title: heptoid gland adenoma (HGA), 9  [h31 RNA-seq]

status: Public on Mar 21 2024

city: Berlin

first: Alexander

middle: F. H.

last: Haake

address: Robert-von-Ostertag-Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

data_processing:
The FASTQ sequencing files were preprocessed (adapter trimmed, filtered) using Cutadapt and  aligned to the NCBI Reference Sequence (RefSeq) assembly for the dog (Canis lupus familiaris) CanFam3.1 with the STAR aligner. Read counts per gene were generated with two rounds of featureCounts to mitigate the effect of too short 3' UTR annotations. Reads that remained unassigned in the first round were subjected to the second round of featureCounts on an adjusted annotation with a 3' extension by 2 kilobases. Differential gene expression analysis for the comparison apocrine gland anal sac adenocarcinoma (AGASAC) versus hepatoid gland adenoma (HGA) was performed with R using DESeq2. Significance thresholds were drawn at a log2(fold change) of ≤ -1 or ≥ 1 and an adjusted p-value of ≤ 0.05.
https://www.lexogen.com/wp-content/uploads/2019/03/015UG009V0251_QuantSeq_Illumina.pdf
Assembly: CanFam3.1 (NCBI RefSeq assembly: GCF_000002285.3)
Supplementary files format and content: tab-delimited text file including raw and normalised counts and differential gene expression data for each sample

organism: Canis lupus familiaris

source_name: archival FFPE tumour tissue

extract_protocol:
Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA). After DNase I treatment 500 - 1000 ng total RNA was used for library construction.
QuantSeq 3' mRNA-Seq FWD Library Preparation Kit (Lexogen GmbH, Vienna, Austria) was used according to the manufacturer's guidelines (user guide 015UG009V0251) using the low-quality RNA protocol.

value: archival FFPE tumour tissue

tag: animal

value: male

tag: breed

value: Mixed-breed

tag: age (years)


title: heptoid gland adenoma (HGA), 8  [h29 RNA-seq]

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: female, neutered

value: Australian Shepherd


title: heptoid gland adenoma (HGA), 7  [h28 RNA-seq]

value: Golden Retriever


title: heptoid gland adenoma (HGA), 10  [h33 RNA-seq]

value: male, neutered

value: Groenendael


title: apocrine gland anal sac adenocarinoma (AGASAC), 11  [a36 RNA-seq]

value: Shih Tzu


title: apocrine gland anal sac adenocarinoma (AGASAC), 9  [a17 RNA-seq]


title: heptoid gland adenoma (HGA), 3  [h5 RNA-seq]

value: female

value: Jack Russell Terrier-mix


title: heptoid gland adenoma (HGA), 1  [h2 RNA-seq]

value: Boxer-mix


title: heptoid gland adenoma (HGA), 5  [h7 RNA-seq]

value: Border Collie-mix


title: apocrine gland anal sac adenocarinoma (AGASAC), 10  [a31 RNA-seq]

value: Pug


title: heptoid gland adenoma (HGA), 4  [h6 RNA-seq]

value: Husky


title: apocrine gland anal sac adenocarinoma (AGASAC), 8  [a15 RNA-seq]

value: Eurasier


title: heptoid gland adenoma (HGA), 6  [h24 RNA-seq]

value: Hunting dog-mix


title: apocrine gland anal sac adenocarinoma (AGASAC), sublumbal lymph node metastasis from 4  [a5.2 RNA-seq]

value: archival FFPE tumour tissue

value: Labrador Retriever


title: apocrine gland anal sac adenocarinoma (AGASAC), 7  [a14 RNA-seq]

value: Munsterlander


title: apocrine gland anal sac adenocarinoma (AGASAC), 6  [a10 RNA-seq]

value: female, neutered

value: Shepherd


title: apocrine gland anal sac adenocarinoma (AGASAC), 4  [a5.1 RNA-seq]


title: apocrine gland anal sac adenocarinoma (AGASAC), 5  [a8 RNA-seq]

value: Shepherd-mix


title: apocrine gland anal sac adenocarinoma (AGASAC), sublumbal lymph node metastasis from 1  [a1.2 RNA-seq]

value: Rhodesian Ridgeback


title: apocrine gland anal sac adenocarinoma (AGASAC), 2  [a2.1 RNA-seq]

value: male, neutered

value: Border Collie


title: apocrine gland anal sac adenocarinoma (AGASAC), sublumbal lymph node metastasis from 3  [a4.2 RNA-seq]

value: Mixed-breed


title: apocrine gland anal sac adenocarinoma (AGASAC), 3  [a4.1 RNA-seq]


title: apocrine gland anal sac adenocarinoma (AGASAC), sublumbal lymph node metastasis from 2  [a2.2 RNA-seq]


title: apocrine gland anal sac adenocarinoma (AGASAC), 1  [a1.1 RNA-seq]


title: heptoid gland adenoma (HGA), 2  [h3 RNA-seq]

value: Beagle


title: hepatoid gland adenoma (HGA), 8 [h29]

type: RNA

hyb_protocol: 150 to 250 ng of total RNA was hybridised to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridised samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.

scan_protocol: Samples were transferred to the nCounter MAX Digital Analyzer (NanoString) for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).

data_processing: Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolver 4.0 Analysis Software. Quality control and normalisation followed default settings.

label: not provided

label_protocol: not provided

extract_protocol: Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA).

value: FFPE tumour tissue

value: Australian Shepherd


title: hepatoid gland adenoma (HGA), 7 [h28]

value: male

value: Golden Retriever


title: apocrine gland anal sac adenocarcinoma (AGASAC), 10 [a31]

value: Pug


title: hepatoid gland adenoma (HGA), 10 [h33]

value: Groenendael


title: hepatoid gland adenoma (HGA), 6 [h24]

value: Hunting dog-mix


title: hepatoid gland adenoma (HGA), 2 [h3]


title: apocrine gland anal sac adenocarcinoma (AGASAC), 11 [a36]

value: Shih Tzu


title: hepatoid gland adenoma (HGA), 3 [h5]

value: female

value: Jack Russell Terrier-mix


title: hepatoid gland adenoma (HGA), 9 [h31]


title: apocrine gland anal sac adenocarcinoma (AGASAC), 7 [a14]

value: Münsterländer


title: apocrine gland anal sac adenocarcinoma (AGASAC), 9 [a17]


title: apocrine gland anal sac adenocarcinoma (AGASAC), 5 [a8]

value: female, neutered

value: Shepherd-mix


title: hepatoid gland adenoma (HGA), 4 [h6]

value: Husky


title: apocrine gland anal sac adenocarcinoma (AGASAC), 6 [a10]

value: Shepherd


title: apocrine gland anal sac adenocarcinoma (AGASAC), 8 [a15]

value: Eurasier


title: hepatoid gland adenoma (HGA), 1 [h2]

value: Boxer-mix


title: apocrine gland anal sac adenocarcinoma (AGASAC), 4 [a5.1]

value: FFPE tumour tissue

value: Labrador Retriever


title: apocrine gland anal sac adenocarcinoma (AGASAC), 3 [a4.1]

value: male, neutered

value: Mixed-breed


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 2 [a2.2]

value: Border Collie


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 3 [a4.2]


title: hepatoid gland adenoma (HGA), 5 [h7]

value: Border Collie-mix


title: apocrine gland anal sac adenocarcinoma (AGASAC), 2 [a2.1]


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 4 [a5.2]


title: Prostate Cancer Patient 10

status: Public on Mar 01 2024

city: Houston

first: Ana

last: Aparicio

state: TX

address: 1515 Holcombe Blvd

department: Genitourinary Medical Oncology

country: USA

institute: MD Anderson Cancer Center

data_processing:
The raw sequencing read files were processed using FastQC (v.0.11.5) and RNA-SeQC (v.1.1.8) to generate a series of quality control metrics.  56 cores from 56 patients passed quality control filters (i.e., RNA total reads ≥60 million, exonic rates ≥0.7, and ≥20,000 genes detected) and are presented here. The reads were aligned to GRCh37 genome assembly (UCSC genome browser: https://genome.ucsc.edu/) using STAR 2-pass alignment (v.2.6.0) with default parameters to generate aligned BAM files.
Supplementary files format and content: tab-delimited text files include count values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: prostate cancer

extract_protocol: Purified double-stranded cDNA was generated from 150 ng of RNA and amplified using 3’ poly(A) selection and random priming throughout the transcriptome. Depending on the degree of sample degradation, double-stranded cDNA products generated with the NuGEN Ovation RNA-Seq System were sheared using the Covaris E220 Focused-ultrasonicator. The fragment sizes were confirmed on the Agilent Bioanalyzer High Sensitivity DNA chip to verify proper shearing. A double-stranded DNA library was created using 100 ng of sheared, double-stranded cDNA, preparing the fragments for hybridization onto a flow cell. Libraries were then pooled in equimolar amounts based on the qPCR quantification and a qPCR was run on the pooled libraries to determine the concentration of the pool for bridge amplification. Using the concentration from the Bio-Rad qPCR instrument, 15 pM of the library pool was loaded onto a flow cell and amplified by bridge amplification using the Illumina cBot instrument. A paired-end 100 bp run was used to sequence the flow cell on a HiSeq 4000 or NovaSeq6000 Sequencing platforms.

tag: Sex

value: male

tag: disease

value: prostate cancer

tag: tumor tissue_site

value: Retroperitoneal mass|Lymph Nodes

tag: tumor tissue_type

value: Distant mets

tag: trial module_assignment


title: Prostate Cancer Patient 9

value: pelvic bone


title: Prostate Cancer Patient 20

value: Iliac Lymph nodes|mass


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 1 [a1.2]

value: female, neutered

value: Rhodesian Ridgeback


title: Prostate Cancer Patient 8

value: Ilium


title: Prostate Cancer Patient 24


title: Prostate Cancer Patient 7


title: apocrine gland anal sac adenocarcinoma (AGASAC), 1 [a1.1]


title: Prostate Cancer Patient 5

value: bone

value: 3* (Patient who did not receive chemotherapy for various reasons, but would have nevertheless qualified for module 3)


title: Prostate Cancer Patient 3


title: Prostate Cancer Patient 55

value: Pelvic mass | Lymphnodes

value: Local Regional Recurrence


title: Prostate Cancer Patient 56


title: Prostate Cancer Patient 54

value: Liver


title: Prostate Cancer Patient 53


title: Prostate Cancer Patient 52

value: Pelvic bone


title: Prostate Cancer Patient 51

value: lymph node


title: Prostate Cancer Patient 49

value: Lymph Node NOS


title: Prostate Cancer Patient 47

value: male

value: Inguinal Lymph nodes|mass


title: Prostate Cancer Patient 17

value: prostate cancer


title: Prostate Cancer Patient 46

value: Retroperitoneal mass|Lymph Nodes

value: Distant mets


title: Prostate Cancer Patient 6

value: prostate bed recurrence


title: Prostate Cancer Patient 38


title: Prostate Cancer Patient 40


title: Prostate Cancer Patient 39

value: Other


title: Prostate Cancer Patient 44


title: Prostate Cancer Patient 32


title: Prostate Cancer Patient 35


title: Prostate Cancer Patient 43


title: Prostate Cancer Patient 30


title: Prostate Cancer Patient 45


title: Prostate Cancer Patient 42


title: Prostate Cancer Patient 37


title: Prostate Cancer Patient 31


title: Prostate Cancer Patient 27


title: Prostate Cancer Patient 36


title: Prostate Cancer Patient 41


title: Prostate Cancer Patient 25


title: Prostate Cancer Patient 22


title: Prostate Cancer Patient 50


title: Prostate Cancer Patient 26


title: Prostate Cancer Patient 48


title: Prostate Cancer Patient 29

value: Cervical Lymph nodes


title: Prostate Cancer Patient 21

value: Pleura


title: bulk RNAseq of tagged library: received ligand, replicate 2, clone5

status: Public on Mar 10 2025

city: Philadelphia

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

description:
Library name: cl5_HyT_2
Cell pellets were frozen on dry ice and submitted for standard RNA sequencing by Azenta Life Sciences. RNA was purified by PolyA selection and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)

data_processing:
For single cell experiments, CellRanger v7 was used
For bulk sequencing experiments, the nf-core/rnaseq pipeline was used
Assembly: GRCh38-2020-A
Supplementary files format and content: sc_data.tar.gz, contains the counts, cell barcodes, and feature names for sample listed in "library name". Sequence guide RNA counts are appended to the counts.
Supplementary files format and content: out_counts_remap.csv, contains the nf-core/rnaseq pipeline output, renamed to match library ids

source_name: HEK 293

growth_protocol: Cells were lifted with TrypLE Express (Thermo Fisher Scientific, 12605010), pelleted for 5 minutes at 300 × g, and washed in PBS with 0.04% BSA. Cells were diluted and strained through a 40 μm strainer.

extract_protocol:
Samples were processed with the Chromium Next GEM Single Cell 3' HT Kit (10x Genomics, CG000416 Rev C). Pooled tag libraries treated with HyT36 were loaded across 3 GEM wells at 88 k cells each per timepoint with the goal of recovering 39 k singlets per well after filtering. Vehicle and untagged controls were loaded each into a single well at 30.5 k and 14.5 k cells, respectively, with the goal of recovering 17 k and 8 k singlets after filtering
Chromium Next GEM Single Cell 3' HT Kit

treatment_protocol: We treated cells with 25 μM HyT36 for 2 and 12 hours in order to capture the breadth of acute responses to misfolding stress across the different cell compartments.

value: HEK 293

tag: cell line

tag: cell type

tag: treatment


title: Prostate Cancer Patient 34


title: Prostate Cancer Patient 33

value: Adrenal


title: Prostate Cancer Patient 19


title: Prostate Cancer Patient 28

value: Pelvic mass | Lymphnodes


title: Prostate Cancer Patient 18


title: Prostate Cancer Patient 11


title: Prostate Cancer Patient 13

value: Prostate

value: Primary


title: Prostate Cancer Patient 12

value: Local Regional Recurrence


title: Prostate Cancer Patient 15

value: Pelvic bone


title: Prostate Cancer Patient 14


title: Prostate Cancer Patient 16


title: Prostate Cancer Patient 4

value: 3* (Patient who did not receive chemotherapy for various reasons, but would have nevertheless qualified for module 3)


title: MOLM13_RNA_CC220_1uM_72h_REP2_210421_TATAAT_S5

status: Public on Feb 20 2024

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description:
Illumina NextSeq 37bp paired-end RNAseq
MOLM13_allSamples_CC220_vs_DMSO_72h_diffexp_sorted_rmdup.csv

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: GRCh38/hg38
Supplementary files format and content: tdf

growth_protocol: MOLM13 cells  were cultured in RPMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), and 1x L-glutamine (Life Technologies) and treated with the prespective drugs dissolved in DMSO.

extract_protocol:
For RNA isolation from cell lines, 1x10^6 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

treatment_protocol: Molm13 cells were treated with Iberdomide/CC-220 (1uM), Mezigdomide/CC-92480 (50nM) or DMSO for a total of 3 days. Samples for RNA-isolation were taken at day 3.

value: acute myeloid leukemia

tag: time

value: 72 hours


title: Prostate Cancer Patient 1

value: male

value: prostate cancer


title: Prostate Cancer Patient 2


title: MOLM13_RNA_CC92480_50nM_72h_REP2_210421_TCGAAG_S8

description:
Illumina NextSeq 37bp paired-end RNAseq
MOLM13_allSamples_CC92480_vs_DMSO_72h_diffexp_sorted_rmdup.csv


title: MOLM13_RNA_CC92480_50nM_72h_REP3_210421_TCGGCA_S9


title: MOLM13_RNA_DMSO_72h_REP2_210421_GACGAC_S2

description: Illumina NextSeq 37bp paired-end RNAseq

value: DMSO


title: MOLM13_RNA_DMSO_72h_REP1_210421_GTGATC_S1

description: Illumina NextSeq 37bp paired-end RNAseq


title: Prostate Cancer Patient 23

value: lymph node

value: Distant mets


title: MOLM13_RNA_CC220_1uM_72h_REP3_210421_TCATTC_S6


title: MOLM13_RNA_CC92480_50nM_72h_REP1_210421_TCCCGA_S7


title: DBD+ Micro-C rep 2

status: Public on Feb 01 2024

city: Columbus

first: Ariunaa

last: Bayanjargal

state: OH

address: 700 Children's Dr

institute: Nationwide Childrens Hospital

library_source: genomic

data_processing:
*library strategy: Micro-C
Fastq files were aligned to hg19 reference genome using BWA-MEMalgorithmwith options -5SP tomapmates independently
Parse module from pairtools was used to find ligation junctions in Micro-C libraries with options min-mapq 40 and max-inter-align-gap 30.
The parsed pair is then sorted using pairtools sort and PCR duplicates were removed with pairtools dedup.
The pairtools split command was used to split the final .pairsam into .bam (then sorted with samtools sort) and .pairs files.
Using Juicer Tools, .pairs files were converted into HiC contact matrices.
Assembly: hg19
Supplementary files format and content: A text file with stats of processing steps.
Supplementary files format and content: HiC files created with Juicer Tools
Supplementary files format and content: TSV files of GI objects used in plotting MDS
Supplementary files format and content: Bedpe files of differentially interacting regions compared to KD at 500kb
Supplementary files format and content: Bed files of TADs called at 10, 25, 50 and 100kb resolutions combined.
Supplementary files format and content: Bed files of loops called with Mustache
Supplementary files format and content: Bed files of differential loops called with Mustache

molecule: genomic DNA

source_name: muscle

growth_protocol: A673 cells were grown at 37C, 5% CO2 in DMEM with 10% fetal bovine serum, 1% P/S/Q, and 1% sodium pyruvate.

extract_protocol:
Micro-C kits (Catalog 21006) purchased from Dovetail Genomics were used to prepare Micro-C libraries. Specifically, the cells were lysed and the chromatin was captured with beads to perform proximity ligation
Libraries were prepared per the protocol of Micro-C kit and each library was indexed with unique primer pairs from IDT (10009816 and 10010147)

treatment_protocol: For knockdown of endogenous EWS::FLI in A673, cells were infected with RNAi virus and subsequently infected with the cDNA-containing virus to rescue the cells. After 48 hours, cells were selected with puromycin (100 μg/ul) and hygromycin (150 μg/ul); and allowed to grow for 7-8 days prior to collection

value: muscle

value: Ewing sarcoma cell line

tag: genotype

value: KD + DBD+ rescue

value: DBD+ rescue


title: DBD+ Micro-C rep 1


title: DBD Micro-C rep 2

value: KD + DBD rescue

value: DBD rescue


title: KD Micro-C rep 1

value: KD of EWS::FLI

value: empty vector rescue


title: Liver, LbNOX, EtOH Gavage, Rep 3

status: Public on Jan 02 2024

first: Russell

last: Goodman

address: 55 Fruit st, Thier Building, 11th Floor

institute: Massachusetts General Hospital

data_processing:
Raw tranascript pseudocounts were generated using Salmon v 1.5.1
Salmon files were then processed with DESeq2 v. 1.30.1 to generate normalized transcript abundance
Assembly: mm10
Supplementary files format and content: tab-delmited text files of normalized counts for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

value: Liver

value: LbNOX

value: ETOH Gavage


title: DBD Micro-C rep 1


title: Liver, Luciferase, EtOH Gavage, Rep 3

value: Luciferase


title: Liver, LbNOX, EtOH Gavage, Rep 2


title: MOLM13_RNA_DMSO_72h_REP3_210421_TAATCG_S3

description: Illumina NextSeq 37bp paired-end RNAseq

value: acute myeloid leukemia

value: 72 hours


title: Liver, LbNOX, EtOH Gavage, Rep 1


title: Liver, LbNOX, H2O Gavage, Rep 4

value: H2O Gavage


title: Liver, Luciferase, EtOH Gavage, Rep 1


title: Liver, LbNOX, H2O Gavage, Rep 2


title: Liver, Luciferase, H2O Gavage, Rep 3


title: Liver, Luciferase, H2O Gavage, Rep 5


title: Liver, Luciferase, H2O Gavage, Rep 1


title: Liver, Luciferase, H2O Gavage, Rep 2


title: MOLM13_RNA_CC220_1uM_72h_REP1_210421_TACAGC_S4


title: Liver, LbNOX, H2O Gavage, Rep 3


title: Liver, ChREBP WT, H2O Gavage, Rep 2

value: ChREBP WT


title: Liver, Luciferase, H2O Gavage, Rep 4


title: Liver, ChREBP WT, EtOH Gavage, Rep 3


title: Liver, ChREBP WT, EtOH Gavage, Rep 2


title: Liver, ChREBP WT, EtOH Gavage, Rep 1


title: Liver, LbNOX, H2O Gavage, Rep 1


title: KD Micro-C rep 2


title: Liver, ChREBP WT, EtOH Gavage, Rep 4


title: Liver, ChREBP KO, H2O Gavage, Rep 3

value: ChREBP KO


title: Liver, ChREBP KO, H2O Gavage, Rep 4


title: Liver, ChREBP KO, H2O Gavage, Rep 2


title: Liver, ChREBP KO, EtOH Gavage, Rep 5

value: EtOH Gavage


title: Liver, ChREBP KO, H2O Gavage, Rep 1


title: Liver, Luciferase, EtOH Gavage, Rep 2


title: Liver, ChREBP KO, EtOH Gavage, Rep 2


title: Liver, ChREBP KO, EtOH Gavage, Rep 3


title: Liver, ChREBP KO, EtOH Gavage, Rep 1


title: Liver, ChREBP WT, H2O Gavage, Rep 3


title: GFP, rep 1

data_processing:
Raw tranascript pseudocounts were generated using Salmon v 1.5.1
Salmon files were then processed with DESeq2 v. 1.30.1 to generate normalized transcript abundance
Assembly: mm10
Supplementary files format and content: comma-delmited text files of normalized counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

value: GFP


title: GFP, rep 4


title: GFP, rep 2


title: Liver, ChREBP WT, H2O Gavage, Rep 1


title: EcSTH, rep 2

value: EcSTH


title: EcSTH, rep 3


title: EcSTH, rep 4


title: GFP, rep 3


title: sciMETcap 6k cells, standard capture conditions

status: Public on Dec 19 2023

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
Raw reads were demultiplexed using unidex
Reads were trimemd using a wrapper for Trim Galore
Trimmed reads were aligned using BSBolt and then duplicate removed
Methylation calls on a per cell basis were then extracted
Methylation calls were used to generate window matrixes used for dimensionality reduction, clustering and visualization
Assembly: hg38
Supplementary files format and content: gzipped tar archives that contain bed files of methylation calls split by chromosome
Supplementary files format and content: gzipped tar archives that contain tab delimited text files for processed matrixes and other analytics
Library strategy: sciMET-cap

source_name: PBMCs

extract_protocol:
Nuclei were extracted using nuclei isolation buffer according to protocols detailed in Nichols et al 2022
Nuclei were isolated and processed using the sciMETv2.SL protocol described in Nichols et al 2022 followed by target capture using the Twist methylome panel

value: PBMCs


title: EcSTH, rep 1


title: Liver, ChREBP KO, EtOH Gavage, Rep 4


title: 22Rv1_RNA_ENZ3w_Dex_rep3

status: Public on Nov 07 2023

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
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: VCaP and 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 16 (ENZ2w) or 21 days (ENZ3w) before the start of hormone treatments. VCaP and 22Rv1 cells were treated with vehicle (EtOH), 1 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for 18 h before the start of RNA extraction.

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

tag: enz treatment

value: 3 weeks

tag: hormone treatment

value: dexamethasone

tag: hormone concentration


title: 22Rv1_RNA_ENZ3w_Dex_rep2


title: 22Rv1_RNA_ENZ3w_Dex_rep1


title: 22Rv1_RNA_Dex_rep2


title: 22Rv1_RNA_ENZ3w_EtOH_rep3

value: EtOH vehicle


title: 22Rv1_RNA_Dex_rep1


title: 22Rv1_RNA_EtOH_rep3


title: 22Rv1_RNA_ENZ3w_EtOH_rep1


title: 22Rv1_RNA_ENZ3w_EtOH_rep2


title: 22Rv1_RNA_Dex_rep3


title: 22Rv1_RNA_EtOH_rep2


title: 22Rv1_RNA_EtOH_rep1


title: VCaP_RNA_ENZ3w_Dex_rep3

source_name: VCaP

value: Vertebral Cancer of the Prostate

value: VCaP


title: VCaP_RNA_ENZ3w_Dex_rep2


title: VCaP_RNA_ENZ3w_EtOH_rep3


title: VCaP_RNA_ENZ3w_EtOH_rep1


title: VCaP_RNA_ENZ3w_EtOH_rep2


title: MEP_MXIE_r2

status: Public on Nov 28 2023

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description: Megakaryocyte Erythroid Progenitor MXIE overexpression rep 2

hyb_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

data_processing: samples were RMA normalised in GenePattern using NormalizeAffymetrixST 2.2 (RMA, core probesets, controls included,Affymetrix_MoGene_1_1_st_v1.na33.2.mm9.transcript.chip).

label: biotin

source_name: MEP (group B) MXIE

growth_protocol: Cell were FACS sorted from primiary receipent mice 16 weeks post transplantation of retrovirally overexpressed immature bone marrow cells.

tag: cell population

value: FACS Sorted BM Lin-C-Kit+Sca-1-CD16/32-CD34- cells

tag: pool

value: B

value: Bone Marrow

value: megakaryote erythorid progenitors (MEP)

tag: overexpression

value: control vector (MXIE)

tag: background strain

tag: biological replicate


title: CMP (group D) Hoxa1mut

description: Common Myeloid Progenitor Hoxa1 mutant rep 4

scan_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

tag: cell sort information

value: FACS Sorted BM  LKS-CD34+CD16/32-

value: D

tag: tissue

value: CMP

tag: overexpression??

tag: genetic background


title: CMP (group D) Hoxa1

description: Common Myeloid Progenitor Hoxa1 overexpression rep 3

label_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.


title: MEP_MXIE_r1

description: Megakaryocyte Erythroid Progenitor MXIE overexpression rep 1

source_name: MEP (group A) MXIE

extract_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

value: A


title: MEP_MXIE_r4

description: Megakaryocyte Erythroid Progenitor MXIE overexpression rep 4

source_name: MEP (group D) MXIE


title: CMP (group A) MXIE

description: Common Myeloid Progenitor MXIE overexpression rep 1

value: MXIE


title: CMP (group D) MXIE

description: Common Myeloid Progenitor MXIE overexpression rep 4


title: VCaP_RNA_Dex_rep3

tag: cell line


title: CMP (group B) MXIE

description: Common Myeloid Progenitor MXIE overexpression rep 2


title: CMP (group B) Hoxa1mut

description: Common Myeloid Progenitor Hoxa1 mutant rep 2


title: CMP (group A) Hoxa1mut

description: Common Myeloid Progenitor Hoxa1 mutant rep 1


title: CMP (group B) Hoxa1

description: Common Myeloid Progenitor Hoxa1 overexpression rep 2


title: MEP_Hoxa1mut_r1

description: Megakaryocyte Erythroid Progenitor Hoxa1 mutant rep 1

source_name: MEP (group A) Hoxa1mut

tag: cell type

value: Mutant Hoxa1 (MUT-Hoxa1)


title: CMP (group C) Hoxa1

description: Common Myeloid Progenitor Hoxa1 mutant rep 3

value: C


title: VCaP_RNA_Dex_rep1


title: VCaP_RNA_ENZ3w_Dex_rep1

value: 3 weeks


title: VCaP_RNA_Dex_rep2

value: dexamethasone


title: VCaP_RNA_EtOH_rep2

value: EtOH vehicle


title: 22Rv1_GR_ENZ3w_Dex_rep2

data_processing:
Basecalls performed using CASAVA, and FASTX-toolkit was used to trim low quality reads.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: VCaP and 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the VCaP cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. VCaP and 22Rv1 cells were treated with vehicle (EtOH), 1 nM of dihydrotestosterone (DHT), 100 nM of DHT, or 100 nM of Dexamethasone (Dex) for 1 h before the start of ChIPs.

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

tag: sirna treatment

tag: chip antibody

value: GR (Cell Signaling, 12041)


title: 22Rv1_GR_ENZ3w_Dex_rep1


title: MEP_Hoxa1mut_r4

description: Megakaryocyte Erythroid Progenitor Hoxa1 mutant rep 4

source_name: MEP (group D) Hoxa1mut

value: FACS Sorted BM Lin-C-Kit+Sca-1-CD16/32-CD34- cells


title: CMP (group C) MXIE

description: Common Myeloid Progenitor MXIE overexpression rep 3


title: CMP (group A) Hoxa1

description: Common Myeloid Progenitor Hoxa1 overexpression rep 1


title: MEP_Hoxa1_r4

description: Megakaryocyte Erythroid Progenitor Hoxa1 overexpression rep 4

source_name: MEP (group D) Hoxa1

value: Wild type Hoxa1 (WT- Hoxa1)


title: MEP_Hoxa1_r1

description: Megakaryocyte Erythroid Progenitor Hoxa1 overexpression rep 1

source_name: MEP (group A) Hoxa1

value: Bone Marrow


title: VCaP_RNA_EtOH_rep3

value: Vertebral Cancer of the Prostate

value: VCaP


title: MEP_Hoxa1mut_r3

description: Megakaryocyte Erythroid Progenitor Hoxa1 mutant rep 3

source_name: MEP (group C) Hoxa1mut

value: megakaryote erythorid progenitors (MEP)


title: VCaP_GR_ENZ3w_Dex_rep2


title: MEP_MXIE_r3

description: Megakaryocyte Erythroid Progenitor MXIE overexpression rep 3

source_name: MEP (group C) MXIE

value: control vector (MXIE)


title: 22Rv1_GR_Dex_rep2


title: 22Rv1_GR_Dex_rep1


title: MEP_Hoxa1_r2

description: Megakaryocyte Erythroid Progenitor Hoxa1 overexpression rep 2

source_name: MEP (group B) Hoxa1

value: B


title: VCaP_GR_ENZ3w_Dex_rep1


title: WTC11 iPSC, differentiated to VECs, rep 3

status: Public on Oct 16 2023

city: New York

first: Clifford

middle: Z.

last: Liu

state: NY

address: 1470 Madison Ave, Hess 8-301

institute: Icahn School of Medicine at Mount Sinai

data_processing:
2-pass mapping with STAR v2.7.10a
Duplicate reads removed with Picard v2.26.10.
Read counts generated with HTSeq v 2.0.2.
Assembly: NCBI build 38/ UCSC hg38
Supplementary files format and content: Gene counts, .txt file

extract_protocol:
Total RNA extracted with the Qiagen RNeasy Kit, following proteinase K incubation.
Poly A selection without strand specificity (performed by Novogene)

value: Valvular Endothelial Cell

tag: genotype

value: WT


title: VCaP_GR_Dex_rep2

tag: enz treatment


title: MEP_Hoxa1mut_r2

description: Megakaryocyte Erythroid Progenitor Hoxa1 mutant rep 2

source_name: MEP (group B) Hoxa1mut

value: Mutant Hoxa1 (MUT-Hoxa1)


title: WTC11 iPSC, differentiated to VECs, rep 2


title: VCaP_GR_Dex_rep1

tag: hormone treatment


title: WTC11 iPSC, differentiated to VICs, rep 3

value: Valvular Interstitial Cell


title: WTC11 iPSC, differentiated to endothelial cells (control), rep 3

value: Endothelial Cell


title: WTC11 iPSC, differentiated to endothelial cells (control), rep 2


title: WTC11 iPSC, differentiated to endocardial cells, rep 3

value: Endocardial Cell


title: WTC11 iPSC, differentiated to VICs, rep 2


title: MSN02-4 iPSC, differentiated to VECs, rep 3


title: MSN02-4 iPSC, differentiated to VECs, rep 2


title: WTC11 iPSC, differentiated to endocardial cells, rep 2


title: VCaP_RNA_EtOH_rep1

value: EtOH vehicle

tag: hormone concentration


title: MSN02-4 iPSC, differentiated to endothelial cells (control), rep 3


title: MSN02-4 iPSC, differentiated to endocardial cells, rep 3


title: MSN02-4 iPSC, differentiated to VICs, rep 2


title: MSN02-4 iPSC, differentiated to endothelial cells (control), rep 2


title: MSN02-4 iPSC, differentiated to VICs, rep 3


title: MSN02-4 iPSC, differentiated to endocardial cells, rep 2


title: ChIA-PET from HCT116 (ENCLB851LXB)

status: Public on Sep 07 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR741AGK/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, BRD4 tag and IAA treated
experiment encode accession: ENCSR741AGK
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB851LXB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS347WDW at ENCODE; https://www.encodeproject.org/ENCBS347WDW/


title: ChIA-PET from HCT116 (ENCLB715PYX)

description:
https://www.encodeproject.org/experiments/ENCSR263OBH/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CDK7 tag and IAA treated
experiment encode accession: ENCSR263OBH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB715PYX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: ENCBS387RXX at ENCODE; https://www.encodeproject.org/ENCBS387RXX/


title: ChIA-PET from T-cell (ENCLB990RKF)

description:
https://www.encodeproject.org/experiments/ENCSR743YTL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD3_Resting_donor4
experiment encode accession: ENCSR743YTL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB990RKF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: primary cell

value: female

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS828FLM at ENCODE; https://www.encodeproject.org/ENCBS828FLM/


title: ChIA-PET from Calu3 (ENCLB229PMX)

description:
https://www.encodeproject.org/experiments/ENCSR723YJG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Calu-3
experiment encode accession: ENCSR723YJG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB229PMX
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens Calu3 cell line

value: CTCF

value: cell line

value: not applicable

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS994KFQ at ENCODE; https://www.encodeproject.org/ENCBS994KFQ/


title: ChIA-PET from HCT116 (ENCLB061GWQ)

description:
https://www.encodeproject.org/experiments/ENCSR956HZZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, MED14 tag and IAA treated
experiment encode accession: ENCSR956HZZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB061GWQ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS176UGT at ENCODE; https://www.encodeproject.org/ENCBS176UGT/


title: ChIA-PET from Caco-2 (ENCLB031SUN)

description:
https://www.encodeproject.org/experiments/ENCSR185PEE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Caco-2
experiment encode accession: ENCSR185PEE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB031SUN
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens Caco-2 cell line

value: colorectal adenocarcinoma

value: 72 year

value: ENCBS369RNF at ENCODE; https://www.encodeproject.org/ENCBS369RNF/


title: ChIA-PET from HCT116 (ENCLB012HOG)

description:
https://www.encodeproject.org/experiments/ENCSR180DXE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SMARCA5 tag and IAA treated
experiment encode accession: ENCSR180DXE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB012HOG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: not applicable

value: ENCBS823TPL at ENCODE; https://www.encodeproject.org/ENCBS823TPL/


title: ChIA-PET from Caco-2 (ENCLB860BXS)

description:
https://www.encodeproject.org/experiments/ENCSR185PEE/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Caco-2
experiment encode accession: ENCSR185PEE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB860BXS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: Mats Ljungman, UMichigan

value: ENCBS933BLN at ENCODE; https://www.encodeproject.org/ENCBS933BLN/


title: ChIA-PET from WTC11 (ENCLB785KWP)

description:
https://www.encodeproject.org/experiments/ENCSR972JTN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11
experiment encode accession: ENCSR972JTN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB785KWP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens WTC11 cell line

value: male

value: 30 year

value: Charles Lee

value: Coriell

value: ENCBS770SCV at ENCODE; https://www.encodeproject.org/ENCBS770SCV/


title: ChIA-PET from T-cell (ENCLB884IGJ)

description:
https://www.encodeproject.org/experiments/ENCSR722NQM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD3_Resting_donor11
experiment encode accession: ENCSR722NQM
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB884IGJ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens male adult (35 years) T-cell primary cell

value: T-cell

value: primary cell

value: adult

value: 35 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS844FBG at ENCODE; https://www.encodeproject.org/ENCBS844FBG/


title: ChIA-PET from Caco-2 (ENCLB224AJH)

description:
https://www.encodeproject.org/experiments/ENCSR713NCY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Caco-2
experiment encode accession: ENCSR713NCY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB224AJH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: not applicable

value: colorectal adenocarcinoma

value: 72 year

value: ATCC

value: ENCBS566DIR at ENCODE; https://www.encodeproject.org/ENCBS566DIR/


title: ChIA-PET from HCT116 (ENCLB423AAA)

description:
https://www.encodeproject.org/experiments/ENCSR956HZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, MED14 tag and IAA treated
experiment encode accession: ENCSR956HZZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB423AAA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS496XOF at ENCODE; https://www.encodeproject.org/ENCBS496XOF/


title: ChIA-PET from Calu3 (ENCLB457IZH)

description:
https://www.encodeproject.org/experiments/ENCSR723YJG/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Calu-3
experiment encode accession: ENCSR723YJG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB457IZH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: Lung adenocarcinoma

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: ENCBS874QBV at ENCODE; https://www.encodeproject.org/ENCBS874QBV/


title: ChIA-PET from WTC11 (ENCLB174FMF)

description:
https://www.encodeproject.org/experiments/ENCSR176OZL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11_clone6
experiment encode accession: ENCSR176OZL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB174FMF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR

value: cell line

value: not applicable

value: 30 year

value: Charles Lee

value: Coriell

value: ENCBS704QHP at ENCODE; https://www.encodeproject.org/ENCBS704QHP/


title: ChIA-PET from HCT116 (ENCLB571KVD)

description:
https://www.encodeproject.org/experiments/ENCSR711IEI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, BRD4 tag and IAA untreated, control
experiment encode accession: ENCSR711IEI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB571KVD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: male

value: colorectal carcinoma

value: ENCBS978VFN at ENCODE; https://www.encodeproject.org/ENCBS978VFN/


title: ChIA-PET from Caco-2 (ENCLB039MZD)

description:
https://www.encodeproject.org/experiments/ENCSR713NCY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in Caco-2
experiment encode accession: ENCSR713NCY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB039MZD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: colorectal adenocarcinoma

value: 72 year

value: ATCC

value: ENCBS987HOX at ENCODE; https://www.encodeproject.org/ENCBS987HOX/


title: ChIA-PET from activated T-cell (ENCLB573ICW)

description:
https://www.encodeproject.org/experiments/ENCSR538SBO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD3_Activated_donor1
experiment encode accession: ENCSR538SBO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB573ICW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: adult

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS415KTK at ENCODE; https://www.encodeproject.org/ENCBS415KTK/


title: ChIA-PET from HCT116 (ENCLB786RVU)

description:
https://www.encodeproject.org/experiments/ENCSR741AGK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, BRD4 tag and IAA treated
experiment encode accession: ENCSR741AGK
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB786RVU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: cell line

value: not applicable

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS189PYR at ENCODE; https://www.encodeproject.org/ENCBS189PYR/


title: ChIA-PET from IMR-90 (ENCLB755BXA)

description:
https://www.encodeproject.org/experiments/ENCSR966RPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in IMR90
experiment encode accession: ENCSR966RPQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-01-31
lab: Charles Lee
library encode accession: ENCLB755BXA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens IMR-90 cell line

tag: description

value: fetal lung fibroblasts

value: female

value: unknown

value: embryonic

value: 16 week

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS844OYT at ENCODE; https://www.encodeproject.org/ENCBS844OYT/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: ChIA-PET from embryonic stem cell (ENCLB443HVH)

description:
https://www.encodeproject.org/experiments/ENCSR214BLK/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in 129S1CastF1
experiment encode accession: ENCSR214BLK
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB443HVH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Mus musculus strain 129S1CastF1 male embryo embryonic stem primary cell

value: CTCF

value: embryonic stem cell

value: primary cell

value: male

value: Charles Lee

value: The Jackson Laboratory

value: ENCBS355CPY at ENCODE; https://www.encodeproject.org/ENCBS355CPY/


title: ChIA-PET from HCT116 (ENCLB917GYN)

description:
https://www.encodeproject.org/experiments/ENCSR711IEI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, BRD4 tag and IAA untreated, control
experiment encode accession: ENCSR711IEI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB917GYN
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: not applicable

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS121KTD at ENCODE; https://www.encodeproject.org/ENCBS121KTD/


title: ChIA-PET from embryonic stem cell (ENCLB844IKU)

description:
https://www.encodeproject.org/experiments/ENCSR214BLK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in 129S1CastF1
experiment encode accession: ENCSR214BLK
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB844IKU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: embryonic

value: unknown

value: ENCBS648RIM at ENCODE; https://www.encodeproject.org/ENCBS648RIM/


title: ChIA-PET from embryonic stem cell (ENCLB368TZH)

description:
https://www.encodeproject.org/experiments/ENCSR466YGP/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in B6CASTF1J
experiment encode accession: ENCSR466YGP
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB368TZH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Mus musculus strain B6CASTF1/J male embryo embryonic stem primary cell

value: CTCF

value: embryonic stem cell

value: ENCBS985DGR at ENCODE; https://www.encodeproject.org/ENCBS985DGR/


title: ChIA-PET from HCT116 (ENCLB752DAQ)

description:
https://www.encodeproject.org/experiments/ENCSR263OBH/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CDK7 tag and IAA treated
experiment encode accession: ENCSR263OBH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB752DAQ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: male

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS354DNN at ENCODE; https://www.encodeproject.org/ENCBS354DNN/


title: ChIA-PET from HCT116 (ENCLB554BAD)

description:
https://www.encodeproject.org/experiments/ENCSR918GSZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, BRD4 tag and IAA treated
experiment encode accession: ENCSR918GSZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB554BAD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: ENCBS632ZLW at ENCODE; https://www.encodeproject.org/ENCBS632ZLW/


title: ChIA-PET from HCT116 (ENCLB272PCU)

description:
https://www.encodeproject.org/experiments/ENCSR918GSZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, BRD4 tag and IAA treated
experiment encode accession: ENCSR918GSZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB272PCU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: not applicable

value: colorectal carcinoma

value: ENCBS671YQM at ENCODE; https://www.encodeproject.org/ENCBS671YQM/


title: ChIA-PET from WTC11 (ENCLB899ENP)

description:
https://www.encodeproject.org/experiments/ENCSR176OZL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11_clone6
experiment encode accession: ENCSR176OZL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB899ENP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: adult

value: 30 year

value: Charles Lee

value: Coriell

value: ENCBS149LXT at ENCODE; https://www.encodeproject.org/ENCBS149LXT/


title: ChIA-PET from embryonic stem cell (ENCLB848JLS)

description:
https://www.encodeproject.org/experiments/ENCSR466YGP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in B6CASTF1J
experiment encode accession: ENCSR466YGP
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB848JLS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: primary cell

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS665NEM at ENCODE; https://www.encodeproject.org/ENCBS665NEM/


title: ChIA-PET from activated T-cell (ENCLB786AAF)

description:
https://www.encodeproject.org/experiments/ENCSR538SBO/
***************
biological replicate number: 1
technical replicate number: 2
description: RNAPII ChIA-PET in CD3_Activated_donor1
experiment encode accession: ENCSR538SBO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB786AAF
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: activated T-cell

value: male

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS415KTK at ENCODE; https://www.encodeproject.org/ENCBS415KTK/


title: ChIA-PET from activated T-cell (ENCLB549YFA)

description:
https://www.encodeproject.org/experiments/ENCSR165FXG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD3_Activated
experiment encode accession: ENCSR165FXG
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB549YFA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens male adult (35 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: not applicable

value: adult

value: 35 year

value: ENCBS247ZXC at ENCODE; https://www.encodeproject.org/ENCBS247ZXC/


title: ChIA-PET from HCT116 (ENCLB531PPC)

description:
https://www.encodeproject.org/experiments/ENCSR910WPE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, RAD21 tag and IAA untreated, control
experiment encode accession: ENCSR910WPE
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB531PPC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: CTCF

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS685QCW at ENCODE; https://www.encodeproject.org/ENCBS685QCW/


title: ChIA-PET from HCT116 (ENCLB450BQE)

description:
https://www.encodeproject.org/experiments/ENCSR674UYO/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control
experiment encode accession: ENCSR674UYO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB450BQE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: male

value: ENCBS957DPF at ENCODE; https://www.encodeproject.org/ENCBS957DPF/


title: ChIA-PET from Panc1 (ENCLB776ESZ)

description:
https://www.encodeproject.org/experiments/ENCSR447IUA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Panc1
experiment encode accession: ENCSR447IUA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB776ESZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens Panc1 cell line

value: pancreatic carcinoma

value: 56 year

value: Charles Lee

value: ATCC

value: ENCBS895GAX at ENCODE; https://www.encodeproject.org/ENCBS895GAX/


title: ChIA-PET from embryonic stem cell (ENCLB024EQR)

description:
https://www.encodeproject.org/experiments/ENCSR067GFU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in B6CASTF1J
experiment encode accession: ENCSR067GFU
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB024EQR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: embryonic stem cell

value: primary cell

value: not applicable

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS580XDG at ENCODE; https://www.encodeproject.org/ENCBS580XDG/


title: ChIA-PET from AG04450 (ENCLB606QMT)

description:
https://www.encodeproject.org/experiments/ENCSR037FPN/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in AG04450
experiment encode accession: ENCSR037FPN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Yijun Ruan, JAX
library encode accession: ENCLB606QMT
size range: 350-600
instrument models: Illumina MiSeq,Illumina HiSeq 4000

source_name: Homo sapiens AG04450 cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/f7779792-9403-4396-9ff6-8e859edd608c/@@download/attachment/In-situ%20chiapet_Ruan%20Lab_final.pdf
extraction method: SDS

value: CTCF

value: cell line

value: apparently healthy

value: 12 week

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS097WVO at ENCODE; https://www.encodeproject.org/ENCBS097WVO/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/


title: ChIA-PET from Patski (ENCLB479IQT)

description:
https://www.encodeproject.org/experiments/ENCSR564BAB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in Patski
experiment encode accession: ENCSR564BAB
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB479IQT
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Mus musculus strain Patski Patski cell line

value: Patski

value: male

value: Charles Lee

value: ENCBS771FMN at ENCODE; https://www.encodeproject.org/ENCBS771FMN/


title: ChIA-PET from Patski (ENCLB310SCO)

description:
https://www.encodeproject.org/experiments/ENCSR564BAB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in Patski
experiment encode accession: ENCSR564BAB
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB310SCO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: not applicable

value: ENCBS804AKM at ENCODE; https://www.encodeproject.org/ENCBS804AKM/


title: ChIA-PET from HCT116 (ENCLB660TLR)

description:
https://www.encodeproject.org/experiments/ENCSR674UYO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control
experiment encode accession: ENCSR674UYO
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB660TLR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS357ENO at ENCODE; https://www.encodeproject.org/ENCBS357ENO/


title: ChIA-PET from embryonic stem cell (ENCLB042PDH)

description:
https://www.encodeproject.org/experiments/ENCSR543IIL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in 129S1SvImJ
experiment encode accession: ENCSR543IIL
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB042PDH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Mus musculus strain 129S1/SvImJ male embryo embryonic stem primary cell

value: embryonic stem cell

value: primary cell

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS933HBL at ENCODE; https://www.encodeproject.org/ENCBS933HBL/


title: ChIA-PET from spleen (ENCLB634TDO)

description:
https://www.encodeproject.org/experiments/ENCSR314BGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in C57BL6J spleen tissue
experiment encode accession: ENCSR314BGZ
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB634TDO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Mus musculus strain C57BL/6J male embryo spleen tissue

value: CTCF

value: spleen

value: tissue

value: male

value: ENCBS468AJT at ENCODE; https://www.encodeproject.org/ENCBS468AJT/


title: ChIA-PET from embryonic stem cell (ENCLB608DLR)

description:
https://www.encodeproject.org/experiments/ENCSR067GFU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in B6CASTF1J
experiment encode accession: ENCSR067GFU
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB608DLR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: not applicable

value: Charles Lee

value: ENCBS355BZY at ENCODE; https://www.encodeproject.org/ENCBS355BZY/


title: ChIA-PET from HCT116 (ENCLB125MRH)

description:
https://www.encodeproject.org/experiments/ENCSR160MHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA treated
experiment encode accession: ENCSR160MHZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB125MRH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS120ZXG at ENCODE; https://www.encodeproject.org/ENCBS120ZXG/


title: ChIA-PET from embryonic stem cell (ENCLB691YVK)

description:
https://www.encodeproject.org/experiments/ENCSR309NAP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in 129S1CastF1
experiment encode accession: ENCSR309NAP
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB691YVK
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: embryonic stem cell

value: primary cell

value: embryonic

value: unknown

value: The Jackson Laboratory

value: ENCBS996HDK at ENCODE; https://www.encodeproject.org/ENCBS996HDK/


title: ChIA-PET from Panc1 (ENCLB421RYW)

description:
https://www.encodeproject.org/experiments/ENCSR447IUA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in Panc1
experiment encode accession: ENCSR447IUA
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB421RYW
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: male

value: pancreatic carcinoma

value: 56 year

value: ATCC

value: ENCBS687JHX at ENCODE; https://www.encodeproject.org/ENCBS687JHX/


title: ChIA-PET from embryonic stem cell (ENCLB129WQY)

description:
https://www.encodeproject.org/experiments/ENCSR309NAP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in 129S1CastF1
experiment encode accession: ENCSR309NAP
assay title: ChIA-PET
assembly: mm10
encode release date: 2022-01-21
lab: Charles Lee
library encode accession: ENCLB129WQY
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: not applicable

value: Charles Lee

value: ENCBS206CFD at ENCODE; https://www.encodeproject.org/ENCBS206CFD/


title: ChIA-PET from activated T-cell (ENCLB792MUR)

description:
https://www.encodeproject.org/experiments/ENCSR891IMI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in CD3_Activated_donor3
experiment encode accession: ENCSR891IMI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB792MUR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens female adult (41 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: female

value: adult

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS755WRA at ENCODE; https://www.encodeproject.org/ENCBS755WRA/


title: ChIA-PET from HCT116 (ENCLB458RUB)

description:
https://www.encodeproject.org/experiments/ENCSR440JFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, MED14 tag and IAA untreated, control
experiment encode accession: ENCSR440JFJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB458RUB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

value: CTCF

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS710FUV at ENCODE; https://www.encodeproject.org/ENCBS710FUV/


title: ChIA-PET from HCT116 (ENCLB467YIP)

description:
https://www.encodeproject.org/experiments/ENCSR160MHZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA treated
experiment encode accession: ENCSR160MHZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB467YIP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: not applicable

value: male

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS464LPU at ENCODE; https://www.encodeproject.org/ENCBS464LPU/


title: ChIA-PET from activated T-cell (ENCLB291OYR)

description:
https://www.encodeproject.org/experiments/ENCSR411UEL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD3_Activated
experiment encode accession: ENCSR411UEL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB291OYR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: activated T-cell

value: primary cell

value: adult

value: 35 year

value: ENCBS247ZXC at ENCODE; https://www.encodeproject.org/ENCBS247ZXC/


title: ChIA-PET from HCT116 (ENCLB494WJS)

description:
https://www.encodeproject.org/experiments/ENCSR641SOU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control
experiment encode accession: ENCSR641SOU
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB494WJS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS922EWC at ENCODE; https://www.encodeproject.org/ENCBS922EWC/


title: ChIA-PET from HCT116 (ENCLB702LKP)

description:
https://www.encodeproject.org/experiments/ENCSR440JFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, MED14 tag and IAA untreated, control
experiment encode accession: ENCSR440JFJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB702LKP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF

value: ENCBS861SVA at ENCODE; https://www.encodeproject.org/ENCBS861SVA/


title: ChIA-PET from activated T-cell (ENCLB750NCO)

description:
https://www.encodeproject.org/experiments/ENCSR411UEL/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIA-PET in CD3_Activated
experiment encode accession: ENCSR411UEL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB750NCO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;


title: ChIA-PET from Panc1 (ENCLB911KQI)

description:
https://www.encodeproject.org/experiments/ENCSR145PYF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in Panc1
experiment encode accession: ENCSR145PYF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB911KQI
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: pancreatic carcinoma

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS471WLS at ENCODE; https://www.encodeproject.org/ENCBS471WLS/


title: ChIA-PET from PC-9 (ENCLB397BNB)

description:
https://www.encodeproject.org/experiments/ENCSR863QCN/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in PC-9
experiment encode accession: ENCSR863QCN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB397BNB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens PC-9 cell line

value: not applicable

value: not collected

value: unknown

value: Sigma

value: ENCBS449UGD at ENCODE; https://www.encodeproject.org/ENCBS449UGD/


title: ChIA-PET from PC-9 (ENCLB325ZZH)

description:
https://www.encodeproject.org/experiments/ENCSR863QCN/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in PC-9
experiment encode accession: ENCSR863QCN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB325ZZH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS442RTD at ENCODE; https://www.encodeproject.org/ENCBS442RTD/


title: ChIA-PET from A673 (ENCLB350NDM)

description:
https://www.encodeproject.org/experiments/ENCSR623KNI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in A673
experiment encode accession: ENCSR623KNI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB350NDM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens A673 cell line

value: female

value: child

value: 15 year

value: ENCBS336SUN at ENCODE; https://www.encodeproject.org/ENCBS336SUN/


title: ChIA-PET from A673 (ENCLB624DLP)

description:
https://www.encodeproject.org/experiments/ENCSR623KNI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in A673
experiment encode accession: ENCSR623KNI
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB624DLP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: Charles Lee

value: ENCBS186FLS at ENCODE; https://www.encodeproject.org/ENCBS186FLS/


title: ChIA-PET from HCT116 (ENCLB344XQB)

description:
https://www.encodeproject.org/experiments/ENCSR106EOT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CTCF tag and IAA untreated, control
experiment encode accession: ENCSR106EOT
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-03-14
lab: Charles Lee
library encode accession: ENCLB344XQB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: CTCF

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS013IOY at ENCODE; https://www.encodeproject.org/ENCBS013IOY/


title: ChIA-PET from HCT116 (ENCLB688BPZ)

description:
https://www.encodeproject.org/experiments/ENCSR407ATL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, POLR2A tag and IAA treated
experiment encode accession: ENCSR407ATL
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB688BPZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: not applicable

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS177WXY at ENCODE; https://www.encodeproject.org/ENCBS177WXY/


title: ChIA-PET from T-cell (ENCLB681OQV)

description:
https://www.encodeproject.org/experiments/ENCSR592BWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in CD3_Resting_donor11
experiment encode accession: ENCSR592BWZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB681OQV
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens male adult (35 years) T-cell primary cell

value: T-cell

value: primary cell

value: 35 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS844FBG at ENCODE; https://www.encodeproject.org/ENCBS844FBG/


title: ChIA-PET from T-cell (ENCLB046IYJ)

description:
https://www.encodeproject.org/experiments/ENCSR592BWZ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIA-PET in CD3_Resting_donor11
experiment encode accession: ENCSR592BWZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-29
lab: Charles Lee
library encode accession: ENCLB046IYJ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: CTCF


title: ChIA-PET from PC-3 (ENCLB480EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR854YJR/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in PC-3
experiment encode accession: ENCSR854YJR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB480EOZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens PC-3 cell line

value: cell line

value: male

value: grade IV, adenocarcinoma

value: 62 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS065UHY at ENCODE; https://www.encodeproject.org/ENCBS065UHY/


title: ChIA-PET from OCI-LY7 (ENCLB869XVD)

description:
https://www.encodeproject.org/experiments/ENCSR401JWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in OCI-LY7
experiment encode accession: ENCSR401JWQ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB869XVD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens OCI-LY7 cell line

value: not applicable

value: B cell lymphoma

value: adult

value: 48 year

value: Charles Lee

value: DSMZ

value: ENCBS309RTL at ENCODE; https://www.encodeproject.org/ENCBS309RTL/


title: ChIA-PET from PC-3 (ENCLB109ONH)

description:
https://www.encodeproject.org/experiments/ENCSR854YJR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in PC-3
experiment encode accession: ENCSR854YJR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB109ONH
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS347JFR at ENCODE; https://www.encodeproject.org/ENCBS347JFR/


title: ChIA-PET from HCT116 (ENCLB510OGP)

description:
https://www.encodeproject.org/experiments/ENCSR641SOU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA untreated, control
experiment encode accession: ENCSR641SOU
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB510OGP
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: colorectal carcinoma

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS710KFY at ENCODE; https://www.encodeproject.org/ENCBS710KFY/


title: ChIA-PET from OCI-LY7 (ENCLB632REQ)

description:
https://www.encodeproject.org/experiments/ENCSR882BUM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in OCI-LY7
experiment encode accession: ENCSR882BUM
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB632REQ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: male

value: ENCBS568NQM at ENCODE; https://www.encodeproject.org/ENCBS568NQM/


title: ChIA-PET from OCI-LY7 (ENCLB747FLM)

description:
https://www.encodeproject.org/experiments/ENCSR882BUM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in OCI-LY7
experiment encode accession: ENCSR882BUM
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB747FLM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS397YHA at ENCODE; https://www.encodeproject.org/ENCBS397YHA/


title: ChIA-PET from WTC11 (ENCLB395AJM)

description:
https://www.encodeproject.org/experiments/ENCSR972JTN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in WTC11
experiment encode accession: ENCSR972JTN
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB395AJM
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

source_name: Homo sapiens WTC11 cell line

value: 30 year

value: Coriell

value: ENCBS062USM at ENCODE; https://www.encodeproject.org/ENCBS062USM/


title: ChIA-PET from HCT116 (ENCLB011LWR)

description:
https://www.encodeproject.org/experiments/ENCSR394XYY/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, BRD4 tag and IAA untreated, control
experiment encode accession: ENCSR394XYY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB011LWR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: CTCF

value: not applicable

value: adult

value: ENCBS287MEN at ENCODE; https://www.encodeproject.org/ENCBS287MEN/


title: ChIA-PET from HCT116 (ENCLB309VYD)

description:
https://www.encodeproject.org/experiments/ENCSR394XYY/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, BRD4 tag and IAA untreated, control
experiment encode accession: ENCSR394XYY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB309VYD
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: 48 year

value: ENCBS328EFM at ENCODE; https://www.encodeproject.org/ENCBS328EFM/


title: ChIA-PET from HCT116 (ENCLB317IJL)

description:
https://www.encodeproject.org/experiments/ENCSR830FZR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA treated
experiment encode accession: ENCSR830FZR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB317IJL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: colorectal carcinoma

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS237ZFD at ENCODE; https://www.encodeproject.org/ENCBS237ZFD/


title: ChIA-PET from HCT116 (ENCLB740ZHU)

description:
https://www.encodeproject.org/experiments/ENCSR388DDH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CDK7 tag and IAA treated
experiment encode accession: ENCSR388DDH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB740ZHU
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS219YEV at ENCODE; https://www.encodeproject.org/ENCBS219YEV/


title: ChIA-PET from PC-3 (ENCLB482TOE)

description:
https://www.encodeproject.org/experiments/ENCSR567RHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in PC-3
experiment encode accession: ENCSR567RHZ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB482TOE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: male

value: grade IV, adenocarcinoma

value: 62 year

value: Charles Lee

value: ATCC

value: ENCBS042UWP at ENCODE; https://www.encodeproject.org/ENCBS042UWP/


title: ChIA-PET from HCT116 (ENCLB153PKR)

description:
https://www.encodeproject.org/experiments/ENCSR388DDH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, CDK7 tag and IAA treated
experiment encode accession: ENCSR388DDH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-03
lab: Charles Lee
library encode accession: ENCLB153PKR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: not applicable

value: adult

value: ENCBS540IRN at ENCODE; https://www.encodeproject.org/ENCBS540IRN/


title: ChIA-PET from mammary epithelial cell (ENCLB623ZAG)

description:
https://www.encodeproject.org/experiments/ENCSR819BBB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HMEC
experiment encode accession: ENCSR819BBB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB623ZAG
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens female adult (19 years) mammary epithelial primary cell

value: CTCF

value: mammary epithelial cell

value: primary cell

value: female

value: 19 year

value: Lonza

value: ENCBS525MJK at ENCODE; https://www.encodeproject.org/ENCBS525MJK/


title: ChIA-PET from HCT116 (ENCLB680YVZ)

description:
https://www.encodeproject.org/experiments/ENCSR830FZR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, SUPT16H tag and IAA treated
experiment encode accession: ENCSR830FZR
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB680YVZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS560COY at ENCODE; https://www.encodeproject.org/ENCBS560COY/


title: ChIA-PET from HCT116 (ENCLB001SKN)

description:
https://www.encodeproject.org/experiments/ENCSR353XNY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, RAD21 tag and IAA untreated, control
experiment encode accession: ENCSR353XNY
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB001SKN
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: not applicable

value: male

value: ENCBS502JWV at ENCODE; https://www.encodeproject.org/ENCBS502JWV/


title: ChIA-PET from HCT116 (ENCLB725VYR)

description:
https://www.encodeproject.org/experiments/ENCSR356GHP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, CTCF tag and IAA treated
experiment encode accession: ENCSR356GHP
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB725VYR
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: CTCF

value: adult

value: ENCBS135CKE at ENCODE; https://www.encodeproject.org/ENCBS135CKE/


title: ChIA-PET from Panc1 (ENCLB817GBZ)

description:
https://www.encodeproject.org/experiments/ENCSR145PYF/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in Panc1
experiment encode accession: ENCSR145PYF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB817GBZ
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens Panc1 cell line

value: pancreatic carcinoma

value: 56 year

value: Charles Lee

value: ATCC

value: ENCBS076COS at ENCODE; https://www.encodeproject.org/ENCBS076COS/


title: ChIA-PET from WTC11 (ENCLB445EBE)

description:
https://www.encodeproject.org/experiments/ENCSR353ASS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in WTC11_clone6
experiment encode accession: ENCSR353ASS
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB445EBE
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR

value: cell line

value: 30 year

value: Coriell

value: ENCBS113MUR at ENCODE; https://www.encodeproject.org/ENCBS113MUR/


title: ChIA-PET from HCT116 (ENCLB921FFB)

description:
https://www.encodeproject.org/experiments/ENCSR553HMH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, MED14 tag and IAA treated
experiment encode accession: ENCSR553HMH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB921FFB
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS062SRG at ENCODE; https://www.encodeproject.org/ENCBS062SRG/


title: ChIA-PET from HCT116 (ENCLB629BHO)

description:
https://www.encodeproject.org/experiments/ENCSR557OAJ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control
experiment encode accession: ENCSR557OAJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB629BHO
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: CTCF

value: not applicable

value: male

value: adult

value: ENCBS619KCC at ENCODE; https://www.encodeproject.org/ENCBS619KCC/


title: ChIA-PET from HCT116 (ENCLB000KYC)

description:
https://www.encodeproject.org/experiments/ENCSR557OAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SMARCA5 tag and IAA untreated, control
experiment encode accession: ENCSR557OAJ
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB000KYC
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS892FTF at ENCODE; https://www.encodeproject.org/ENCBS892FTF/


title: ChIA-PET from HCT116 (ENCLB154CUA)

description:
https://www.encodeproject.org/experiments/ENCSR553HMH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNAPII ChIA-PET in HCT116, MED14 tag and IAA treated
experiment encode accession: ENCSR553HMH
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-02-15
lab: Charles Lee
library encode accession: ENCLB154CUA
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: ENCBS974TVC at ENCODE; https://www.encodeproject.org/ENCBS974TVC/


title: ChIA-PET from WTC11 (ENCLB745IPL)

description:
https://www.encodeproject.org/experiments/ENCSR779QAB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIA-PET in WTC11_clone28
experiment encode accession: ENCSR779QAB
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2021-09-09
lab: Charles Lee
library encode accession: ENCLB745IPL
fragmentation methods: sonication (Branson Sonifier 250)
size range: 350-600

value: cell line

value: Charles Lee

value: ENCBS019CAD at ENCODE; https://www.encodeproject.org/ENCBS019CAD/


title: ChIA-PET from A673 (ENCLB582HLK)

description:
https://www.encodeproject.org/experiments/ENCSR549TMF/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in A673
experiment encode accession: ENCSR549TMF
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-05-30
lab: Charles Lee
library encode accession: ENCLB582HLK
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

source_name: Homo sapiens A673 cell line

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS487VGN at ENCODE; https://www.encodeproject.org/ENCBS487VGN/


title: ChIA-PET from HCT116 (ENCLB468SZS)

description:
https://www.encodeproject.org/experiments/ENCSR326KGW/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIA-PET in HCT116, SUPT16H tag and IAA treated
experiment encode accession: ENCSR326KGW
assay title: ChIA-PET
assembly: GRCh38
encode release date: 2022-06-27
lab: Charles Lee
library encode accession: ENCLB468SZS
fragmentation methods: sonication (Branson Sonifier 250)
size range: 300-600

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS600VSU at ENCODE; https://www.encodeproject.org/ENCBS600VSU/