

tag: Sex


title: WRKY18_B5_Rep3


title: GRH160

description: total small RNA

value: ovary

tag: genotype

tag: temperature


title: NAP_B5_Rep3

value: 10 days

value: NAP


title: EV_B5_Rep3


title: genomic DNA from sample 504

description: whole blood control sample

tag: snp based principle component 1

tag: cellcount-nk

tag: cellcount-mono


title: genomic DNA from sample 113

description: whole blood case sample

tag: diagnosis

value: case

tag: tissue


title: EV_B6_Rep2

tag: age


title: NAP_B5_Rep2


title: genomic DNA from sample 276

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-bcell


title: GRH77

description: total small RNA

value: BX2OFF, P(TARGET)


title: WRKY18_B5_Rep2

tag: organ


title: genomic DNA from sample 316

description: whole blood control sample

tag: cellcount-gran


title: EV_B5_Rep2

tag: ecotype

tag: treatments


title: hasset_DMUCA_A

city: Aurora

first: Michael

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

data_processing: Microarray data were generated using Affymetrix protocols. Probe set summarization (.CHP) files were generated using the Affymetrix Microarray Suite (MAS 5.0) algorithm. Background-corrected perfect match intensities were computed for each perfect match cell on every GeneChip and base-2 logarithm of each background-corrected perfect match intensity was obtained. These background-corrected and log-transformed perfect match intensities were normalized using the quantile normalization method. Tukey's median polish was used to obtain estimates that serve as the log-scale expression measures associated with the particular probe set. These data were imported into Transcriptome Analysis Console (Affymetrix version 3.0.0) Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Signal estimates for each transcript cluster for each condition was calculated using Tukey's Bi-weight Average Algorithm. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. Finally, the mean value of the signal log ratios from each comparison file was calculated.  Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than or equal to 1 for down-regulated transcripts were kept in the final list of genes. Signal log ratio values were converted from log2 and expressed as fold changes.

label: biotin

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 ∆mucA grown under growth protocol

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol (end labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix))

growth_protocol: transcriptional profiling experiments using wild-type PAO1, mucA22 and ∆mucA bacteria were grown for 24 hr under anaerobic conditions in LBN, pH 6.5, followed by treatment of each organism with 15 mM A-NO2- for 20 min.

extract_protocol: Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

treatment_protocol: Cells were treated with RNAprotect (Qiagen) and frozen at -80°C.

tag: genotype/variation

value: {deleta}mucA (mucA deletion)


title: genomic DNA from sample 455

description: whole blood case sample

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
Processed data in Series matrix table: Funnorm normalized

tag: education level

tag: history of myocardial infarction

value: whole blood


title: genomic DNA from sample 506

description: whole blood control sample

tag: Sex

value: M


title: hasset_DMUCA_C

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: HAT22_B5_Rep1

value: root

value: Nitrogen, Cycloheximide, Dexamethasone

tag: transfection


title: hasset_MUCA22_B

source_name: PAO1 mucA22 grown under growth protocol


title: hasset_MUCA22_C


title: hasset_DMUCA_B


title: hasset_MUCA22_A


title: genomic DNA from sample 388

description: whole blood case sample

tag: snp based principle component 1


title: hasset_PAO1_A

source_name: PAO1 WT grown under growth protocol

value: wild type


title: WRKY18_B5_Rep1


title: genomic DNA from sample 52

description: whole blood case sample

value: F

tag: cellcount-nk


title: 20.endo.2

city: Rochester

first: Purna

last: Kashyap

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
MAPRSeq 2.1.1, aligner tophat 2.1.0 and expression counts collated with HTSeq
Genome_build: Homo_sapiens.GRCh38.78.mod.gtf

source_name: post intervention

extract_protocol:
Biopsy samples were thawed on ice, homogenized and centrifuged at 13000 RPM and the supernatant was transferred to a new tube.  RNA was prepared using the RNeasy Mini Kit (QIAGEN, Hilden, Germany), using protocol instructions
Samples were stored at -20 and submitted to the Medical Genome Facility at Mayo Clinic, Rochester, MN for library preparation and sequencing on the Illumina HiSeq 2500 Rapid Run

treatment_protocol: This was a pilot prospective single-center dietary intervention study in healthy volunteers consuming a high fiber diet at baseline. The study was registered with clinicaltrials.gov NCT03266536.

tag: subject status

tag: gender

tag: time point

value: post dietary intervention (to reduce fiber intake for 1 week)

value: duodenum


title: 20.endo.1

source_name: baseline

value: healthy volunteers consuming a high fiber diet

tag: age

value: baseline

tag: tissue


title: hasset_PAO1_C


title: HAT22_B5_Rep2


title: 19.endo.2


title: EV_B5_Rep1

value: empty vector


title: 19.endo.1


title: genomic DNA from sample 218

description: whole blood case sample

tag: diagnosis

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-mono


title: LBD38_B4Rep3

data_processing:
Raw reads were trimmed to remove low quality bases (q<10) and adapter contamination.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the TopHat (v2) package and estimating read counts by the GenomicFeatures/Alignments package.
Genes responding significantly (FDR adjusted p-val <0.05) to each of the "N-early response" TFs  relative to the empty vector control were identified using DESeq2 with a ~TF+Batch model.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts output from GenomicFeatures/Alignments package

tag: organ

tag: ecotype

tag: treatments


title: NAP_B5_Rep1


title: genomic DNA from sample 119

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: cellcount-gran


title: genomic DNA from sample 397

description: whole blood case sample

tag: Sex

tag: snp based principle component 1


title: ERF060_B4Rep3

tag: transfection


title: genomic DNA from sample 536

description: whole blood case sample

tag: cellcount-nk


title: 17.endo.1

tag: subject status

tag: gender

tag: time point


title: genomic DNA from sample 475

description: whole blood control sample

tag: diagnosis

value: control

tag: age

tag: tissue


title: 16.endo.2


title: ASR3_B4Rep3

value: 10 days


title: hasset_PAO1_B

tag: genotype/variation


title: 16.endo.1


title: genomic DNA from sample 253

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 319

description: whole blood control sample

tag: education level


title: 15.endo.2


title: EV_B4Rep3

tag: organ

tag: ecotype

tag: treatments


title: LBD38_B4Rep2


title: 17.endo.2


title: genomic DNA from sample 247

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1

tag: cellcount-gran


title: genomic DNA from sample 166

description: whole blood control sample

tag: cellcount-nk


title: ASR3_B4Rep2

tag: transfection


title: ERF060_B4Rep2


title: 15.endo.1

tag: subject status

tag: gender

tag: time point


title: genomic DNA from sample 473

description: whole blood control sample

tag: diagnosis

tag: age

tag: tissue


title: 13.endo.2


title: 13.endo.1


title: 12.endo.2


title: EV_B4Rep2


title: genomic DNA from sample 54

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 75

description: whole blood case sample

tag: education level


title: LBD38_B4Rep1

tag: organ

tag: ecotype

tag: treatments


title: 12.endo.1


title: NAC4_B4Rep2


title: NAC4_B4Rep3


title: 11.endo.2


title: ERF060_B4Rep1


title: 11.endo.1


title: genomic DNA from sample 58

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: genomic DNA from sample 6

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-gran


title: ASR3_B4Rep1

tag: transfection


title: 9.endo.2

tag: subject status

tag: gender

tag: time point


title: genomic DNA from sample 471

description: whole blood case sample

tag: diagnosis

tag: age

tag: tissue


title: EV_B4Rep1


title: genomic DNA from sample 360

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 68

description: whole blood case sample

tag: education level


title: 8.endo.2


title: bZIP3_B4Rep3

tag: organ

tag: ecotype

tag: treatments


title: HHO2_B4Rep3


title: genomic DNA from sample 95

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: ZFP4_B4Rep3

tag: transfection


title: genomic DNA from sample 72

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-gran


title: 7.endo.2

tag: subject status

tag: gender

tag: time point


title: 7.endo.1

tag: age

tag: tissue


title: genomic DNA from sample 318

description: whole blood control sample

tag: diagnosis

tag: snp based principle component 2

tag: cellcount-bcell


title: genomic DNA from sample 173

description: whole blood control sample

tag: education level

tag: cellcount-mono


title: 8.endo.1


title: C2H2_B4Rep3

tag: organ

tag: ecotype

tag: treatments


title: 5.endo.2


title: 6.endo.1


title: genomic DNA from sample 195

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: genomic DNA from sample 17

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-gran


title: bZIP3_B4Rep2

tag: transfection


title: 6.endo.2

tag: subject status

tag: gender

tag: time point


title: genomic DNA from sample 208

description: whole blood case sample

tag: diagnosis

tag: age

tag: tissue


title: NAC4_B4Rep1


title: 5.endo.1


title: CDF1_B4Rep3


title: 3.endo.1


title: 3.endo.2


title: ZFP4_B4Rep2


title: genomic DNA from sample 248

description: whole blood control sample

tag: education level

tag: snp based principle component 2

tag: cellcount-bcell


title: HHO2_B4Rep2

tag: organ

tag: ecotype


title: C2H2_B4Rep2

tag: treatments


title: 2.endo.2


title: genomic DNA from sample 431

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-mono


title: genomic DNA from sample 326

description: whole blood control sample

tag: snp based principle component 1

tag: cellcount-nk

tag: cellcount-gran


title: bZIP3_B4Rep1

tag: transfection


title: genomic DNA from sample 529

description: whole blood case sample


title: CDF1_B4Rep2


title: genomic DNA from sample 90

description: whole blood case sample


title: HHO2_B4Rep1


title: 2.endo.1

tag: subject status

tag: gender

tag: time point


title: 1.endo.2

tag: age

tag: tissue


title: genomic DNA from sample 488

description: whole blood case sample

tag: diagnosis

tag: education level

tag: snp based principle component 2


title: 1.endo.1


title: CDF1_B4Rep1

tag: organ

tag: ecotype


title: C2H2_B4Rep1

tag: treatments


title: ZFP4_B4Rep1


title: genomic DNA from sample 464

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: cellcount-bcell


title: genomic DNA from sample 256

description: whole blood control sample

tag: snp based principle component 1

tag: cellcount-nk

tag: cellcount-mono


title: HYH_B3Rep3

tag: transfection

value: HYH


title: genomic DNA from sample 38

description: whole blood case sample

value: case

tag: cellcount-gran


title: TGA4_B3Rep3


title: genomic DNA from sample 505

description: whole blood control sample


title: genomic DNA from sample 20

description: whole blood case sample


title: CRF4_B3Rep3