title: 3 month rep1


title: OG1 wild type s4

status: Public on Mar 08 2024

type: SRA

city: MILWAUKEE

first: CHRIS

last: KRISTICH

state: WI

address: 8701 WATERTOWN PLANK RD

country: USA

institute: MCW

library_source: transcriptomic

data_processing:
Illumina Casava 1.7 software used for basecalling.
TrimGalore v. 0.6.6 used to quality filter and trim reads
Bowtie 2 v. 2.3.4.3 used to align trimmed reads to reference (OG1RF: NC_017316.1)
Samtools v. 1.11 used to convert SAM to BAM and sort alignments
featureCounts was used to count reads; stranded set to reverse (-s 2), -t gene -g gene_id
DESeq2 was used for differential expression testing.
Assembly: NC_017316.1
Supplementary files format and content: tab-delimited file containing raw counts (output of featureCounts) of all samples

molecule: total RNA

organism: Enterococcus faecalis

source_name: bacterial culture

growth_protocol: Exponentially growing bacterial cultures in Mueller-Hinton broth in shaking flasks at 37 C

extract_protocol:
Total RNA was purified from cells, then subjected to rRNA depletion
TruSeq stranded libraries were prepared using standard Illumina protocols

treatment_protocol: No treatment applied

tag: strain

tag: genotype

value: wild type


title: RNA

city: Milan

first: Paolo

last: Gandellini

state: Milan

address: Via celoria 26

department: Bioscience

country: Italy

institute: University of Milan

description: bulk

data_processing:
RNA-seq reads were aligned to NCBI RefSeq GRCh38/hg38 genome using STAR.
Gene intensities were computed using RSEM-1.3.1 software.
Assembly: hg38
Supplementary files format and content: tab-delimited genes.results files include raw counts for each sample.
Supplementary files format and content: tab-delimited genes.results files include TPM values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: lung

growth_protocol: H520 cells were maintained in RPMI 1640 with stable L-Glutamine (Euroclone S.p.A., Pero, Italy) culture medium supplemented with 10% fetavl bovine serum and 25 mM Hepes (Euroclone S.p.A., Pero, Italy), and cultured at 37°C and 98% relative humidity in a 5% CO2 atmosphere.

extract_protocol:
H520 cells at 48 hours after Gapmer antisense oligonucleotide transfection and CRISPR edited and non-edited clones were washed with PBS Dulbecco’s Phosphate Buffered Saline (Euroclone S.p.A., Pero, Italy) and incubated with Trypsin/EDTA 1X in Phosphate Buffered Saline (Euroclone S.p.A., Pero, Italy) at 37°C for 5 min. Cells were collected and pelleted. Total RNA was isolated from cellular pellets using QIAzol Lysis Reagent and miRNeasy Mini Kit (QIAGEN, Hilden, Germany) with DNase I digestion (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. RNA integrity was checked through agarose gel electrophoresis. RNA yield and A260/A280 ratio were monitored with Nabi - UV/VIS Nano Spectrophotometer MicroDigital (TWIN HELIX SRL, Rho, Italy). For gene-expression profiling studies, RNA integrity numbers were also measured using 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA).
Total RNA was purified through oligo-dT-based RNA capturing, randomly fragmented and transformed into cDNA with NEB library preparation protocol. Library preparation was performed by Novogene, UK.

tag: tissue

value: lung

tag: cell line

tag: cell type

value: lung squamous carcinoma cells

value: WT


title: OG1 wild type s3


title: MDA-MB-468 WT cells biol rep 1

city: boston

first: Shizhong

last: Ke

state: Massachusetts

address: 3 BLACKFAN CIRCLE, CLS0428D

institute: Beth Israel Deaconess Medical Center (BIDMC)

data_processing:
Quality Control (QC) of Raw Data: The first step is to check the quality of the raw sequence data.
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to human_hg38
raw counts of sequencing reads extraction and normalization were performed
Assembly: human_hg38
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for each sample

growth_protocol: breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human breast cancer


title: 22 month rep1

city: Hefei

first: Ding

middle: feng

last: Li

address: Huang shan road 443

country: China

institute: USTC

data_processing:
Sequencing quality was examined by FastQC
Trimmed reads pass Illumina quality filter, trimmed 3¡¯-adaptor bases by cutadapt
Trimmed reads were aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb using NovoAlign software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized tsRNA expression for each group

organism: Mus musculus

source_name: brain

extract_protocol:
Total RNA was extracted by Trizol. Total amount of 2 ug RNA per sample was used as input material for the RNA sample preparations. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50-bp single-read at 10M reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: age

value: 22 months


title: OG1 wild type s1


title: MDA-MB-468 WT cells biol rep 2


title: Human_PBMC_59

status: Public on Mar 07 2024

type: RNA

city: Chicago

first: Anthony

last: Reder

state: IL

address: 5841 S Maryland Ave

department: Neurology

institute: University of Chicago Medicine

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

data_processing: Raw CEL files from arrays were imported, log2-transformed,  and normalized; gene expression was analyzed as described  previously (Feng et al, 2019a). Transcriptome Analysis  Console (TAC) version 4.02 (ThermoFisher) identified differentially expressed genes (DEGs).

label: biotin

source_name: Healthy Control

label_protocol: Affymetrix protocol

growth_protocol: PBMC were isolated by density gradient centrifugation (Lympholyte, Cedarlane Laboratories, Burlington, NC) within 1–4 h of phlebotomy. Cell lysates were stored at -80!C  in ‘‘buffer RLT plus’’ (Qiagen) for <12 months.

extract_protocol: Total RNA was purified using RNeasy (Qiagen).

treatment_protocol: 10 SPMS patients treated with IFN-beta-1a (Rebif) for 4 hours.

tag: Sex

value: F

tag: treatment duration (hours)

tag: ms-type


title: Human_PBMC_58

scan_protocol: Samples were randomized and hybridized to highly sensitive comprehensive  Clariom D microarrays (ThermoFisher Scientific)

value: M


title: Human_PBMC_57


title: Human_PBMC_56


title: Human_PBMC_53


title: Human_PBMC_54


title: Human_PBMC_52


title: Human_PBMC_51


title: Human_PBMC_50


title: Human_PBMC_49

source_name: MS Patient

value: Untreated

value: RRMS-s


title: Human_PBMC_47


title: Human_PBMC_44


title: OG1 wild type s2


title: Human_PBMC_45


title: Human_PBMC_40

value: Rebif 4h

value: SPMS-s


title: Human_PBMC_39

value: SPMS-a


title: Human_PBMC_38


title: Human_PBMC_43


title: Human_PBMC_46


title: Human_PBMC_42


title: Human_PBMC_37


title: Human_PBMC_41


title: Human_PBMC_36


title: MDA-MB-231 normal mouse igG

city: Guangzhou

first: Man-Li

last: Luo

address: No.107 Yanjiang West Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen Memorial Hospital

data_processing:
Sequencing were performed using Illumina HiSeqTM 4000.
RIP-seq reads were aligned to the Ensembl_release100 genome using Bowtie version 2.2.8. Only uniquely mapping reads with at most two mismatches were retained.
The reconstruction of transcripts was carried out with software StringTie3, which allows to identify splice variants.
Peaks were called using RIPSeeker with the significance cut-off eFDR < 0.05
Processed data files were based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold   enrichment between two experiment > 2 was used to selected different genes.
Assembly: Ensembl_release100
Supplementary files format and content: tab-delimited text files include fold change values for each RNA precipitation Sample normalised to input respectively.
Supplementary files format and content: Peak related genes were used to analyse differences between two samples, different genes analysis was based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold enrichment between two experiment> 2 was used to selected different genes. Using the same method, different genes associated with peaks were identified, and also do GO and KEGG enrichment analysis.

growth_protocol: Breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina Ribo-Zero Gold（Human/Mouse/Rat）kit following manufacturer's protocols

treatment_protocol: We produced FLAG tagged-MDM2 protein in MDA-MB-231 and MCF-7 cells by transfection of FLAG tagged plasmids into cells. Cells were lysed by RIP lysis buffer, and incubated at 4 °C with antibody-conjugated Protein A/G Dynabeads overnight. Specific anti-FLAG antibody (Sigma) and normal mouse IgG (Santa Cruz) were used for the retrieval of RNA. RNA was extracted for subsequent sequencing analysis.

value: Flag-tagged MDM2 protein was expressed

tag: treatment

value: IgG antibody immunoprecipitation


title: Human_PBMC_35


title: Human_PBMC_33

value: SPMS


title: Human_PBMC_32


title: Human_PBMC_34


title: Human_PBMC_31


title: Human_PBMC_30

value: Rebif 0h


title: Human_PBMC_55


title: Human_PBMC_29


title: Human_PBMC_28


title: Human_PBMC_26


title: Human_PBMC_25


title: Human_PBMC_27


title: Human_PBMC_48


title: Human_PBMC_24


title: Human_PBMC_22


title: Human_PBMC_23


title: Human_PBMC_19


title: Human_PBMC_18


title: Human_PBMC_20


title: Human_PBMC_17


title: Human_PBMC_15


title: Human_PBMC_13


title: Human_PBMC_14


title: Human_PBMC_12


title: Human_PBMC_9


title: placenta_80

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

data_processing:
Each sample was sequenced with >= 60 million reads and quality control of raw sequence performed by FastQC.
FASTQ sequence data was preprocessed with Trimmomatic and aligned to GRCh38_Ensembl using STAR stranded  alignment to generate a table of counts per transcript. After trimming and alignment additional  QC was performed using RNA-SeQC. Raw count data was transformed to log counts per million  (logcpm) and transcripts with low read counts removed by requiring a minimum of 0.2 logcpm in  >=18 samples, based on the smallest sample group (never-smokers).
Differential expression analysis was performed with EdgeR
Assembly: Human_GRCh38_Ensembl
Supplementary files format and content: "VCSIP_counts_raw.csv" contains raw counts aligned to Human_GRCh38_Ensembl

source_name: placenta

extract_protocol:
DNA, RNA, and miRNA were simultaneously extracted from placenta, powdered under liquid N2, using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).
Total RNA was sent to MedGenome Inc. (Foster City, CA, USA) for RNA QC, library preparation, and sequencing. cDNA libraries were generated using the Illumina Stranded Total RNA kit (Illumina, CA, USA) and sequenced using 100bp paired-end reads on the HiSeq 2500 platform (Illumina, CA, USA).

value: placenta

tag: status

value: non-smoker


title: Human_PBMC_16


title: Human_PBMC_10


title: Human_PBMC_8


title: placenta_78


title: Human_PBMC_11


title: placenta_79


title: placenta_76


title: placenta_77


title: Human_PBMC_6


title: placenta_75


title: placenta_74


title: Human_PBMC_4


title: placenta_72


title: Human_PBMC_5


title: Human_PBMC_21


title: Human_PBMC_3


title: Human_PBMC_2


title: placenta_71


title: placenta_70


title: Human_PBMC_1


title: Human_PBMC_7


title: placenta_68


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t8 ICRF-193 + Merb R1

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

library_source: genomic

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) reads.
Assembly: hg38

molecule: genomic DNA

source_name: uterine/cervical adenocarcinoma cell line

growth_protocol: HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 and 200uM Merbarone was added at t2hr. Cells were fixed at t8hr.

value: HeLa-S3 (CCL-2.2)


title: placenta_67


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t4 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr. Cells were fixed at t4hr.


title: placenta_73


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t8 DMSO R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr. Cells were fixed at t8hr.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t4 ICRF-193 + Merb R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 and 200uM Merbarone was added at t2hr. Cells were fixed at t4hr.


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t2 R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. Cells were fixed at t2hr.


title: placenta_64


title: placenta_65


title: placenta_66


title: TKO3

city: jiangsunantong

first: hu

middle: han

last: jing

address: Chongchuan District Xincheng Bridge street

institute: nantonguniversity

data_processing:
HISAT2 is a second-generation sequencing sequence alignment software, which can compare the whole genome, transcriptome and exome data with the reference genome. Using the improved BWT algorithm, the sequencing Reads can be efficiently compared to the reference genome. In this project, the HISAT2 software was used to sequence Clean Reads with a specified genome to obtain information about their location on the reference genome. The HISAT2 algorithm is mainly divided into three parts: (1) The whole sequencing sequence is compared to the single exon of the genome; (2) Segmented alignment of the sequencing sequence to two exons of the genome; (3) Segmenting the sequencing sequence to more than three (including three) exons of the genome.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: fpkm, tpm, read counts

extract_protocol:
Total RNA was extracted by TRIzol(Takara)
After the sample was qualified, eukaryotic mRNA was enriched with magnetic beads with Oligo (dT) connections. mRNA was then randomly interrupted by fragmentation buffer. Using mRNA as template, the first strand of cDNA was synthesized with six-base random primers, then the second strand of cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I, and then the double-stranded cDNA was purified by AMPure XP beads. The purified double-stranded cDNA was then end-repaired, A-tailed and sequenced, and then treated with AMPure XP beads were used for fragment size selection and PCR enrichment to obtain the final cDNA library.

value: neuroblastoma cells

value: TDP-43 knock out


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 + Merb added at t2: t0 Mitotic R1

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole.


title: NC1

value: NC


title: NC3


title: TKO2


title: JM8.N4 mESC, clone D ∆ZFP143 3h, PRO-seq, rep. 1

city: Cambridge

first: Domenic

last: Narducci

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
*library strategy: PRO-seq
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to a concatenation of the UCSC mm39 and dm6 genomes using bowtie2.
Spike-in and primary reads were independently deduplicated using UMI-tools and sorted using samtools 1.3.1 -n. These were converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl), and subsequently converted to bigwig format.
Assembly: mm39; dm6
Supplementary files format and content: bedGraph file has data based on all uniquely aligning non-duplicate reads
Library strategy: PRO-seq

molecule: nuclear RNA

growth_protocol: mESCs were cultured under 5% CO2 at 37°C under feeder-free conditions. The mESCs were grown in medium consisting of KnockOut DMEM (ThermoFisher #10829-018) supplemented with 15% FBS, 1000 U/mL LIF (homemade), 1 mM MEM Non-Essential Amino Acid Solution (ThermoFisher #11140050), 2 mM GlutaMAX supplement (ThermoFisher #35050061), 100 μg/mL Penicillin-Streptomycin (ThermoFisher #15140122), 0.1 mM 2-mercaptoethanol (ThermoFisher #31350010), 10 μM MEK inhibitor (Tocris #PD0325901), and 3 μM GSK inhibitor (Sigma-Aldrich #SML1046) on plates pre-coated with sterile 0.1% gelatin (Sigma-Aldrich, G1890). The mESCs were passaged every 2 days by dissociation with TrypLE Express Enzyme (ThermoFisher #12605028), and half the medium was replaced daily.

extract_protocol:
Cells were permeabilized using a combination of 0.1% (v/v) Igepal CA-630 and 0.05% (v/v) Tween-20. Subsequently, biotin-11 dNTPs were incorporated into the 3’ end of nascent RNA transcripts in a biotin run-on reaction. The run-on was stopped and total RNA was extracted using the Norgen Biotek Total RNA Purification Kit. The RNA was chemically fragmented and biotin-enriched using streptavidin beads.
The 3’ and 5’ adapters were ligated to the extracted RNA. The adapter-ligated RNA was converted to a cDNA library by reverse transcription using the SSIV RTase. Libraries were indexed by PCR using the NEBNext Ultra II Q5 Master Mix and custom primers from IDT. Libraries were purified using ProNex (Promega) beads. Purified libraries were quantified by qPCR and pooled in a 1:1 ratio. Following qPCR quantification, libraries were submitted for sequencing.

treatment_protocol: For depletion of ZFP143 in the clone A and clone B cell lines, the cells were incubated in media containing 100 μM 5-Ph-IAA (MedChemExpress #HY-134653) and 300 nM HaloPROTAC3 (Promega # GA3110), and for depletion of CTCF in the same lines the, the cells were incubated in media containing 100 nM dTAG-13 (Tocris # 6605) for 3 hours. For the depletion of ZFP143 in the clone D cell line, the cells were incubated in media containing 100 nM dTAG-13, and for the depletion of ZNF143 in the clone 30 HEK293T cell line, the cells were incubated in media containing 500 μM IAA for 3 hours.

value: Mouse embryonic stem cell

tag: spike-in reference_organism

value: Drosophila melanogaster

tag: spike-in cell_line

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF

value: 100nM dTAG-13

tag: time

value: 3 hours


title: placenta_63


title: JM8.N4 mESC, clone D untreated, PRO-seq, rep. 2


title: NC2


title: JM8.N4 mESC, clone D untreated, PRO-seq, rep. 1


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 2

value: Clone B, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3/100nM dTAG-13


title: placenta_69


title: placenta_62


title: TKO1


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs DMSO R3

data_processing:
Library strategy: MC-3C
PacBio SMRTLink software was used to call circular consensus sequences (CCS). Fastq files containing CCS were mapped to the hg38 genome using minimap2. Mapped C-walks were then annotated both at the fragment and the C-walk level for further filtering and analysis, including number of fragments per C-walk, number of chromosomes and compartment types visited, proximity of each fragment to the largest step in each C-walk, the size of the largest step for each C-walk, the distance of each direct pairwise interaction, the total span of each C-walk, and other features.
Tab delimited text file containing mapped and annotated C-walks. All HeLa S3 samples are combined in one processed data file. The table contains the first 2-10 fragments of all C-walks, organized based on number of fragments. Note that there is overlap between the length classes, e.g. 2 fragment C-walks in this table include C-walks with only 2 fragments as well as the first 2 fragments of C-walks 3 fragments and longer, etc.
Assembly: hg38

extract_protocol:
For each MC-3C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cells were then crosslinked with 3mM DSG for 45 minutes at room temperature, and DSG crosslinking was quenched with Tris. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until MC-3C library generation.
MC-3C was performed as described in Tavares-Cadete and Norouzi et al, Nature Structural and Molecular Biology. Restriction enzyme: DpnII

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.

value: uterine/cervical adenocarcinoma cell line


title: JM8.N4 mESC, clone B ∆ZFP143 3h, PRO-seq, rep. 2

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3


title: JM8.N4 mESC, clone B untreated, PRO-seq, rep. 2


title: placenta_61


title: JM8.N4 mESC, clone D ∆ZFP143 3h, PRO-seq, rep. 2


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 2

value: Clone A, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF


title: placenta_60

value: smoker


title: JM8.N4 mESC, clone A ∆CTCF 3h, PRO-seq, rep. 2


title: JM8.N4 mESC, clone A ∆ZFP143 3h, PRO-seq, rep. 2


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs ICRF-193 R3

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t4hr. G1 cells were isolated by FACS.


title: placenta_59

value: placenta


title: DpnII MC-3C on HeLa S3 MR: t0 Mitotic R3

extract_protocol:
For each MC-3C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cells were then crosslinked with 3mM DSG for 45 minutes at room temperature, and DSG crosslinking was quenched with Tris. Cell pellets were frozen at -80C until MC-3C library generation.
MC-3C was performed as described in Tavares-Cadete and Norouzi et al, Nature Structural and Molecular Biology. Restriction enzyme: DpnII


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs ICRF-193 R3

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t2hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.


title: DpnII MC-3C on HeLa S3 MR: t2 R3


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 1


title: JM8.N4 mESC, clone A untreated, PRO-seq, rep. 2


title: JM8.N4 mESC, clone B ∆CTCF 3h, PRO-seq, rep. 1


title: placenta_57


title: placenta_56


title: JM8.N4 mESC, clone B untreated, PRO-seq, rep. 1


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs ICRF-193 R2


title: JM8.N4 mESC, clone B ∆CTCF 3h, PRO-seq, rep. 2


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, PRO-seq, rep. 1


title: JM8.N4 mESC, clone A ∆CTCF 3h, PRO-seq, rep. 1


title: JM8.N4 mESC, clone B ∆ZFP143 3h, PRO-seq, rep. 1


title: placenta_58


title: JM8.N4 mESC, clone A ∆ZFP143 3h, PRO-seq, rep. 1


title: placenta_55


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs DMSO R2


title: JM8.N4 mESC, clone A untreated, PRO-seq, rep. 1


title: placenta_54


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs DMSO R2

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t2hr, and cells were fixed at t4hr. G1 cells were isolated by FACS.


title: JM8.N4 mESC, clone D ∆ZFP143 3h, Input, rep. 2

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to a concatenation of the UCSC mm39 and hg38 genomes using bowtie2 v2.2.5 with --no-mixed --no-discordant.
Uniquely aligned reads were filtered for PCR duplicates using sambamba markdup. Reads for each condition were randomly subsambled using normalization factors based on hg38 spike-in. Normalization factors were corrected using the ratio of human to mouse read counts in corresponding input samples.
Assembly: mm39;hg38
Supplementary files format and content: bigwig file has data based on all uniquely aligning non-duplicate reads

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 mins. Following quenching, chromatin was sonicated and then reverse crosslinked. Naked DNA was further sonicated to the 400-800bp range.
DNA from ZNF143 ChIP, CTCF ChIP, or input chromatin was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with a number of PCR cycles according to the manufacturer's protocol on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified twice using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, libraries were submitted for sequencing.

value: Homo sapiens

tag: chip antibody

tag: antibody info


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs ICRF-193 R2

value: HeLa-S3 (CCL-2.2)


title: JM8.N4 mESC, clone D untreated, Input, rep. 2


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs DMSO R3


title: JM8.N4 mESC, clone D untreated, Input, rep. 1


title: JM8.N4 mESC, clone D ∆ZFP143 3h, Input, rep. 1


title: DpnII MC-3C on HeLa S3 MR: t2 R2


title: placenta_53


title: DpnII MC-3C on HeLa S3 MR: t0 Mitotic R2


title: placenta_51


title: JM8.N4 mESC, clone B ∆CTCF 3h, Input, rep. 2


title: placenta_52


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs DMSO R1


title: JM8.N4 mESC, clone A untreated, Input, rep. 2


title: JM8.N4 mESC, clone B ∆ZFP143 3h, Input, rep. 2


title: placenta_49


title: JM8.N4 mESC, clone A ∆ZFP143 3h, Input, rep. 2


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Input, rep. 2


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs ICRF-193 R1


title: placenta_50


title: JM8.N4 mESC, clone B ∆CTCF 3h, Input, rep. 1


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Input, rep. 2


title: JM8.N4 mESC, clone B ∆ZFP143 3h, Input, rep. 1


title: placenta_48


title: DpnII MC-3C on HeLa S3 MR: 2-4hrs DMSO R1


title: JM8.N4 mESC, clone B untreated, Input, rep. 1


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Input, rep. 1


title: JM8.N4 mESC, clone B untreated, Input, rep. 2


title: placenta_47


title: DpnII MC-3C on HeLa S3 MR: t2 R1


title: JM8.N4 mESC, clone A ∆CTCF 3h, Input, rep. 1


title: DpnII MC-3C on HeLa S3 MR: 2-8hrs ICRF-193 R1


title: placenta_46


title: JM8.N4 mESC, clone A ∆ZFP143 3h, Input, rep. 1


title: JM8.N4 mESC, clone A ∆CTCF 3h, Input, rep. 2


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Input, rep. 1


title: JM8.N4 mESC, clone A untreated, Input, rep. 1


title: placenta_45


title: JM8.N4 mESC, clone D ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2


title: placenta_43


title: placenta_41


title: JM8.N4 mESC, clone B ∆CTCF 3h, ZNF143 ChIP-seq, rep. 2


title: JM8.N4 mESC, clone D untreated, ZNF143 ChIP-seq, rep. 2


title: JM8.N4 mESC, clone D untreated, ZNF143 ChIP-seq, rep. 1


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 2


title: JM8.N4 mESC, clone D ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1


title: Kidney, Normal,  Vehicle,  rep3

city: GRONINGEN

first: Marco

last: Demaria

state: Groningen

address: Antonius Deusinglaan, 1

country: Netherlands

institute: umcg

data_processing:
The FastQC 0.11.3 and Trim Galore 0.6.6 (bioinformatics.babraham.ac.uk) wereused to control the quality of raw sequencing data with parameter nextseq 25 and length 36.Trimmed reads were mapped to the genome using Salmon 1.3.0 with the control of gcBias and gencode.vM26.transcripts decoy index. The Bioconductor 3.11 package DESeq2 1.30.1 was used to conduct the differential gene expression analysis with genes less than 3 reads prefiltered.
Assembly: GRCm39
Supplementary files format and content: Comma-separated text file includes raw counts for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from kidney samples via an ISOLATE II RNA mini kit (Bioline, Cat: BIO-52073) according to the manufacturer’s instructions. Nanodrop was used for the quantification of the extracted RNA and the quality was measured via BioAnalyzer RNA chip (Agilent). In order to enrich for messenger RNA (mRNA), poly-A tail selection was carried out using the NEXTflex Poly(A) Beads kit (Bioo Scientific Corp, cat #512980)
RNA-Seq library preparation was accomplished using NEXTflex Rapid Directional qRNA-Seq kit (Bioo Scientific, cat# 5130-05D)

value: kidney

value: male

value: 12 weeks

tag: injury model

value: Normal

value: Vehicle


title: Kidney, Normal,  Vehicle,  rep4

tag: strain


title: placenta_44


title: Kidney, Normal,  Vehicle,  rep2


title: JM8.N4 mESC, clone A ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2

value: Mouse embryonic stem cell

tag: genotype


title: Kidney, Normal,  Vehicle,  rep1

tag: tissue


title: JM8.N4 mESC, clone B untreated, ZNF143 ChIP-seq, rep. 2

tag: cell line


title: JM8.N4 mESC, clone A untreated, ZNF143 ChIP-seq, rep. 2

tag: cell type


title: placenta_39


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 2


title: placenta_42


title: JM8.N4 mESC, clone A ∆CTCF 3h, ZNF143 ChIP-seq, rep. 2

value: 100nM dTAG-13


title: DpnII MC-3C on HeLa S3 MR: t0 Mitotic R1


title: JM8.N4 mESC, clone B ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1

value: 3 hours


title: Kidney, Normal,  PJ34,  rep3

tag: age


title: Kidney, Normal,  PJ34,  rep2

tag: Sex


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 1

value: Clone B, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF


title: JM8.N4 mESC, clone B ∆CTCF 3h, ZNF143 ChIP-seq, rep. 1


title: Kidney, Normal,  PJ34,  rep1


title: JM8.N4 mESC, clone B ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 2


title: Kidney, Normal,  PJ34,  rep4


title: placenta_40


title: JM8.N4 mESC, clone B untreated, ZNF143 ChIP-seq, rep. 1


title: placenta_37


title: placenta_36


title: placenta_35


title: placenta_38


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, ZNF143 ChIP-seq, rep. 1

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3/100nM dTAG-13


title: JM8.N4 mESC, clone D ∆ZFP143 3h, CTCF ChIP-seq, rep. 2

value: CTCF

value: Millipore-Sigma (#07-725)

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF


title: JM8.N4 mESC, clone A untreated, ZNF143 ChIP-seq, rep. 1

value: Clone A, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF


title: JM8.N4 mESC, clone A ∆CTCF 3h, ZNF143 ChIP-seq, rep. 1


title: JM8.N4 mESC, clone D untreated, CTCF ChIP-seq, rep. 1


title: Kidney, Ischemia Reperfusion,  Vehicle,  rep3

value: Ischemia Reperfusion


title: JM8.N4 mESC, clone B ∆CTCF 3h, CTCF ChIP-seq, rep. 2

value: Homo sapiens


title: Kidney, Ischemia Reperfusion,  Vehicle,  rep1


title: JM8.N4 mESC, clone D untreated, CTCF ChIP-seq, rep. 2


title: JM8.N4 mESC, clone D ∆ZFP143 3h, CTCF ChIP-seq, rep. 1


title: placenta_33

value: placenta

value: smoker


title: placenta_34


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 2


title: Kidney, Ischemia Reperfusion,  PJ34,  rep4

value: kidney

value: male


title: Kidney, Ischemia Reperfusion,  Vehicle,  rep4

value: 12 weeks


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 2


title: placenta_32


title: Kidney, Ischemia Reperfusion,  Vehicle,  rep2

value: Vehicle


title: placenta_31


title: Kidney, Ischemia Reperfusion,  PJ34,  rep2


title: JM8.N4 mESC, clone B untreated, CTCF ChIP-seq, rep. 2

value: Mouse embryonic stem cell


title: JM8.N4 mESC, clone A ∆ZFP143 3h, ZNF143 ChIP-seq, rep. 1

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3


title: JM8.N4 mESC, clone A ∆CTCF 3h, CTCF ChIP-seq, rep. 2

value: 100nM dTAG-13

value: 3 hours


title: placenta_30


title: JM8.N4 mESC, clone A ∆ZFP143 3h, CTCF ChIP-seq, rep. 2


title: JM8.N4 mESC, clone B ∆ZFP143 3h, CTCF ChIP-seq, rep. 2

value: Clone B, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF


title: JM8.N4 mESC, clone A untreated, CTCF ChIP-seq, rep. 2

value: CTCF


title: LSK, LFD, IgG, replicate 4, CUT&RUN

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

data_processing:
FASTQ files were processed using the nf-core-cutandrun pipeline (v3.1).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm38 (NCBI, p.6, release 108) and duplicates were removed for only control samples using picard.
Generally speaking, "peaks" refer to regions where at least one of the target samples significantly exceeds its matched control for a given genomic region. Here, peaks were called with macs2 (normalization mode: CPM).
Peaks were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: narrowPeak (except for IgG samples)
Library strategy: CUT&Tag

source_name: LSK

growth_protocol: Mouse bone marrow cells were harvested from tibias and femurs. LSK cells were FACS sorted in Upstate Flow Core following magnetic enrichment.

extract_protocol:
We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: LSK

tag: cut&tag antibody

tag: diet

value: LFD


title: placenta_28


title: JM8.N4 mESC, clone B ∆ZFP143 3h, CTCF ChIP-seq, rep. 1

value: Millipore-Sigma (#07-725)

tag: treatment


title: placenta_26

tag: status


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 1

tag: spike-in reference_organism

value: Clone A, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3/100nM dTAG-13


title: Kidney, Ischemia Reperfusion,  PJ34,  rep1

value: Ischemia Reperfusion


title: placenta_29

value: placenta

value: smoker


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, CTCF ChIP-seq, rep. 1

value: Homo sapiens

tag: spike-in cell_line


title: JM8.N4 mESC, clone D ∆ZFP143 3h, Micro-C, rep. 2

data_processing:
Assembly: mm39
*library strategy: Micro-C
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. These filtered reads were subsequently converted to .cool format using cooler (v0.9.1) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Assembly: mm39;hg38
Supplementary files format and content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-10 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF

tag: time


title: LSK, HFD, IgG, replicate 3, CUT&RUN

value: HFD


title: JM8.N4 mESC, clone B ∆CTCF 3h, CTCF ChIP-seq, rep. 1

value: Mouse embryonic stem cell

tag: chip antibody


title: Kidney, Ischemia Reperfusion,  PJ34,  rep3

value: kidney

value: male

value: 12 weeks


title: placenta_27


title: LSK, HFD, IgG, replicate 2, CUT&RUN


title: placenta_24


title: placenta_23


title: LSK, LFD, IgG, replicate 2, CUT&RUN


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Micro-C, rep. 2

value: Clone B, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF

value: 3 hours


title: JM8.N4 mESC, clone A ∆CTCF 3h, CTCF ChIP-seq, rep. 1

value: CTCF

tag: antibody info

value: 100nM dTAG-13


title: JM8.N4 mESC, clone A ∆ZFP143 3h, CTCF ChIP-seq, rep. 1

value: Millipore-Sigma (#07-725)

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3


title: JM8.N4 mESC, clone D untreated, Micro-C, rep. 2


title: LSK, LFD, IgG, replicate 1, CUT&RUN

value: LSK

value: LFD


title: LSK, HFD, IgG, replicate 1, CUT&RUN


title: JM8.N4 mESC, clone D ∆ZFP143 3h, Micro-C, rep. 1


title: JM8.N4 mESC, clone B ∆CTCF 3h, Micro-C, rep. 2


title: JM8.N4 mESC, clone B untreated, CTCF ChIP-seq, rep. 1


title: placenta_21

value: placenta


title: JM8.N4 mESC, clone B untreated, Micro-C, rep. 2


title: placenta_25

value: smoker


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Micro-C, rep. 2

value: Clone A, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF

value: 100uM 5-Ph-IAA/300nM HaloPROTAC3/100nM dTAG-13


title: JM8.N4 mESC, clone A ∆ZFP143 3h, Micro-C, rep. 2


title: LSK, LFD, IgG, replicate 3, CUT&RUN


title: placenta_20


title: JM8.N4 mESC, clone D untreated, Micro-C, rep. 1

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF


title: LSK, LFD, H3K4me3, replicate 1, CUT&RUN


title: placenta_22


title: JM8.N4 mESC, clone B ∆CTCF 3h, Micro-C, rep. 1

value: Mouse embryonic stem cell


title: LSK, LFD, H3K4me3, replicate 3, CUT&RUN


title: placenta_18


title: JM8.N4 mESC, clone B ∆ZFP143 3h, Micro-C, rep. 1


title: JM8.N4 mESC, clone A ∆CTCF 3h, Micro-C, rep. 2


title: JM8.N4 mESC, clone A untreated, Micro-C, rep. 2


title: placenta_17


title: placenta_19


title: LSK, HFD, H3K4me3, replicate 3, CUT&RUN

value: HFD


title: JM8.N4 mESC, clone A ∆CTCF 3h, Micro-C, rep. 1


title: placenta_16


title: JM8.N4 mESC, clone B ∆ZFP143/∆CTCF 3h, Micro-C, rep. 1


title: LSK, LFD, H3K4me3, replicate 2, CUT&RUN


title: LSK, LFD, H3K4me3, replicate 4, CUT&RUN


title: JM8.N4 mESC, clone B untreated, Micro-C, rep. 1


title: placenta_15


title: Jejunum-2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
quality control was done with fastqc (v0.12.0)
reads weremapped to the mm39 reference genome using the STAR (v2.7.0a) aligner with the --quantMode GeneCounts option to immediatly obtain counts per genes for each sample
The DESeq2 package was used to process the counts and determine differential gene expression
Assembly: mm39
Supplementary files format and content: atab delimited tekst file with raw counts for each sample

source_name: small intestine

growth_protocol: Mice wer kept in an SPF animal housing with at libitum access to food and water

extract_protocol:
A piece of the duodenum, jejunum and ileum was isolated from each mouse and processed into a single cel suspension. Cells were sorted using a FACS and paneth cells were collected for RNA isolation. RNA was isolated using an aurum total RNA mini kit accorting to the manufacturers instructions
library preparation was done with the illumina truseq stranded mRNA library kit according to the manufacturers instructions

value: small intestine

value: paneth cells

value: WT


title: LSK, HFD, H3K4me3, replicate 2, CUT&RUN


title: placenta_14


title: JM8.N4 mESC, clone A ∆ZFP143/∆CTCF 3h, Micro-C, rep. 1

value: 3 hours


title: Jejunum-1


title: placenta_13


title: LSK, HFD, H3K4me3, replicate 1, CUT&RUN


title: JM8.N4 mESC, clone B ∆ZFP143 3h, Micro-C, rep. 2

value: Clone B, Homozygous Rosa26-OsTIR1(F74G), Homozygous ZFP143-mAID2-HaloTag-V5, Homozygous FLAG-SNAPftag-FKBP12(F36V)-CTCF


title: JM8.N4 mESC, clone A ∆ZFP143 3h, Micro-C, rep. 1


title: Jejunum-4


title: SYN_11452

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Sequencing reads were mapped to hg38 following the processing steps described by Pidsley and colleagues [PMID: 36178085].
Adaptor sequences and poor quality bases were removed using Trim Galore (v0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters. bwa-meth (v0.10) was used to align reads to hg19 using default parameters. PCR duplicates were removed using Picard (v1.91, http://broadinstitute.github.io/picard). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using the ‘tabulate’ module of bwa-meth and BisSNP (v0.82.2) with default parameters.
Assembly: hg38
Supplementary files format and content: tsv file containing counts of C (methylated) and coverage at each CpG site assayed

source_name: Prostate tumour

extract_protocol:
Fresh-frozen tissue cores (10x5mm) were retrieved and matched H&E slides reviewed by a specialist pathologist to identify areas of tumour. Regions of high tumour content were microdissected from the core and DNA extracted using the Qiagen AllPrep kit (Qiagen).
Whole genome bisulphite sequencing libraries were prepared for prostate cancer tissue samples using the CEGX TrueMethyl Whole-Genome kit (v3.1) (Cambridge Epigenetics, UK) with minor improvements as described by Nair and colleagues [PMID: 29807544]. Libraries were run on the HiSeq X Ten with one sample per lane.

value: Prostate tumour


title: SYN_5656


title: JM8.N4 mESC, clone A untreated, Micro-C, rep. 1


title: Jejunum-3


title: Ileum-1


title: SYN_16599


title: Duodenum-4


title: Ileum-4


title: Ileum-2


title: Ileum-3


title: Duodenum-3


title: SYN_12543


title: placenta_11


title: SYN_10651


title: Duodenum-1


title: JM8.N4 mESC, clone A untreated, CTCF ChIP-seq, rep. 1

value: Homo sapiens

value: CTCF

value: Millipore-Sigma (#07-725)


title: SYN_15917


title: placenta_9


title: placenta_7


title: Duodenum-2


title: placenta_10


title: HEK293T, SF3B4, rep1

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
Upstream data analysis pipeline was based on the published eCLIP article.
Raw reads were demultiplexing based on barcodes with clipper scripts.
Reads were trimmed twice with cutadapt (v3.4).
Repetitive elements were removed with STAR (v2.7.0d).
Clean reads were aligned to hg19 genome with STAR (v2.7.0d)
PCR duplicate were removed with clipper scripts.
Aligned reads were used to call peaks and normalizing peaks with clipper scripts.
All PQS were analyzed with custom scripts.
Assembly: hg19;  hg38.bw files aligned to hg38
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
Total RNA was harvested using RIPA-Strong (Beyotime Biotechnology).
library was constructed according to the previous reported articl (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP)

treatment_protocol: HEK293T cells were grown in 15 cm dishes at 70 to 80% confluency. Cells were transfected with pIRES2-G4PID-EGFP plasmid or pIRES2-miniTurboID-EGFP using lipofectamine 3000 (Thermo Scientific) and replaced the fresh DMEM after 6 h. The transfected cells were cultured for 24 h before labeling. Biotin (Sigma-Aldrich) was dissolved in DMSO as 500 mM stock solution and added to the warm DMEM media to a final concentration of 500 μM. The cells (~ 20 million) were treated with biotin (500 μM) for 30 min at 37℃, labeling reaction was stopped by moving the cells onto the ice and washing five times with 5 mL ice-cold PBS. The cell pellets were either treated directly or frozen at –80°C until use.

tag: antibody


title: placenta_12


title: HEK293T, input, rep1


title: tdTom neg cells, Het3

city: Stockholm

first: David

last: Grommisch

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

data_processing:
Samples were sequenced using a NovaSeq6000 platform (Illumina) on a single lane with 2x50bp reads. A quality check (Fast QC/0.11.5) was run on raw sequencing reads. Reads were aligned using the mm10 reference genome (GRCm38, vM25 annotation) and star alignment tool (v2.7.2b), indexed and sorted using samtools (v1.10) and featurecount matrix created using subread (v2.0.0).
Data was analyzed using DESeq2 (v 1.30.0) using tdTOMATO+ cells of TroyWT/KI and TroyKI/KI mice as a contrast. Only genes with a total count >10 were kept for subsequent analysis. Regularized logarithm transformed data was used for data visualization. clusterProfiler (v 3.18.0) was utilized for GO enrichment analysis with a simplified cutoff of 0.5.
Assembly: mm10
Supplementary files format and content: txt files for raw counts and annotation

source_name: oesophagus

extract_protocol:
The esophageal muscle layer and submucosa were removed mechanically and after enzymatic treatment. The epithelium was minced and incubated in DNaseI and LiberaseTM. After incubation, the cells were filtered and stained with CD324-PE/Cy7  and CD104-A647. Using FACS, the progenitor cells (CD324+CD104+) were isolated based on tdTomato reporter expression.
RNA of 2000 cells per sample was isolated and libraries prepared according to Picelli et al. (Picelli, Simone, et al. "Smart-seq2 for sensitive full-length transcriptome profiling in single cells." Nature methods 10.11 (2013): 1096-1098).

value: oesophagus

tag: strain

value: epithelial

value: 1% Tamoxifen in ethanol 24 hours prior to euthanasia

value: 10-14 weeks


title: esophageal epithelial cells, lane2

library_source: transcriptomic single cell

data_processing:
Samples were sequenced using a NovaSeq6000 platform (Illumina). The sample was run on two lanes of the same flowcell. 10X's CellRanger v3.0.1 pipeline was used for pre-processing of the data by NGI-Sweden. The reads were mapped to mm10 reference genome with Cell Ranger pipeline (version 3.0.1) with default parameters.
Only cells which met the following criteria were included for further analysis: more than 2000 read counts in more than 1000 genes and having less than 25% mitochondrial genes. 9309 out of 11164 cells were kept. Genes that were not expressed were filtered out. The UMI count matrix was analyzed by RaceID v0.1.3 to identify cell clusters.
Assembly: mm10
Supplementary files format and content: matrix and rds files

source_name: esophagus

extract_protocol:
The esophageal muscle layer and submucosa were removed mechanically and after enzymatic treatment. The epithelium was minced and incubated in DNaseI and LiberaseTM. After incubation, the cells were filtered and stained with CD49f-PE and CD104-A647. Using FACS, double-positive cells (CD49f+CD104+) were isolated.
RNA isolation and library preparation of the sorted CD104/CD49f double positive epithelial cell solution for the 10X Chromium platform were conducted by NGI-Sweden (National Genomic Infrastructure) at SciLifeLab, Stockholm.

value: esophagus

tag: genotype

value: TroyWT/WT


title: HEK293T, input, rep2


title: tdTom pos cells, Het3

tag: tissue


title: esophageal epithelial cells, lane1


title: placenta_4

value: placenta

value: smoker


title: placenta_8


title: tdTom neg cells, Het4


title: tdTom neg cells, Het2


title: HEK293T, SF3B4, rep2

tag: cell line


title: tdTom pos cells, Het2

tag: cell type


title: tdTom pos cells, Het4

tag: age


title: placenta_5


title: HEK293T, G4PID, rep2

value: anti-HA (Thermo, #88836)


title: placenta_6


title: HEK293T, G4PID, rep1


title: AB2

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

institute: UVA

data_processing:
Reads were aligned to Danio rerio reference genome using  using DESeq2.
Assembly: GRCz11
Supplementary files format and content: tsv files with estimated counts (est_counts) and transcripts per million (tpm) for each gene

organism: Danio rerio

source_name: liver

extract_protocol:
Adult fish were euthanized, livers were dissected and collected in PBS. RNA was extracted using TRIzol and Direct-zol RNA MiniPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: wild type AB

tag: Stage

value: adult


title: AB1


title: tdTom pos cells, Het1


title: tdTom neg cells, KO4


title: AG1B, HGPS, Passage14, 1

city: Ottawa

first: William

middle: L.

last: Stanford

state: Ontario

address: 501 Smyth

department: The Sprott Centre for Stem Cell Research,

country: Canada

institute: The Ottawa Hospital Research Institute

data_processing:
HISAT2 was used to map the reads to the GRCh38 genome using the Gencode v27 transcript annotations to guide alignment to spliced transcripts, plus the ERCC spike-in transcript sequences and transcript definitions
Individual count files generated by featureCount
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

growth_protocol: Vascular smooth muscle cells were maintained in VSMC differentiation medium (Medium 231) and differentiation growth supplement

extract_protocol:
RNA was harvested using Nucleospin RNA kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using HiSeq SBS V4 kit following manufacturer's protocols.

treatment_protocol: To differentiate iPSCs to VSMCs, embryoid bodies (EB) were generated from iPSCs by treatment with Collagenase IV for 30min before being dislodged with cell scraper. Dislodged cell clusters were then plated for 7-10days in EB medium. EBs were plated on 0.1% gelatin coated plates for 3-5 days. EB outgrowths were trypsinized and cells were plated on Medium 231 and differentiation growth supplement.

tag: condition

value: Hutchinson-Gilford Progeria syndrome (HGPS)

value: vascular smooth muscle cells

value: LMNA c.1824C>T

value: vascular smooth muscle cells differentiation


title: placenta_1

extract_protocol:
DNA, RNA, and miRNA were simultaneously extracted from placenta, powdered under liquid N2, using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).
Total RNA was sent to MedGenome Inc. (Foster City, CA, USA) for RNA QC, library preparation, and sequencing. cDNA libraries were generated using the Illumina Stranded Total RNA kit (Illumina, CA, USA) and sequenced using 100bp paired-end reads on the HiSeq 2500 platform (Illumina, CA, USA).


title: AG1B, HGPS, Passage7, 2


title: 3b2

value: capn3b-/- mutant


title: tdTom pos cells, KO4

value: oesophagus


title: tdTom neg cells, Het1

value: epithelial


title: AB3


title: placenta_3


title: tdTom neg cells, KO3

value: 1% Tamoxifen in ethanol 24 hours prior to euthanasia


title: AG1B, HGPS, Passage7, 1


title: AG1B, HGPS, Passage14, 2


title: 0031C, HGPS, Passage14, 2


title: 3b3


title: Caco2 185+2.7kb del5.1kb #297 viewpoint +48.9kb Rep. 1

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 4C-seq library with the CFTR +48.9kb region as the viewpoint

data_processing:
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: Aligned 4C-seq of each sample of at a single viewpoint in bigWig format

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925).
All libraries were constructed with Illumina sequencing adapters as per PMID: 31351925.
4C-seq

value: human colorectal adenocarcnioma cell line


title: 3b1


title: Caco2 185+2.7kb del5.1kb #297 viewpoint +48.9kb Rep. 2


title: tdTom neg cells, KO2

value: 10-14 weeks


title: 0031C, HGPS, Passage7, 2


title: tdTom pos cells, KO2


title: Caco2 185+2.7kb del5.1kb #297 viewpoint int1 Rep. 2

description: 4C-seq library with the CFTR intron 1 region as the viewpoint


title: BJ1C, Control, Passage14, 2

value: Control

value: LMNA


title: Caco2 185+2.7kb del5.1kb #297 viewpoint int1 Rep. 1


title: 0031C, HGPS, Passage7, 1


title: tdTom neg cells, KO1


title: 0031C, HGPS, Passage14, 1


title: BJ1C, Control, Passage14, 1


title: tdTom pos cells, KO1


title: Caco2 185+2.7kb del5.1kb #297 viewpoint prom Rep. 2

description: 4C-seq library with the CFTR promoter region as the viewpoint


title: tdTom pos cells, KO3


title: Caco2 185+2.7kb del5.1kb #297 viewpoint -20.9kb Rep. 2

description: 4C-seq library with the CFTR -20.9kb region as the viewpoint


title: BJ1C, Control, Passage7, 1


title: Dox, biol rep 2

city: Clayton

first: Michael

last: Uckelmann

state: Victoria

address: 23 Innovation Walk

department: Biochemistry

institute: Monash University

description: biological replicate 2

data_processing:
reads were quality-trimmed and adapeters were removed with Trimgalore using paired-end mode and default settings
Reads were aligned to the mouse mm10 reference genome using bowtie2 in "very-sensitive" mode
mitochondrial reads were removed using a pythion script from https://github.com/harvardinformatics/ATAC-seq, PCR duplicates were removed using Picard
read pairs were fixed with Samtools fixmate
BigWig files were calculated using BamCoverage with CPM normalisation
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: broadPeak file conataing peak location

source_name: mES cells

growth_protocol: DMEM, 20 % FBS, 1x non-essential amino acids (Gibco #11140-050), 1x Glutamax (Gibco #35050-061),  PenStrep 100 u/ml (Thermo Fischer), 0.5 x EmbryoMax 2-Mercaptoethanol (Merck Millipore #ES-007-E), 2.5 ug/ml Plasmocin (Invivogen), 1000 U/ml ESGRO Leukemia Inhibitory Factor (LIF) (Merck Millipore)

extract_protocol: according to ATAC-seq kit from Diagenode (Diagenode cat nr. C01080002).

treatment_protocol: 6 days of either 1 ug/ml Doxycycline or an equivalent volume of Water

value: mES cells

value: mouse embryonic stem cells

value: TetO CP15 reporter gene casset and TetR-CBX8

value: Doxycyclin 1ug/ml


title: Caco2 185+2.7kb del5.1kb #297 viewpoint -20.9kb Rep. 1


title: Dox,  biol rep 1

description: biological replicate 1


title: Caco2 185+2.7kb del5.1kb #297 viewpoint prom Rep. 1


title: BJ1C, Control, Passage7, 2


title: Control,  biol rep 2

description: biological replicate 2


title: Gar15-13_Decitabine_1

type: genomic

description:
human breast cancer patient derived xenografts
GSM5218257

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

scan_protocol: Standard Illumina Protocol

data_processing:
All arrays were processed and normalised using the Sesame pipeline (Zhou et al. 2018) with functions inferInfiniumIChannel(), dyeBiasNL(), pOOBAH() and noob() with default arguments.
Unmethylated and methylated signal intensities are taken from the “UR” and “UG” columns respectively from the sample SigDF object
Normalised beta values from sesame::getBetas().

label: Cy5 and Cy3

source_name: Breast tumour PDX

label_protocol: Standard Illumina Protocol

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. MCF7 and TAMR cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol: For the LNCaP, PrEC, TAMR and MCF7 cells and PDX samples genomic DNA was isolated using the QIAamp DNA Mini kit (Qiagen). For the prostate tumour samples fresh-frozen tissue cores (10x5mm) were retrieved, and matched H&E slides reviewed by a specialist pathologist to identify areas of tumour. Regions of high tumour content were microdissected from the core and DNA extracted using the Qiagen AllPrep kit (Qiagen).

treatment_protocol: For the breast cancer PDX model mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC) and treated until ethical end-point. For the TAMR cell experiments cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35.

value: Breast cancer PDX model Gar15-13

value: Decitabine


title: 0901C, Control, Passage14, 2

value: vascular smooth muscle cells


title: Control, biol rep 1

description: biological replicate 1


title: hub1, rep3

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

data_processing:
Raw reads were trimmed using cutadapt v4.4 with parameters -q 15,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 20
Clean reads were aligned to the TAIR10 genome using STAR v2.7.10b with default options
Gene counts were obtained using featureCounts from subread v2.0.3 with options -s 2 -Q 5 and using the Araport11 annotation
Differential expression analyses were performed using DESeq2 v1.38.0
Assembly: TAIR10
Supplementary files format and content: Raw counts

organism: Arabidopsis thaliana

source_name: whole seedlings

extract_protocol:
Total RNA from whole seedlings was extracted using the NucleoSpin RNA Plant (Machery Nagel).
Libraries were prepared using Trueseq Stranded mRNA Illumina.

value: whole seedlings

value: 7-day-old seedlings


title: Caco2 185+2.7kb del5.1kb #297 viewpoint -80.1kb Rep. 2

description: 4C-seq library with the CFTR -80.1kb region as the viewpoint


title: hub1, rep2


title: Cerebellum, TRAP, WT, rep3

city: New York

first: Kärt

last: Mätlik

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Reads were mapped to mm10 using Rsubread (version 1.30.6) (Liao et al., 2019)
Transcript abundance was calculated using Salmon (version 0.8.2) (Patro et al., 2017)
Counts were retrieved using Tximport (version 1.8.0) (Love et al., 2016)
Normalized, fragment extended signal bigWigs were created using rtracklayer (version 1.40.6) (Lawrence et al., 2009)
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes transcript counts for each sample
Supplementary files format and content: bigWig

source_name: Cerebellum

extract_protocol:
TRAP was performed as described in (Doyle et al. 2008 and Heiman et al. 2008). Briefly, Streptavidin MyOne T1 Dynabeads were coated with biotinylated protein L for 35 min at room temperature, washed with 3% IgG and Protease-free BSA in 1× PBS and subsequently incubated with 50 µg each of 19C8 and 19F7 anti-GFP monoclonal antibodies (Memorial Sloan-Kettering Monoclonal Antibody Facility) in 0.15 M KCl TRAP wash buffer (10 mM HEPES-KOH at pH 7.4, 5 mM MgCl2, 150 mM KCl, 1% NP-40, supplemented with 100 µg/mL cycloheximide in methanol, 0.5 mM DTT, 20 U/mL RNasin) for 30 min at room temperature using end-over-end rotation. After antibody binding, the beads were washed three times with 0.15 M KCl TRAP wash buffer and resuspended in 0.15 M KCl TRAP wash buffer. Each reaction was supplemented with 30 mM DHPC. Cerebella from P21 Tg(Pcp2-Egfp-L10a) mice were dissected and placed in TRAP dissection buffer (2.5 mM HEPES-KOH at pH 7.4, 35 mM glucose, 4 mM NaHCO3 in 1× HBSS, supplemented with 100 µg/mL cycloheximide). The tissue was homogenized in chilled TRAP lysis buffer (10 mM HEPES-KOH at pH 7.4, 5 mM MgCl2, 150 mM KCl, supplemented with 0.5 mM DTT, 100 µg/mL cycloheximide, protease inhibitor cocktail, 40 U/mL RNasin, and 20 U/mL Superasin). The homogenate was centrifuged at 2000g for 10 min at 4°C. 3% of the supernatant was set aside as an input. The rest of the supernatant was supplemented with NP-40 to a final concentration of 1% and with DHPC to a final concentration of 30 mM and incubated for 5 min on ice. The samples were centrifuged at 20,000g for 10 min at 4°C, and the supernatant was used for immunoprecipitation with GFP-conjugated beads overnight at 4°C with end-over-end rotation. Subsequently, the beads were washed four times in 0.35 mM KCl TRAP wash buffer (10 mM HEPES-KOH at pH 7.4, 5 mM MgCl2, 350 mM KCl, 1% NP-40, supplemented with 100 µg/mL cycloheximide, 0.5 mM DTT, and 20 U/mL RNasin) and resuspended in 100 µL of RLT buffer from the RNeasy Micro Kit supplemented with 1% β-mercaptoethanol. The resuspended beads were incubated at room temperature for 10 min, placed on a magnet, and the supernatant containing the RNA was collected and purified using the RNeasy Micro Kit, including dsDNAse treatment. RNA integrity was determined using Bioanalyzer RNA 6000 Pico kit (Agilent) prior to RNAseq library preparation.
RNA-seq libraries were prepared from 100 ng RNA/sample using the NEBNext Ultra II RNA library preparation kit for Illumina in conjunction with the NEBNext poly(A) mRNA magnetic isolation module and NEBNext multiplex oligos for Illumina. The quality of the sequencing libraries was evaluated using the Agilent 2200 TapeStation with D1000 High-Sensitivity ScreenTape. The samples were sequenced at the Rockefeller University Genomics Resource Center using NovaSeq 6000 to obtain 50-bp single-end reads. Samples with a sufficient number of reads after QC were included in the analysis.

value: Cerebellum

value: Purkinje cells

value: WT

tag: Sex

value: male


title: 0901C, Control, Passage7, 2

tag: treatment

value: vascular smooth muscle cells differentiation


title: elf7, rep3


title: Cerebellum, TRAP, WT, rep2


title: Caco2 185+2.7kb del5.1kb #201 viewpoint +48.9kb Rep. 2

value: human colorectal adenocarcnioma cell line


title: 0901C, Control, Passage7, 1

value: Control


title: Cerebellum, TRAP, WT, rep1

value: female


title: Gar15-13_Vehicle_3

description:
human breast cancer patient derived xenografts
GSM5218255

value: Vehicle


title: HCI-005_Vehicle_1

description:
human breast cancer patient derived xenografts
GSM5218272

value: Breast cancer PDX model HCI-005


title: Caco2 185+2.7kb del5.1kb #201 viewpoint +48.9kb Rep. 1


title: elf7, rep2


title: HCI-005_Decitabine_1

description:
human breast cancer patient derived xenografts
GSM5218275


title: HCI-005_Vehicle_2

description:
human breast cancer patient derived xenografts
GSM5218273


title: Gar15-13_Decitabine_2

description:
human breast cancer patient derived xenografts
GSM5218258


title: hub1, rep1


title: Caco2 185+2.7kb del5.1kb #201 viewpoint int1 Rep. 1


title: TAMR

description: Tamoxifen-resistant MCF7

source_name: TAMR cells

value: Cell line


title: AS-sh-2

city: Guangzhou

first: Jianyou

middle: No

last: Gu

state: Guangdong

address: 253 Gongye Middle Avenue, Haizhu District

department: No

institute: Zhujiang Hospital, Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts and FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly (A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human pancreatic cancer cells

tag: genotype/variation

value: shTMPRSS4 lentivirus


title: elf7, rep1


title: Gar15-13_Vehicle_4

description:
human breast cancer patient derived xenografts
GSM5218256

value: Breast cancer PDX model Gar15-13


title: AS-sh-3


title: Cerebellum, TRAP, Astn2KO, rep4

value: Astn2 KO


title: Caco2 185+2.7kb del5.1kb #201 viewpoint int1 Rep. 2


title: Caco2 185+2.7kb del5.1kb #297 viewpoint -80.1kb Rep. 1


title: AS-NC-3

source_name: AsPC-1_TMPRSS4 NC

value: TMPRSS4 NC

value: control lentivirus


title: HCI-005_Decitabine_3

description:
human breast cancer patient derived xenografts
GSM5218277

value: Decitabine


title: Cerebellum, TRAP, Astn2KO, rep3

value: Cerebellum

value: Purkinje cells


title: SYN_16599

description: prostate tumour

value: Prostate tumour


title: WT, rep3

value: whole seedlings

value: 7-day-old seedlings

value: wild type


title: AS-sh-1


title: AS-NC-2


title: SYN_15917

description: prostate tumour


title: Cerebellum, input, WT, rep4

value: whole cerebellum

value: WT

value: male


title: Caco2 185+2.7kb del5.1kb #201 viewpoint -20.9kb Rep. 2

value: human colorectal adenocarcnioma cell line


title: SYN_11452

description: prostate tumour


title: SYN_5656

description: prostate tumour


title: Caco2 185+2.7kb del5.1kb #201 viewpoint prom Rep. 2


title: Cerebellum, TRAP, Astn2KO, rep1

value: female


title: Caco2 185+2.7kb del5.1kb #201 viewpoint prom Rep. 1


title: WT, rep1


title: PolII_elf7, rep1

data_processing:
Raw reads were trimmed using cutadapt v4.4 with parameters -q 15,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 20
Clean reads were aligned to the TAIR10 genome using bowtie2 v2.5.1 with default parameters
Duplicates were marked with sambamba v1.0. Alignments were filtered using samtools (v1.17) view with options -q 5 -F 4 -F 1024
BigWig files were obtained using bedtools (v2.31.0) genomecov and UCSC bedGraphToBigWig. Bigwigs were scaled to their normalization factors using wiggletools (v1.2.11) scale
For FLAG-ELF7, GFP-VIP3 and Pol II ChIPs, samples were scaled by sequencing depth (CPM). H2Bub samples were normalized by the amount of Drosophila reads in the IP and the input as in Nassrallah et al. 2018
Peaks were called using macs2 v2.2.7.1 with options --keep-duplicates all --nomodel --extsize 200 --broad --broad-cutoff 0.05 -gs 119144248
Assembly: TAIR10
Supplementary files format and content: Raw bigwigs
Supplementary files format and content: broadPeaks

extract_protocol:
H2B and H2Bub ChIP-Rx were conducted in parallel using the same two biological replicates of 7-day-old WT and elf7-3 seedlings grown under standard conditions. For each biological replicate, two immunoprecipitations (IP) were performed using an anti-H2Bub antibody (MM-0029-P, Medimabs) and one using an anti-H2B (ab1790, abcam). 100 µg of Arabidopsis chromatin mixed with 3 µg of Drosophila chromatin was used for each IP. DNA eluted from the two technical replicates of H2Bub IP was pooled before library preparation. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). Flag-ELF7 and GFP-VIP3 ChIP-seq was performed using 7-day-old seedlings and an anti-Flag M2 antibody (F1804, Sigma). We used double in vitro crosslinking using 1.5 mM ethylene glycol bis (succinimidyl succinate) for 20 min and then with 1% formaldehyde for 10 min at room temperature. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). ChIP-seq for RNAPII was done using the anti-NRPB1 antibody (active motif, Clone: 4H8) using similar growth conditions and protocol than for H2Bub profiling without Drosophila cells spike-in. Library preparation and sequencing were carried out by the Epigenomics platform at IPS2 (Paris, France).
Libraries were prepared using commercial kits as follows: GFP-VIP3, H2B and H2Bub with NEBNext® Ultra DNA Library Prep for Illumina® kit, PolII with NEBNext® Ultra II DNA Library Prep for Illumina® kit, and Flag-ELF7 with Ovation Ultralow System V2.

value: anti-NRPB1 (active motif, Clone:4H8)


title: Caco2 185+2.7kb del5.1kb #201 viewpoint -20.9kb Rep. 1


title: PolII_elf7, rep2


title: GB3

first: Jie

last: Yu

state: Hubei

address: Zhijinchangshan Road No.2, Jinkou, Jiangxia District

department: Institute of Animal Science and Veterinary Medicine

institute: Wuhan Academy of Agricultural Sciences

data_processing:
Use fastp (v0.21.0) (https://github.com/OpenGene/fastp) to process the raw data in fastq format to obtain clean data (clean reads).
Clean reads were mapped to the NCBI Rfam database, and rRNA sequences were removed by Bowtie2 (v2.33)(parameter default).
The sequences after ribosome removal were aligned to the Bos taurus reference genome ARS-UCD1.2  by Hisat2 (v2.2.1) software (parameter default).
RSEM (v1.3.3) was applied to obtain the read counts for each gene. Fragments per kilobase of exon per million mapped reads (FPKM) of genes in each sample were calculated to estimate gene expression levels.
Differentially expressed genes between two groups were screened with DESeq2 package (v1.34.0)（parameter |log2(Fold Change)|>1 and FDR<0.05）.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Bos taurus

source_name: endometrium

growth_protocol: BEND were cultured with DMEM/F12(Gibco, USA) containing 10% FBS(Gibco, USA) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using HiPure Universal RNA Mini Kit（Magen）. 0.6 ug of total RNA was used for the construction of sequencing libraries.
The mRNAseq library was generated using the ALFA-SEQ Directional RNaLib Prep Kit following the manufacturer's recommendations.

treatment_protocol: Comparative gene expression profiling analysis of RNA-seq data for the BEND treated with E2 (10-9 M, Sigma),P4 (10-7 M, Sigma, USA)  and IFNT (100ng/mL, Cell sicences, USA) for 12 h.

value: endometrium

value: Primary bovine endometrial epithelial cells

value: Primary epithelial cells

value: E2,P4 and IFNT stimulation


title: MCF7

description: MCF7 breast cancer cells

source_name: MCF7 cells

value: Cell line


title: AS-NC-1

value: Human pancreatic cancer cells

value: TMPRSS4 NC

value: control lentivirus


title: SYN_10651

description: prostate tumour

value: Prostate tumour


title: Cerebellum, input, WT, rep2

value: Cerebellum


title: PolII_WT, rep2

value: whole seedlings

value: 7-day-old seedlings

value: wild type


title: 0901C, Control, Passage14, 1

value: Control

value: vascular smooth muscle cells

value: LMNA

value: vascular smooth muscle cells differentiation


title: Cerebellum, input, WT, rep3

value: whole cerebellum

value: WT

value: male


title: GB2

value: endometrium

value: Primary bovine endometrial epithelial cells

value: Primary epithelial cells

value: E2,P4 and IFNT stimulation


title: PolII_WT, rep1

value: anti-NRPB1 (active motif, Clone:4H8)


title: Caco2 185+2.7kb del5.1kb #201 viewpoint -80.1kb Rep. 2

value: human colorectal adenocarcnioma cell line


title: Caco2 185+2.7kb del5.1kb #195 viewpoint +48.9kb Rep. 2


title: Cerebellum, input, Astn2KO, rep3

value: Cerebellum

value: Astn2 KO


title: GB1


title: Caco2 185+2.7kb del5.1kb #201 viewpoint -80.1kb Rep. 1


title: Cerebellum, input, Astn2KO, rep2

value: female


title: Cerebellum, input, WT, rep1


title: GA3

value: E2 and P4 stimulation


title: Caco2 185+2.7kb del5.1kb #195 viewpoint +48.9kb Rep. 1


title: GA2


title: BMSCs-derived BMAds lineage cells, EsrraKO4

city: Shenzhen

first: Tongling

address: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences  1068 Xueyuan Avenue,Shenzhen University Town,  Nanshan District, Shenzhen, China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: xls include FPKM values for each Sample

source_name: bone marrow stromal /stem cell

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: bone marrow adipocyte

value: adipocyte-specific ESRRA deficiency

value: adipogenic induction for 7days


title: GA1


title: Caco2 185+2.7kb del5.1kb #195 viewpoint int1 Rep. 2


title: CON3

value: normal


title: Caco2 185+2.7kb del5.1kb #195 viewpoint int1 Rep. 1


title: Cerebellum, TRAP, Astn2KO, rep2

value: Purkinje cells


title: LNCaP

description:
transformed prostate cancer cell line
GSM2309171

source_name: LNCaP cells

value: Cell line


title: Caco2 185+2.7kb del5.1kb #195 viewpoint prom Rep. 2


title: SYN_12543

description: prostate tumour

value: Prostate tumour


title: CON2

value: endometrium

value: WT


title: PrEC_Rep2

description:
primary cell culture of prostate epithelial cells
GSM2309173

source_name: PrEC cells


title: WT, rep2

value: whole seedlings

value: 7-day-old seedlings

value: wild type


title: BMSCs-derived BMAds lineage cells, EsrraKO2

institute: Shenzhen Institute of Advanced Technology


title: CON1

value: Primary bovine endometrial epithelial cells

value: Primary epithelial cells


title: Cerebellum, input, Astn2KO, rep1

value: Cerebellum

value: whole cerebellum

value: Astn2 KO


title: Caco2 185+2.7kb del5.1kb #195 viewpoint prom Rep. 1

value: human colorectal adenocarcnioma cell line


title: BMSCs-derived BMAds lineage cells, EsrraKO1

value: bone marrow adipocyte

value: adipocyte-specific ESRRA deficiency


title: Caco2 185+2.7kb del5.1kb #195 viewpoint -20.9kb Rep. 2


title: BMSCs-derived BMAds lineage cells, EsrraFLOX4

value: adipogenic induction for 7days


title: Caco2 185+2.7kb del5.1kb #195 viewpoint -20.9kb Rep. 1


title: H1_Hypoxic_Primed_Batch2

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Cyanine 3-labeled cRNAs were hybridized onto Agilent Whole Human Genome kit 4 x 44K slides (Catalog number G4112F, Agilent Technologies) containing 44,397 oligonucleotide probes in 2X Hi-RPM Hybridization buffer (Catalog number 5188-5242, Agilent Technologies) at 65°C for 17 hours at 10 r.p.m. as recommended.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Sample amplification and labeling were carried out using the Low Input Quick Amp labeling Kit (Catalog number 5190-2305, Agilent Technologies, Santa Clara, CA). Briefly, total RNAs (200 ng) were reverse transcribed into cDNAs using T7 primer mix in 5X First Strand Buffer, 0.1 M DTT, 10 mM dNTP Mix, and Affinity Script RNase Block Mix. The cDNAs were used to synthesize Cy3-labeled cRNAs in a reaction containing nuclease-free water, 5X Transcription Buffer, 0.1 M DTT, NTP Mix, T7 RNA polymerase blend, and Cyanine 3-CTP. The RNeasy Mini Kit (QIAGEN) was used to purify the linearly amplified cRNA samples. Cyanine 3-labeled cRNAs were measured using the NanoDrop Spectrophotometer.

growth_protocol: Three NIH registered human embryonic stem cell (hESC) lines, H1 (WA01, registration number 0043), H7 (WA07, registration number 0061), and H9 (WA09, registration number 0062), were used in this study. All three hESC lines were obtained from WiCell Research Institute (Madison, WI) and previously extensively characterized in our NIH Stem Cell Unit (Chen et al., 2014a; Chen et al., 2012; Mallon et al., 2013). More detailed information regarding these hESC lines is available at the website of the NIH Stem Cell Unit (stemcells.nih.gov/research/).

extract_protocol: RNA was extracted by using the basic Trizol protocol (Invitrogen Inc., Carlsbad, CA) with slight modifications. Briefly, hESCs per sample were dissolved in 1 mL of the Trizol solution and stored in - 80°C freezer prior to use. HESC lysates were further subjected to chloroform extraction and isopropanol precipitations. A DNA-Free kit (Applied Biosystems/Ambion, Austin, TX) was used to remove genomic DNA contamination. The quality of RNAs was agarose gel verified. RNA concentration was determined by using the ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies Wilmington, DE).

treatment_protocol: The human primed hESC lines H1, H7, and H9 (at passages 55, 57, and 56, respectively) were used to generate naïve-like hESCs. After 3-day induction or selection of primed hESCs in RSeT medium, the cell colonies (in each well) were dissociated as a single-cell suspension by TrypLE™ Express (ThermoFisher Scientific, REF number 12604-013) and passaged on mouse embryonic fibroblast (MEF) feeder in a 1:6 split ratio. The cells were grown in a humidified incubator with 5% CO2, 3% O2 (hypoxia), and 20% O2 (normoxia). The ROCK inhibitor Y-27632 (10 µM) was added to enhance single-cell plating efficiency for the initial 3 passages. The RSeT naïve-like hESCs were fully characterized at passages 4 and 10 in this study. Two batches (Batch1 and Batch2) of primed hESCs (at passages 55, 56, and 57) were used as controls for comparison.

tag: line

tag: growth condition

value: Hypoxic

tag: state

value: Primed

tag: passage

tag: batch


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t4 DMSO R2

city: Worcester

first: Job

last: Dekker

address: 368 Plantation Street

institute: University of Massachusetts Medical School/HHMI

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) reads.
Assembly: hg38

source_name: uterine/cervical adenocarcinoma cell line

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

value: HeLa-S3 (CCL-2.2)


title: BMSCs-derived BMAds lineage cells, EsrraKO3


title: H9_Hypoxic_RSeT_Passage10

value: Naive-like


title: BMSCs-derived BMAds lineage cells, EsrraFLOX3


title: BMSCs-derived BMAds lineage cells, EsrraFLOX2


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t0 Mitotic R2


title: H9_Hypoxic_Primed_Batch2


title: Caco2 185+2.7kb del5.1kb #195 viewpoint -80.1kb Rep. 2


title: H7_Hypoxic_Primed_Batch2


title: Caco2 185+2.7kb del5.1kb #195 viewpoint -80.1kb Rep. 1


title: H7_Hypoxic_RSeT_Passage10


title: H9_Normoxia_Primed_Batch2

value: Normoxia


title: H1_Normoxia_Primed_Batch2


title: H1_Hypoxic_RSeT_Passage10


title: Caco2 185+5.7kb del2.1kb #318 viewpoint +48.9kb Rep. 2


title: H7_Normoxia_Primed_Batch2


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: ICRF-193 R3

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38

source_name: colorectal carcinoma cell line

growth_protocol: HCT116 + Rad21-mAID-mClover cells were cultured in glutamax McCoy's 5A Modified Medium supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were treated with 30uM ICRF-193 and Ethanol for 2 hours before fixation. G1 cells were isolated by FACS.

value: colorectal carcinoma cell line


title: Caco2 185+5.7kb del2.1kb #318 viewpoint +48.9kb Rep. 1


title: α-cdKO, Replicate 2, scRNAseq

first: Robert

middle: S.

last: Krauss

address: One Gustave L. Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequenced fastq files were aligned, filtered, barcoded and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 7.1.0, by 10X Genomics with Cell Ranger, GRCm38 database (version 2020-A) as the mouse genome reference
Each dataset was filtered to retain cells with ≥ 1000 UMIs, ≥ 400 genes expressed, and <15% of the reads mapping to the mitochondrial genome
The top 2000 most highly variable genes were identified using the “vst” selection method of “FindVariableFeatures” function and counts were scaled using the “ScaleData” function from the Seurat package (version 4.0.3) (Hao et al., 2021).
Assembly: mm10
Supplementary files format and content: Tab-separated filtered values files and matrix files

source_name: skeletal muscle

extract_protocol:
Cells were pelleted at 300g for 5 minutes before washing with ice cold Hanks’ Balanced Salt Solution without magnesium and calcium supplemented with 2% FBS and 1mM EDTA (HBSS+), pelleting again, and resuspending in 4ml of HBSS+. Samples were kept on ice and counterstained with SYTOX Blue before FACS isolation of MuSCs. Each sample was pooled from two littermate mice of the same genotype with 2 samples sequenced per genotype. A Sony MA900 equipped with a 100μm nozzle and 20 psi pressure was used for FACS isolation.
Droplet-based scRNA-seq (Chromium, 10x Genomics) was applied to single-cell suspensions of tdTomato+ cells from 2 WT and 2 α-cdKO samples (2 mice pooled per sample); 3 × 10^4 cells were loaded per well for each of the 4 samples, and partitioning and library preparation were performed according to the manufacturer’s protocol for the 3′ v.3 chemistry.

value: skeletal muscle

value: 3-4 months old

value: MuSC

value: a-cdKO


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA R3

treatment_protocol: Cells were treated with DMSO and 500uM IAA for 2 hours before fixation. G1 cells were isolated by FACS.


title: DpnII Hi-C on HeLa S3 MR DMSO or Merb added at t2: t4 Merb R2

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 200uM Merbarone was added at t2hr. Cells were fixed at t4hr.


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: Control R3

treatment_protocol: Cells were treated with DMSO and Ethanol for 2 hours before fixation. G1 cells were isolated by FACS.


title: H9_Normoxia_RSeT_Passage10


title: Caco2 185+5.7kb del2.1kb #318 viewpoint int1 Rep. 1


title: Control, Replicate 2, scRNAseq

value: control


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA + ICRF-193 R3

treatment_protocol: Cells were treated with 30uM ICRF-193 and 500uM IAA for 2 hours before fixation. G1 cells were isolated by FACS.


title: α-cdKO, Replicate 1, scRNAseq


title: H7_Normoxia_RSeT_Passage10


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: ICRF-193 R2


title: Caco2 185+5.7kb del2.1kb #318 viewpoint int1 Rep. 2


title: H1_Normoxia_RSeT_Passage10


title: Caco2 185+5.7kb del2.1kb #318 viewpoint prom Rep. 2


title: H9_Hypoxic_Primed_Batch1


title: BMSCs-derived BMAds lineage cells, EsrraFLOX1

value: wild type


title: Control, Replicate 1, scRNAseq


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA + ICRF-193 R2


title: Caco2 185+5.7kb del2.1kb #318 viewpoint -20.9kb Rep. 2


title: C_BI15_mCD45

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

description: 10x Genomics

data_processing:
Data analysis was executed utilizing the Cell Ranger Software Suite (10x Genomics). The binary base call (BCL) files extracted from the sequencer were employed as inputs for the Cell Ranger pipeline to produce the digital expression matrix for each sample. Subsequently, the matrix, along with the features and barcodes, was imported into R using the read10X() and CreateSeuratObject functions to construct the count matrix and Seurat objects for further downstream analysis.
Assembly: hg38
Supplementary files format and content: Cell-gene matrix, barcodes and genes

source_name: Immune cells

extract_protocol:
Bone marrow cells (the tumor site) harvested from experimental animals at Day 28 were subjected to FACS sorting for isolating mouse immune cells (mouse CD45+; Sample_01: blank mice, Sample_02: vehicle treated, Sample_03: BCAR-T treated, Sample_04: Allo15BCAR-NKT treated). Cells isolated from 10 experimental mice were combined for each group.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Bone marrow

tag: time point

value: Immune cells


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: IAA R2


title: DpnII Hi-C on HCT116 + Rad21-mAC async 2hr: Control R2


title: Caco2 185+5.7kb del2.1kb #318 viewpoint prom Rep. 1

value: human colorectal adenocarcnioma cell line


title: C_Blank_m45

description: 10x Genomics


title: Caco2 185+5.7kb del2.1kb #318 viewpoint -20.9kb Rep. 1


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA + ICRF-193 R2

treatment_protocol: Cells were treated with 30uM ICRF-193 and 500uM IAA for 1 hour before fixation. G1 cells were isolated by FACS.


title: C_ctrl_m45

description: 10x Genomics


title: H7_Hypoxic_RSeT_Passage4


title: H9_Hypoxic_RSeT_Passage4


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: ICRF-193 R2

treatment_protocol: Cells were treated with 30uM ICRF-193 and Ethanol for 1 hour before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #318 viewpoint -80.1kb Rep. 2


title: H1_Hypoxic_RSeT_Passage4


title: Caco2 185+5.7kb del2.1kb #318 viewpoint -80.1kb Rep. 1


title: intestinal organoids, NIBR_LTSi_3

city: Basel

first: Clara

last: Baader

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

data_processing:
Sequenced reads were aligned using the qAlign tool
Raw counts were optained using the qCount tool (QuasR package, version 1.32.0)
Count table was filtered to only keep genes which had at least 1 cpm in at least 3 samples
Differential gene expression was calculated edgeR (Bioconductor, version 3.34.0)
Assembly: BSgenome.Mmusculus.UCSC.mm10
Supplementary files format and content: Raw counts expression matrix .txt file

source_name: small intestine

extract_protocol:
Organoids were digested to single cells and RNA extracted using RNeasy RNA purification Kit.
200ng of total RNA was used as input for the Illumina Stranded mRNA Prep

treatment_protocol: Organoids were treated for 24h with 5uM of NIBR-LTSi or corresponding amounts of DMSO

value: small intestine

value: organoid

value: NIBR-LTSi


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: IAA R2

treatment_protocol: Cells were treated with DMSO and 500uM IAA for 1 hour before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #314 viewpoint +48.9kb Rep. 2


title: DpnII Hi-C on HCT116 + Rad21-mAC async 1hr: Control R2

treatment_protocol: Cells were treated with DMSO and Ethanol for 1 hour before fixation. G1 cells were isolated by FACS.


title: Caco2 185+5.7kb del2.1kb #314 viewpoint +48.9kb Rep. 1


title: H9_Normoxia_Primed_Batch1

value: Primed