title: Yap, ChIP, Yap-activated tumor, 2

data_processing:
For ChIP-Seq, the filtered single-end reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with default parameters. ChIP-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Assembly: mm10
Supplementary files format and content: The .bed files contain ChIP-Seq peak summits generated by MACS2. The .bw files contain normalized genome-wide ChIP-Seq signal.

extract_protocol:
Gastric corpus is dissected and epithelial cells are isolated using EDTA. Isolated epithelial cells were fixed and frozen by liquid nitrogen. Frozen tissues were thawed, lysed and sonicated to obtain genomic DNA, on which ChIP is performed. Immunoprecipitated DNA are eluted and purified using phenol/chloroform.
Library is prepared using ThruPLEX DNA-Seq kit (Rubicon Genomics, R400428) according to manufacturer's protocol
ChIP-Seq (50bp PE)

tag: chip antibody

value: Yap (Cell Signaling Technology, 14074, LOT 4)


title: 0.5% DMSO rep7 [S49]

status: Public on Nov 07 2023

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: transcriptomic

data_processing:
*library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Normalization was performed with DESeq2 R package v1.30.1
Log2 fold change shrinkage was performed using the ashr method.
Potential false positive DEGs were removed using filtering criteria defined in the Omics Data Analysis Frameworks for Regulatory application
Assembly: Genome_build: Biospyder S1500 Gene Set
Supplementary files format and content: Comma-delimited text file with genes by counts matrix

molecule: total RNA

organism: Homo sapiens

source_name: KGN

growth_protocol: KGN cells were maintained in DMEM/F12 medium supplemented with 10% charcoal-stripped fetal bovine serun (FBS) and 0.5% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: No RNA extraction was done. Cells were directly lysed with 1X TempO-Seq lysis buffer and TempO-Seq libraries were constructed directly from cell lysates according to the TempO-Seq Assay User Guide (Version 2.1)

treatment_protocol: Cells were exposed for 48 h to vehicle control (0.5% dimethyl sulfoxide; DMSO) or various concentrations of test chemicals (ranging from 0.1 to 50 μM).

tag: cell line

value: KGN

tag: cell type

value: Human ovarian granulosa cells

tag: treatment

value: 0.5% DMSO


title: BPDP 0.32uM rep1 [S118]

value: BPDP 0.32uM


title: RNASeq, Normal Stomach, rep2

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and the raw read count matrix was used for differential gene expression analysis by DESeq2.
Assembly: mm10
Supplementary files format and content: The .txt file contains raw read counts of all RNASeq samples.

organism: Mus musculus

source_name: Gastric corpus epithelial cells

growth_protocol: Cells were isolated without culturing

extract_protocol:
Gastric corpus is dissected and epithelial cells are isolated using EDTA. Total RNA was then extracted using RNeasy mini kit (QIAGEN, 74104).
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.
RNA-Seq (50bp PE)

treatment_protocol: Mice were administered 2mg tamoxifen intraperitoneally for 5 consecutive days, and were subsequently fed DOX food for 14 days directly before endpoint

tag: disease state

value: Normal Stomach

tag: tissue

value: Gastric corpus epithelium

tag: genotype

value: WT


title: Yap, ChIP, Normal Stomach, 1

library_source: genomic

molecule: genomic DNA


title: 0.5% DMSO rep4 [S161]


title: Yap, ChIP, Normal Stomach, 2


title: H3K27ac, ChIP, Yap-activated tumor

value: Yap-activated gastric cancer


title: Yap, ChIP, Yap-activated tumor, 1


title: 0.5% DMSO rep6 [S25]


title: 0.5% DMSO rep3 [S151]


title: 0.5% DMSO rep5 [S177]


title: 0.5% DMSO rep9 [S73]


title: 0.5% DMSO rep2 [S110]


title: H3K27ac, ChIP, Normal Stomach


title: 0.5% DMSO rep1 [S108]


title: 0.5% DMSO rep8 [S55]


title: Breast tumors, 92-21325

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

country: USA

institute: NCI

data_processing:
We used the R/Bioconductor package edgeR to generate CPM_TMM normalized counts. Briefly, starting with the data in the raw count file, any gene that did not have a CPM value of 0.5 in two or more samples was filtered out. calcNormFactors was then used to calculate the normalization factors for the remaining genes using the TMM normalization method. CPM was then calculated while using the TMM normalization factors for these remaining genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes CPM_TMM normalized values for each Sample

source_name: frozen breast tumors

extract_protocol:
RNA isolation was done using TRIzol method . Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina HiSeq machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: race

value: AA

tag: er status

value: POS

tag: diabetes info

value: Yes

tag: diabetes type

value: II

tag: disease grade

value: breast tumors


title: Breast tumors, 93-22307

value: No


title: HEK293,WT,H1.5 IP

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

description: H1.5_WTcell line_IP

data_processing:
Read quality was evaluated using FASTQC
The adaptor sequences were trimmed using Cutadapt v2.3
Processed reads were aligned to the University of California, Santa Cruz (UCSC) Genome Sequencing Consortium (https://genome.ucsc.edu) reference genome (human genome assembly 19 (hg19)) using the Bowtie2 program v2.4.1
PCR duplicated reads and low mapping quality reads were filtered out using samtools v.1.10 rmdup and samtools –q 30 functions, respectively
Sam-formatted files were converted to Bam with samtools and sorted
H1 coverage signal (subtraction of IP and input) were calculated for each sample, and samples were normalized by RPKM (reads per kilobase per million) using deepTools v3.5.1
Assembly: hg19
Supplementary files format and content: bigWig,subtraction of IP and input

extract_protocol:
Cells were fixed using 1% formaldehyde, and then were harvested, and sonicated using a Vibra-Cell VCX600.
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Human embryonic kidney

value: Abcam 18208

value: WT,H1.5 IP


title: Breast tumors, 91-20967


title: HEK293,WT, Input for H1.5 IP experiment

description: Input_for_H1.5_WTcell line_IP

value: no treatment


title: HEK293,WT, Input for H1.2 IP experiment

description: Input_for_H1.2_WTcell line_IP


title: HEK293,WT,H1.2 IP

description: H1.2_WTcell line_IP

value: Abcam 4086

value: WT,H1.2 IP


title: Breast tumors, 87-20874


title: Breast tumors, 88-20878

value: NEG


title: HEK293,WT,H1.X IP

description: H1.X_WTcell line_IP

value: Abcam 31972

value: WT,H1.X IP


title: 22Rv1_RNA_ENZ3w_DHT_rep3

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.

molecule: polyA RNA

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: dihydrotestosterone

tag: hormone concentration

value: 1 nM


title: HEK293,WT, Input for H1.X IP experiment

description: Input_for_H1.X_WTcell line_IP


title: Breast tumors, 96-26666

value: AA

value: POS

value: Yes


title: Breast tumors, 85-20736

value: I

value: breast tumors


title: Breast tumors, 83-20695

value: No


title: 22Rv1_RNA_ENZ3w_DHT_rep2


title: Breast tumors, 86-20805

value: II


title: Breast tumors, 84-20698


title: 22Rv1_RNA_ENZ3w_DHT_rep1


title: Breast tumors, 78-20170


title: Breast tumors, 72-19943


title: Breast tumors, 76-20040

value: CC


title: Breast tumors, 75-19999


title: Breast tumors, 74-19989


title: 22Rv1_RNA_DHT_rep3


title: Breast tumors, 73-19952


title: 22Rv1_RNA_DHT_rep2


title: Breast tumors, 77-20069


title: Breast tumors, 71-19842


title: 22Rv1_RNA_DHT_rep1


title: Breast tumors, 70-19826


title: Breast tumors, 89-20925


title: Breast tumors, 68-19743


title: Breast tumors, 65-19576


title: Breast tumors, 61-19526


title: Breast tumors, 59-19436


title: VCaP_RNA_ENZ3w_DHT_rep3

source_name: VCaP

value: Vertebral Cancer of the Prostate

value: VCaP


title: VCaP_RNA_ENZ3w_DHT_rep2


title: Breast tumors, 57-19311

value: NEG


title: VCaP_RNA_ENZ3w_DHT_rep1


title: Breast tumors, 56-19297


title: VCaP_RNA_ENZ3w_EtOH_rep5

value: EtOH vehicle


title: VCaP_RNA_ENZ3w_EtOH_rep4


title: Breast tumors, 55-19277


title: Breast tumors, 54-19274


title: VCaP_RNA_DHT_rep3


title: VCaP_RNA_DHT_rep2


title: Breast tumors, 47-18669


title: Breast tumors, 51-19065


title: VCaP_RNA_DHT_rep1


title: VCaP_RNA_EtOH_rep5


title: Breast tumors, 45-18243


title: VCaP_RNA_EtOH_rep4


title: Breast tumors, 50-19048


title: Breast tumors, 66-19703


title: Breast tumors, 43-17952


title: Breast tumors, 41-17624


title: Breast tumors, 46-18395


title: Breast tumors, 64-19566


title: Breast tumors, 40-17351


title: Breast tumors, 62-19554


title: VCaP_RNA_ENZ2w_Dex_rep3

value: 2 weeks

value: dexamethasone


title: Breast tumors, 39-17268


title: VCaP_RNA_ENZ2w_Dex_rep2


title: Breast tumors, 36-16666


title: VCaP_RNA_ENZ2w_Dex_rep1


title: Breast tumors, 35-16404


title: Breast tumors, 49-18996


title: Breast tumors, 48-18973


title: Breast tumors, 34-16301


title: VCaP_RNA_ENZ2w_EtOH_rep2


title: VCaP_RNA_ENZ2w_EtOH_rep1


title: Breast tumors, 25-15047


title: Breast tumors, 29-15800


title: Breast tumors, 24-15046


title: Breast tumors, 28-15703


title: Breast tumors, 27-15425


title: Breast tumors, 33-16087


title: Breast tumors, 32-16086


title: Breast tumors, 38-17014


title: Breast tumors, 23-13583


title: Breast tumors, 20-12424


title: 22Rv1_H3K27ac_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

value: 3 weeks

tag: sirna treatment

value: H3K27ac (Active Motif, 39133)


title: Breast tumors, 21-12645


title: 22Rv1_H3K27ac_ENZ3w_Dex_rep1

tag: chip antibody


title: 22Rv1_input_Dex_rep1

tag: cell line


title: Breast tumors, 37-16718


title: 22Rv1_input_ENZ3w_Dex_rep1

tag: cell type


title: VCaP_RNA_ENZ2w_EtOH_rep3


title: 22Rv1_H3K27ac_ENZ3w_EtOH_rep2


title: 22Rv1_H3K27ac_ENZ3w_EtOH_rep1


title: Breast tumors, 18-9791

value: AA


title: 22Rv1_H3K27ac_Dex_rep2


title: SCEACono2 cell line, rep3

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

data_processing:
Raw sequencing data includnig adapter sequences or low-quality sequences was filtered using SOAPnuke software with the following parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim".
The filtered sequenced reads were aligned to the human reference genome hg38 using STAR v2.7.9a with Gencode v38 annotations.
Read count data for each gene was calculated usng RSEM v1.3.1.
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing read count data of each gene. Gene names are represented as Ensembl Gene IDs.

extract_protocol:
The extraction of RNA from SCEACono2, HSC4, and SCC9 cell lines were performed using a NucleoSpinTM RNA plus kit (MachereyHagel, Düren, Germany).
Library preparation was performed using DNBSEQ Eukaryotic Strand-specific mRNA library kit.

value: external auditory canal squamous cell carcinoma


title: Breast tumors, 16-9763


title: Breast tumors, 30-15842

value: POS

value: Yes


title: 22Rv1_H3K27ac_Dex_rep1


title: SCEACono2 cell line, rep1


title: 22Rv1_H3K27ac_EtOH_rep2


title: Breast tumors, 15-9525

value: I

value: breast tumors


title: 22Rv1_FOXA1_ENZ3w_Dex_rep2

value: FOXA1 (Abcam, ab23738)


title: SCC9 cell line, rep3

value: head and neck squamous cell carcinoma


title: 22Rv1_FOXA1_ENZ3w_Dex_rep1


title: 22Rv1_H3K27ac_EtOH_rep1


title: 22Rv1_FOXA1_ENZ3w_EtOH_rep1


title: 22Rv1_FOXA1_ENZ3w_EtOH_rep2


title: 22Rv1_FOXA1_Dex_rep2


title: Breast tumors, 13-9255

value: CC

value: No


title: HSC4 cell line, rep2


title: 22Rv1_FOXA1_Dex_rep1


title: HSC4 cell line, rep1


title: Breast tumors, 10-8254

value: NEG

value: II


title: Breast tumors, 12-9246


title: 22Rv1_FOXA1_DHT_rep2

value: dihydrotestosterone

value: 1 nM


title: 22Rv1_FOXA1_EtOH_rep2

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: EtOH vehicle


title: SCEACono2 cell line, rep2


title: MDAMB468_HG_H4

data_processing:
We used the R/Bioconductor package edgeR to generate CPM_TMM normalized counts. Briefly, starting with the data in the raw count file, any gene that did not have a CPM value of 0.5 in two or more samples was filtered out. calcNormFactors was then used to calculate the normalization factors for the remaining genes using the TMM normalization method. CPM was then calculated while using the TMM normalization factors for these remaining genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM_TMM normalized values for each Sample

source_name: Breast cancer cell line

growth_protocol: Breast cancer cells (MDA-MB-231 and MDA-MB-468) were cultured under low (5mM) and high glucose (25mM)

extract_protocol:
RNA isolation was done using RNeasy Plus Mini Kits from Qiagen. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina HiSeq machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For each experimental group there were four replicates.  In brief, 5×105cells in a T25 flask were treated with low or high glucose for 48 hrs before RNA was isolated.

value: Breast cancer cell line

value: ER negative

tag: treatment

value: high glucose


title: Breast tumors, 7-8126


title: 22Rv1_FOXA1_DHT_rep1


title: MDAMB468_HG_H3


title: 22Rv1_FOXA1_EtOH_rep1


title: Breast tumors, 6-7553

value: AA


title: MDAMB468_HG_H2


title: Breast tumors, 5-6335

value: POS

value: Yes


title: Breast tumors, 14-9520

value: breast tumors


title: Breast tumors, 4-6076


title: SCC9 cell line, rep1


title: MDAMB468_LG_G4

value: low glucose


title: Breast tumors, 3-4663


title: MDAMB468_LG_G3


title: 22Rv1_AR_ENZ3w_1nM-DHT_rep2

value: 3 weeks

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


title: 22Rv1_AR_ENZ3w_1nM-DHT_rep1


title: Breast tumors, 8-8142

value: CC

value: No


title: MDAMB468_LG_G2


title: Breast tumors, 1-3275

value: NEG


title: 22Rv1_AR_100nM-DHT_rep2

value: dihydrotestosterone


title: MDAMB231_HG_B4


title: HCC1500, HG4

source_name: breast cancer cell lines

growth_protocol: Breast cancer cells (MDA-MB-175, ZR7530 and HCC1500) were cultured under low (5mM) and high glucose (25mM)

value: breast cancer cell

value: ER positive


title: MDAMB468_LG_G1


title: HCC1500, HG3


title: 22Rv1_AR_100nM-DHT_rep1

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line


title: 22Rv1_AR_1nM-DHT_rep2

value: 1 nM


title: MDAMB231_HG_B2

value: Breast cancer cell line

value: ER negative


title: 22Rv1_AR_1nM-DHT_rep1


title: MDAMB468_HG_H1

value: high glucose


title: MDAMB231_HG_B3


title: HCC1500, HG1


title: 22Rv1_AR_EtOH_rep2

value: EtOH vehicle


title: MDAMB231_HG_B1


title: MDAMB231_LG_A4


title: HCC1500, LG3


title: HCC1500, LG4


title: Breast tumors, 2-3279

value: AA

value: Yes

value: II


title: VCaP_input_ENZ3w_siFOXA1_Dex_rep1

value: Vertebral Cancer of the Prostate

value: VCaP

value: 3 weeks

value: ON-TARGETplus Human FOXA1 siRNA (Dharmacon, L-010319-00-0050)

value: dexamethasone


title: 22Rv1_GR_EtOH_rep1

value: GR (Cell Signaling, 12041)


title: MDAMB231_LG_A3

value: low glucose


title: MDAMB231_LG_A2


title: VCaP_input_ENZ3w_siNON_Dex_rep1

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


title: 22Rv1_AR_EtOH_rep1

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

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


title: HCC1500, HG2

value: breast cancer cell

value: ER positive


title: HCC1500, LG1


title: VCaP_input_siFOXA1_Dex_rep1


title: ZR7530, HG4

value: high glucose


title: ZR7530, HG3


title: VCaP_TLE3_ENZ3w_siFOXA1_Dex_rep2

value: TLE3 (Abcam, ab94972)


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO,H1.4KO

data_processing:
Cutadapt (v3.4, https://doi.org/10.14806/ej.17.1.200) was used to trim adapter sequences from paired-end reads and to remove low-quality bases and reads shorter than 20 nt with -m20 -q 30,30.
Processed reads were first aligned to the Drosophila genome assembly dm3 using Bowtie2 v1.2.3 with --trim5 6 -p 20 --score-min C,-13,0.
To perform spike-in normalization in all samples, we counted the primary aligned mapped reads to the dm3 genome assembly using samtools view (v1.12) with the -c and -F260 options.
Paired reads that did not align to dm3, were aligned to the hg19 genome assembly using STAR v2.7.10b with the following parameters: --outMultimapperOrder Random --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outSAMtype BAM SortedByCoordinate --alignSJoverhangMin 8 –outFileNamePrefix --outFilterMismatchNmax 5.
To analyze the RNAPII elongation rate, we isolated the active elongation sites from paired-end bam files using bedtools genomecov (v2.29.1) with the following specifications: 5′ positions (-5), single-base resolution (-d), and strand-specificity (-strand).
Output files were converted to bedgraph format using ‘in-house’ bash script, and then to bigwig format using the UCSC tool bedGraphToBigWig (http://hgdownload.soe.ucsc.edu/admin/exe/).
Bwtool matrix v1.0 was used to cast the PRO-seq-read density on gene bodies (protein-coding) including TSSs, exon-intron junctions (excluding first and last exons), and TESs. Correct orientation was achieved by casting the forward and reverse bigwig files on coordinates of the opposite strands.
Assembly: hg19
Supplementary files format and content: big wig data of the RNA polymerase II active elongation sites in a single-base resulution

extract_protocol:
For library generation, 1 x 106 cells were spiked with 5% permeabilizedDrosophilaS2 cells for data normalization and used as input for PRO-seq. Nascent RNA was labeled through a biotin-NTP run-on as follows: Permeabilized cells were added to an equal volume of a 2X run-on reaction mix. and incubated at 30 °C for 5 min. RNA was isolated using TRIzol Reagent. Isolated RNA was fragmented by base hydrolysis with 0.25 N NaOH for 9 min on ice, followed by neutralization with one volume of 1 M Tris-HCl, pH 6.8. To select for nascent RNA, 48 μL of washed Streptavidin M-280 magnetic beads in binding buffer were added to the fragmented RNA, and samples were rotated at room temperature for 20 min. The Streptavidin M-280 magnetic beads were washed twice in each of the following three buffers: high salt buffer , binding buffer, and low salt buffer. Beads were resuspended in TRIzol LS Reagent  and heated at 65 °C for 5 min, cooled to room temperature, and heated at 65 °C for 5 min again to elute the RNA from the beads.
Nascent RNA was resuspended in 10 µM of the VRA3 3′ end adapter in T4 Ligase buffer and was 3′ end ligated with T4 RNA ligase I for 2 h at room temperature. The sample was enriched for ligated nascent RNAs by binding to Streptavidin M-280 magnetic beads as described above. The beads were washed twice in high, binding, and low salt buffers, then once in 1X ThermoPol Buffer. To prepare the nascent RNA for 5′ end adapter ligation, the 5′ ends of the RNA were decapped using RppH suspended in RppH buffer, then 5′ end was recapped with RNA 5′ pyrophosphohydrolase at 37 °C for 1 h in T4 ligase buffer. Beads were then washed in high salt buffer, low salt buffer, and 1X T4 PNK Reaction Buffer. Samples were treated with T4Poly-nucleotideKinase for 1 h at 37 °C, and the reverse 5′ RNA adapter VRA5 was ligated to the RNA by incubation with T4 RNA ligase I for 2 h at room temperature. Following the 5′ end ligation, beads were washed twice in high, binding, and low salt buffers, then once in 0.25X FSS Buffer . Reverse transcription was performed using Superscript IV Reverse Transcriptase with 25 pmol of the Illumina TRU-seqRP1Primer. The RT product was eluted from the beads by heating the samples twice at 95°C for 30 s. All libraries were amplified by 12 cycles of PCR with 12.5 pmol of Illumina TRU-seq RPI-index primers, excess RP1 primer, and Q5 DNA Polymerase. The samples were sequenced using a HiSeq instrument with a mid-output 150bp cycle run.
Six nucleotide Barcode specific primers were used in order to isolate the results from each of the specific samples (WT, 1-KO, 2-KO, 4-KO and 5-KO).

value: Human embryonic kidney


title: VCaP_input_siNON_Dex_rep1


title: VCaP_TLE3_ENZ3w_siFOXA1_Dex_rep1


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO


title: ZR7530, HG1


title: ZR7530, LG4


title: ZR7530, HG2


title: HEK293,H1.2KO

value: H1.2 knockout


title: VCaP_TLE3_ENZ3w_siFOXA1_EtOH_rep1

value: EtOH vehicle


title: HEK293,H1.2KO,H1.3KO

value: (H1.2 and H1.3) knockout


title: ZR7530, LG3


title: VCaP_TLE3_ENZ3w_siFOXA1_EtOH_rep2

value: Vertebral Cancer of the Prostate

value: VCaP


title: HEK293,WT

value: WT


title: HEK293,KO,H1.X IP

description: H1.X_KOcell line_IP

value: Abcam 31972


title: ZR7530, LG2


title: VCaP_TLE3_ENZ3w_siNON_Dex_rep2

value: 3 weeks

value: dexamethasone


title: VCaP_TLE3_ENZ3w_siNON_Dex_rep1

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


title: HEK293,KO, Input for H1.X IP experiment

description: Input_for_H1.X_KOcell line_IP


title: HCC1500, LG2

value: low glucose


title: HEK293,KO,H1.5-HA IP

value: Abcam 9110


title: MDA-MB-175, HG4

value: breast cancer cell


title: MDAMB231_LG_A1

value: Breast cancer cell line

value: ER negative


title: MDA-MB-175, HG3

value: ER positive

value: high glucose


title: HEK293, KO,Input for H1.5-HA IP experiment

value: Human embryonic kidney


title: VCaP_TLE3_siFOXA1_Dex_rep2

value: ON-TARGETplus Human FOXA1 siRNA (Dharmacon, L-010319-00-0050)

value: TLE3 (Abcam, ab94972)


title: VCaP_TLE3_ENZ3w_siNON_EtOH_rep1

value: Vertebral Cancer of the Prostate

value: EtOH vehicle


title: MDA-MB-175, HG2


title: HEK293,KO,H1.4-HA IP


title: VCaP_TLE3_siFOXA1_Dex_rep1

value: VCaP


title: MDA-MB-175, HG1


title: HEK293,KO, Input for H1.4-HA IP experiment


title: VCaP_TLE3_siFOXA1_EtOH_rep2


title: HEK293,KO,H1.3-HA IP


title: MDA-MB-175, LG4


title: VCaP_TLE3_siNON_Dex_rep2


title: HEK293,KO, Input for H1.3-HA IP experiment


title: MDA-MB-175, LG3


title: MDA-MB-175, LG2


title: HEK293,KO,H1.2-HA IP


title: VCaP_TLE3_siNON_Dex_rep1


title: HEK293, KO, Input for H1.2-HA IP experiment


title: ZR7530, LG1


title: VCaP_TLE3_ENZ3w_siNON_EtOH_rep2


title: MDA-MB-175, LG1


title: HEK293,KO,H1.0-HA IP


title: VCaP_TLE3_siNON_EtOH_rep2


title: HEK293, KO, Input for H1.0-HA IP experiment


title: VCaP_TLE3_siNON_EtOH_rep1


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO,H1.4KO,rep2

data_processing:
The quality of sequenced reads was evaluated using the FASTQC tool
Sequenced reads were aligned to the University of California, Santa Cruz (UCSC) Genome Sequencing Consortium (https://genome.ucsc.edu) reference genome (human genome assembly 19 (hg19)) using TopHat v2.1.1 66 while adding gene annotations (refgene) table downloaded from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables) in GTF format in addition to the default parameters
Sequenced reads were also aligned to the UCSC Genome Sequencing Consortium reference genome (human hg19) using the vast-tools v2.5.1 67 align command with default options.
Quality metrics from the alignment of samples were obtained from the vast-tools and expression table, normalized by quantile normalization, cRPKM (corrected for mapability, Reads per kbp, and Million mapped reads) values obtained for each sample.
Assembly: hg19
Supplementary files format and content: tab-delimited files including cRPKM values for each Sample , no quantile normalization

extract_protocol: RNA was extracted by adding 100µl BCP (1-bromo 3-chloro propane) and vigorous shaking (20s) followed by a 15minute 12,000g centrifugation at 4ºC. The top transparent liquid phase containing the RNA was transferred to a new tube, 0.5ml isopropanol was added and the sample was centrifuged as before for 8minutes at 4ºC. The RNA pellet was washed with 1ml 70% ethanol, re-suspended in Rnase free DDW and treated with Dnase (ThermoFisher), to eliminate residual DNA. A sample of 1500-2000ng of total RNA, was used to generate cDNA by oligo(dT) primers and SuperScript III reverse transcriptase. RNA libraries were prepared for sequencing using standard Illumina protocols.


title: VCaP_GR_ENZ3w_siFOXA1_Dex_rep2

value: GR (Cell Signaling, 12041)


title: Soluble MNase, SDC-inositol, Replicate 2

city: Evanston

first: Jason

last: Brickner

state: IL

address: Hogan 1-500, 2205 Tech Drive

institute: Northwestern University

data_processing:
Trimmomatic 0.39 ILLUMINACLIP:2:30:10 LEADING:30 TRAILING:30 MINLEN:25
Bowtie2
samtools view -@ 7 -b -u -q 10
ChEC-seq2 Peak Finder
Assembly: R64 sacCer3
Supplementary files format and content: bigwig files represent CPM-normalized coverage from the 5' base of each read (MNase cleavage site).  Telomeres and the rDNA locus were masked due to repetitive sequence and inability to accurately map reads.
Supplementary files format and content: csv file with peak locations identified using local maxima
Supplementary files format and content: csv file with peaks locations that remain after comparison to soluble MNase
Supplementary files format and content: csv file with peak locations that remain after comparison to Soluble MNase signal and selection for doublets
Library strategy: ChEC-seq2

organism: Saccharomyces cerevisiae

extract_protocol:
genomic DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1), pH 7.5
ChEC-seq2 method, which produces Illumina-compatible libraries with Nextera indexes

tag: strain

value: MATa leu2delta0 ura3delta0 met15delta0 SolubleMNase:HIS3


title: Soluble MNase, SDC-inositol, Replicate 1


title: Soluble MNase, SDC-inositol, Replicate 3


title: VCaP_GR_ENZ3w_siFOXA1_Dex_rep1

value: 3 weeks

value: dexamethasone


title: HEK293,H1.2KO,H1.3KO,H1.2Rescue,H1.3Rescue

value: (H1.2 and H1.3)knockout and (H1.2,H1.3) cDNA administration


title: VCaP_GR_ENZ3w_siNON_Dex_rep2

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


title: Soluble MNase, YPD, Replicate 3


title: VCaP_TLE3_siFOXA1_EtOH_rep1


title: HEK293,H1.2KO,H1.2Rescue

value: H1.2 knockout and H1.2 cDNA administration


title: Soluble MNase, YPD, Replicate 2


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO,H1.4KO,rep1


title: Soluble MNase, YPD, Replicate 1


title: VCaP_GR_siFOXA1_Dex_rep2


title: VCaP_GR_siFOXA1_Dex_rep1


title: HEK293,H1.2KO,H1.3KO

value: (H1.2 and H1.3)knockout


title: Rap1-MNase, YPD, Replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 Rap1-3xFLAG-MNase:KanMX


title: Rap1-MNase, YPD, Replicate 2


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO


title: VCaP_GR_siNON_Dex_rep2


title: HEK293,H1.2KO

extract_protocol: RNA was extracted by adding 100µl BCP (1-bromo 3-chloro propane) and vigorous shaking (20s) followed by a 15minute 12,000g centrifugation at 4ºC. The top transparent liquid phase containing the RNA was transferred to a new tube, 0.5ml isopropanol was added and the sample was centrifuged as before for 8minutes at 4ºC. The RNA pellet was washed with 1ml 70% ethanol, re-suspended in Rnase free DDW and treated with Dnase (ThermoFisher), to eliminate residual DNA. A sample of 1500-2000ng of total RNA, was used to generate cDNA by oligo(dT) primers and SuperScript III reverse transcriptase. RNA libraries were prepared for sequencing using standard Illumina protocols

value: H1.2 knockout


title: VCaP_GR_siNON_Dex_rep1


title: Prp20-MNase, SDC-histidine, Replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 Prp20-3xFLAG-MNase:KanMX


title: VCaP_input_ENZ3w_Dex_rep1


title: Rap1-MNase, YPD, Replicate 1


title: HEK293,WT

value: Human embryonic kidney

value: WT


title: ATACseq_SKNMC_shCHD4#2_48h_rep3

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Illumina adaptors of sequencing reads were trimmed off using trimmomatic v0.36 and quality control was performed with FastQC v0.11.7.
The paired-end reads were aligned separately to the human (GRCh38) and Drosophila  (dm6) reference genomes using the BWA mem algorithm and Samtools v1.9.
Mapping quality was assessed by QualiMap v2.2.1 and quality control of ATACseq was performed using ATACseqQC.
GRCh38-aligned tags were normalized using correction factors generated from dm6-aligned tags in each sample and stored in bigWig files using the bamCoverage function from deepTools v3.2.1.
Peak calling was performed using HHMRATAC and reproducible peaks amongst all replicates were identified using ChIP-R v1.1.0.
Assembly: GRCh38 and dm6
Supplementary files format and content: bigwig normalized to drosophila counts
Supplementary files format and content: bed files with reproducible peaks per sample identified in all three biological replicates

source_name: SKNMC

growth_protocol: SKNMC cells were cultured in RPMI (Roswell Park Memorial Institute, Sigma-Aldrich) supplemented with 10% fetal bovine serum (#F7524, Sigma-Aldrich), 2 mM L-glutamine (Bioconcept AG) and 100 U/ml penicillin/streptomycin (Thermo Fisher Scientific AG), in 5% CO2 at 37°C.

extract_protocol:
Insect cells were spiked-in: for each sample, 100,000 SKNMC cells were collected and mixed with 100 Drosophila Schneider 2 (S2) cells.
ATACseq assays were performed using the ATAC-seq kit (#53150, Active Motif) according with manufacturer’s instructions. Samples were paired-end sequenced on an Illumina HiSeq2500 at the Functional Genomics Center Zurich.

treatment_protocol: SKNMC shScramble, shCHD4#1 and shCHD4#2 cells were cultured in the presence of 100ng/ml doxycycline (Sigma-Aldrich) to induce shRNA expression. For each assay, three biological replicates were performed.

value: SKNMC

value: Ewing Sarcoma

value: CHD4 knockdown

tag: time


title: ATACseq_SKNMC_shCHD4#2_48h_rep2

tag: genotype


title: Prp20-MNase, SDC-histidine, Replicate 2


title: HBV_1

city: Wuhan

first: Shuang

last: Ding

address: 262 Jinlong Street

country: China

institute: Wuhan Institute of Virology

data_processing:
Raw reads were first processed with fastp (version 0.23.0) to remove the residual adaptor sequences and the reads with low quality scores.
Then the clean reads were mapped to the reference genome and the duplicated reads were removed using Bismark (version 0.22.3).
The depth and coverage on chromosomes were calculated with mosdepth (version 0.3.1) and RSeQC(version 4.0.0)
The methylation detection along the whole genome were conducted by Bismark which calculates the proportion of methylated reads at every genome site.
Supplementary files format and content: GRCh38
Supplementary files format and content: *.mC.site.anno.xls

source_name: liver

growth_protocol: huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)at 37 ℃ in a 5% CO2 environment

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）. DNA digestion was carried out after RNA extraction by DNaseI. 2 μg total RNAs were used for mRNA enrichment by KAPA mRNA Capture Kit (Roche, KK8441).
The conversion of unmethylated cytosines to thymidines of enriched mRNA was carried out using the EZ RNA Methylation Kit (Zymo Research, Cat. No. R5001) . Sequencing libraries were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Huh7 cells transfected with Poly I:C and HBV 1.1-mer for 18 hours

tag: tissue

value: liver

value: human hepatocellular carcinoma cell

value: polyI:C and HBV 1.1 mer plasmid transfected


title: HBV_3


title: HBV_2


title: Prp20-MNase, SDC-histidine, Replicate 1


title: Vector_3

value: polyI:C and vector transfected


title: VCaP_FOXA1_ENZ3w_Dex_rep2

value: Vertebral Cancer of the Prostate

value: VCaP

value: 3 weeks

value: dexamethasone

value: FOXA1 (Abcam, ab23738)


title: Vector_2


title: ATACseq_SKNMC_shCHD4#2_48h_rep1


title: VCaP_FOXA1_ENZ3w_Dex_rep1


title: Prp20-MNase, SDC, Replicate 3


title: VCaP_GR_ENZ3w_siNON_Dex_rep1

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

value: GR (Cell Signaling, 12041)


title: ATACseq_SKNMC_shCHD4#1_48h_rep3


title: VCaP_input_Dex_rep1


title: Prp20-MNase, SDC, Replicate 2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 Prp20-3xFLAG-MNase:KanMX


title: Prp20-MNase, SDC, Replicate 1


title: Vector_1


title: ATACseq_SKNMC_shCHD4#1_48h_rep1


title: VCaP_FOXA1_ENZ3w_EtOH_rep1

value: EtOH vehicle


title: ATACseq_SKNMC_shCHD4#1_48h_rep2


title: multiome-human-cerebellum-donor01

city: Stanford

first: Siavash

last: Moghadami

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

institute: Stanford University

description:
liger_objects.tar
liger_k100_cell_annotation.txt
liger_k150_cell_annotation.txt
liger_k50_cell_annotation.txt
archr_objects.tar

library_source: other

data_processing:
library strategy: scRNA-seq/scATAC-seq
For 10x Multiome data, please see README_multiome.md. For Dip-C data, please see https://github.com/tanlongzhi/dip-c.
Assembly: hg19 and mm10
Supplementary files format and content: For 10x Multiome data, data are in ArchR (https://www.archrproject.com) and LIGER (https://github.com/welch-lab/liger) formats. For Dip-C data, data are in pairs (https://github.com/4dn-dcic/pairix), hic (https://www.aidenlab.org/juicebox), and Dip-C (https://github.com/tanlongzhi/dip-c) formats.

molecule: other

source_name: lateral cerebellum

extract_protocol: Dip-C

value: lateral cerebellum

tag: Sex

value: male


title: multiome-human-cerebellum-donor02


title: Gcn4-MNase, SDC-histidine, Replicate 2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 Gcn4-3xFLAG-MNase:KanMX


title: Gcn4-MNase, SDC-histidine, Replicate 3


title: VCaP_FOXA1_Dex_rep3


title: multiome-human-cerebellum-donor03


title: ATACseq_SKNMC_shScramble_48h_rep2

value: SKNMC

value: Ewing Sarcoma

value: wildtype

value: shScramble


title: Gcn4-MNase, SDC-histidine, Replicate 1


title: multiome-human-cerebellum-donor04

source_name: cerebellum crus 1

value: cerebellum crus 1


title: multiome-human-cerebellum-donor05


title: VCaP_FOXA1_Dex_rep2

value: Vertebral Cancer of the Prostate


title: ATACseq_SKNMC_shScramble_48h_rep1


title: Gcn4-MNase, SDC, Replicate 3


title: VCaP_FOXA1_DHT_rep1

value: VCaP

value: dihydrotestosterone


title: VCaP_FOXA1_EtOH_rep3


title: Gcn4-MNase, SDC, Replicate 1


title: VCaP_FOXA1_ENZ3w_EtOH_rep2

value: 3 weeks


title: multiome-human-cerebellum-donor13


title: Gcn4-MNase, SDC, Replicate 2


title: dipc-human-experiment11-cerebellum

description:
human.contacts_female.pairs.gz.tar.gz
human.contacts_female.seg.gz.tar.gz
human.contacts_male.pairs.gz.tar.gz
human.contacts_male.seg.gz.tar.gz
human.contacts_unisex.hic.tar.gz
human.contacts_unisex.info.tar.gz
human.contacts_unisex.pairs.gz.tar.gz
human.contacts_unisex.seg.gz.tar.gz
human.cpg_b1m.color2.tar.gz
human.x2a.txt.tar.gz

data_processing:
For 10x Multiome data, please see README_multiome.md. For Dip-C data, please see https://github.com/tanlongzhi/dip-c.
Assembly: hg19 and mm10
Supplementary files format and content: For 10x Multiome data, data are in ArchR (https://www.archrproject.com) and LIGER (https://github.com/welch-lab/liger) formats. For Dip-C data, data are in pairs (https://github.com/4dn-dcic/pairix), hic (https://www.aidenlab.org/juicebox), and Dip-C (https://github.com/tanlongzhi/dip-c) formats.

source_name: cerebellum

value: cerebellum


title: WM164 Q61K Input-2

city: Woolloongabba

first: Helmut

last: Schaider

state: Queensland

address: level 7, 37 Kent Street

department: Diamantina Institute

country: Australia

institute: The University Of Queensland

data_processing:
Reads were first trimmed for quality (Phred score >20) and Illumina adapters using fastq-mcf
Reads were then aligned to the human genome GRCh37 (hg19) version using BWA
Alignment were converted to sorted BAM file using SAMtools
Peaks were called using Macs2 (2.1.2) callpeak
ChIP-seq signals were normalized for sequencing depth and effective length using deepTools (2.5.4)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig format: Binary file showing the read coverage normalized to 1x sequencing depth . Sequencing depth is normalized by the effective human genome length (2451960e3).
Supplementary_files_format_and_content: NarrowPeak is BED6+4 format. Columns are the following: Chromosome, Start, End, peak name, Integer score for display calculated as int(-10*log10qvalue),  Fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start.

source_name: cell line

growth_protocol: Cells were maintained in RPMI-1640 medium, supplemented with 5% fetal bovine serum, 2% L-glutamine and 2% Pen/Strep.

extract_protocol:
Chromatin immune precipitation was performed using the Active Motif ChIP-IT® Express Chromatin Immunoprecipitation Kits (53009). WM164 parent, IDTC colonies and dabrafenib resistant cells were fixed using 4% paraformaldehyde for 10 minutes followed by chromatin preparation according to the manufacturer’s protocol. 15 microgram DNA containing chromatin was used as input per reaction.
The libraries were prepared using ThruPLEX DNA-seq kit (Takara Bio) according to the manufacturer’s protocol. All libraries were uniquely indexed and pooled for single-read sequencing across 8 lanes of HiSeq 2500 High Output, V4 chemistry (Illumina, Inc.), generating 50bp reads.

treatment_protocol: Cells  were exposed to dabrafenib 50nM for 45 days (colony) or more than 90 days (resistant). Drug treatments were re-applied every 3 days. Parental samples were exposed to the corresponding volume of DMSO 3 days before sample extraction.

value: BRAF mutant melanoma

tag: treatment duration


title: WM164 Q61K Input-1


title: ATACseq_SKNMC_shScramble_48h_rep3


title: WM164 Q61K H3K4me3-2

value: H3K4me3 Active motif  (39159)


title: WM164 Q61K H3K4me3-1


title: dipc-human-experiment10-cerebellum


title: dipc-human-experiment09-cortex

source_name: cerebral cortex

value: cerebral cortex

value: pooled male and female


title: WM164 GFP Input-2


title: Htz1-MNase, SDC-inositol, Replicate 2

value: MATa his3delta1 leu2delta1 met15delta0 ura3delta0 Htz1-MNase:KanMX


title: Htz1-MNase, SDC-inositol, Replicate 1


title: VCaP_FOXA1_DHT_rep2

value: FOXA1 (Abcam, ab23738)


title: dipc-human-experiment07-cerebellum

value: male


title: WM164 GFP Input-1


title: Ino2-MNase, SDC-inositol, Replicate 2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 Ino2-3xFLAG-MNase:KanMX


title: Ino2-MNase, SDC-inositol, Replicate 3


title: WM164 GFP H3K4me3-2


title: dipc-human-experiment08-cerebellum


title: WM164 GFP H3K4me3-1


title: VCaP_AR_ENZ3w_1nM-DHT_rep2

value: 1 nM

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


title: VCaP_AR_ENZ3w_1nM-DHT_rep1


title: multiome-human-cerebellum-donor06

value: lateral cerebellum


title: VCaP_FOXA1_EtOH_rep2

value: EtOH vehicle


title: WM164 Resist Input-2

value: dabrafenib 50 nM

value: more than 90 days


title: Htz1-MNase, SDC-inositol, Replicate 3


title: Ino2-MNase, SDC, Replicate 3


title: dipc-human-experiment05-cerebellum


title: Ino2-MNase, SDC-inositol, Replicate 1


title: WM164 Resist Input-1


title: dipc-human-experiment04-cerebellum


title: WM164 Resist H3K4me3-2


title: VCaP_AR_1nM-DHT_rep1

value: Vertebral Cancer of the Prostate

value: VCaP

value: dihydrotestosterone


title: 22Rv1_ATAC_ENZ3w_naked-DNA_rep1

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 transposase treated naked DNA sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) 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. VCaP and 22Rv1 cells were treated with vehicle (EtOH), 1 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for 1 h before the start of nuclei extraction.

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: 3 weeks


title: Ino2-MNase, SDC, Replicate 2


title: Htz1-MNase, SDC, Replicate 3


title: WM164 Resist H3K4me3-1

value: BRAF mutant melanoma

value: H3K4me3 Active motif  (39159)


title: Ino2-MNase, SDC, Replicate 1


title: dipc-human-experiment03-cortex

value: cerebral cortex

value: pooled male and female


title: dipc-human-experiment02-cerebellum

value: cerebellum


title: 22Rv1_ATAC_naked-DNA_rep1


title: WM164 Colony Input-2

value: 45 days


title: dipc-human-experiment01-cerebellum

value: female


title: Htz1-MNase, SDC, Replicate 2

value: MATa his3delta1 leu2delta1 met15delta0 ura3delta0 Htz1-MNase:KanMX


title: 22Rv1_ATAC_ENZ3w_100nM-Dex_rep2

value: dexamethasone


title: WM164 Colony Input-1


title: dipc-human-experiment06-cerebellum


title: Htz1-MNase, SDC, Replicate 1


title: HepG2_siANP32B_mH2A1_rep2

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Paired end reads were adapter and quality trimmed with trimgalore using --stringency 3
Reads were aligned using Bowtie2 (Langmead, et al 2009) to UCSC hg38 (no alternative contigs) with the following options: --very-sensitive --no-discordant --no-mixed -X 700 –dovetail. The resulting alignment bam files were filtered to retain only concordant proper pair alignments using samtools and sam flag 0x2.
Coverage signal profiles in bigwig format were generated using the bamCoverage function from deepTools (Ramírez et al., 2014) with a Counts-Per-Million per-sample normalization using a bin of 1bp, ignoring ChrM for normalization and excluding reads falling into described “blacklisted” regions for CUT&RUN (Nordin et al., 2023).
Epic2 (Stovner et al., 2019) was used to perform peak calling in the form of broad domain detection on the filtered aligned reads using the IgG controls as background, a bin size of 1000bp and the following options: --guess-bampe -kd -fdr 0.0001 –gaps-allowed 5.
Differentially bound regions were identified using the R package csaw (Lun et al., 2016), which is based on counting reads into sliding windows across the genome. The analysis was performed following the workflow guidelines provided by the authors (Lun, Smyth, 2015). The filtered bam files for each sample were used as input, setting as parameters: paired-end data, a maximum fragment length of 700bp, restricted analysis to standard chromosomes. A stringent blacklist of regions was obtained by merging the CUT&RUN blacklisted regions within 10kb (Nordin et al., 2023) and the ENCODE blacklist (Amemiya et al., 2019). Reads falling into the blacklist were discarded for quantification. Sliding windows for read counting were set at 10kb with a spacing of 1kb. Only windows with a fold-change of at least 3 over the IgG background were kept for further analysis using the filterWindowsGlobal function. The filtered windows were normalized for compositional bias using the normFactors function. Dispersion estimates and differential binding testing was performed with edgeR as described in the package documentation, using in the model a single experimental condition with two levels (siControl, siANP32B). Individual windows were merged and corrected for multiple testing with the mergeResults function and a 1000bp maximum gap. Only regions with a combined FDR < 0.05 were considered differentially bound.
Assembly: hg38
Supplementary files format and content: .bw, BigWig files with signal coverage profiles
Supplementary files format and content: .bed, regions called as peaks by epic2
Supplementary files format and content: .tab, table with results of the differential binding analysis
Library strategy: CUT&RUN

source_name: Liver

growth_protocol: Cells were cultured in humidified incubators at 37oC and 5% CO¬2 using high glucose DMEM (Sigma) culture media supplemented with 10% Fetal Calf Serum (FCS, GIBCO), 2 mM glutamine (GIBCO) and 1% penicillin/streptomycin (GIBCO).

extract_protocol:
CUT&RUN reactions were performed as described in Meers et al., 2019 following the “Standard CUT&RUN” protocol. Briefly, approximately 1M cryopreserved HepG2 cells were thawed and bound to concanavalin-A paramagnetic beads (Epicypher), then split equally, resuspended in antibody binding buffer and incubated overnight with either home-made macroH2A1 antibodies (described in Buschbeck et al., 2009 and Douet et al., 2017) and an IgG non-targeting control (Abcam ab46540). Both antibodies were diluted 1:100 in the binding reaction. Samples were then washed and bound with pA/G-MNase (Epicypher), chromatin digestion started by addition of CaCl and stopped after 30min with STOP buffer containing chelating agents. Samples were then incubated for 30min at 37oC to release CUT&RUN fragments, incubated 1h at 50oC with proteinase K and purified using ChIP DNA Clean & Concentrator (Zymo Research).
Sequencing libraries were prepared with the KAPA HyperPrep kit (Roche) and NEXTflex DNA barcodes for Illumina (Bioo Scientific).

treatment_protocol: RNAi experiments were performed with RNAiMax (Invitrogen) according to the manufacturer’s protocol 3 days before cell harvesting or fixation. siControl: 5′-UGGUUUACAUGUCGACUAA-3′, siANP32B: 5’UGACUACCGAGAGAGUGUCUU-3’.

value: Liver

value: Human Hepatoblastoma

tag: antibody


title: VCaP_AR_1nM-DHT_rep2

value: 1 nM

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


title: Soluble MNase, SDC-histidine, Replicate 3

value: MATa leu2delta0 ura3delta0 met15delta0 SolubleMNase:HIS3


title: 22Rv1_ATAC_ENZ3w_1nM-DHT_rep2

value: dihydrotestosterone


title: HepG2_siControl_mH2A1_rep2

value: siControl


title: WM164 Colony H3K4me3-2

value: dabrafenib 50 nM


title: 22Rv1_ATAC_ENZ3w_100nM-Dex_rep1

value: CWR22 xenograft derived human prostate carcinoma epithelial cell line

value: 3 weeks


title: WM164 Colony H3K4me3-1

value: BRAF mutant melanoma

value: H3K4me3 Active motif  (39159)


title: HepG2_siANP32B_mH2A1_rep1


title: Soluble MNase, SDC-histidine, Replicate 2


title: WM164 parent Input-2


title: Soluble MNase, SDC-histidine, Replicate 1


title: 22Rv1_ATAC_ENZ3w_0nM_rep2

value: EtOH vehicle


title: HepG2_siControl_mH2A1_rep1


title: WM164 parent Input-1


title: Soluble MNase, SDC, Replicate 3


title: 22Rv1_ATAC_ENZ3w_0nM_rep1


title: WM164 parent H3K4me3-2


title: HepG2_siANP32B_IgG_rep2

value: IgG


title: 22Rv1_ATAC_100nM-Dex_rep2


title: Soluble MNase, SDC, Replicate 2


title: HepG2_siControl_IgG_rep2


title: Soluble MNase, SDC, Replicate 1


title: HepG2_siANP32B_IgG_rep1


title: 22Rv1_ATAC_100nM-Dex_rep1


title: WM164 parent H3K4me3-1


title: 22Rv1_ATAC_ENZ3w_1nM-DHT_rep1


title: OVCA420 cells, 7 day TGFB1 treatment

first: Edward

last: Yakubovich

address: 451 Smyth Rd

institute: Ottawa Hospital Research Institute

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using CellRanger v2.0.1 and the GRCh38 build of the human genome. Default settings were used for both libraries.
Assembly: GRCh38/hg38
Supplementary files format and content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. Cellranger barcode list: Cellranger barcode list from filtered_feature_bc_matrix directory. Cellranger gene list: Cellranger gene list output from filtered_feature_bc_matrix directory. Cellranger UMI matrix: Cellranger UMI matrix output from filtered_feature_bc_matrix directory.

extract_protocol:
OVCA420 cells were washed with PBS then incubated with trypsin for 5 minutes and quenched using normal growth media (DMEM + 10% FBS) . The suspension was filtered, and  large aggregates were further disrupted using a syringe plunger on a 70μm filter in order to generate a single-cell suspension. Cells were counted to assess viability (Trypan-blue exclusion) prior to staining.
Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ RNA-seq kit (v3), loaded to target a yield of 10,000 cells per sample. Cell cDNA libraries were prepared according to the manufacturer’s protocol and libraries were assessed using the Fragment Analyzer (Agilent).
3' scRNA-seq


title: 22Rv1_ATAC_1nM-DHT_rep2


title: No MNase, SDC, Replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: HepG2_siControl_IgG_rep1


title: OVCA420 cells, 3 day TGFB1 treatment


title: No MNase, SDC, Replicate 1


title: No MNase, SDC, Replicate 2


title: 22Rv1_ATAC_1nM-DHT_rep1


title: 22Rv1_ATAC_0nM_rep2


title: A375 cells, shPRMT1_1,rep2

city: Hangzhou

first: Liyuan

last: Zhou

state: 杭州市

address: 国科大杭州高等研究院

institute: University of Chinese Academy of Sciences

data_processing:
FastQC was used to qualified the reads.
The  qualified reads were mapped on homo sapiens genome hg38 by STAR(2.7.10b).
The gene counts were quantified  by featureCounts (subread 2.0.1).
Gtf files were generated using stringtie.
Gtf files were imported into ASprofile to compare multiple transcripts of the same gene for identification of variable indirect events
Assembly: hg38

growth_protocol: B16-F10 and A375 cells were maintained in DMEM medium containing 1% Penicillin/Streptomycin  and 10% FBS andcultured in 37°C incubator with 5%CO2.

extract_protocol:
The total RNA from B16-F10 or A375 cells was extracted by trizol(Vazyme) according to manufacturer’s protocol for RNA-seq.  For chip-seq, B16-F10 cells were fixed by 1% formaldehyde for 10 minutes. Then, chromatin from cells lysate was digested by Micrococcal Nuclease  into DNA fragments between 150-900 bp in length and released by sonication for antibody enrichment.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina(Vazyme) following manfacturer's protocl.

value: cell line

value: melanoma cells

value: PRMT1 knockdown


title: OVCA420 cells, Control

value: Control


title: 22Rv1_ATAC_0nM_rep1


title: VCaP_ATAC_ENZ3w_naked-DNA_rep1

value: Vertebral Cancer of the Prostate

value: VCaP


title: TL_rep2

city: Guelph

first: Terence

last: Van Raay

address: 50 stone road east

department: MCB

institute: University of Guelph

data_processing:
Rsubread v2.2.6
reads were aligned using the Rsubread align function to the Ensembl Genome Browser assembly ID: GRCz11
reads were filtered using EdgeR 3.30.3 filterByExpr function
Assembly: GRCz11
Supplementary files format and content: csv for counts of all genotypes

organism: Danio rerio

source_name: 50% epiboly

extract_protocol:
10 embryos at 50% epiboly were extracted using the FroggaBio GENEzol TriRNA pure kit following manufacturers instructions.
NEBNext Ultra II DNA library prep kit for illumina (New England BioLabs)

value: 50% epiboly


title: A375 cells, shNC,rep3

value: WT


title: Pol II ChIP_Rep1_Sth1-AID +Aux+Met [Pol II_cn9_S9]

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_cn9_S9

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive --no-mixed --no-unal, to map sequences up to 1 kb with maximum accuracy.
The PCR duplicates were removed by Samtool Rmdup tool
The average ORF occupancies for Pol II, Spt6, and Spt16 and TBP occupancies at TATA box or TATA-like sequences were calculated using modified scripts
The spike-in factor was calculated by dividing the average of S. pombe reads for all the samples by the average S. pombe reads for the replicate samples.
Assembly: SacCer3 2011
Supplementary files format and content: wig format

growth_protocol: Cells were grown in Synthetic Complete media deficient for methionine (SC/Met-) media to an A600 of 0.7

extract_protocol:
Sonicated extracts were used to ChIP for either Rpb3, Spt16, Spt6 or TBP antibodies. ChIPs samples were reverse-crosslinked, extracted with chloroform:IAA, then precipitated with ethanol.
Libraries were constructed using NEBNext Ultra II kit and Biooscientific NEXTFLEX ChIP-Seq adapters. Protocol was slightly modified from NEBNext manufacturer instuctions.

treatment_protocol: Cell with OD at 600nm were treated with methionine and 3-indole acetic acid (3-IAA) one hour before formaldehyde crosslinking. The cells were disrupted and sonicated to shear chromatin to approximately 25-350 base pairs.

tag: lane info

value: Run in 1st lane

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6

value: Auxin+Methionine


title: A375 cells, shPRMT1_1,rep1


title: A375 cells, shNC,rep2


title: VCaP_ATAC_ENZ3w_100nM-Dex_rep2

value: 3 weeks

value: dexamethasone


title: TL_rep1


title: A375 cells, shNC,rep1


title: Pol II ChIP_Rep1_Sth1-AID/Sth1-KR [Pol II_cn7_S7]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_cn7_S7

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1


title: A375 cells, shPRMT1_1,rep3


title: VCaP_ATAC_naked-DNA_rep1

value: EtOH vehicle


title: OVCA420 cells, 1 day TGFB1 treatment


title: VCaP_ATAC_ENZ3w_100nM-Dex_rep1


title: Tu_rep1


title: AID-WT_ZNF143,HiChIP

city: Shanghai

first: Mo

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Jiaotong University

data_processing:
*library strategy: HiChIP
HiChIP raw data was treated using the HiC-Pro pipeline
The aligned reads from HiC-Pro and ChIP-nexus peaks files were used to call loops with hichipper pipeline (v0.7.7).
The loops that length < 20Kb or the number of paired-end reads < 2 were filtered.
Assembly: hg19
Supplementary files format and content: bedpe

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). Human HCT-116 RAD21-AID-mClover cells (Natsume et al., 2016) were cultured in RPMI Medium 1640 L-Glutamine (Gibco), 1% penicillin-streptomycin (Gibco 15140122) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
Cells were fixed by 1% formaldehyde for 10 minutes at room temperature with slow rotation and quenched by 125 mM glycine. Cells were centrifuged at 800g for 5 minutes and washed once using ice-cold PBS. Cells were suspended using 1 mM ice-cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, 1x protease inhibitors) for 15 minutes at 4 ℃ with slow rotation and centrifuged at 2,500g, 4 ℃ for 5 minutes to remove supernatant. The above lysis step was repeated again used to fully lyse cells. 100 μL of 0.5% SDS solution was used to resuspend cells and incubation at 62 ℃ for 10 minutes. 240 μL water and 50 μL of 10 % Triton x-100 was added to quench reaction and incubated for 15 minutes at 37 ℃. Chromatin was digested for 2 hours at 37 ℃ with slow rotation by adding 50 μL of 10 x NEB buffer 2 and 15 μL of MboI (NEB R0147M). After heat inactivate MboI by incubating at 62 ℃ for 20 minutes, the DNA ends was marked by biotin using fill-in master mix (37.5 μL 0.4 mM biotin-dATP, 1.5 μL 10 mM dCTP, 1.5 μL 10 mM dGTP, 1.5 μL 10 mM dTTP, 10 μL 5U/μL DNA Polymerase I, Large (Klenow) Fragment) for 1 hour at 37 ℃ with slow rotation. 948 μL of ligation master mix (150 μL 10X NEB T4 DNA ligase buffer with 10 mM ATP, 125 μL 10% Triton X-100, 3 μL 50 mg/mL BSA, 10 μL 400 U/μL T4 DNA Ligase, 660 μL Water) was using to connect proximal DNA ends at room temperature for 4 hours with slow rotation. After centrifuging at 2,500g for 5 minutes, cell pellet was washed once with 1mL ChIP buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl, 1x protease inhibitors), and resuspended using 0.7 mL ChIP buffer with 10 minutes incubation on ice. The cell pellet was sonicated using Bioruptor Plus Sonicator by high intensity, 30 seconds on, 30 seconds rest, 15 cycles. The protein-DNA complexes was pre-clean using 25 μL of protein G beads with incubation at 4 ℃ for 1 hour. The primary antibody was added and incubation at 4 ℃ overnight with slow rotation. Beads washing, DNA elution, and precipitation were the same as ChIP-seq and DNA fragment was dissolved using 10 μL of water.
VAHTS Universal DNA Library Prep Kit (Vazyme ND607-01) was used for library construction. After end-repair and adaptor were performed under kit protocols. 10 μL Streptavidin T1 beads were washed twice with Tween washing buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended with 10 μL of 2X Biotin Binding Buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl). The ligated DNA was mixed with streptavidin beads suspension and incubated at room temperature for 15 minutes with slow rotation to enrich biotin labeled DNA. Beads-DNA complexes were washed twice with 500 μL of Tween washing buffer at 55 ℃ for 2 minutes with 1000 rpm shaking. Beads-DNA complexes were washed with 100 μL TE buffer (10mM Tris-HCl pH7.5, 5 mM MgCl2, 10% Dimethylformamide) and resuspended with 20 μL water. The DNA was amplified by PCR (95°C, 3 min; 98°C, 20 s, 60°C, 15 s, 72°C, 30 s for 13 cycles; and a final extension at 72°C, 5 min), and the DNA fragments were select by AMPure XP beads (0.7 x and 0.3 x). The DNA was dissolved using 20 μL H2O.

treatment_protocol: In order to degrade protein labeled with AID in TiR1 expression cells, IAA was added to final concentration of 500 μM for 6-24 hours.

value: ZNF143 (Proteintech, #16618-1-AP)

value: Human Uterine Adenocarcinoma Cells

value: CTCF-AID

value: IAA, 0h


title: Tu_rep3


title: Pol II ChIP_Rep1_Sth1-AID/Sth1-KR+Aux+Met [Pol II_cn5_S5]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_cn5_S5


title: Tu_rep2


title: Pol II ChIP_Rep2_Sth1-AID/Sth1-KR+Aux+Met [Pol II_cn6_S6]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_cn6_S6


title: TBP ChIP_Rep2_Sth1-AID/Sth1-KR [TBP_cn-61]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
TBP_cn-61


title: AID-CTCFd_ZNF143,HiChIP

value: IAA, 24h


title: Pol II ChIP_Rep2_Sth1-AID +Aux+Met [Pol II_cn10_S10]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_cn10_S10


title: Pol II ChIP_Rep2_Sth1-AID/Sth1-KR [Pol II_cn8_S8]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_cn8_S8


title: VCaP_ATAC_ENZ3w_1nM-DHT_rep2

value: dihydrotestosterone

value: 1 nM


title: TBP ChIP_Rep1_Sth1-AID/Sth1-KR [TBP_cn-60]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
TBP_cn-60


title: Double_KO_rep3


title: ZNF143KO_CTCF,HiChIP

value: CTCF (Abcam, #Ab70303)


title: Double_KO_rep2

value: 50% epiboly


title: VCaP_ATAC_ENZ3w_0nM_rep1

value: Vertebral Cancer of the Prostate

value: VCaP


title: VCaP_ATAC_100nM-Dex_rep2


title: Double_KO_rep1


title: TBP ChIP_Rep1_Sth1-AID/Sth1-KR+Aux+Met [TBP_cn-58]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
TBP_cn-58


title: WT_CTCF,HiChIP

value: wild type


title: Nkd1_KO_rep3


title: VCaP_ATAC_ENZ3w_1nM-DHT_rep1


title: TBP ChIP_Rep2_Sth1-AID [TBP_cn-57]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
TBP_cn-57

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6


title: ZNF143KO_RAD21,HiChIP

value: RAD21 (Abcam, #Ab992)


title: VCaP_ATAC_100nM-Dex_rep1

value: dexamethasone


title: WT_ZNF143,HiChIP


title: TBP ChIP_Rep1_Sth1-AID [TBP_cn-56]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
TBP_cn-56


title: Nkd1_KO_rep1


title: AID-CTCFd,Hi-C

data_processing:
library strategy: In situ Hi-C
Raw reads were mapped to GRCh37/hg19 to generate contact maps using HiC-Pro (v3.0.0)
The produced allValidPairs file was transformed to a hic file using the hicpro2juicebox script from HiC-Pro for further analyses with Juicer tools.
The hic file was converted to cool format using Hic2cool.
The Hi-C contact matrix was balanced using the Knight-Ruiz (KR) method and normalized to a depth of 100 million contacts.
TAD domains were called using HMM (hidden Markov models) method as previously described.
Assembly: hg19
Supplementary files format and content: mcool

extract_protocol:
About 5 million cross-linked cells were lysed with lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% NP-40) to obtain nuclei. Nuclei were incubated with SDS and quenched by adding Triton X-100. Samples DNA was digested with MboI (NEB R0147M) for overnight at 37℃. After heat inactivation at 62℃, restriction fragment overhangs were filled and marked with biotin-14-dATP (Thermo 19524016), dCTP, dTTP, dGTP, and DNA Polymerase I, Large (Klenow) Fragment (NEB M0210L). After Proximity ligation using T4 DNA ligase (NEB M0202S), samples were reverse cross-links at 68℃ for overnight. DNA samples were precipitated with ethanol and then sonicated to fragmentize DNA. DNA fragment size selection was performed by using AMPure XP Beads (Beckman A63881), and 300-500 bp DNA fragments were used for the next step. M-280 Streptavidin beads (Thermo 11206D) were used to select DNA fragments marked with biotin.
Library construction steps were performed while DNA samples were still bound to the bead interval with strict washing. NEB end-repair module (NEB E6050S) was used to blunt DNA end and dA-Tailing DNA reaction performed with Klenow exo- (NEB M0212S). Illumina U-type adaptors were adopted to add adaptor for DNA, and USER enzyme (NEB M5505S) was used for adaptor cleavage. After 10-12 of cycles PCR amplification, DNA samples were purified with AMPure XP Beads (Beckman A63881).


title: Axin2_KO_rep3


title: VCaP_ATAC_ENZ3w_0nM_rep2

value: 3 weeks


title: VCaP_ATAC_1nM-DHT_rep1


title: AID-ZNF143KO&CTCFd,Hi-C

value: CTCF-AID, ZNF143KO


title: Nkd1_KO_rep2


title: TBP ChIP_Rep2_Sth1-AID +Aux+Met [TBP_cn-55]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
TBP_cn-55

value: Auxin+Methionine


title: VCaP_ATAC_1nM-DHT_rep2


title: AID-ZNF143KO,Hi-C

value: Human Uterine Adenocarcinoma Cells


title: Axin2_KO_rep2


title: TBP ChIP_Rep2_Sth1-AID/Sth1-KR+Aux+Met [TBP_cn-59]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
TBP_cn-59

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1


title: VCaP_ATAC_0nM_rep2

value: EtOH vehicle


title: VCaP_ATAC_0nM_rep1


title: WT_RAD21,HiChIP


title: TBP ChIP_Rep1_Sth1-AID +Aux+Met [TBP_cn-54]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
TBP_cn-54


title: Axin2_KO_rep1


title: Spt6 ChIP_Rep1_Sth1-AID/Sth1-KR [Spt6_L19]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt6_L19


title: HS578T, Dia4

data_processing:
We used the R/Bioconductor package edgeR to generate CPM_TMM normalized counts. Briefly, starting with the data in the raw count file, any gene that did not have a CPM value of 0.5 in two or more samples was filtered out. calcNormFactors was then used to calculate the normalization factors for the remaining genes using the TMM normalization method. CPM was then calculated while using the TMM normalization factors for these remaining genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes CPM_TMM normalized values for each Sample

growth_protocol: We orthotopically injected estrogen receptor (ER)-negative breast cancer cells (MDA-MB-231, MDA-MB-468 and Hs578T) into the mammary fat pad of mice for tumor growth. Eight weeks old diabetic and non-diabetic mice were injected unilaterally with 5×106 cells in 100 µL of Matrigel/PBS (50∶50) into the fourth abdominal fat pad by subcutaneous injection. The tumor-growing mice (n=4 from each group) were sacrificed at 5 weeks (for MDA-MB-231 xenografts), 6 weeks (for MDA-MB-468 xenografts), or 8 weeks (for Hs578T xenografts) after the initial inoculation of the breast cancer cells into the fat pads. Tumors were obtained and were immediately frozen in liquid nitrogen for subsequent RNA isolation. mRNA profiles of above xenograft tissues were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

extract_protocol:
RNA isolation was done using RNeasy Plus Mini Kits from Qiagen. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina HiSeq machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast cancer cell

tag: er status

value: ER Negative

tag: disease state

value: diabetic


title: Sample6_asthmatic model3

city: China

first: Chunxia

last: Gong

address: 117 Meishan Road, Shushan District, Hefei City, Anhui Province,

institute: The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine

data_processing:
After library construction, PCR amplification was used to enrich the library fragments, and then the library was selected according to the fragment size, and the library size was 450 bp.
Then, the Agilent 2100 Bioanalyzer was used for quality control of the library, and then the total concentration of the library and the effective concentration of the library were detected. Then, according to the effective concentration of the library and the amount of data required for the library, the libraries containing different Index sequences (each sample is added with a different Index, and finally the downstream data of each sample is distinguished according to the Index) are mixed proportionally. The mixed libraries are uniformly diluted to 2nM and denatured by base denaturation to form single-stranded libraries.
After RNA extraction, purification and library construction, the libraries were subjected to paired-end (PE) sequencing using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform.
The raw downstream data (Raw Data) is filtered, and the filtered high-quality sequences (Clean Data) are compared to the reference genome of the species.
Based on the comparison results, the expression amount of each gene was calculated. On this basis, the samples were further analyzed for expression difference analysis, enrichment analysis and cluster analysis. The Reads on the comparison were spliced and the transcript sequences were reduced.
Supplementary files format and content: processed date.xls

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Total RNA was extracted and purified by the mirVana™ miRNA Isolation Kit (catalog number: AM1561; Ambion, Austin, TX, USA) according to manufacturer instructions. RNA quality was evaluated by a spectrophotometer (Nanodrop™; Thermo Fisher Scientific, Waltham, MA, USA) and a bioanalyzer (2100 series; Agilent Technologies, Santa Clara, CA, USA).
The mRNA with polyA structure in the total RNA was enriched by Oligo(dT) magnetic beads, and ion interruption was used to break the RNA to a fragment of about 300bp in length. The fragment with a length of 300bp was chosen because the length of the junction is fixed, and if the length of the interrupted fragment is short, it will lead to a high proportion of the junction sequence, which will reduce the proportion of valid data; if the length of the interrupted fragment is long, it will be unfavorable to the generation of clusters in the process of on-line sequencing. The first strand of cDNA was synthesized using RNA as template with 6-base random primer and reverse transcriptase, and the first strand cDNA was used as template for the second strand cDNA synthesis.

value: lung

tag: strain background

value: Sprague Dawley

value: male

value: asthmatic model


title: Sample5_asthmatic model2


title: Spt6 ChIP_Rep2_Sth1-AID/Sth1-KR+Aux+Met [Spt6_L18]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt6_L18


title: HS578T, Dia2


title: HS578T_HG4

data_processing:
We used the R/Bioconductor package edgeR to generate CPM_TMM normalized counts. Briefly, starting with the data in the raw count file, any gene that did not have a CPM value of 0.5 in two or more samples was filtered out. calcNormFactors was then used to calculate the normalization factors for the remaining genes using the TMM normalization method. CPM was then calculated while using the TMM normalization factors for these remaining genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM_TMM normalized values for each Sample

growth_protocol: Breast cancer cells (Hs578T) were cultured under low (5mM) and high glucose (25mM)

value: Breast cancer cell line

value: ER negative

value: high glucose


title: HS578T, Dia3


title: WT,Hi-C

value: wild type


title: Spt6 ChIP_Rep1_Sth1-AID/Sth1-KR+Aux+Met [Spt6_L17]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt6_L17


title: HS578T_HG3


title: Spt6 ChIP_Rep2_Sth1-AID/Sth1-KR [Spt6_L20]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt6_L20


title: Sample2_normal2

value: normal


title: Spt16 ChIP_Rep1_Sth1-AID/Sth1-KR [Spt16_L-33]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt16_L-33


title: Spt16 ChIP_Rep2_Sth1-AID/Sth1-KR+Aux+Met [Spt16_L-32]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt16_L-32


title: Spt16 ChIP_Rep2_Sth1-AID/Sth1-KR [Spt16_L-34]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt16_L-34


title: HS578T, Cont4

value: control


title: HS578T, Dia1


title: HS578T, Cont3


title: HS578T, Cont2


title: HS578T_HG2


title: Sample3_normal3


title: AID-WT,Hi-C

value: CTCF-AID

value: IAA, 0h


title: HS578T_HG1


title: HS578T_Cont4

value: low glucose


title: ZNF143KO,Hi-C

value: Human Uterine Adenocarcinoma Cells


title: Spt16 ChIP_Rep1_Sth1-AID/Sth1-KR+Aux+Met [Spt16_L-31]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Spt16_L-31

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1

value: Auxin+Methionine


title: Sample4_asthmatic model1


title: HS578T, Cont1

value: breast cancer cell

value: ER Negative


title: Pol II ChIP_Rep2_Sth1-AID [Pol II_Run2-cn12_S12]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_Run2-cn12_S12

value: Run in 2nd lane

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6


title: HS578T_Cont3


title: MDAMB468, Dia4

value: diabetic


title: lung tumor, RPR2;Nfibf/f, JHK1399

first: Julie

last: Ko

address: 265 Campus Drive G2065

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fatq files and de-multiplexed using Illumina bcl2fastq 2.20 software.
Sequenced reads were trimmed for adapter sequences.
Transcript quantification was conducted using Salmon v0.12.0 with GRCm38 mouse genome
Tximeta package (v1.12.4) running on R (v4.1.0) was used for mapping Ensembl transcript IDs to gene symbols and for quantifying scaledTPM values.
Assembly: GRCm38
Supplementary files format and content: csv of scaled TPM values for each sample

source_name: lung tumor

extract_protocol:
Tumors from lungs and livers were macrodissected at morbidity and snap-frozen. Total RNA extraction, polyA selection, and quality control were performed by Azenta Inc.
RNA library was constructed by Azenta Inc. using NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New Englad Biolabs, Ipswich, MA, USA).

value: lung tumor

tag: mouse tag


title: HS578T_Cont2

first: Stefan

last: Ambs

address: Building 37, Room 3050B

value: Breast cancer cell line

value: ER negative


title: liver metastasis, RPR2;Nfibf/f, JHK1399

source_name: liver metastasis

value: liver metastasis


title: Pol II ChIP_Rep2_Sth1-AID +Aux+Met [Pol II_Run2-cn10_S10]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_Run2-cn10_S10


title: Pol II ChIP_Rep1_Sth1-AID [Pol II_Run2-cn11_S11]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_Run2-cn11_S11


title: Sample1_normal1

value: lung

value: Sprague Dawley

value: male

value: normal


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO,H1.5Rescue

first: Gil

last: Ast

address: Haim Levanon 55

description: The UMIs for each sample are under the relevantR2.fastqfile

data_processing:
The quality of sequenced reads was evaluated using the FASTQC tool
Sequenced reads were aligned to the University of California, Santa Cruz (UCSC) Genome Sequencing Consortium (https://genome.ucsc.edu) reference genome (human genome assembly 19 (hg19)) using TopHat v2.1.1 66 while adding gene annotations (refgene) table downloaded from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables) in GTF format in addition to the default parameters
Sequenced reads were also aligned to the UCSC Genome Sequencing Consortium reference genome (human hg19) using the vast-tools v2.5.1 67 align command with default options.
Quality metrics from the alignment of samples were obtained from the vast-tools and expression table, normalized by quantile normalization, cRPKM (corrected for mapability, Reads per kbp, and Million mapped reads) values obtained for each sample.
Assembly: hg19
Supplementary files format and content: tab-delimited files including cRPKM values for each Sample , no quantile normalization

extract_protocol: RNA was extracted by adding 100µl BCP (1-bromo 3-chloro propane) and vigorous shaking (20s) followed by a 15minute 12,000g centrifugation at 4ºC. The top transparent liquid phase containing the RNA was transferred to a new tube, 0.5ml isopropanol was added and the sample was centrifuged as before for 8minutes at 4ºC. The RNA pellet was washed with 1ml 70% ethanol, re-suspended in Rnase free DDW and treated with Dnase (ThermoFisher), to eliminate residual DNA. A sample of 1500-2000ng of total RNA, was used to generate cDNA by oligo(dT) primers and SuperScript III reverse transcriptase. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human embryonic kidney

value: (H1.2,H1.3,H1.0,H1.5) knockout and H1.5 cDNA administration


title: HS578T_Cont1

value: low glucose


title: Pol II ChIP_Rep1_Sth1-AID +Aux+Met [Pol II_Run2-cn9_S9]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_Run2-cn9_S9

value: Auxin+Methionine


title: MDAMB468, Dia1

value: breast cancer cell


title: MDAMB468, Dia3

value: ER Negative


title: HEK293,H1.2KO,H1.3KO,H1.0KO,H1.5KO,H1.0Rescue

value: (H1.2,H1.3,H1.0,H1.5) knockout and H1.0 cDNA administration


title: lung tumor, RPR2;Nfibf/f, JHK1398


title: liver metastasis, RPR2;Nfibf/f, JHK1398


title: lung tumor, RPR2, JHK1548


title: Pol II ChIP_Rep2_Sth1-AID/Sth1-KR [Pol II_Run2-cn8_S8]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_Run2-cn8_S8

value: Run in 2nd lane

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1


title: MDAMB468, Cont4

value: control


title: MDAMB468, Dia2

value: diabetic


title: TL_rep3

value: 50% epiboly


title: HEK293,H1.2KO,H1.3KO,H1.3Rescue

value: (H1.2 and H1.3)knockout and H1.3 cDNA administration


title: liver metastasis, RPR2, JHK1394

value: liver metastasis


title: Pol II ChIP_Rep2_Sth1-AID/Sth1-KR+Aux+Met [Pol II_Run2-cn6_S6]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_Run2-cn6_S6


title: MDAMB468, Cont3


title: SKNMC_H3K4me3

data_processing:
Illumina adaptors of sequencing reads were trimmed off using trimmomatic v0.36 and quality control was performed with FastQC v0.11.7.
Reads were aligned to the human reference genome (GRCh38) using the BWA mem algorithm v.0.7.17 (default settings), sorted and indexed using Samtools v1.9.
Quality control of ChIPseq data was performed using SSP v1.2.3. Mapping quality was assessed by QualiMap v2.2.1.
Aligned reads were stored in bigwig files using the bamCoverage function from deepTools v3.2.1.
Peak calling was performed using the MACS algorithm (v2.1.2, default parameters for narrow transcription factor peaks were used, --keep-dup 1, ENCODE blacklist regions were excluded using BEDTools v2.27.1).
Assembly: GRCh38
Supplementary files format and content: bigwig CPM normalized
Supplementary files format and content: narrowPeak (except for Input)

extract_protocol:
ChIPseq assays were performed using the iDeal ChIP-seq kit for Transcription factors (C01010054, Diagenode) according to the manufacturer’s instructions. Briefly, cells were grown to confluence in 15cm dishes, fixed with ChIP Cross-link Gold (C01019027, Diagenode) for 30 min and with 1.1% formaldehyde for 15 min, harvested, lysed and sonicated with the Bioruptor Pico (B01060010, Diagenode) for 5-10 cycles (30sec ON, 30sec OFF). Sonicated lysates were then quantified and 30µg of chromatin were incubated overnight at 4°C with 3-15µg of antibody. DNA was purified according to the manufacturer’s instructions.
Libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7370L, New England BioLabs) at the Functional Genomics Center Zurich, Switzerland.

value: SKNMC

value: Ewing Sarcoma

value: wildtype

value: H3K4me3 (#ab8580, Abcam)


title: MDAMB468, Cont2


title: lung tumor, RPR2, JHK1373

value: lung tumor


title: Pol II ChIP_Rep1_Sth1-AID/Sth1-KR+Aux+Met [Pol II_Run2-cn5_S5]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_Run2-cn5_S5


title: Pol II ChIP_Rep2_Sth1-AID [Pol II_cn12_S12]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_cn12_S12

value: Run in 1st lane

value: MATa trp1{delta}1 can1{delta}100 leu2{delta}3-112 his3{delta}11-15 ura3{delta}0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6


title: MDAMB468, Cont1

value: breast cancer cell


title: lung tumor, RPR2, JHK1394


title: MDAMB231, Dia4

value: ER Negative


title: liver metastasis, RPR2, JHK1373


title: SKNMC_H3K4me1

value: H3K4me1 (#39297, Active Motif)


title: Pol II ChIP_Rep1_Sth1-AID/Sth1-KR [Pol II_Run2-cn7_S7]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6 STH1K501R-PK3::TRP1
Pol II_Run2-cn7_S7

value: Run in 2nd lane


title: K_WT_Venus_plus_45

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.10a was used to align the reads to the GRCm39 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 100
Assembly: GRCm39 version 106
Supplementary files format and content: Tab-delimited gene counts

source_name: trigeminal ganglia

extract_protocol:
Tissues were microdissected in ice-cold PBS and stored at -80°C in 1ml TRIZOL (Thermofisher). RNA was extracted using the illustra RNAspin Mini RNA isolation kit from GE Healthcare (25-0500-70). RNA-sequencing was performed  at the NGS- Integrative Genomics (NIG) Core Unit Institute of Human Genetics of University Medical Center Göttingen (UMG).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: trigeminal ganglia

tag: age

value: Prdm12+/+; Sox10 Venus+


title: Pol II ChIP_Rep1_Sth1-AID [Pol II_cn11_S11]

description:
ChIP-DNA
MATa trp1∆1 can1∆100 leu2∆3-112 his3∆11-15 ura3∆0 GAL psi+ pADH1-OsTIR1-9myc::ADE2 URA2::pMET3::STH1-IAA17::KanMX6
Pol II_cn11_S11


title: SKNMC_H3K27ac

tag: chip antibody

value: H3K27ac (#39685, Active Motif)


title: K_WT_Venus_plus_35


title: K_WT_Venus_plus_32


title: SKNMC_FLI1

tag: cell line

value: FLI1 (C-19, #sc-356, Santa Cruz)


title: SKNMC_RBBP4

tag: cell type

value: RBBP4 (#A-2703-050, Epigentek)


title: MDAMB231, Dia3

institute: NCI

value: diabetic


title: MDAMB231, Dia2


title: MDAMB231, Dia1


title: K_WT_Venus_plus_22


title: SKNMC_HDAC2

value: SKNMC

value: HDAC2 (#ab7029, Abcam)


title: MDAMB231, Cont4

value: control


title: SKNMC_H3K27me3

value: Ewing Sarcoma

value: wildtype

value: H3K27me3 (#39157, Active Motif)


title: SKNMC_MTA2

value: MTA2/PID (#ab8106, Abcam)


title: lung tumor, RPR2;Nfibf/f, JHK997

value: lung tumor


title: SKNMC_FlagCHD4

value: Flag (clone M2, #F1804, Sigma-Aldrich)


title: MDAMB231, Cont2

value: breast cancer cell

value: ER Negative


title: F_Ko49

value: trigeminal ganglia

value: Prdm12-/-; Sox10 Venus+


title: F_Ko50


title: SKNMC_input_biolrep2


title: SKNMC_input_biolrep1


title: F_Ko42


title: MDAMB231, Cont1


title: MDAMB231, NCML 4

treatment_protocol: mRNA profiles of breast cancer cells (MDA-MB-231)  exposed with 1micro molar Carboxymethyllysine (CML) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

value: ER negative

tag: treatment

value: CML


title: F_Ko29

tag: strain


title: K_WT_Venus_plus_24

value: Prdm12+/+; Sox10 Venus+


title: MDAMB231, NCML 3


title: MDA-MB-157, HG4

growth_protocol: Breast cancer cells (MDA-MB-157) were cultured under low (5mM) and high glucose (25mM)

treatment_protocol: For each experimental group there were four replicates.  In brief, 5×10^5cells in a T25 flask were treated with low or high glucose for 48 hrs before RNA was isolated.

value: high glucose


title: MDA-MB-157, HG3


title: MDAMB231, Cont3


title: MDA-MB-157, HG2


title: seedlings, nol12_rep3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
The reads for each sample were aligned to the TAIR10 A. thaliana genome from ensembl (release v29) using HISAT2 (v2.0.4) with the following command-line parameters: --fr --rna-strandness RF --known-splicesite-infile.
Mapped reads were sorted using samtools sort (v1.1).
Reads were counted with htseq-count (v0.6.0) and the following command-line parameters: -a 0 -s reverse using Araport11 gene annotation (release 201604).
Assembly: TAIR10
Supplementary files format and content: raw counts

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: Seeds were surface-sterilized with 30% bleach/0.02% Triton-X100 solution and stratified for 2 days at 4°C on half-strength MS (Murashige and Skoog, 1962) basal salt medium supplemented with 1% (w/v) sucrose and 0.3% phytagel (Sigma-Aldrich). Seddlings were grown in Percival growth chambers at 22/19°C on a 16-h-light and 8-h-dark (long-day) photoperiod.

extract_protocol:
Total RNA was isolated from 14-day-old seedlings using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf).

value: 14-day-old seedlings


title: F_Ko16


title: MDAMB231, NCML 1

city: Bethesda


title: MDA-MB-157, HG1


title: MDAMB231, control 4


title: MDA-MB-157, LG4

value: low glucose


title: MDA-MB-157, LG3


title: seedlings, nol12_rep1


title: seedlings, nol12_rep2


title: MDAMB231, NCML 2


title: MDAMB231, control 3

value: control


title: seedlings, Col0_rep3

value: wild type (Col-0)


title: MDAMB231, control 2


title: MDA-MB-157, LG2


title: seedlings, Col0_rep2


title: MDAMB231, control 1


title: Intestine, Saliva 2 (Treatment)

status: Public on Nov 06 2023

city: Ciudad Real

first: Rita

last: Vaz-Rodrigues

address: Ronda de Toledo 12

department: SaBio

institute: Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM)

data_processing:
Around 18.4 to 49.3 million (M) of total reads were generated from each library for the RNA sequencing (RNA-Seq) data.
The Read 1 and Read 2 FASTQ files were analyzed by FastQC (0.11.5) and primary quality control (QC) was performed.
The UMI reads were identified, and adapter and poly A/T sequences were trimmed by using UMI-tools (1.1.2) and Cutadapt (3.7).
The STAR (2.7.3) aligner was used to align reads to the Danio Rerio reference genome (GRCz11.107).
After alignment, the final BAM files were deduplicated with UMI-tools and quantified with featureCounts function available in Bioconductor R package Rsubread by GRCz11.107 annotations.
Assembly: Danio Rerio reference genome (GRCz11.107)
Supplementary files format and content: MS Excel spreadsheet contains raw counts for each sample.

source_name: Intestine

extract_protocol:
Total mRNA was isolated from samples using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany), following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the CORALL mRNA-Seq V1 Library Prep Kit (Lexogen, Wien, Austria), following manufacturer's protocol.

value: Intestine

value: tick saliva


title: Intestine, PBS 1 (Control)

value: Control


title: Intestine, PBS 2 (Control)


title: Intestine, PBS 3 (Control)


title: HOM_S2, scRNAseq

city: Dallas

first: Jeffrey

middle: Marc

last: Zigman

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger 5 pipeline as recommended by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)
Assembly: mm10
Supplementary files format and content: Cellranger output files

source_name: Pancreas

extract_protocol:
Following decapitation, pancreata were inflated in situ with freshly prepared collagenase (~ 5 mL of a 0.65 mg/mL solution) that was injected into the bile duct under a dissecting microscope (Supplemental Figure 9). Each inflated pancreas was dissected, placed in a 50 mL centrifuge tube, and then incubated in a 37°C water bath for 15 min. Four digested pancreases of each genotype were pooled together, after which islets were isolated by Histopaque density gradient (Sigma-Aldrich, Cat# 10771 and 11191) centrifugation (1200 rpm, 4°C for 30 min). All detectable islets were handpicked under a microscope (at 10x magnification) and placed into a 15 mL centrifuge tube containing 1 mL of 1x HBSS media (GibcoTM, ThermoFisher Scientific, Waltham, MA; Cat# 14025-076). Single cell dispersion was then carried out as follows: islets were centrifuged (200 rpm, 4°C for 3 min), supernatant was removed, islets were incubated with 2 mL Accutase® solution (Innovative Cell Technologies, Inc. San Diego, CA; Cat# AT104) in a 37°C water bath for 15 min, after which cells were dispersed by pipetting up and down ten times using a 1 mL micropipette every 5 min x 3. The digestion was stopped by adding 10 mL of prewarmed RPMI-1640 (GibcoTM, ThermoFisher Scientific, Waltham, MA; Cat# 11875-085) containing 10% FBS (Atlanta Biologicals, Flowery Branch, GA; Cat# S11150). The cell solution was filtered through a 40 μm cell strainer and centrifuged (200 rpm at 4°C for 3 min), after which the cells were resuspended with 2 mL of fresh media. A total of three washes were performed before the final resuspension of islet cells in 0.5 mL of serum containing media. The cells were placed on ice and then submitted for fluorescence-activated cell sorting (FACS) within 20 minutes.
cDNA and single-cell libraries were prepared with the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index) (10x Genomics, Pleasanton, CA), as per manufacturer’s instructions: Cells in suspension were first prepared as gel beads in emulsion (GEMs) on a Single Cell 3’ Chip G (10x Chromium) using the Chromium Controller (10x Genomics). For this, ~1,600-1,800/µL cells were loaded, aiming for 10,000 cells per channel. Barcoded RNA transcripts in each single cell were reverse transcribed within GEM droplets. cDNA in GEM reaction mixture was purified with DynaBeads MyOneTM Silane beads (ThermoFisher Scientific, Waltham, MA). Read 1 primer sequence was added and full-length barcoded cDNA was amplified for subsequent library construction. cDNA quality was verified by Agilent Tapestation 4200 (Agilent Technologies, Santa Clara, CA) using DNAHS 5000 tape, and concentration was determined with a Qubit 4 Fluorometer (ThermoFisher Scientific) using the DNA HS assay before sequencing. Sequencing libraries were prepared by fragmentation, end-repair, ligation with indexed adapters, and PCR amplification using the Chromium Single Cell 3’ library kit v3.1 (10x Genomics). Nucleic acid was cleaned up using Ampure XP beads (Beckman Coulter Inc, Brea, CA). Post library preparation quality control was performed using DNA 1000 tape on the Agilent Tapestation 4200 and quantified by Qubit and real-time quantitative PCR on a LightCycler 96 System (Roche, Basel, Switzerland). Pooled libraries were sequenced at 1.6 pM on the Illumina NextSeq 2000 P2 100 Flowcell at a configuration of 28 x 90 x 10 x 10 base-pair, which codes for 28 base-pair Cell Barcodes, 90 base-pair Read, 10 base-pair unique molecular identifiers (UMI) and 10 base-pair Sample index. Cell Ranger Single-Cell Software Suite (v 5.0.1, 10X Genomics) was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized data across samples

value: Pancreas

value: Islet cells

value: Ghrelin knockout


title: Intestine, Saliva 3 (Treatment)


title: Intestine, Saliva 1 (Treatment)


title: WT_S1, scRNAseq

description: 10x Genomics

value: Wildtype


title: CD8 TRM_RNA seq#4 Donor12-treatment3_48h

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
75 cycle
D12_T3_48h

data_processing:
Reads were aligned to human genome by STAR2
Raw read counts were conducted by HTSeq-count
Digintal expression normalization was done with DEseq2
Assembly: hg38
Supplementary files format and content: Raw read count in tab-delimited text format

source_name: PBMC

growth_protocol: All cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA was extracted using the Qiagen AllPrep DNA/RNA 96-well system
Libraries were generated using ThruPLEX DNA-Seq Library Preparation Kit (Takara Bio, USA)

value: PBMC

value: Primary

value: OKT3 + MAdCAM + RA + TGFβ


title: CD8 TRM_RNA seq#4 Donor12-treatment2_48h

description:
75 cycle
D12_T2_48h

value: OKT3 + MAdCAM + RA