title: DM30-2

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the SST-RMA algorism using a Transcriptome Analysis Console Software (Affymetrix Inc.)

organism: Mus musculus

source_name: exposure group

label_protocol: The total RNA (500 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmented and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mouse neuroblastoma Neuro-2a cells (IFO50081) were obtained from Japanese Collection of Research Bioresources Cell Bank (JCRB) and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C in humidified air with 5% CO2.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® XS RNA isolation kit (MACHEREY-NAGEL, GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies, Inc.). The RNA samples with RIN (RNA integrity number) values >9.0 were considered acceptable.

treatment_protocol: Semi-confluent cells were exposued to 30 µM DM or vehicle (0.1%DMSO) dossolved in medium for 24 hours.

tag: strain

value: Albino strain A

tag: cell line

value: neuroblastoma Neuro-2a cells (IFO50081)

value: DM


title: prostate_cancer_primary_294

status: Public on Jun 03 2021

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

country: USA

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: tissue

value: FFPE prostate cancer

tag: primary gleason

tag: secondary gleason

tag: decipher risk group

value: Lower

tag: race

value: African American


title: PRISM_Control_250Control

type: genomic

city: Doha

first: Omar

middle: M E

last: Albagha

address: Luqta Street, Education City

department: Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: DNA CpG sites

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
The R package RnBeads version 1.10.8 was used for quality control. Samples with low methylated or unmethylated median intensity (<11.0) were excluded (n=35) along with samples with sex mismatch between reported and predicted sex (n=0). Probes with the following criteria were excluded: detection P value >0.05, cross reactive probes, containing a SNP within 3 bp of nucleotide extension site, or those located on sex chromosomes. Additionally, 723 sites were further excluded from the dataset for previously established association with smoking. A total of 56,356 probes were excluded from the initial 485,512 leaving 429,156 CpGs for analysis.
The Enmix method from RnBeads was used for background correction whilst
SWAN from RnBeads was used for between and within array normalization
The M-values, derived using the formulae log2((methylated signal+1)/(unmethylated signal+1)), were used

label: Cy3, Cy5

molecule: genomic DNA

source_name: white blood cells

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using standard protocols. Bisulfite conversion was performed on 500µg of DNA using Zymo EZ-96 DNA methylation Kit (Zymo Research, USA). DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturer’s protocol

tag: mmed

tag: umed

tag: phenotype

value: Control

tag: array

tag: slide

value: white blood cells


title: DM30-1

tag: treatment


title: prostate_cancer_primary_310

value: Higher


title: visit 1 (baseline), group A  1_B9

city: Oslo

first: Stine

middle: Marie

last: Ulven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of oslo

description:
visit 1 (baseline), group A
wk 0

hyb_protocol: Illumina HumanHT-12 Expression BeadChips (Illumina Inc., CA, USA)

scan_protocol: Illumina HiScann instrument (Illumina Inc., CA, USA)

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PBMC, visit 1 (baseline), group A

label_protocol: Illumina Total Prep RNA Amplification Kit (Thermo Fisher Scientific, MA, USA)

extract_protocol: Total RNA was isolated from all PBMC samples using RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.RNA quantity measurements were performed using a Nanodrop ND-1000 Spectrometer (Thermo Fisher Scientific, Gothenburg, Sweden) and RNA integrity number (RIN) value was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to check the RNA quality.

tag: cell type

value: PBMC


title: visit 1 (baseline), group A  1_C1

description:
visit 1 (baseline), group A
wk 0


title: Ctrl-2

source_name: control group

value: control group


title: visit 1 (baseline), group B  1_B7

description:
visit 1 (baseline), group B
wk 0

source_name: PBMC, visit 1 (baseline), group B


title: prostate_cancer_primary_287


title: PRISM_Control_345Control

description: DNA CpG sites


title: visit 2 (end of study), group B  1_B8

description:
visit 2 (end of study), group B
wk 8

source_name: PBMC, visit 2 (end of study), group B


title: visit 1 (baseline), group B  1_C11

description:
visit 1 (baseline), group B
wk 0


title: DXA1226_334Control

description: DNA CpG sites


title: E80 skeletal muscle input DNA

type: SRA

city: Guangzhou

first: Renqiang

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road

country: China

institute: SUN YAT-SEN UNIVERSITY

library_source: genomic

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Samtools (v 1.3.1) was used to remove potential PCR duplicates.
Peaks were identified with MACS2 algorithms.
Super-enhancers were defined using the standard ROSE algorithms.
Genome_build: Sscrofa11.1

organism: Sus scrofa

source_name: skeletal muscle

extract_protocol:
Samples were  were washed with PBS and incubated in lysis buffer. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). The histone-DNA complexes were isolated with H3K27ac.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the Illumina TruSeq ChIP Sample Prep Set A and sequenced on Illumina HiSeq X Ten with PE150 method

tag: breed

value: Luchuan pig

tag: tissue type

value: longissimus dorsi muscle

tag: age

value: embryonic day 80

tag: Sex

value: female

tag: chip antibody

tag: restriction enzyme


title: Ctrl-1

tag: strain

tag: cell line


title: prostate_cancer_primary_284

tag: tissue

tag: primary gleason

tag: secondary gleason

tag: decipher risk group


title: E80 skeletal muscle H3K27ac

value: H3K27ac antibodies (ab4732, Abcam)


title: PRISM_Control_251Control

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype


title: DXA2019_93Control

description: DNA CpG sites

tag: array

tag: slide


title: E35 skeletal muscle input DNA

tag: breed

value: embryonic day 35


title: prostate_cancer_primary_285

tag: race


title: prostate_cancer_primary_283

value: Average


title: DXA1864_283Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_B6

description:
visit 2 (end of study), group A
wk 8

source_name: PBMC, visit 2 (end of study), group A

tag: cell type


title: E35 skeletal muscle H3K27ac replicate_2

tag: tissue type

tag: age

tag: Sex

value: H3K27ac antibodies (ab4730, Abcam)


title: visit 2 (end of study), group B  1_B4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_282


title: E35 skeletal muscle H3K27ac replicate_1

tag: chip antibody

value: H3K27ac antibodies (ab4729, Abcam)

tag: restriction enzyme


title: visit 1 (baseline), group B  1_B3

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_120Control

description: DNA CpG sites

tag: tissue


title: prostate_cancer_primary_281

value: FFPE prostate cancer

tag: primary gleason


title: PRISM_Control_113Control

description: DNA CpG sites


title: prostate_cancer_primary_280

tag: secondary gleason


title: E80 skeletal muscle RNA-seq replicate_3

library_source: transcriptomic

data_processing:
Sequence reads are aligned to pig reference genome (Sscrofa 11.1) by alignment tool STAR (version 2.6.0c).
The aligned reads of these samples were assembled using Cufflinks (version 2.1.1).
Kallisto (v 0.44.0) was used to quantify gene expression and obtain TPM expression values.
Genome_build: Sscrofa11.1

extract_protocol:
Skeletal muscles were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent
rRNA depletion protocol (Ribo-Zero kit, Epicentre) and Illumina TruSeq stranded RNA-Seq library protocol are used to construct the RNA-Seq libraries. cDNA libraries were  sequenced on HiSeq X Ten (Illumina) platform to produce  150-bp paired-end raw reads.


title: E80 skeletal muscle RNA-seq replicate_2


title: DXA1349_313Control

description: DNA CpG sites


title: PRISM_Control_407Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_B2

description:
visit 2 (end of study), group A
wk 8


title: E80 skeletal muscle RNA-seq replicate_1


title: visit 2 (end of study), group B  1_B12

description:
visit 2 (end of study), group B
wk 8


title: DXA1437_348Control

description: DNA CpG sites


title: E35 skeletal muscle RNA-seq replicate_3


title: visit 1 (baseline), group B  1_B11

description:
visit 1 (baseline), group B
wk 0


title: prostate_cancer_primary_278

tag: decipher risk group


title: prostate_cancer_primary_279


title: DXA2027_332Control

description: DNA CpG sites

tag: mmed


title: visit 2 (end of study), group A  1_B10

description:
visit 2 (end of study), group A
wk 8


title: prostate_cancer_primary_277


title: visit 1 (baseline), group A  1_B5

description:
visit 1 (baseline), group A
wk 0


title: E35 skeletal muscle RNA-seq replicate_1


title: visit 1 (baseline), group A  1_B1

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_293


title: visit 2 (end of study), group B  1_A8

description:
visit 2 (end of study), group B
wk 8


title: DXA1140_182Control

description: DNA CpG sites

tag: umed


title: Epithelium 3

city: Cambridge

first: Linda

middle: G.

last: Griffith

state: MA

address: 77 Massachusetts Avenue, Building 16-429

institute: Massachusetts Institute of Technology

data_processing:
Illumina HiSeq Control Software  v. 2.2.58 used for basecalling.
Quality control: Reads were aligned against GRCh38  (Sept. 2011) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against canFam3 and read density across genomic features were estimated for RNA-Seq-specific quality control metrics.
RNA-Seq mapping and quantitation: Reads were aligned against GRCh38 / ENSEMBL 89 annotation using STAR v. 2.5.3a with flags -runThreadN 8 --runMode alignReads  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM with --genomeDir pointing to a 75nt-junction GRCh38 STAR suffix array.
Gene expression was quantitated using RSEM v. 1.3.0 with the following flags for all libraries: rsem-calculate-expression --calc-pme --alignments -p 8  --forward-prob 0 against an annotation matching the STAR SA reference. Posterior mean estimates (pme) of counts and estimated RPKM were retrieved.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing log2-transformed RPKM values for all GRCh38 annotated genes (ENSEMBL 89) in each sample (RSEM pme_RPKM output).

source_name: Colon Epithelium from healthy donor

growth_protocol: Physiomimetic platform 3XGL  [Fabrication and assembly]    The physiomimetic technology was developed in-house and described previously (Chen et al.,  2017; Edington et al., 2018). Briefly, iterations of the system were designed in CAD and  commercially machined. The pneumatic plates were machined in acrylic and solvent bonded to  form two-layer manifolds, while the fluidic plates were machined from monolithic polysulfone. The  pneumatic plates were processed with vapor polishing and fluidic plates were cryo-deburred to  remove sharp burrs. 50 micron thick polyurethane membranes are supplied by American Polyfilm  Inc. and mounted onto grip rings (Ultron Systems UGR-12) to provide uniform tension. Mounted  membranes were laser cut to remove material around screw holes. After cutting, they were rinsed  in 10% 7x solution followed by DI water and then sterilized using ethylene oxide gas. All hardware  components, with the exception of the polyurethane membranes, are reusable. Flow of media  between compartments on the platform is achieved by pumping driven from outside the incubator  by a microcontroller and a pneumatic solenoid manifold that controls the tubing run through the  back of the incubator to intermediary connectors. Moreover, the system allows for safe circulation  of CD4 T cells within and between compartments at high velocities and preserved T cell viability.  Inside the incubator, tubing is attached to the platform through valved breakaway couplings to  allow removal from the incubator for media changes and sampling. Flow rates and calibration  factors are set through a graphical user interface and are sent to a customized microcontroller  (National Instruments myRIO-1900) over USB or WiFi.  [Operation]    4 days prior to experimentation, sterile platforms were assembled in a laminar flow hood. They  were primed with 1% bovine serum albumin (Sigma, cat. no. A9576) and Pen/Strep in PBS. Pump  function and tubing connections were visually confirmed by pumping from the mixer to each dry  compartment, then by running the recirculation pumps backwards to clear all air from the  channels. Platforms were run overnight in the incubator to passivate and confirm full operation  before the addition of the gut and/or liver MPS as well as the circulating Treg/Th17 cells. On the  day of the experiment, priming media was replaced with serum-free CM (see Gut MPS methods)  with the volume of each compartment being as follows: gut MPS 2 ml (apical 0.5 ml, basal 1.5  ml), liver MPS 1.6 ml and the mixer compartment 2.3 ml. The layout of the platform and flow  parameters are indicated in Figure S2A. The duration of interaction studies was 4 days with  complete media changes every 48 hours. TEER was measured just prior to the interaction and at  the end on day 4 to minimize monolayer manipulation. However, TEER was measured on control  gut MPSs in isolation at day 2 to monitor innate monolayer behavior. During the media change  and at the end of the interaction studies on day 4, common media was collected from the apical  and basal gut compartment, liver compartment above the scaffold and mixer. Circulating  Treg/Th17 cells that were collected with the media during the 48 h media change were returned  to each original platform equally distributed among the 3 compartments. Media samples were  collected in low-binding tubes, supernatants were spun down at 10,000 g for 5 min to remove cell  debris, BSA was added to a final concentration of 0.5% (except to the samples reserved for  metabolomic analysis) and the samples transferred to a -80 °C freezer. Cytokine/chemokine,  metabolomic and albumin measurements during interaction studies were performed on the media  collected from the apical gut compartments (for studies of SCFA distribution only) and the mixer  compartments that distribute the media between the gut and liver MPSs. Each condition was  performed in 3 biological replicates.

extract_protocol:
Epithelial tissue from the gut MPSs and hepatocytes with Kupffer cells from the liver MPSs, as  well as Treg/Th17 cells were collected and mRNA was extracted using the PureLink RNA mini kit  (Thermo Fisher, cat. no. 12183018A).
Total RNA was analyzed and quantified using the Fragment  Analyzer (Advanced Analytical), and Illumina libraries were prepared with Kapa RNA HyperPrep  with RiboErase (Kapa Biosystems, cat. no. 08098107702). After cDNA fragmentation (Covaris  S2), cDNA was end-repaired and adaptor-ligated using the SPRI-works Fragment Library System  I (Beckman Coulter Genomics). Adaptor-ligated cDNA was then indexed during PCR  amplification, and the resulting libraries were quantified using the Fragment Analyzer and qPCR  before being sequenced on the Illumina HiSeq 2000 (Illumina) in High Output mode. 4 lanes 40-50 nt single-end read  with an average depth of 15-20 million or 5 million reads per sample were sequenced.

value: Colon Epithelium from healthy donor (in vitro)

tag: interaction

value: Epithelium isolated under static conditions

tag: treatment

value: Epithelium alone


title: E35 skeletal muscle RNA-seq replicate_2


title: prostate_cancer_primary_275

value: African American


title: prostate_cancer_primary_274


title: visit 1 (baseline), group A  1_A9

description:
visit 1 (baseline), group A
wk 0


title: DXA1404_36Control

description: DNA CpG sites

tag: phenotype

value: Control

tag: array

tag: slide

value: white blood cells


title: prostate_cancer_primary_273

value: Higher

tag: race


title: PRISM_Control_212Control

description: DNA CpG sites


title: PRISM_Control_491Control

description: DNA CpG sites


title: Epithelium 2

tag: cell type


title: Epithelium 1


title: PRISM_Control_328Control

description: DNA CpG sites


title: Tr/Th17+IFN/IL-12+SCFA

source_name: T cells

value: T cells (in vitro)

value: T cells in vitro

value: In vitro-differentiated Thr/Th17 from peripheral blood T cells  were  seeded in combination (2.4x10e5 cells/ml of Tregs and 1.2x10e5 cells/ml of Th17 cells) in 1ml of CM  on 24-well plates. Cells were activated with 10 ng/ml of IFN-gamma and IL-12 ((R&D Systems, cat. no 212-IL/285-IF) and challenged with 1mM of total SCFA (0.7mM acetate, 0.2mM  propionate, 0.1mM butyrate).


title: visit 2 (end of study), group A  1_A6

description:
visit 2 (end of study), group A
wk 8

value: PBMC


title: prostate_cancer_primary_272

value: Lower


title: visit 1 (baseline), group B  1_A7

description:
visit 1 (baseline), group B
wk 0


title: visit 1 (baseline), group A  1_A5

description:
visit 1 (baseline), group A
wk 0


title: prostate_cancer_primary_276


title: prostate_cancer_primary_286


title: prostate_cancer_primary_270


title: PRISM_Control_466Control

description: DNA CpG sites


title: Tr/Th17+IFN/IL-12

value: In vitro-differentiated Thr/Th17 from peripheral blood T cells  were  seeded in combination (2.4x10e5 cells/ml of Tregs and 1.2x10e5 cells/ml of Th17 cells) in 1ml of CM  on 24-well plates. Cells were activated with 10 ng/ml of IFN-gamma and IL-12 ((R&D Systems, cat. no 212-IL/285-IF).


title: DXA1199_155Control

description: DNA CpG sites


title: prostate_cancer_primary_269

value: Average


title: PRISM_Control_476Control

description: DNA CpG sites


title: LCB5 D4

source_name: Liver (Hepatocytes + Kupffer cells)

value: Liver (Hepatocytes + Kupffer cells)

value: Liver MPS isolated

tag: time

value: Day 4

value: Control Liver tissue


title: visit 1 (baseline), group B  1_A3

description:
visit 1 (baseline), group B
wk 0


title: PRISM_Control_76Control

description: DNA CpG sites


title: visit 2 (end of study), group A  1_A2

description:
visit 2 (end of study), group A
wk 8


title: LCB4 D4


title: prostate_cancer_primary_268

value: FFPE prostate cancer


title: visit 2 (end of study), group B  1_A12

description:
visit 2 (end of study), group B
wk 8


title: LCB3 D4


title: visit 1 (baseline), group B  1_A11

description:
visit 1 (baseline), group B
wk 0


title: LCB2 D4


title: visit 2 (end of study), group B  1_A4

description:
visit 2 (end of study), group B
wk 8


title: prostate_cancer_primary_271


title: PRISM_Control_472Control

description: DNA CpG sites


title: prostate_cancer_primary_266


title: PRISM_Control_211Control

description: DNA CpG sites


title: LCB1 D4


title: prostate_cancer_primary_267


title: visit 2 (end of study), group A  1_A10

description:
visit 2 (end of study), group A
wk 8


title: visit 1 (baseline), group A  1_A1

description:
visit 1 (baseline), group A
wk 0


title: DXA1424_19Control

description: DNA CpG sites


title: LCA5 D4


title: prostate_cancer_primary_265


title: PRISM_Control_321Control

description: DNA CpG sites


title: LCA4 D4


title: prostate_cancer_primary_262


title: DXA1004_406Control

description: DNA CpG sites


title: prostate_cancer_primary_264


title: PRISM_Control_323Control

description: DNA CpG sites


title: 4L3Sl D4

treatment_protocol: Treg and Th17 cells were differentiated from naïve CD4 T cells derived from the same Leuko Pak  donor (StemCell, cat. no. 70500) as the dendritic cells and macrophages in the gut MPS. Naïve  CD4 T cells were isolated with the EasySep Human Naïve CD4+ T Cell Isolation Kit II (StemCell,  cat. no. 17555). Cells were differentiated to Tregs or Th17 cells in RPMI 1640 medium (Gibco)  supplemented with Pen/Strep, heat-inactivated 10% heat-inactivated FBS, 1% MEM Non-  Essential Amino Acid Solution, 1 mM sodium pyruvate, 1% GlutaMax, 2.5% ImmunoCult Human  CD3/CD28 T cell activator (StemCell, cat. no. 10971) and 5 ng/ml human TGF-beta (R&D  Systems, cat. no. 240-B/CF). Additionally Tregs received 100 UI/ml IL-2 (R&D Systems, cat. no.  202-IL) and 10 nM retinoic acid (Sigma, cat. no. R2625-50MG); while for Th17 cell differentiation,  10 ng/ml each of human IL-6 and IL-1 beta (R&D Systems, cat. no. 206-IL, 201-LB) were added.  After 7 days of differentiation at 37 °C, cells were harvested into CM and added in a physiological  2:1 ratio of Treg/Th17 cells to either the basal side of gut MPS for isolation studies (total of 4 x  104 Tregs/2 x 10e4 Th17 cells/transwell) or equally distributed among the compartments on the  3XGL platform (total of 2.4 x 10e5 Tregs and 1.2 x 10e5 Th17 cells/interaction lane). Treg/Th17 ratio  in human peripheral blood varies from 0.2 to 1 in healthy individuals and total Treg numbers  varying from 7 x 10e4 to 5 x 10e5/ml (Eastaff-Leung et al., 2010; Ratajczak et al., 2010). While T cells  were prevented to come into direct contact with the epithelium grown on microporous membranes,  their contact was enabled with antigen presenting cells of the gut MPS and the liver MPS.

value: Gut-Liver-Treg/Th17-SCFA Interaction (Platform 4)

value: Each platform houses 3 replicates of the gut-liver interaction.


title: PRISM_Control_10Control

description: DNA CpG sites

value: Control


title: DXA0933_67Control

description: DNA CpG sites

value: white blood cells


title: 4L2Sl D4


title: prostate_cancer_primary_260

value: African American


title: 4L1Sl D4


title: LCB6 D4


title: DXA1901_53Control

description: DNA CpG sites


title: prostate_cancer_primary_261


title: 3L3l D4

value: Gut-Liver-Treg/Th17 Interaction (Platform 3)


title: PRISM_Control_218Control

description: DNA CpG sites


title: prostate_cancer_primary_259


title: 3L2l D4


title: prostate_cancer_primary_258


title: prostate_cancer_primary_256


title: prostate_cancer_primary_257


title: 3L1l D4


title: prostate_cancer_primary_255


title: DXA1379_49Control

description: DNA CpG sites


title: DXA0118_26Control

description: DNA CpG sites


title: PRISM_Control_458Control

description: DNA CpG sites


title: 2L3S D4

treatment_protocol: The liver MPS was prepared as previously described (Chen et al., 2017). Single donor human  primary hepatocytes were purchased from BioIVT (cat. No. AQL) and Kupffer cells, as the innate  immune component of the liver MPS, were obtained from Thermo Fisher (cat. no. HMCSTS). The  cells were seeded on liver scaffolds which are thin (0.25 mm) polystyrene discs perforated with  301 channels (diameter = 0.3 mm) (Clark et al., 2016). Scaffolds were soaked in 70% EtOH for  15 min, washed twice with PBS, and coated with 30 μg/mL rat tail collagen I in PBS for 1 hour at  room temperature. Collagen-coated scaffolds were air dried and then punched into the 3XGL  platforms for interaction experiments or in the LiverChipâ (CN Bio Innovations) for experiments  in isolation. 3 days prior to interaction experiments, hepatocytes and Kupffer cells were thawed in  21  Cryopreserved Hepatocyte Recovery Medium (Thermo Fisher, cat. no. CM7000), centrifuged at  100 × g for 8 min, and seeded on the scaffolds at a 10:1 ratio, 6 × 10e5:6 × 10e4 cells/well, in  hepatocyte seeding medium (250 mL William’s E medium, 9 mL Gibco Cocktail A, 12.5 mL FBS)  and cultured under flow at 37°C. After 1 day, the media was changed to 250 mL William’s E  medium and 10 mL Gibco Cocktail B. At day 3 after seeding, the media was changed to CM and  the interaction studies with the gut MPS begun. The CM was also added to the LiverChipâ . To  evaluate the physiological status of the liver, samples from all compartments but the apical gut  MPS (i.e., liver, directly above the scaffold; basal gut MPS: and mixer) were taken at every  medium change (every 48 hours) and assayed for albumin via ELISA (Bethyl Laboratories, cat.  no. E80-129).

value: Gut-Liver-SCFA Interaction (Platform 2)


title: prostate_cancer_primary_254

value: Higher


title: prostate_cancer_primary_263


title: DXA1427_343Control

description: DNA CpG sites


title: PRISM_Control_468Control

description: DNA CpG sites


title: prostate_cancer_primary_251


title: 1L2 D4

value: Gut-Liver Interaction (Platform 1)


title: 2L1S D4


title: 2L2S D4


title: DXA1005_256Control

description: DNA CpG sites


title: prostate_cancer_primary_252

value: Lower


title: prostate_cancer_primary_249


title: H460 Hydrocortisone Rep 2 4C

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

description:
h460_hc_ceres_vp.wig
h460_hc_promoter_vp.wig

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
For ChIP sequencing reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed. Peaks were called MACS peak caller version 2 (Zhang Y et al. Genome Biol 2008;9(9):R137). MACS2 was run with the default parameters.
For 4C sequencing the alignment of the sequencing reads was done using bowtie2 with default parameters. We use samtools to filter for mapped reads with a minimum mapping quality score of 1. Next we extract from the reference genome all possible 4C capture sequences (in FASTA format) with the exact same length as the observed 4C captures from the sequencing run. We map and filter these reference capture sequences with the same parameters as the observed 4C reads using bowtie2 and samtools. In subsequent analysis we only include the thus mappable 4C fragment ends.
Genome_build: RNA-Seq: Hg38
Genome_build: ChIP-Seq: Hg19

source_name: Lung cancer cell line

growth_protocol: A549 mentained in DMEM/F12 + 10%FCS + 1%P/S. H2122/H1944/H1975/H460 mentained in RPMI + 10%FCS + 1%P/S. H1944 cells were injected to NOD-SCID mice and after engraftment treated with either Vehicle or Dexamethason (4 mg/kg).

extract_protocol:
The 4C procedure was performed according to the published protocol (van de Werken et al., 2012, Nature Methods (PMID 22961246)).
The 4C library constuction was performed according to the published protocol (van de Werken et al., 2012, Nature Methods (PMID 22961246)).

treatment_protocol: Cells were serum starved for 3 days, subsequently the cells either remained untreated or were treated for 2 (ChIP and 4C) or 8 (RNA seq) hours with hydrocortisone and processed for downstream analysis.

tag: crispr cell line features

tag: grna

tag: antibody

tag: viewpoints

value: Viewpoint CDKN1C and Viewpoint CERES enhancer

value: Hydrocortisone (2,75 μM)

tag: replicate

value: Replicate 2


title: PRISM_Control_174Control

description: DNA CpG sites

tag: tissue


title: LCA3 D4

value: Liver (Hepatocytes + Kupffer cells)

value: Liver MPS isolated


title: prostate_cancer_primary_248

tag: primary gleason

tag: secondary gleason

tag: decipher risk group


title: 1L3 D4

tag: interaction

value: Day 4


title: prostate_cancer_primary_247

value: FFPE prostate cancer


title: H460 Vehicle Rep 2 4C

description:
h460_veh_ceres_vp.wig
h460_veh_promoter_vp.wig

tag: treatment

value: Vehicle


title: H1975 Hydrocortisone Rep 2 4C

description:
h1975_hc_ceres_vp.wig
h1975_hc_promoter_vp.wig


title: DXA1900_473Control

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype


title: PRISM_Control_42Control

description: DNA CpG sites

tag: array

tag: slide


title: H1975 Vehicle Rep 2 4C

description:
h1975_veh_ceres_vp.wig
h1975_veh_promoter_vp.wig


title: SF9402_K27me3

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey 7-400

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq reads were aligned to hg38 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq reads were aligned to hg38 genome assembly using Bowtie2;H3K27ac, H3K27M ChIP-Seq were called using MACS2. For the H3K27ac ChIP-Seq, the peak length were fixed to 500 bp. For replicates, we used overlap optimal peaksets provided from the ENCODE ChIP-seq pipeline.
Hi-C raw FASTQ files and then mapped the trimmed files against hg38 human reference genome using runHiC pipeline. Hi-C matrix was generated using juicer Pre.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.

growth_protocol: Cell lines were maintained in culturing media recommended by cell line providers. All cells were grown in an incubator with 5% CO2 at 37°C.

extract_protocol:
Briefly, 30-50 million cells were crosslinked using 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes at room temperature. Cells were then rinsed, harvested, and resuspended in extraction buffer for ten minutes at 4°C, then centrifuged at 1,350xg for five minutes at 4°C. Cell pellet was resuspended and transferred to a one mL milliTUBE (520135, Covaris). After sonication (Covaris E220 ultrasonicator), samples were spun down and supernatant containing chromatin was collected. Chromatin was de-crosslinked for three hours at 65°C and DNA was extracted (28104, Qiagen). 10% sample was saved as input. Chromatin was incubated with primary antibody overnight at 4°C. The following day, protein A/G agarose beads (sc-2003, Santa Cruz Biotech) were added to the samples and incubated for 3 hours. Beads were centrifuged and washed with one mL of RIPA buffer four times. The beads and the ten mL input were eluted for 30 minutes at 65°C then spun down. Supernatant was de-crosslinked overnight 65°C. DNA was extracted and submitted for library preparation.
ChIP-Seq libraries were prepared with the KAPA Library preparation kit (KK8234, Kapa Biosystems) and NETflex DNA barcodes (514104, Bioo Scientific). A total of ten mg DNA was used as starting material for input and immunoprecipitation samples. Libraries were amplified with a thermocycler for 13 cycles. Post-amplification libraries were size-selected at 250-45bp in length using the Agencourt AMPure XP beads (A63881, Beckman Coulter).

tag: chip-antibody


title: PRISM_Control_389Control

description: DNA CpG sites


title: 1L1 D4

tag: cell type

tag: time

value: Each platform houses 3 replicates of the gut-liver interaction.


title: H460 Hydrocortisone Rep 1 4C

tag: crispr cell line features

tag: grna

tag: antibody

value: Replicate 1


title: prostate_cancer_primary_253

tag: tissue

tag: race


title: Neuron_D58_3

city: Exeter

first: Jennifer

last: Imm

state: Devon

address: Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader using recommended scanner settings

data_processing: Data loaded into R using methylumi, and then was then pre-processed in the R package wateRmelon using the dasen function.

label: Cy3 and Cy5

source_name: Terminally Differentiated Neuron

label_protocol: Standard Illumina Protocol

growth_protocol: iPSCs were differentiated into NPCs for 16 days before being terminally differentiated into neurons where they were maintained for either a further 37 or 58 days before final collection.

extract_protocol: Genomic DNA was extracted from cell sample using a standard phenol-chloroform protocol

treatment_protocol: iPSCs were differentiated into NPCs using LDN 193189, SB431542 and IWR1 in culture media. NPCs were terminally differentiated into neurons using synaptojuice SCM1/2 protocol.

tag: developmental stage

value: Terminally Differentiated Neuron

tag: gender

value: Female


title: prostate_cancer_primary_250

tag: primary gleason

tag: secondary gleason

tag: decipher risk group

value: African American


title: PRISM_Control_433Control

description: DNA CpG sites

tag: mmed

tag: umed

value: Control

value: white blood cells


title: XIII_K27me3

source_name: DIPGXIII


title: NHA_K27me3

source_name: NHA


title: SF7761_K27me3


title: prostate_cancer_primary_246

value: Average


title: PRISM_Control_330Control

description: DNA CpG sites

tag: phenotype

tag: array


title: SF9427_K27me3

tag: chip-antibody


title: H1975 Vehicle Rep 1 4C

tag: viewpoints

tag: treatment

tag: replicate


title: prostate_cancer_primary_242

value: Lower


title: PRISM_Control_329Control

description: DNA CpG sites

tag: slide


title: H460 Vehicle Rep 1 4C

tag: crispr cell line features

tag: grna

tag: antibody

value: Viewpoint CDKN1C and Viewpoint CERES enhancer


title: Neuron_D58_4

tag: developmental stage


title: KNS42_K27me3


title: Neuron_D58_1

tag: gender


title: PRISM_Control_128Control

description: DNA CpG sites

tag: tissue


title: prostate_cancer_primary_245

tag: primary gleason

tag: secondary gleason

value: Higher

tag: race


title: prostate_cancer_primary_241

tag: decipher risk group


title: prostate_cancer_primary_244


title: SHR rat strain, male, 7 month of age, liver, high fat diet [SHR4]

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Liver expression data obtained from SHR strain.

hyb_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC version 4.0.1, Affymetrix, Santa Clara, CA, USA) using GC-MRA as normalization method.

organism: Rattus norvegicus

source_name: liver sample from SHR rat strain after high fat diet administration

growth_protocol: All strains were bred in-house. Rats were kept under  12 hours light-dark cycle, fed standard laboratory chow and given access to water ad libitum. After 6 months rats were fed HFD (Ssniff EF R/M with 30% fat, containing saturated fattyacids (FAs), short to long chain FAs, corresponding to approximately 50% of energy) for additional four weeks. Subsequently rats were anesthetized and decapitated. Organs were snap frozen in liquid nitrogen, and liver tissue was used for RNA extraction and further analysis.

extract_protocol: Total liver RNA was isolated using TRIzol reagent (Invitrogen) and purification was performed using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. UV measurements at 280 and 260 nm and 2100 Bioanalyzer runs using the RNA-6000 Nano-LabChip (Agilent, Böblingen, Germany) were used to ensure the quality and quantity of the extracted RNA Only samples showing RNA integrity numbers (RIN) above 8 were used for furhter analysis.

value: Liver tissue

tag: diet

value: high fat diet

tag: Sex

value: male


title: hNSC_K27me3

source_name: hNSC

tag: chip-antibody


title: DXA1336_94Control

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype

tag: array


title: PRISM_Control_255Control

description: DNA CpG sites

tag: slide


title: DIPG1114_K27me3


title: DXA1097_233Control

description: DNA CpG sites


title: NPC_2

source_name: NPC

value: Neuronal Precursor Cell


title: prostate_cancer_primary_243

source_name: FFPE prostate cancer

value: FFPE prostate cancer


title: PRISM_Control_141Control

description: DNA CpG sites

source_name: white blood cells


title: DIPG007_K27me3


title: SHR rat strain, male, 7 month of age, liver, high fat diet [SHR3]

label_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual


title: DXA2014_195Control

description: DNA CpG sites


title: prostate_cancer_primary_240


title: Neuron_D37_1


title: H1975 Hydrocortisone Rep 1 4C

tag: crispr cell line features

tag: grna

tag: viewpoints

tag: treatment

value: Hydrocortisone (2,75 μM)

tag: replicate


title: Neuron_D58_2

tag: developmental stage

tag: gender


title: SHR rat strain, male, 7 month of age, liver, high fat diet [SHR2]

tag: tissue


title: E3CD3col6

city: Baltimore

first: Joshua

middle: M

last: Popp

state: Maryland

address: 3100 Wyman Park Drive South Wing, Room S249

department: Biomedical Engineering

institute: Johns Hopkins University

description:
collection_metadata.txt
cell_counts.mtx
cell_counts_sctransform.mtx
pearson_residuals_sctransform.tsv

data_processing:
Paired-end reads were combined to form a (cells x genes) UMI counts matrix using dropseqRunner (https://github.com/aselewa/dropseqRunner)
Transcripts were aligned to the genome (GRCh38) using STAR-solo (Dobin et al. 2013)
featureCounts (Liao et al. 2014) assigned each read to a genomic feature, and umi_tools (Smith et al. 2017) created a count matrix representing the frequency of each feature in the dataset
Demuxlet (Kang et al. 2018) was used to demultiplex the pooled single cell data, and assign to each cell a probability that the cell was a doublet as well as a maximum likelihood donor (cell line) assignment
Genes were removed that were detected in fewer than 10 cells, and cells were removed if they were assigned by demuxlet to have a posterior probability of doublet assignment greater than 0.3, were not assigned to a single cell line donor, had more than 25% reads mapping to mitochondrial genes, or had fewer than 300 unique genes detected. This left a total of 38,943 genes (of 60,668) and 230,786 cells (of 564,362)
Seurat v3 and SCTransform were used to normalize the expression data while accounting for overdispersion and cell cycle effects. Cell cycle scoring was performed with the Seurat package, assigning a S phase and G2/ M phase score to each cell. The difference between these two scores was regressed out during normalization of the expression data.
Genome_build: GRCh38
Supplementary_files_format_and_content: cell_counts.mtx contains the raw UMI counts for each cell (in the MatrixMarket format). The files cell_indices.tsv and gene_indices.tsv are used for interpreting the matrix files.
Supplementary_files_format_and_content: cell_counts_sctransform.mtx contains the expected UMI counts for each cell (in the MatrixMarket format) after normalizing the data using SCTransform (Hafemeister et al. 2019). These adjusted counts were used to aggregate pseudobulk
Supplementary_files_format_and_content: pearson_residuals_sctransform.tsv contains the Pearson residuals for each cell (in the MatrixMarket format) after normalization using SCTrasnform (Hafemeister et al. 2019). These Pearson residuals were used for visualization, cell type annotation, and pseudotime inference
Supplementary_files_format_and_content: experimental_design.txt describes the mapping of cell lines to their pooled collections. Columns are 'Exp' (experimental round, 1-3); 'CD' (collection day, 1-3); 'col' (collection, 1-6 for experiments 1 and 3, 1-7 for experiment 2), 'Line' (cell line), 'Day' (differentiation day)
Supplementary_files_format_and_content: collection_metadata.txt contains metadata for each collected sample. Rows are samples, columns are 'Line' (cell line), 'Differentiation Day' (differentiation day), 'Feeder Passage', 'FF Passage' (feeder free passage), 'Date' , 'CD' (collection day), 'col' (collection), 'orig.ident' (exp/collection day/collection), 'Experiment Batch', 'Diff Start  Batch', "How many wells collected", "Confluence when collected as percent", "Day 0 Confluence (%)", "Beating on day of collection Y 1/N 0", "Day this well started beating", "% beating when collected", "First day beating for this line/diff start", "avg. day this line/diffStart started beating", "Networks+Stringy (0- none noted, 1--thin, 2- chunky, if no adjective-1)", "flash freezing or cryopreserve (flash-0, cryo-1)", "Sheets vs. clumps (0-no notes, 1- clumps, 2- sheets, 3-both)", "debris (0-none or not noted, 1-some, 2- lots)", "swirls/semi-circles/background (not noted-0, noted-1)"
Supplementary_files_format_and_content: cell_metadata.tsv contains metadata for each cell. Rows are cells, columns are 'cell', 'exp.grp' (experiment group), 'sample' (sample),  'diffday' (differentiation day), 'individual' (cell line), 'S.Score' (S score, computed in Seurat), 'G2M.Score' (G2/M score, computed in Seurat), 'CC.Difference' (G2M.Score - S.Score, regressed out during SCTransform normalization), 'demux.dbl.prb' (demuxlet posterior probability of doublet assignment), 'leiden' (leiden assignment from scanpy), 'type' (assigned cell type, based on leiden clustering), 'dpt_pseudotime' (inferred diffusion pseudotime)

molecule: polyA RNA

growth_protocol: Feeder-free iPSC cultures were maintained on Matrigel Growth Factor Reduced Matrix with Essential 8 Medium and Penicillin/Streptomycin.

extract_protocol:
Samples were collected using a 125 um Drop-seq microfluidic device. Single cells were captured in droplets along with a cell-specific barcode bead. After collection, RNA molecules were reverse transcribed and cDNA amplification performed according to the Drop-seq protocol (Macosko et al 2015).
Library preparation was performed using the Illumina Nextera XT DNA Library Preparation Kit, for paired-end sequencing using the Illumina NextSeq 500.

treatment_protocol: To begin cardiomyocyte differentiation, E8 media was replaced with "heart media"--RPMI with B27 supplement minus insulin, 2mM GlutaMAX, and 100mg/ml Penicllin/Streptomycin--along with 1:100 Matrigel hESC-qualifed Matrix and 12uM of CHIR99021 trihydrochloride on Day 0. On Day 1, this media was removed and fresh "heart media" was added. On Day 3, new "heart media" was added along with 2uM of Wnt-C59. On Days 5, 7, 10, 12, and 14, old media was removed and replaced with fresh "heart media."

tag: cell line

value: multiplexed sample (pool of 19127, 19209, 18499)

tag: differentiation day

value: multiplexed sample (pool of 15, 11, 0 respectively)


title: prostate_cancer_primary_239

tag: primary gleason

tag: secondary gleason

tag: decipher risk group

tag: race


title: PRISM_Control_64Control

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype


title: E3CD3col5

value: multiplexed sample (pool of 19108, 18499, 19127)


title: iPSC_2

source_name: iPSC

value: iPSC

value: Female


title: NPC_4


title: prostate_cancer_primary_237

value: African American


title: E3CD3col4

value: multiplexed sample (pool of 18870, 19127, 19108)


title: Neuron_D37_4

value: Terminally Differentiated Neuron


title: prostate_cancer_primary_236


title: E3CD3col3

value: multiplexed sample (pool of 19193, 19108, 18870)


title: Neuron_D37_2


title: E3CD3col2

value: multiplexed sample (pool of 19209, 18870, 19193)


title: PD rat strain, male, 7 month of age, liver, high fat diet [PD3]

description: Liver expression data obtained from PD strain.

source_name: liver sample from PD rat strain after high fat diet administration

tag: diet

tag: Sex


title: PD rat strain, male, 7 month of age, liver, high fat diet [PD2]


title: E3CD3col1

value: multiplexed sample (pool of 18499, 19193, 19209)


title: prostate_cancer_primary_235

value: Higher


title: DXA1253_434Control

description: DNA CpG sites

value: Control

tag: array

tag: slide

value: white blood cells


title: PD rat strain, male, 7 month of age, liver, high fat diet [PD1]

value: Liver tissue

value: high fat diet

value: male


title: DXA1102_40Control

description: DNA CpG sites


title: PRISM_Control_460Control

description: DNA CpG sites


title: NPC_1

value: Neuronal Precursor Cell


title: E3CD2col6

value: multiplexed sample (pool of 19127, 19209, 19193)

value: multiplexed sample (pool of 11, 7, 5 respectively)


title: BN rat strain, male, 7 month of age, liver, high fat diet [BN4]

description: Liver expression data obtained from BN strain.

source_name: liver sample from BN rat strain after high fat diet administration


title: prostate_cancer_primary_233

value: FFPE prostate cancer

value: Lower


title: prostate_cancer_primary_232

value: African American


title: prostate_cancer_primary_234


title: Neuron_D37_3

value: Female


title: PRISM_Control_341Control

description: DNA CpG sites


title: PRISM_Control_369Control

description: DNA CpG sites


title: E3CD2col4

value: multiplexed sample (pool of 18870, 19127, 18499)


title: prostate_cancer_primary_238

value: Average


title: Mut_D868N

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ sequencing reads were adaptor-trimmed and quality-filtered with Cell Ranger
Gene count normalization and differential gene expression have been done with Seurat 4.01
Low-dimensional embedding of high-dimensional data was done by uniform manifold approximation and projection for dimension reduction (Umap).
Genome_build: hg38

source_name: human cortical organoids

growth_protocol: Celebral organoids protocol according to "Generation of cerebral organoids from human pluripotent stem cells", Madeline A Lancaster & Juergen A Knoblich Nature Protocols, 2014

extract_protocol:
mRNA isolation and library prep were performed by Chromium Single Cell Gene Expression (10x Genomics)
single-cell RNA-seq

treatment_protocol: Isogenic WT line production with mutation correction using crispr/cas9 genome editing technology

tag: genotype

value: SEBP1 D686N (Mut)


title: iPSC_1

tag: developmental stage

value: iPSC


title: BN rat strain, male, 7 month of age, liver, high fat diet [BN2]


title: prostate_cancer_primary_231

value: Higher


title: E3CD2col3

value: multiplexed sample (pool of 19193, 19108, 19127)


title: WT_D686D

value: SEBP1 D686D (WT)


title: DXA1957_298Control

description: DNA CpG sites

value: Control

value: white blood cells


title: E3CD2col2

value: multiplexed sample (pool of 19209, 18870, 19108)


title: E3CD2col1

value: multiplexed sample (pool of 18499, 19193, 18870)


title: PRISM_Control_84Control

description: DNA CpG sites


title: BN rat strain, male, 7 month of age, liver, high fat diet [BN3]

value: Liver tissue

value: high fat diet

value: male


title: WTC_Resp_226

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to hg19 reference build with refGene GTF annotation version 25 using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file with raw counts

source_name: blood

extract_protocol:
RNA samples were extracted using Qiagen miRNeasy mini kit as per as per manufacturer's instructions. Quantitative assessment of the purified total RNA is then accomplished by using a Qubit Broad Range RNA kit (Thermofisher), and concentration is determined by Ribogreen fluorescent binding to isolated RNA.  The RNA is further evaluated qualitatively on the 4200 Tapestation (Agilent technologies), where sizing of the RNA is determined, and a qualitative numerical score (RINe) is assigned.
Whole transcriptome (RNA-Seq) libraries were prepared using HyperPrep Kit with RiboErase (HMR)kit (Roche Sequencing Solutions), from 100ng total RNA following manufacturer's instructions. The libraries are quantitated using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria.  Each pool is denatured and diluted to 350pM with 1% PhiX control library added.  The resulting pool is then sequenced on Illumina  NovaSeq 6000 sequencer for 100PE sequencing following the manufacturer’s recommended protocol (Illumina Inc.).

tag: subject gender

tag: subject race/ethnicity

value: caucasian

tag: pcl

value: blood


title: prostate_cancer_primary_229

tag: tissue

value: FFPE prostate cancer

value: African American


title: PRISM_Control_29Control

description: DNA CpG sites


title: prostate_cancer_primary_228

tag: primary gleason


title: BN rat strain, male, 7 month of age, liver, high fat diet [BN1]


title: WTC_Resp_225


title: PRISM_Control_228Control

description: DNA CpG sites


title: E3CD1col6

tag: cell line

value: multiplexed sample (pool of 19127, 19209, 19193)

tag: differentiation day

value: multiplexed sample (pool of 7, 3, 1 respectively)


title: PRISM_Control_366Control

description: DNA CpG sites


title: PD rat strain, male, 7 month of age, liver, high fat diet [PD4]


title: prostate_cancer_primary_226

tag: secondary gleason

tag: decipher risk group

tag: race


title: E3CD1col5

value: multiplexed sample (pool of 19108, 18499, 19209)


title: PRISM_Control_15Control

description: DNA CpG sites

tag: mmed

tag: umed

tag: phenotype


title: prostate_cancer_primary_227

value: Higher


title: WTC_Resp_223


title: WTC_Resp_224


title: WTC_Resp_222


title: E3CD1col3

value: multiplexed sample (pool of 19193, 19108, 19127)


title: E3CD1col4

value: multiplexed sample (pool of 18870, 19127, 18499)


title: DXA1822_316Control

description: DNA CpG sites

value: Control

tag: array


title: WTC_Resp_221


title: E3CD1col2


title: E3CD2col5

value: multiplexed sample (pool of 11, 7, 5 respectively)


title: WTC_Resp_220


title: WTC_Resp_219


title: E3CD1col1


title: prostate_cancer_primary_225

value: Lower


title: E2CD3col6

value: multiplexed sample (pool of 18489, 19190, 18517)

value: multiplexed sample (pool of 15, 11, 0 respectively)


title: prostate_cancer_primary_222


title: WTC_Resp_217


title: E2CD3col7

value: multiplexed sample (pool of 18517, 18855, 19190)


title: NPC_3

value: Neuronal Precursor Cell

tag: gender

value: Female


title: WTC_Resp_216

value: male

value: caucasian

value: blood


title: prostate_cancer_primary_224

value: FFPE prostate cancer

value: African American


title: WTC_Resp_215


title: prostate_cancer_primary_220


title: prostate_cancer_primary_230


title: E2CD3col5

value: multiplexed sample (pool of 19159, 18517, 18489)


title: prostate_cancer_primary_221

value: Higher


title: E2CD3col4

value: multiplexed sample (pool of 18505, 18489, 19159)


title: prostate_cancer_primary_218


title: prostate_cancer_primary_219


title: WTC_Resp_214


title: E2CD3col3

value: multiplexed sample (pool of 18907, 19159, 18505)


title: SHR rat strain, male, 7 month of age, liver, high fat diet [SHR1]

value: Liver tissue

tag: diet

value: high fat diet

tag: Sex


title: prostate_cancer_primary_216

value: Average


title: WTC_Resp_218

tag: subject gender


title: prostate_cancer_primary_223


title: prostate_cancer_primary_215


title: WTC_Resp_213

tag: subject race/ethnicity


title: E2CD3col1

value: multiplexed sample (pool of 19190, 18907, 18855)


title: WTC_Resp_212

tag: pcl


title: E2CD2col7

value: multiplexed sample (pool of 18517, 18855, 18907)

value: multiplexed sample (pool of 11, 7, 5 respectively)


title: prostate_cancer_primary_214

tag: tissue


title: E2CD2col6

value: multiplexed sample (pool of 18489, 19190, 18855)


title: WTC_Resp_211


title: E2CD3col2

value: multiplexed sample (pool of 18855, 18505, 18907)

value: multiplexed sample (pool of 15, 11, 0 respectively)


title: WTC_Resp_210

value: male

value: caucasian


title: E2CD2col5

value: multiplexed sample (pool of 19159, 18517, 19190)


title: WTC_Resp_208

value: blood


title: E2CD2col3

value: multiplexed sample (pool of 18907, 19159, 18489)


title: E2CD2col2

value: multiplexed sample (pool of 18855, 18505, 19159)


title: E2CD2col1

value: multiplexed sample (pool of 19190, 18907, 18505)


title: WTC_Resp_209


title: E2CD2col4

value: multiplexed sample (pool of 18505, 18489, 18517)


title: WTC_Resp_206


title: WTC_Resp_205


title: E2CD1col6

value: multiplexed sample (pool of 7, 3, 1 respectively)


title: E2CD1col7


title: WTC_Resp_204


title: WTC_Resp_203


title: WTC_Resp_207


title: prostate_cancer_primary_213

value: FFPE prostate cancer

tag: primary gleason

value: Higher

value: African American


title: prostate_cancer_primary_217

value: Average


title: WTC_Resp_202


title: prostate_cancer_primary_212


title: prostate_cancer_primary_211

value: Lower


title: E2CD1col4

tag: cell line


title: prostate_cancer_primary_205


title: E2CD1col5

tag: differentiation day


title: prostate_cancer_primary_208

tag: secondary gleason


title: prostate_cancer_primary_210

tag: decipher risk group


title: prostate_cancer_primary_204

tag: race


title: WTC_Resp_201


title: prostate_cancer_primary_207


title: prostate_cancer_primary_206


title: E2CD1col3


title: WTC_Resp_200


title: E2CD1col2


title: WTC_Resp_199


title: prostate_cancer_primary_202


title: WTC_Resp_198


title: E1CD3col6

value: multiplexed sample (pool of 18511, 18858, 19093)


title: E1CD3col5

value: multiplexed sample (pool of 18508, 19093, 18511)


title: E2CD1col1


title: prostate_cancer_primary_201


title: WTC_Resp_197


title: WTC_Resp_196


title: E1CD3col4

value: multiplexed sample (pool of 18520, 18511, 18508)

value: multiplexed sample (pool of 15, 11, 0 respectively)


title: WTC_Resp_195

value: male

value: caucasian


title: E1CD3col3

value: multiplexed sample (pool of 18912, 18508, 18520)


title: WTC_Resp_193

value: blood


title: E1CD3col2

value: multiplexed sample (pool of 18858, 18520, 18912)


title: WTC_Resp_194


title: prostate_cancer_primary_203


title: prostate_cancer_primary_198


title: E1CD3col1

value: multiplexed sample (pool of 19093, 18912, 18858)


title: WTC_Resp_192


title: E1CD2col6

value: multiplexed sample (pool of 18511, 18858, 18912)

value: multiplexed sample (pool of 11, 7, 5 respectively)


title: WTC_Resp_190


title: prostate_cancer_primary_199

value: FFPE prostate cancer


title: prostate_cancer_primary_194


title: prostate_cancer_primary_197


title: prostate_cancer_primary_193

value: Higher


title: prostate_cancer_primary_200

value: African American


title: E1CD2col4

value: multiplexed sample (pool of 18520, 18511, 19093)


title: E1CD2col3

value: multiplexed sample (pool of 18912, 18508, 18511)


title: prostate_cancer_primary_195

value: Lower


title: prostate_cancer_primary_196


title: prostate_cancer_primary_191


title: prostate_cancer_primary_192


title: E1CD2col5

value: multiplexed sample (pool of 18508, 19093, 18858)


title: WTC_Resp_191


title: WTC_Resp_188


title: prostate_cancer_primary_189


title: WTC_Resp_187


title: WTC_Resp_189


title: prostate_cancer_primary_190


title: WTC_Resp_186


title: WTC_Resp_185


title: E1CD2col2

value: multiplexed sample (pool of 18858, 18520, 18508)


title: E1CD1col5

value: multiplexed sample (pool of 7, 3, 1 respectively)


title: WTC_Resp_184

value: male


title: E1CD1col6


title: E1CD1col4


title: prostate_cancer_primary_209


title: WTC_Resp_183

value: caucasian


title: WTC_Resp_181


title: prostate_cancer_primary_187


title: WTC_Resp_182


title: E1CD1col3


title: E1CD2col1

value: multiplexed sample (pool of 19093, 18912, 18520)


title: prostate_cancer_primary_188


title: prostate_cancer_primary_186


title: WTC_Resp_180

value: blood


title: prostate_cancer_primary_184


title: E1CD1col1


title: prostate_cancer_primary_183

value: Average


title: E1CD1col2


title: DIPG007-RNAseq-rep2

extract_protocol:
Cells were harvested at 80% confluency and washed with PBS twice. Cells were homogenized with QIAshredder (79654, Qiagen). Homogenized whole cell lysate then were used for RNA isolation via the manufacturer’s protocol (74104, Qiagen). Extracted RNA was stored in -80°C or proceed directly to library construction.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit (RS-122-2201) with ribo-depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit (5067-1511). A total of one mg total RNA was used as starting material. 1 ug of RNA was used as starting material.

tag: chip-antibody


title: WTC_Resp_178


title: prostate_cancer_primary_182


title: DIPG007-RNAseq-rep1


title: DIPG1114-RNAseq-rep3


title: prostate_cancer_primary_185


title: prostate_cancer_primary_181


title: prostate_cancer_primary_180


title: DIPG1114-RNAseq-rep2


title: prostate_cancer_primary_179


title: WTC_Resp_179


title: DIPG1114-RNAseq-rep1


title: WTC_Resp_176


title: WTC_Resp_175


title: SF7761-RNAseq-rep2


title: prostate_cancer_primary_178


title: SF7761-RNAseq-rep3


title: SF7761-RNAseq-rep1


title: WTC_Resp_174


title: WTC_Resp_173


title: WTC_Resp_177


title: WTC_Resp_172


title: prostate_cancer_primary_177


title: prostate_cancer_primary_176


title: SF8628-RNAseq-rep2


title: WTC_Resp_171


title: SF8628-RNAseq-rep3


title: prostate_cancer_primary_175


title: prostate_cancer_primary_174


title: SF9402-RNAseq-rep3


title: SF8628-RNAseq-rep1


title: WTC_Resp_169


title: WTC_Resp_168


title: SF9402-RNAseq-rep2


title: SF9402-RNAseq-rep1


title: WTC_Resp_167


title: WTC_Resp_166


title: SF9427-RNAseq-rep3


title: prostate_cancer_primary_173


title: SF9427-RNAseq-rep2


title: SF9427-RNAseq-rep1


title: prostate_cancer_primary_172


title: WTC_Resp_164


title: WTC_Resp_170


title: prostate_cancer_primary_170


title: prostate_cancer_primary_171


title: prostate_cancer_primary_167


title: DIPGIV-RNAseq-rep3

source_name: DIPGIV


title: prostate_cancer_primary_169


title: WTC_Resp_163


title: prostate_cancer_primary_166


title: DIPGIV-RNAseq-rep2


title: DIPGIV-RNAseq-rep1


title: WTC_Resp_160


title: WTC_Resp_161


title: prostate_cancer_primary_165


title: prostate_cancer_primary_168


title: WTC_Resp_159


title: KNS42-RNAseq-rep3


title: prostate_cancer_primary_162


title: WTC_Resp_165


title: prostate_cancer_primary_160


title: KNS42-RNAseq-rep2


title: prostate_cancer_primary_161


title: prostate_cancer_primary_163


title: WTC_Resp_162


title: KNS42-RNAseq-rep1


title: NHA-RNAseq-rep3


title: WTC_Resp_157


title: NHA-RNAseq-rep2


title: WTC_Resp_158


title: WTC_Resp_156


title: WTC_Resp_155


title: WTC_Resp_154


title: NHA-RNAseq-rep1


title: WTC_Resp_153


title: DIPGXIII-RNAseq-rep3


title: DIPGXIII-RNAseq-rep2


title: DIPGXIII-RNAseq-rep1


title: prostate_cancer_primary_164


title: prostate_cancer_primary_159


title: WTC_Resp_152


title: hNSC-RNAseq-rep3


title: WTC_Resp_151


title: WTC_Resp_150


title: WTC_Resp_149


title: hNSC-RNAseq-rep1


title: WTC_Resp_148


title: VCaP_AR_siFOXA1_DHT_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim low quality reads and sequence duplicates were collapsed
For ChIP-seq, the reads were aligned to human reference genome version hg38 by using Bowtie software version 0.12.9. Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Input sample from VCaP cells cells was used as control for SMARCA4 ChIP samples. EtOH treated AR ChIP sample from VCaP cells was used as control for AR ChIP samples.
For ATAC-seq, the reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Input sample from VCaP cells cells was used as control for ATAC samples.
For RNA-seq, the reads were trimmed using trimmomatic version 0.33 and poly-A tails were removed using homerTools in HOMER. Contaminants reported in iGENOME were removed using Bowtie2 and remaining reads were mapped to human hg38 transcriptome and genome with tophat2 software version 2.0.31. Differential expression of genes was analyzed using DESeq2 using HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: VCaP prostate cancer cells, DHT, siFOXA1, AR ChIP

growth_protocol: VCaP cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using Qiagen RNeasy Mini kit.
For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: VCaP cells were seeded at 70 % confluence in 10-cm plates and allowed to grow in steroid-depleted medium (2.5 %  charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated wither with vechicle (EtOH) or 100 nM of dihydrotestosterone for 1 h prior ChIP or ATAC. For RNA-seq the cells were treated with vehicle (EtOH) or 100 nM of dihydrotestosterone for 6 h prior RNA extraction. For siRNA treatments, the VCaP cells were transfected with siRNA using Lipofectamine RNAiMAX reagent 72 h before hormone treatments.

value: VCaP

tag: cell type

value: Vertebral Cancer of the Prostate

tag: sirna treatment

value: ON-TARGETplus SMARTpool against FOXA1 (Dharmacon, L-010319-00, lot # 190627)

tag: sirna concentration

value: 60 nM

tag: sirna time

tag: hormone treatment

value: dihydrotestosterone

tag: hormone concentration

tag: hormone time

value: 1 h

tag: chip antibody

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: prostate_cancer_primary_158

value: FFPE prostate cancer

value: African American


title: prostate_cancer_primary_156

value: Lower


title: hNSC-RNAseq-rep2


title: prostate_cancer_primary_157

value: Higher


title: prostate_cancer_primary_155


title: WTC_Resp_147

tag: subject gender

tag: subject race/ethnicity

tag: pcl


title: prostate_cancer_primary_153

tag: tissue

tag: primary gleason


title: VCaP_AR_siFOXA1_DHT_rep1

tag: cell line


title: prostate_cancer_primary_152

tag: secondary gleason

tag: decipher risk group


title: VCaP_AR_siNON_DHT_rep4

source_name: VCaP prostate cancer cells, DHT, siNON, AR ChIP

value: Non-targeting control siRNA (Dharmacon, D-001810-10, lot # 2420873)


title: prostate_cancer_primary_154

tag: race


title: prostate_cancer_primary_151


title: WTC_Resp_146

value: male


title: prostate_cancer_primary_150


title: WTC_Resp_143

value: caucasian


title: prostate_cancer_primary_147

value: White (Non-Hispanic)


title: VCaP_AR_siNON_DHT_rep3

tag: cell type


title: prostate_cancer_primary_149


title: VCaP_input_siNON-siSIM2_rep2

source_name: VCaP prostate cancer cells, siNON-siSIM2 mix, control ChIP input

tag: sirna treatment

value: Non-targeting control siRNA and ON-TARGETplus SMARTpool against SIM2

value: 30 nM

value: EtOH vehicle


title: prostate_cancer_primary_148


title: prostate_cancer_primary_145


title: VCaP_input_siNON-siSIM2_rep1

value: VCaP

value: Vertebral Cancer of the Prostate

tag: sirna concentration


title: prostate_cancer_primary_144


title: VCaP_AR_siSIM2_DHT_rep2

source_name: VCaP prostate cancer cells, DHT, siSIM2, AR ChIP

value: ON-TARGETplus SMARTpool against SIM2 (Dharmacon, L-008598-00, lot # 180323)

tag: sirna time


title: WTC_Resp_140

value: blood


title: VCaP_AR_siSIM2_EtOH_rep2

source_name: VCaP prostate cancer cells, vehicle, siSIM2, AR ChIP

tag: hormone treatment

value: 1 h


title: WTC_Resp_138


title: WTC_Resp_141


title: WTC_Resp_144


title: WTC_Resp_139


title: VCaP_AR_siSIM2_EtOH_rep1

tag: hormone concentration

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: WTC_Resp_145


title: VCaP_AR_siSIM2_DHT_rep1

value: dihydrotestosterone

tag: hormone time


title: VCaP_AR_siNON_DHT_rep2

tag: chip antibody


title: WTC_Resp_137

tag: subject gender


title: VCaP_AR_siNON_DHT_rep1


title: WTC_Resp_136

tag: subject race/ethnicity


title: WTC_Resp_135

tag: pcl


title: VCaP_AR_siNON_EtOH_rep2

source_name: VCaP prostate cancer cells, vehicle, siNON, AR ChIP


title: WTC_Resp_142

tag: tissue


title: VCaP_AR_siNON_EtOH_rep1


title: prostate_cancer_primary_143

value: FFPE prostate cancer

tag: primary gleason

value: African American


title: VCaP_RNA_siSIM2_DHT_rep3

source_name: VCaP prostate cancer cells, DHT, siSIM2, RNA

tag: cell line

value: 6 h


title: prostate_cancer_primary_141

tag: secondary gleason

value: Average


title: prostate_cancer_primary_146

tag: decipher risk group

value: Lower


title: prostate_cancer_primary_140

tag: race


title: WTC_Resp_134

value: male

value: caucasian


title: prostate_cancer_primary_138

value: White (Non-Hispanic)


title: prostate_cancer_primary_142


title: prostate_cancer_primary_139


title: WTC_Resp_133


title: prostate_cancer_primary_137


title: prostate_cancer_primary_136


title: WTC_Resp_132


title: VCaP_RNA_siSIM2_DHT_rep1

tag: cell type

value: 30 nM


title: VCaP_RNA_siSIM2_EtOH_rep3

source_name: VCaP prostate cancer cells, vehicle, siSIM2, RNA

tag: sirna treatment

value: EtOH vehicle


title: WTC_Resp_130


title: VCaP_RNA_siSIM2_DHT_rep2

value: VCaP

tag: sirna concentration


title: WTC_Resp_131


title: VCaP_RNA_siSIM2_EtOH_rep2

value: Vertebral Cancer of the Prostate

tag: sirna time


title: prostate_cancer_primary_135


title: WTC_Resp_129


title: prostate_cancer_primary_132


title: VCaP_RNA_siSIM2_EtOH_rep1

value: ON-TARGETplus SMARTpool against SIM2 (Dharmacon, L-008598-00, lot # 180323)

tag: hormone treatment


title: prostate_cancer_primary_134

value: Higher


title: WTC_Resp_128

value: blood


title: prostate_cancer_primary_133


title: VCaP_RNA_siSMARCA4_DHT_rep3

source_name: VCaP prostate cancer cells, DHT, siSMARCA4, RNA

value: ON-TARGETplus SMARTpool against SMARCA4 (Dharmacon, L-010431-00, lot # 180816)

tag: hormone concentration


title: prostate_cancer_primary_131

source_name: FFPE prostate cancer


title: VCaP_RNA_siSMARCA4_DHT_rep2

value: dihydrotestosterone

tag: hormone time


title: WTC_Resp_127


title: prostate_cancer_primary_130

value: FFPE prostate cancer


title: WTC_Resp_125


title: VCaP_RNA_siSMARCA4_EtOH_rep3

source_name: VCaP prostate cancer cells, vehicle, siSMARCA4, RNA

tag: chip antibody


title: VCaP_RNA_siSMARCA4_EtOH_rep2


title: WTC_Resp_123

tag: subject gender


title: WTC_Resp_124

tag: subject race/ethnicity


title: prostate_cancer_primary_128


title: VCaP_RNA_siSMARCA4_EtOH_rep1


title: prostate_cancer_primary_129


title: VCaP_RNA_siNON_DHT_rep3

description: VCaP_RNA_siNON_DHT_rep2 sample was not used in the downstream analyses due to dissimilarity to other biological replicates. VCaP_RNA_siNON_DHT_rep1 and VCaP_RNA_siNON_DHT_rep3 were used in the downstream analyses.

source_name: VCaP prostate cancer cells, DHT, siNON, RNA

value: Non-targeting control siRNA (Dharmacon, D-001810-10, lot # 2420873)


title: prostate_cancer_primary_127

value: African American


title: prostate_cancer_primary_126

value: Average


title: prostate_cancer_primary_125


title: VCaP_RNA_siNON_DHT_rep2

value: 6 h


title: prostate_cancer_primary_124

value: Lower


title: prostate_cancer_primary_123


title: WTC_Resp_121

value: male

value: caucasian

tag: pcl


title: WTC_Resp_120

tag: tissue


title: VCaP_RNA_siNON_DHT_rep1

value: 30 nM


title: VCaP_RNA_siNON_EtOH_rep3

source_name: VCaP prostate cancer cells, vehicle, siNON, RNA

value: EtOH vehicle


title: WTC_Resp_119


title: prostate_cancer_primary_122

tag: primary gleason

value: White (Non-Hispanic)


title: VCaP_RNA_siSMARCA4_DHT_rep1

tag: cell line

value: VCaP

value: Vertebral Cancer of the Prostate


title: WTC_Resp_118


title: WTC_Resp_126


title: VCaP_RNA_siNON_EtOH_rep2


title: prostate_cancer_primary_121

tag: secondary gleason

value: Higher


title: WTC_Resp_117

value: blood


title: VCaP_RNA_siNON_EtOH_rep1


title: VCaP_ATAC_siSIM2_DHT_rep2

source_name: VCaP prostate cancer cells, DHT, siSIM2, ATAC

value: ON-TARGETplus SMARTpool against SIM2 (Dharmacon, L-008598-00, lot # 180323)

value: 1 h


title: VCaP_ATAC_siSIM2_DHT_rep1

value: dihydrotestosterone


title: WTC_Resp_116


title: WTC_Resp_115


title: WTC_Resp_122


title: WTC_Resp_114


title: prostate_cancer_primary_119

value: FFPE prostate cancer

tag: decipher risk group


title: WTC_Resp_113


title: prostate_cancer_primary_120

tag: race


title: VCaP_ATAC_siSIM2_EtOH_rep2

source_name: VCaP prostate cancer cells, vehicle, siSIM2, ATAC

tag: cell type


title: prostate_cancer_primary_116


title: WTC_Resp_112

source_name: blood


title: prostate_cancer_primary_118


title: VCaP_ATAC_siSMARCA4_DHT_rep2

source_name: VCaP prostate cancer cells, DHT, siSMARCA4, ATAC

tag: sirna treatment

value: ON-TARGETplus SMARTpool against SMARCA4 (Dharmacon, L-010431-00, lot # 180816)


title: prostate_cancer_primary_117

value: Average


title: WTC_Resp_111


title: VCaP_ATAC_siSIM2_EtOH_rep1

tag: sirna concentration


title: prostate_cancer_primary_115


title: VCaP_ATAC_siSMARCA4_EtOH_rep2

source_name: VCaP prostate cancer cells, vehicle, siSMARCA4, ATAC

tag: sirna time


title: prostate_cancer_primary_114


title: WTC_Resp_110


title: WTC_Resp_109


title: VCaP_ATAC_siSMARCA4_EtOH_rep1

tag: hormone treatment


title: VCaP_ATAC_siNON_DHT_rep2

source_name: VCaP prostate cancer cells, DHT, siNON, ATAC

value: Non-targeting control siRNA (Dharmacon, D-001810-10, lot # 2420873)

tag: hormone concentration


title: WTC_Resp_108


title: WTC_Resp_107


title: prostate_cancer_primary_111

value: Lower


title: prostate_cancer_primary_109


title: prostate_cancer_primary_110


title: prostate_cancer_primary_112


title: WTC_Resp_105

value: male


title: WTC_Resp_104

value: caucasian


title: VCaP_ATAC_siSMARCA4_DHT_rep1

value: 30 nM

tag: hormone time


title: prostate_cancer_primary_108


title: WTC_Resp_106


title: VCaP_input_rep1

source_name: VCaP prostate cancer cells, control ChIP input

value: EtOH vehicle

tag: chip antibody


title: prostate_cancer_primary_107

value: White (Non-Hispanic)


title: WTC_Resp_103

tag: subject gender


title: VCaP_ATAC_siNON_DHT_rep1

value: VCaP


title: VCaP_SMARCA4_DHT_rep2

source_name: VCaP prostate cancer cells, DHT, SMARCA4 ChIP

value: Vertebral Cancer of the Prostate


title: VCaP_ATAC_siNON_EtOH_rep1

source_name: VCaP prostate cancer cells, vehicle, siNON, ATAC


title: prostate_cancer_primary_113

value: African American


title: WTC_Resp_101

tag: subject race/ethnicity

value: blood


title: VCaP_SMARCA4_DHT_rep1


title: VCaP_SMARCA4_EtOH_rep1

source_name: VCaP prostate cancer cells, vehicle, SMARCA4 ChIP


title: prostate_cancer_primary_105

value: Higher


title: WTC_Resp_102

tag: pcl


title: WTC_Resp_100

tag: tissue


title: VCaP_SMARCA4_EtOH_rep2

value: 1 h


title: prostate_cancer_primary_104

tag: primary gleason


title: prostate_cancer_primary_102


title: VCaP_ATAC_siNON_EtOH_rep2

tag: cell line


title: WTC_Resp_098


title: WTC_Resp_096


title: VCaP_AR_DHT_rep1

source_name: VCaP prostate cancer cells, DHT, AR ChIP

value: dihydrotestosterone

value: AR (rabbit antiserum; Karvonen et al. 1997)


title: VCaP_AR_EtOH_rep1

source_name: VCaP prostate cancer cells, vehicle, AR ChIP


title: WTC_Resp_095


title: WTC_Resp_097


title: WTC_Resp_099


title: WTC_Resp_094


title: VCaP_AR_DHT_rep2


title: prostate_cancer_primary_99

value: FFPE prostate cancer

tag: secondary gleason


title: prostate_cancer_primary_100

tag: decipher risk group


title: prostate_cancer_primary_101

value: Average

tag: race


title: prostate_cancer_primary_106


title: prostate_cancer_primary_103


title: H3K4me2_ChIPseq [HS39-Barretts]

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: ChIP-seq:bowtie2
CHIP-seq peak calling: MACS, version 2.0
Genome_build: hg19
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags

source_name: Barrett's esophagus

extract_protocol:
10 sections of 10 μm thickness were scraped into plastic tubes sonicated, followed by ChIP with 10 µg Ab.
DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) and sequenced on a Nextseq 500 instrument (Illumina)

value: Barrett's esophagus

tag: tissue preparation

value: FFPE

tag: antibody

value: H3K4me2 (Millipore, 07-030)


title: H3K4me2_ChIPseq [HS38-Barretts]


title: prostate_cancer_primary_96

source_name: FFPE prostate cancer

value: Lower


title: H3K4me2_ChIPseq [HS36-Barretts]


title: H3K4me2_ChIPseq [HS37-Barretts]


title: WTC_Resp_093

value: male

value: caucasian


title: VCaP_AR_EtOH_rep2

tag: cell type

tag: sirna treatment

tag: sirna concentration

value: EtOH vehicle


title: prostate_cancer_primary_95

value: White (Non-Hispanic)


title: WTC_Resp_090


title: H3K4me2_ChIPseq [HS35-Barretts]


title: WTC_Resp_092


title: prostate_cancer_primary_94


title: WTC_Resp_091


title: prostate_cancer_primary_98


title: H3K4me2_ChIPseq [HS34-Barretts]


title: WTC_Resp_089


title: prostate_cancer_primary_97


title: WTC_Resp_088


title: WTC_Resp_087


title: WTC_Resp_086


title: WTC_Resp_085


title: Input_DNA [HS3-Gastric-Input]

source_name: Primary gastric corpus mucosa

extract_protocol:
10 sections of 10 μm thickness were scraped into plastic tubes sonicated.
DNA libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics)

value: Primary gastric corpus mucosa

value: none (input)


title: Input_DNA [HS4-Gastric-Input]


title: Input_DNA [HS9-Gastric-Input]


title: Input_DNA [HS6-Ileum-Input]

source_name: Primary intestinal mucosa

value: Primary intestinal mucosa


title: Input_DNA [HS1-Ileum-Input]


title: WTC_Resp_083

value: blood


title: Input_DNA [HS25-Squamous-Input]

source_name: Esophageal squamous epithelium

value: Esophageal squamous epithelium


title: WTC_Resp_082


title: Input_DNA [HS12-Squamous-Input]


title: prostate_cancer_primary_91

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.


title: prostate_cancer_primary_93

value: African American


title: prostate_cancer_primary_92


title: prostate_cancer_primary_90

value: Higher


title: prostate_cancer_primary_88

value: FFPE prostate cancer


title: prostate_cancer_primary_89


title: prostate_cancer_primary_87


title: WTC_Resp_081


title: Input_DNA [HS22-Barretts-Input]


title: prostate_cancer_primary_85


title: Input_DNA [HS7-Ileum-Input]


title: prostate_cancer_primary_86


title: WTC_Resp_080


title: Input_DNA [HS19-Barretts-Input]


title: WTC_Resp_084


title: WTC_Resp_079


title: WTC_Resp_078


title: Input_DNA [HS5-Barretts-Input]


title: WTC_Resp_076


title: H3K4me2_ChIPseq [HS30-Gastric]


title: WTC_Resp_075


title: H3K4me2_ChIPseq [HS28-Gastric]


title: H3K4me2_ChIPseq [HS4-Gastric]


title: H3K4me2_ChIPseq [HS3-Gastric]


title: WTC_Resp_074


title: WTC_Resp_073


title: H3K4me2_ChIPseq [HS31-Ileum]


title: prostate_cancer_primary_80


title: prostate_cancer_primary_81


title: WTC_Resp_072


title: WTC_Resp_071


title: WTC_Resp_077


title: WTC_Resp_070


title: H3K4me2_ChIPseq [HS6-Ileum]


title: prostate_cancer_primary_83


title: H3K4me2_ChIPseq [HS9-Gastric]


title: prostate_cancer_primary_79


title: prostate_cancer_primary_84


title: prostate_cancer_primary_78


title: H3K4me2_ChIPseq [HS35-Squamous]


title: H3K4me2_ChIPseq [HS1-Ileum]


title: prostate_cancer_primary_76


title: H3K4me2_ChIPseq [HS34-Squamous]


title: prostate_cancer_primary_77


title: prostate_cancer_primary_75


title: prostate_cancer_primary_73


title: prostate_cancer_primary_72


title: prostate_cancer_primary_71


title: prostate_cancer_primary_82


title: prostate_cancer_primary_74


title: WTC_Resp_068


title: H3K4me2_ChIPseq [HS25-Squamous]


title: WTC_Resp_066


title: WTC_Resp_067


title: H3K4me2_ChIPseq [HS12-Squamous]


title: H3K4me2_ChIPseq [HS7-Ileum]


title: prostate_cancer_primary_68


title: WTC_Resp_064


title: prostate_cancer_primary_69


title: WTC_Resp_069


title: H3K4me2_ChIPseq [HS24-Barretts]


title: H3K4me2_ChIPseq [HS23-Barretts]


title: WTC_Resp_065


title: WTC_Resp_063


title: prostate_cancer_primary_67


title: WTC_Resp_060


title: WTC_Resp_062


title: Retina CAST/EiJ [TA033]

city: New York

first: Andrei

middle: V.

last: Tkatchenko

department: Edward S. Harkness Eye Institute

institute: Columbia University

data_processing:
The FASTQ raw data files generated by the Illumina sequencing system were imported into Partek Flow software package (Partek), libraries were separated based on their barcodes, adapters were trimmed and remaining sequences were subjected to pre-alignment quality control using the Partek Flow pre-alignment QA/QC module
After the assessment of various quality metrics, bases with the quality score < 34 were removed (≤ 5 bases) from each end.
Sequencing reads were then mapped to the mouse reference genome Genome Reference Consortium Mouse Build 38 (GRCm38/mm10, NCBI) using the STAR aligner resulting in 95.0 ± 0.4% mapped reads per library, which covered 35.4 ± 1.0% of the genome.
Aligned reads were quantified to transcriptome using the Partek E/M annotation model and the NCBI’s RefSeq annotation file to determine read counts per gene/genomic region.
The generated read counts were normalized by the total read count and subjected to the analysis of variance (ANOVA) to detect genes whose expression correlates with either refractive error, susceptibility to myopia or contrast sensitivity
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including matrix table with normalized gene counts for every gene and every sample

source_name: Retina

extract_protocol:
The retinae were washed in RNAlater (Thermo Fisher Scientific) for 5 min., frozen in liquid nitrogen, and stored at -80°C. To isolate RNA, tissue samples were homogenized at 4°C in a lysis buffer using Bead Ruptor 24 tissue homogenizer (Omni). Total RNA was extracted from each tissue sample using miRNAeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Illumina sequencing libraries were constructed from 1 μg of total RNA using the TruSeq Stranded Total RNA LT kit with the Ribo-Zero Gold ribosomal RNA depletion module (Illumina).

tag: strain

value: CAST/EiJ

tag: age

value: postnatal day 28

tag: genotype

value: wild type


title: H3K4me2_ChIPseq [HS22-Barretts]

value: Barrett's esophagus

value: FFPE

value: H3K4me2 (Millipore, 07-030)


title: WTC_Resp_059

tag: subject gender

value: male

value: caucasian


title: WTC_Resp_061

tag: subject race/ethnicity


title: H3K4me2_ChIPseq [HS19-Barretts]


title: Retina CAST/EiJ [TA031]


title: Retina CAST/EiJ [TA032]


title: WTC_Resp_058

tag: pcl


title: H3K4me2_ChIPseq [HS5-Barretts]

tag: tissue


title: prostate_cancer_primary_70

tag: primary gleason

value: White (Non-Hispanic)


title: prostate_cancer_primary_66

value: Lower


title: prostate_cancer_primary_64


title: prostate_cancer_primary_65


title: prostate_cancer_primary_62

value: Average


title: prostate_cancer_primary_61


title: prostate_cancer_primary_60


title: WTC_Resp_057


title: Retina NZO/HlLtJ [TA029]

value: NZO/HlLtJ


title: Retina NZO/HlLtJ [TA030]


title: WTC_Resp_056

value: blood


title: prostate_cancer_primary_59


title: WTC_Resp_055


title: Retina NZO/HlLtJ [TA028]


title: prostate_cancer_primary_58


title: prostate_cancer_primary_63


title: Retina WSB/EiJ [TA027]

value: WSB/EiJ


title: WTC_Resp_053


title: WTC_Resp_054


title: Retina WSB/EiJ [TA026]


title: prostate_cancer_primary_57


title: WTC_Resp_052


title: prostate_cancer_primary_56


title: prostate_cancer_primary_55


title: Retina PWK/PhJ [TA024]

value: PWK/PhJ


title: Retina WSB/EiJ [TA025]


title: prostate_cancer_primary_54


title: WTC_Resp_050


title: Retina PWK/PhJ [TA023]


title: WTC_Resp_049


title: prostate_cancer_primary_53

value: Higher


title: Retina A/J [TA021]

value: A/J


title: Retina A/J [TA020]


title: WTC_Resp_047


title: WTC_Resp_046


title: WTC_Resp_045


title: Retina A/J [TA019]


title: Retina NOD/ShiLtJ [TA018]

value: NOD/ShiLtJ


title: Retina PWK/PhJ [TA022]

value: postnatal day 28


title: WTC_Resp_051


title: prostate_cancer_primary_50

value: FFPE prostate cancer


title: prostate_cancer_primary_51


title: WTC_Resp_044


title: prostate_cancer_primary_52


title: WTC_Resp_043


title: prostate_cancer_primary_48


title: WTC_Resp_048


title: prostate_cancer_primary_46

value: African American


title: prostate_cancer_primary_47


title: Retina NOD/ShiLtJ [TA017]

value: wild type


title: prostate_cancer_primary_49


title: Retina C57BL/6J [TA015]


title: prostate_cancer_primary_45


title: WTC_Resp_042


title: Retina NOD/ShiLtJ [TA016]


title: Retina C57BL/6J [TA014]


title: WTC_Resp_041


title: prostate_cancer_primary_43


title: Retina 129S1/Svlmj [TA012]


title: Retina 129S1/Svlmj [TA010]


title: NHA-1-input-0824

source_name: NHA

tag: chip-antibody


title: Retina C57BL/6J [TA013]


title: WTC_Resp_037

source_name: blood


title: WTC_Resp_038


title: DIPG007-1-input-0824


title: WTC_Resp_035


title: WTC_Resp_039


title: hNSC-1-input-0824

source_name: hNSC


title: WTC_Resp_040


title: WTC_Resp_036


title: prostate_cancer_primary_44

tag: secondary gleason


title: WTC_Resp_033


title: WTC_Resp_034


title: Retina 129S1/Svlmj [TA011]


title: prostate_cancer_primary_40

tag: decipher risk group


title: prostate_cancer_primary_42

tag: race


title: prostate_cancer_primary_39


title: prostate_cancer_primary_38


title: prostate_cancer_primary_41


title: prostate_cancer_primary_37


title: prostate_cancer_primary_36


title: SF7761-1-INPUT-0824


title: WTC_Resp_032


title: prostate_cancer_primary_35


title: WTC_Resp_031


title: WTC_Resp_030


title: WTC_Resp_029


title: DIPG IV-1-INPUT-0914

source_name: DIPGIV


title: KNS42-1-INPUT-0914


title: SF8628-1-INPUT-0914


title: prostate_cancer_primary_33


title: SF9427-H3K27AC Rep 2


title: WTC_Resp_027


title: prostate_cancer_primary_32


title: prostate_cancer_primary_30


title: SF9427-1-INPUT-0824


title: prostate_cancer_primary_29


title: prostate_cancer_primary_28


title: WTC_Resp_026


title: WTC_Resp_025


title: prostate_cancer_primary_34


title: SF9427-H3K27AC Rep 1


title: SF8628-H3K27AC Rep 2


title: prostate_cancer_primary_27


title: prostate_cancer_primary_31


title: WTC_Resp_024


title: SF8628-H3K27AC Rep 1


title: SF7761-H3K27AC Rep 2


title: SF7761-H3K27AC Rep 1


title: WTC_Resp_023


title: WTC_Resp_028


title: prostate_cancer_primary_26


title: NHA-H3K27AC Rep 2


title: prostate_cancer_primary_24


title: prostate_cancer_primary_25


title: WTC_Resp_021


title: prostate_cancer_primary_23


title: NHA-H3K27AC Rep 1


title: KNS42-H3K27AC Rep 1


title: WTC_Resp_019


title: KNS42-H3K27AC Rep 2


title: prostate_cancer_primary_22


title: WTC_Resp_020


title: prostate_cancer_primary_21


title: WTC_Resp_018


title: prostate_cancer_primary_20


title: hNSC-H3K27AC Rep 2


title: WTC_Resp_017


title: DIPG007-H3K27M Rep 1


title: hNSC-H3K27AC Rep 1


title: WTC_Resp_015


title: prostate_cancer_primary_19


title: WTC_Resp_022


title: WTC_Resp_016


title: DIPG007-H3K27AC Rep 1


title: DIPG007-H3K27AC Rep 2


title: WTC_Resp_013


title: WTC_Resp_014


title: WTC_Resp_012


title: prostate_cancer_primary_16


title: prostate_cancer_primary_18


title: prostate_cancer_primary_15


title: DIPG IV-H3K27AC Rep 2


title: WTC_Resp_011


title: WTC_Resp_010


title: DIPG IV-H3K27AC Rep 1


title: prostate_cancer_primary_17


title: WTC_Resp_009


title: SA2 Hi-C rep 1

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

source_name: Hap1 SA2

growth_protocol: Hap1 cells were cultered in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptomycin (Invitrogen) and 0.5% UltraGlutamin (Lonza). NMuMG cells (Gift of J. Jonkers) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptocmycin (Invitrogen) and 0.5% UltraGlutamin (Lonza).

extract_protocol:
TruSeq libraries prepared from 3C template
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: Hap1 SA1 and SA2 knock-out cells were generated using gRNA’s targeting SA1 exon 2 (ACTACTGCCCATTCCGATGC) and SA2 exon 3 (TGATGACCATTCATTCGGTT), which were cloned into PX330. Cells were transfected with PX330 and pDonorTia containing a puromycin resistance gene. Clones were selected using puromycin (2 µg/µl). Colonies were screened for the loss of SA1 and SA2 using PCR and western blot analysis.

tag: cell line

value: SA2 knockout


title: SA2 Hi-C rep 2


title: SA1 Hi-C rep 2

source_name: Hap1 SA1

value: SA1 knockout


title: SA1 Hi-C rep 1


title: WTC_Resp_006

value: male

value: caucasian


title: WTC_Resp_008


title: WTC_Resp_005


title: prostate_cancer_primary_12

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps


title: WTC_Resp_007


title: prostate_cancer_primary_14

value: White (Non-Hispanic)


title: WTC_Resp_004


title: prostate_cancer_primary_13


title: prostate_cancer_primary_9

value: Lower


title: WTC_Resp_003


title: WTC_Resp_002


title: prostate_cancer_primary_10

value: Average


title: WTC_Resp_001

value: blood


title: prostate_cancer_primary_5


title: A3810-N-ATACseq

source_name: tissue

extract_protocol:
Approximately 5mg of tissue was crushed into a fine powder in liquid nitrogen and then suspended in 1 mL cold PBS and spun down. The tissue pellet was resuspended in one mL lysis buffer, followed by isolation of 50,000 nuclei. Then the 50 μL transposition reaction mix was added to the isolated nuclei and incubated at 37 °C for one hour.
The transposal DNA was purified with the Qiagen MinElute PCR Purification Kit (Qiagen, 28006) and then amplified with appropriate number of cycles. Libraries were sequenced on the Illumina HiSeq X Ten PE150 platform.


title: A3810-T-ATACseq


title: WTC11 RBM20 eCLIP R636S replicate 2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
library strategy: eCLIP
Reproducible RBM20 peaks (hg19) obtained from replicate WT and R636S HMZ iPSC-CMs compared to size-matched input controls, were used for all down-stream analyses. Downstream bioinformatics were performed according to the default ENCODE eCLIP bioinformatics pipeline as described at from https://www.encodeproject.org/eclip/.
Genome_build: hg19
Supplementary_files_format_and_content: BED format text files of hg19-aligned RBM20 eCLIP in WT iPSC-CM  peak genomic coordinates and annotations
Supplementary_files_format_and_content: BED format text files of hg19-aligned RBM20 eCLIP in RBM20 R636S-HMZ iPSC-CM  peak genomic coordinates and annotations

growth_protocol: The iPS cell lines were differentiated into iPS-CMs using the method that controls WNT signaling by small molecules 16. Briefly, iPS cells were seeded at 1.25–2.5x104 cells/cm2 onto 12-well plates coated with 80 μg/μl growth factor-reduced Matrigel (BD Biosciences) in mTeSR1 supplemented with 10 μM Y-27632 (Selleckchem) for 24 h (day –3). mTeSR1 medium was changed daily for the next 2 days. On day 0, iPS cells were treated with 12 μM CHIR99021 (CHIR) (Tocris) in RPMI supplemented with B-27 (RPMI/B27) without insulin (Life Technologies) for exactly 24 h. On day 1, the culture medium was replaced with fresh RPMI/B27 without insulin and maintained for 48 h. On day 3, cells were treated with 5 μM IWP2 (Tocris) in RPMI/B27 without insulin and maintained for 48 h. On day 5, fresh RPMI/B27 without insulin was added to the cells, and on day 7, the medium was switched to RPMI/B27 with insulin. Afterward, fresh RPMI/B27 with insulin was added to the cells every 3 days. We used a metabolic selection protocol with glucose-free DMEM containing lactate to purify iPS-CMs. Cells were replated on day 15–18 of differentiation, and then on day 20–22 media were replaced with DMEM (without glucose, with sodium pyruvate, Thermo Fisher Scientific) supplemented with Glutamax, non-essential amino acids, and buffered lactate (4 mM). Stock-buffered lactate solution was prepared by dissolving sodium L-lactate powder (Sigma-Aldrich) at 1 M concentration in 1 M HEPES solution. Lactate media were exchanged 2–3 times, with a total exposure of 48 hours for each treatment. After the final lactate treatment (day 24–28), media were changed to RPMI/B27. The purified iPS-CMs at day 30 were harvested for RNA-Seq or cryopreserved for further analyses.

extract_protocol: The eCLIP protocol was performed as previously described  (Van Nostrand et al., 2016). B47RNA-libraries were sequenced at a depth of 30-40 million reads for each replicate eCLIP sample, on an Illumina HiSeq 2500 (single-end reads).

tag: cell line source

value: a healthy male patient

value: iPS cell-derived cardiomyocytes

tag: differentiation

value: WNT modulation method day 26

tag: purification

value: Lactate method (PMID:23168164)


title: DIPG007-dBET6-HiC

extract_protocol:
Hi-C in cell and tissue was performed following the manufacturer's protocol (A510008, Arima Genomics). Cells were cultured and crosslinked using 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for five minutes at RT. A total of 3 million cells were used for each Hi-C experiment. Tissue samples were frozen with liquid nitrogen and pulverized using mortar and pestle until the sample resembles a fine powder, then crosslinked using the same condition as cell lines.
Hi-C libraries were generated and quality checked per manufacturer's protocol. 300-600M reads per each sample was generated based on total usable reads above 20Kb.

treatment_protocol: DIPG007 cells were treated with 200 nM BRD4 inhibitor (Bristol Myers Squibb, BMS986158), and 1000 nM dBET6 (Selleckchem S8762) for 24 hours. DMSO treatment at 200nM and 1000nM for 24 hours were also included as vehicle controls. For all treatment conditions, 2 million cells were plated in 6 well plates 24 hours prior to drug dosing. 24 hours after administration of drugs, cells were crosslinked with 1% formaldehyde for 10 minutes and quenched with 0.125M glycine for 5 minutes. Cells were then rinsed, harvested, and store in -80°C prior to use.

tag: treatment


title: DIPG007-DMSO-HiC

value: DMSO


title: A3810-HiC


title: DIPG007-BRD4i-HiC

value: BRD4 inhibitor


title: WTC11 eCLIP input-control R636S replicate 2

tag: cell type


title: WTC11 RBM20 eCLIP wild-type replicate 2

source_name: Wild-Type iPSC-cardiomyocytes


title: WTC11 eCLIP input-control R636S replicate 1


title: NHA-HiC


title: SF9427-HiC


title: WTC11 RBM20 eCLIP R636S replicate 1


title: WTC11 eCLIP input-control wild-type replicate 2


title: prostate_cancer_primary_4

first: Elai

last: Davicioni

institute: Veracyte, Inc

value: FFPE prostate cancer

value: Higher


title: prostate_cancer_primary_2

value: African American


title: DIPG007-HiC


title: prostate_cancer_primary_3


title: WTC11 eCLIP input-control wild-type replicate 1


title: prostate_cancer_primary_8


title: prostate_cancer_primary_6


title: WTC11 RBM20 eCLIP wild-type replicate 1


title: prostate_cancer_primary_1


title: H1944 Xenograft Dexamethason Rep 5 RNA seq

source_name: Xenograft models of lung cancer cell line

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)

tag: crispr cell line features

tag: grna

tag: antibody

tag: viewpoints

value: Dexamethasone

tag: replicate

value: Replicate 5


title: DIPGXIII-HiC

source_name: DIPGXIII