title: KO_PA_24h_rep3

city: Gothenburg

first: Marc

last: Pilon

address: Medicinaregetan 9 (BOX462)

department: Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

description: Supplemental_Table_S2_RNASEQ_normalized_counts.txt

data_processing:
Sequencing reads were processed with the bcbio pipeline and mapped to the human genome (hg38).
RNA-seq counts were generated using Salmon [32] which is an alignment free method that maps reads to human transcript sequences.
Counts were imported into R using tximport [33] and collapsed to the gene level.
The raw counts were adjusted using DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates [34].
Normalized counts were imported into Qlucore Omics Explorer n.n (Qlucore AB) for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Duplicates were “collapsed” to median values, resulting in a data set containing 54962 unique symbols (distinct transcripts) with read counts from each replicate. A threshold of 1 was applied to all entries and the counts were log2 transformed. The data were normalized for the purpose of heat map visualization (mean=0; variance=1). GSEA for KEGG and REACTOME pathways v6.1 were done using two group comparisons where the KO24hPA treatment was compared to the other treatments using the following settings: min match set size=15, max match set size=500, permutations=100000, permutation method: variables and enrichment weight=1. The normalized RNAseq counts are provided in supplemental Table S2.

source_name: HEK293 ADIPOR2 Knockout

growth_protocol: HEK293T cells were grown in DMEM containing glucose 1 g/l, pyruvate and GlutaMAX and supplemented with 10% fetal bovine serum, 1% non-essential amino acids, HEPES 10 mM and 1% penicillin and streptomycin (all from Life Technologies) at 37 ̊C in a water-humidified 5% CO2 incubator.

extract_protocol:
RNA was isolated using a RNeasy Mini Kit (Qiagen) with DNase treatment as per the manufacturer’s instructions. RNA concentration and quality was measured on a Fragment Analyser (Advanced Analytical Technologies). RNA integrity number greater than 9 was set as a quality control cut off for library preparation using 1 µg of total RNA.
Poly(A) selected pair-end sequencing libraries were generated using the Illumina TrueSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Library quantification was assessed using the Standard Sensitivity NGS Kit (Advance Analytical Technologies) on a Fragment Analyser. Libraries were pooled and quantified on a Qubit Fluorometer using a DNA HS kit (ThermoFisher) followed by dilution to 1.8 pM before being sequenced using an Illumina NextSeq 500 Sequencer (Illumina).

treatment_protocol: Palmitic acid (PA; 16:0) was dissolved in sterile DMSO then mixed with fatty acid-free bovine serum albumin BSA (all from Sigma) in serum-free medium for 15 min at room temperature. The molecular ratio of BSA to fatty acid was 2.65 for 200 μM of PA. Cells were then cultivated in this serum-free medium containing PA for 3, 6, 9 or 24 h prior to analysis.

tag: cell

value: embryonic kidney cell line

value: 1% BSA + 200µM Palmitic acid

tag: medium

value: Serum-free, 1% BSA


title: H69, replicate 1

status: Public on Jan 18 2021

type: RNA

city: Hospitalet d'Llobregat

first: manuel

last: torres diz

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: PEBC

country: Spain

institute: IDIBELL

description: Gene expression analysis on parental cell line

hyb_protocol: Hibridaded on the Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494

scan_protocol: G2505B DNA microarray scanner

data_processing: Data was procesed with limma R Bioconductor

molecule: total RNA

organism: Homo sapiens

source_name: cell line

label_protocol: 100 ng of total RNA were labeled with Cy3

growth_protocol: All cell lines were growth acording to ATTC recommendations

extract_protocol: RNA was extracted using Maxwell® RSC simplyRNA Tissue Kit (Ref. AS1340) and following

treatment_protocol: None of the cells were treated

tag: cell line


title: KO_PA_24h_rep2

type: SRA

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: KO_PA_24h_rep1


title: F-2

city: Nagoya

first: Kousuke

last: Okimura

address: Furocho

country: Japan

institute: Nagoya University

description: Gene expression under SC condition at 22 hrs later from midnight

data_processing:
RNA-seq reads were aligned to mouse reference genome and annotation (Mus musculus (GRCm38.p6), index and annotation packages) using HISAT2 (version 2.0.4).
Gene expression levels were calculated by RNA-seq by Expectation-Maximization (RSEM)
Genome_build: Mus musculus (GRCm38.p6)
Supplementary_files_format_and_content: Excel file include Gene expression for each sample.

organism: Mus musculus

source_name: SC eyes collected at 22 hrs later from midnight

growth_protocol: Mouse (Mus musculus) were obtained from a local dealer and kept under SC or LW conditions.

extract_protocol:
Total RNA of eyes were isolated with elimination of DNA contamination using DNase.
According to TruSeq Stranded mRNA Sample Preparation Guide (Illumina), the cDNA libraries were prepared using TruSeq stranded mRNA LT sample prep kit (Illumina).

treatment_protocol: Mouse were kept under SC or LW conditions for 4 weeks. After that, mouse eyes were collected every 4 hours from middnight.

tag: strain

value: CBA/N

tag: tissue

value: eye

tag: gender

value: male


title: H1963, replicate 1


title: Fs-1

description: Gene expression under LW condition at 22 hrs later from midnight

source_name: LW eyes collected at 22 hrs later from midnight


title: F-1

value: SC condition at 22 hrs later from midnight


title: KO_PA_9h_rep3


title: Es-2

description: Gene expression under LW condition at 18 hrs later from midnight

source_name: LW eyes collected at 18 hrs later from midnight


title: U2OS WDR5-FKBP(F36V) RNA-seq DMSO rep3 [DMSO_3]

status: Public on Jan 19 2021

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

country: USA

institute: Vanderbilt University Medical Center

description:
4489-AG-3_S1
processed data file: U2OS-WDR5-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each Sample

source_name: U2OS WDR5-FKBP(F36V) RNA-seq DMSO

growth_protocol: All cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment. RNA was submitted to GENEWIZ or the Vanderbilt Technologies for Advanced Genomics Core Laboratory for rRNA reduction, library preparation, and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: engineered genotype

value: endogenous C-terminal tag on WDR5, FKBP(F36V)-2xHA

value: 0.01% DMSO for 24 hours


title: Es-1

value: LW condition at 18 hrs later from midnight


title: E-2

description: Gene expression under SC condition at 18 hrs later from midnight

source_name: SC eyes collected at 18 hrs later from midnight


title: KO_PA_9h_rep2


title: KO_PA_3h_rep1


title: KO_PA_3h_rep2


title: KO_PA_3h_rep3


title: E-1

value: SC condition at 18 hrs later from midnight


title: H446, replicate 3


title: KO_BSA_24h_rep3

value: 1% BSA


title: KO_BSA_24h_rep2


title: HCC33, replicate 1


title: D-2

description: Gene expression under SC condition at 14 hrs later from midnight

source_name: SC eyes collected at 14 hrs later from midnight


title: KO_BSA_9h_rep3


title: KO_BSA_24h_rep1


title: Ds-1

description: Gene expression under LW condition at 14 hrs later from midnight

source_name: LW eyes collected at 14 hrs later from midnight


title: D-1

value: SC condition at 14 hrs later from midnight


title: KO_BSA_9h_rep2


title: KO_PA_9h_rep1


title: H69, replicate 2


title: H446, replicate 1


title: HCC33, replicate 3


title: Cs-2

description: Gene expression under LW condition at 10 hrs later from midnight

source_name: LW eyes collected at 10 hrs later from midnight


title: N417, replicate 1


title: H446, replicate 2


title: N417, replicate 2


title: CORL95, replicate 3


title: CORL95, replicate 2


title: CORL95, replicate 1


title: Cs-1

value: LW condition at 10 hrs later from midnight


title: C-2

description: Gene expression under SC condition at 10 hrs later from midnight

source_name: SC eyes collected at 10 hrs later from midnight


title: KO_BSA_3h_rep3


title: C-1

value: SC condition at 10 hrs later from midnight


title: KO_BSA_3h_rep2


title: Bs-2

description: Gene expression under LW condition at 6 hrs later from midnight

source_name: LW eyes collected at 6 hrs later from midnight


title: Ds-2

value: LW condition at 14 hrs later from midnight


title: B-2

description: Gene expression under SC condition at 6 hrs later from midnight

source_name: SC eyes collected at 6 hrs later from midnight


title: KO_full_rep3

value: Full medium

value: Full medium (10% FBS)


title: KO_full_rep1

value: embryonic kidney cell line


title: KO_BSA_3h_rep1

value: Serum-free, 1% BSA


title: As-2

description: Gene expression under LW condition at 2 hrs later from midnight

source_name: LW eyes collected at 2 hrs later from midnight

value: CBA/N


title: WT_PA_24h_rep3

source_name: HEK293 ADIPOR2 Wildtype

value: 1% BSA + 200µM Palmitic acid


title: KO_full_rep2


title: Bs-1

value: eye

value: male

value: LW condition at 6 hrs later from midnight


title: As-1

value: LW condition at 2 hrs later from midnight


title: WT_PA_24h_rep2


title: B-1

value: SC condition at 6 hrs later from midnight


title: A-2

description: Gene expression under SC condition at 2 hrs later from midnight

source_name: SC eyes collected at 2 hrs later from midnight


title: WT_PA_24h_rep1


title: WT_PA_9h_rep3


title: KO_BSA_9h_rep1


title: A-1

value: SC condition at 2 hrs later from midnight


title: WT_PA_9h_rep2


title: WT_PA_9h_rep1


title: RNA-seq_CTCF0 mutant, rep3

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: strand-specific RNA library

data_processing:
Reads were aligned against Drosophila melanogaster genome assembly release 6 (dm6) using MicMap (v2.0)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using Drosophila melanogaster genome assembly Release 6 gene annotations (dmel_r6.26_FB2019_01) retrieved from Flybase
Genome_build: Drosophila_melanogaster release 6 (dm6)
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts

organism: Drosophila melanogaster

source_name: third instar larval central nervous system

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
60 larval central nervous systems per replicate were homogenized in TRIzol LS with pestles on ice. 1 µg of total RNA was subjected to mRNA enrichment with NEBNext Oligo d(T)25 beads.
Standard RNA-seq libraries were generated with the NEBNext Ultra directional RNA library prep kit

value: central nervous system

tag: age

value: third instar larva

tag: genotype

value: CTCF[0] mutant


title: RNA-seq_CTCF0 mutant, rep2

description: strand-specific RNA library


title: WT_PA_3h_rep3


title: WT_PA_3h_rep2


title: RNA-seq_CTCF0 mutant, rep1

description: strand-specific RNA library


title: RNA-seq_Wildtype control for CTCF0, rep1

description: strand-specific RNA library

value: Wildtype


title: RNA-seq_Wildtype control for CTCF0, rep3

description: strand-specific RNA library


title: Dam-Only Rep 3

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

library_source: genomic

data_processing:
Library strategy: DamID-seq
Unaligned TaDa-seq reads were trimmed using TrimGalore (Version 0.4.2), assessed for general quality control with the FastQC tool (Version 0.11.9), and aligned to the mouse reference genome (mm10) using BWA (Version 0.7.17). Biological replicates were analyzed independently and as a single merged file generated via samtools (Version 1.10).
TaDa-seq peak calling was performed using MACS2 (Version 2.2.5) with model-based peak identification disabled, a p-value cutoff set at less than 0.00001, and the merged Dam-only dataset as a control. Peak calling for individual CHD8 TaDa replicates was performed against the merged Dam-only dataset to identify specific peaks that were enriched in CHD8 TaDa versus non-specific signal in Dam-only experiments. Peak calling for the Dam-only merged dataset was performed without a control dataset as Dam-only is analogous to assays of accessible chromatin. A final set of merged CHD8 TaDa peaks was obtained using bedtools intersect (Version 2.29.2) to select peaks that were present in at least 3 replicates and had a MACS2 FDR less than 0.00001.
Enriched regions from TaDa-seq datasets were annotated to genomic features using custom R scripts and combined UCSC and RefSeq transcript sets. CHD8 target genes were assigned to nearest transcription start site, which for distal peaks was achieved using the bedtools closest command (Version 2.29.2). Bigwig coverage files were generated using deeptools bamCoverage (Version 3.3.1).
Genome-wide signal summary correlation heatmaps were generated using the multiBigwigSummary and plotCorrelation tools from deeptools (Version 3.3.1). Peak loci heatmaps were generated using the deeptools computeMatrix and plotHeatmap tools (Version 3.3.1). Analysis of peaks not captured by the CHD8 TaDa experiments was performed using bedtools intersect (Version 2.29.2) with CHD8 TaDa filtered peak datasets. Promoter-proximal versus promoter-distal and peak set concordance datasets were also obtained using the bedtools intersect tool (Version 2.29.2). Ontology analysis was performed using the GREAT online tool (Version 4.0.4) or goseq (Version 1.36.0). HOMER was used to perform de novo motif discovery with default parameters (Version 4.10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: broadPeak or bed peak files
Supplementary_files_format_and_content: bigWig coverage files

molecule: genomic DNA

source_name: E17.5 Cortex

extract_protocol:
Sample genomic DNA extraction was performed using the Qiagen QIAamp DNA Micro Kit (Qiagen, 56304). Extracted genomic DNA was digested overnight at 37°C with DpnI (NEB, R0176S) to cut adenine-methylated GATC sites. Following digestion, DNA was column purified with the QIAquick PCR Purification Kit (Qiagen, 28104) to remove un-cut genomic DNA. dsADR adaptors (0.05 umole, DST purity, Sigma) were blunt-end ligated to DpnI-digested fragments using T4 DNA ligase (NEB, M0202S; 2 hours at 16°C, heat inactivation at 65°C for 20 minutes) to prepare for PCR amplification. Before PCR amplification, fragments were digested with DpnII (NEB, R0543S) to cut non-methylated GATC sites and prevent amplification of unmethylated regions and purified with a 1:1.5 ratio of Seramag beads (Fisher Scientific, 12326433). PCR amplification of DpnII-digested fragments using MyTaq (Bioline, BIO-21112) enriched for methylated fragments before samples were sonicated and prepped for sequencing. Sonicated samples were subjected to AlwI digestion (NEB, R0513S) to remove previously ligated adaptors and initial GATC sequences from fragments.
A modified TruSeq protocol was used to generate sequencing libraries involving end repair, 3’ end adenylation, sequencing adaptor ligation (0.05 umole, DST purity, Sigma), and DNA fragment enrichment using a reduced number of PCR cycles. TaDa-seq libraries were sequenced on the Illumina HiSeq 1500 platform using a 50bp strategy by the Gurdon Institute Next Generation Sequencing Core.

treatment_protocol: CHD8 TaDa (0.5ug/ul) or Dam-only (0.5ug/ul) and electroporation-control (0.25ug/ul) plasmids were injected into the fetal brain ventricles at embryonic day (E) 13.5 before collection at E17.5.

value: Cortex

tag: developmental stage

value: Dam-Only Construct


title: WT_BSA_24h_rep2

value: 1% BSA


title: Dam-Only Rep 2


title: Dam-Only Rep 1


title: WT_PA_3h_rep1

value: embryonic kidney cell line


title: WT_BSA_24h_rep3

value: Serum-free, 1% BSA


title: CHD8 TaDa-seq Rep 4

value: CHD8-Dam Fusion Construct


title: RNA-seq_Wildtype control for CTCF0, rep2

description: strand-specific RNA library


title: CHD8 TaDa-seq Rep 3


title: WT_BSA_24h_rep1


title: 1818770_mono_input

city: Memphis

first: Yong

last: Cheng

address: 262 Danny Thomas Place

institute: St. Jude Childrens Research Hospital

data_processing:
Single-end reads were mapped to hg19 using BWA mem
narrowPeaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

growth_protocol: HUDEP2 cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
The ChIP assay were performed as previously described (Cheng et al, 2014, PMCID: PMC4343047)
Sequencing libraries were generated using NEBNext UltraII DNA library Prep kit with homemade adaptors

treatment_protocol: For CD34+ cell differentiation, in days 0-7, cells were cultured at a density of 1-8 x105 cells/mL in IMDM medium with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 µg/mL insulin, 200 µg/mL holo-transferrin, 1 IU/ml of EPO, 10 ng/mL human SCF, and 1 ng/mL IL-3. In days 8-12, IL-3 was omitted from the medium. For HUDEP-2 cell differentiation, cells were cultured at 0.7-1.4 million cells/ml of IMDM medium supplemented with 2% FBS, 3% human serum albumin, 3 IU/mL EPO, 10 µg/mL insulin, 1000 µg/mL holo-transferrin, 3 units/mL heparin and 1 µg/mL doxycycline

tag: cell type

value: mono

tag: antibody

value: input


title: 1835427_CD4_CTCF_3

value: CTCF(Millipore, 07-729)


title: CHD8 TaDa-seq Rep 2


title: 1818768_CD8_input


title: 1818769_B_input

value: B


title: WT_BSA_3h_rep3


title: Endometrial_Tissue_Fertile_UIF_24

city: Istanbul

first: Tuba

last: Günel

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü Vezneciler

department: Department of Molecular Biology and Genetics

country: Turkey

institute: Istanbul University

description: Gene expression in the endometrium of UIF patient during the window of implantation

hyb_protocol: Fragmented cRNA samples were hybridized onto Agilent Sure Print G3 8x60K Version 2 Microarray slide, by incubation at 65 C for 17 hours with constant rotation. The microarray slides were then washed in two steps of 1 minute in two washing buffers (Agilent Technologies). In order to enhance reproducibility across the different chemical surfaces used, a reference sample was spotted in duplicate on each type of surface to calculate experimental intra- and inter-coefficient of variation and to optimize the array reading parameters (such as laser intensity, focus mass and mass range).

scan_protocol: The slides were scanned by an Agilent SureScan Microarray Scanner (model G2600D) using one color scan setting for 8x60k array slides.

data_processing: Hybridization signals were extracted using the Agilent Feature Extraction software, version 11.0.1.1. Background correction and quantile normalization was performed using the R package limma.

label_protocol: First-strand cDNAs were transcribed from 100 ng total RNA with the use of T7-Oligo (dT) Promoter Primers. Samples were transcribed in vitro and Cy-3 labeled, all with the Low Input Quick Amp Labeling kit (Agilent Technologies). The labeling reaction typically yielded 120-200 ng/μl of complementary RNA (cRNA) with a specific activity >10.

extract_protocol: Total RNA were extracted from the endometrium tissues samples; as 24 RPL patients, 24 UIF and 24 controls, under cold chain conditions with QIAGEN RNeasy Plus Mini Isolation Kit according to the manufacturer’s instructions. The quantity and quality of obtained total RNA were firstly measured by NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific) and secondly by the Agilent RNA Nano Chip kit on Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).

tag: subject status/group

value: patient with UIF

value: Endometrial tissue


title: WT_BSA_9h_rep1


title: Endometrial_Tissue_Fertile_UIF_17


title: 1818767_CD4_input


title: Endometrial_Tissue_Fertile_UIF_19


title: WT_BSA_9h_rep2


title: Endometrial_Tissue_Fertile_UIF_18


title: Endometrial_Tissue_Fertile_UIF_20


title: 1818764_mono_CTCF_2


title: Endometrial_Tissue_Fertile_UIF_22


title: CHD8 TaDa-seq Rep 1


title: Endometrial_Tissue_Fertile_UIF_21


title: WT_BSA_3h_rep2


title: 1818763_mono_CTCF_1


title: Endometrial_Tissue_Fertile_UIF_16


title: Endometrial_Tissue_Fertile_UIF_15


title: Endometrial_Tissue_Fertile_UIF_14


title: WT_BSA_9h_rep3


title: Endometrial_Tissue_Fertile_UIF_13


title: Endometrial_Tissue_Fertile_UIF_23


title: Endometrial_Tissue_Fertile_UIF_10


title: Endometrial_Tissue_Fertile_UIF_11


title: WT_BSA_3h_rep1


title: Endometrial_Tissue_Fertile_UIF_12


title: 1818762_B_CTCF_2


title: 1818760_CD8_CTCF_2


title: WT_full_rep3

value: Full medium

value: Full medium (10% FBS)


title: WT_full_rep1


title: WT_full_rep2


title: 1818758_CD4_CTCF_2


title: 1818761_B_CTCF_1


title: 1818759_CD8_CTCF_1


title: ZR-75-1, pooled input

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control.
Peaks found in 2 out of the 3 replicates (as determined using BEDTools (Quinlan & Hall, 2010)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two of three replicate experiments. An average enrichment signal from all replicates was generated by merging mapped reads for a given condition (Picard Toolkit, 2018), followed by subsequent conversion to bigwig format using deepTools (Ramirez et al. 2016).

source_name: Breast cancer cell line

growth_protocol: ZR-75-1 cells were grown in hormone-deplete conditions (phenol red-free RPMI-1640 + 5% dextran-coated charcoal-stripped FBS) for 72h

extract_protocol:
ZR-75-1 cells were fixed with 2mM disuccinimidyl glutarate for 20m followed by 1% formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 2.5µg of SRC-3 antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultra-Low Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: ZR-75-1 cells were treated for 6 h with either a vehicle (ethanol), 10 nM E2 or 10 nM E2 + 10 nM DHT

value: Breast cancer cell line ZR-75-1

tag: passages

value: 14-16 (where replicates represent sequential passages)

tag: chip antibody

value: none (Input DNA)

value: Pooled input


title: ZR-75-1, SRC-3 ChIP E2+DHT Consensus

value: SRC-3 (Cell Signaling Technology #2126S)


title: erythroblast_H3K27ac_HiChIP

description: HiChIP

data_processing:
Library strategy: HiChIP
The sequencing reads were mapped to hg19 using HiC-pro (Servant et al., 2015). The output were further processed using Hichipper (Lareau and Aryee, 2018) to identify significant loops
Genome_build: hg19

source_name: Hematopoietic stem/progenitor cells

growth_protocol: To obtain erythroblasts, in days 0-7, CD34+ HSPCs were cultured at a density of 1-8 x105 cells/mL in IMDM medium with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 µg/mL insulin, 200 µg/mL holo-transferrin, 1 IU/ml of EPO, 10 ng/mL human SCF, and 1 ng/mL IL-3. In days 8-12, IL-3 was omitted from the medium.

extract_protocol:
HiChIP samples on 10 million cells each sample using H3K27ac antibody were prepared according to the published protocol (Fang et al., 2016; Mumbach et al., 2016) with the following modification. After proximity ligation, the nuclear lysates were sonicated using a Branson 250 Sonifier (microtip, 100% duty, 20%outpt, 12x10s intervals). 8ug of H3K27ac antibodies were used for each sample. The reverse cross-linked ChIP DNA were purified using DNA clean & concentrator-5 (Zymo Research) and quantified using Qubit (Life Technologies).
The samples were end repaired, dATP labeled and adaptor ligated using NEBNext ultraII DNA library prep kit, followed by streptavidin pull-down and PCR amplification of library. 300-1000bp of PCR products were size selected using E-gel

value: erythroblast

tag: erythropoiesis

value: 12 days

value: H3K27ac (Abcam, ab4729)


title: ZR-75-1, SRC-3 ChIP E2 Consensus


title: GnRH_female_biological rep4

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

description: Gene expression data from GnRH neurons of GnRH-GFP transgenic female mice

hyb_protocol: Hybridization, washing and staining of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

scan_protocol: Staining and scanning of Affymetrix Mouse Genome 430 PM Strip arrays were performed following the manufacturer’s recommendations.

data_processing: Scanned images (DAT files) were transformed into intensities (CEL files) using the AGCC software (Affymetrix). RMA analysis to obtain probe set level expression estimates was performed by means of the Partek Genomics Suite (Partek Inc., St. Louis, MO, USA).

label: biotin

source_name: Hypothalamic GnRH neurons from intact mice

label_protocol: 8 µg cDNA was fragmented by DNase I and biotinylated by terminal transferase obtained from the GeneChip Mapping 250K Nsp Assay Kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: GnRH cell samples collected with LCM were incubated in 200 ul lysis buffer (Tris-HCl, pH 8.0, 10 mM; EDTA 50 mM; NaCl 200 mM; SDS 2,2%; Anti-RNase 1000 U/ml; Prot-K 1 mg/ml) at 56°C for 3 hours. RNA was isolated from the lysate by an optimized proteinase K/acid phenol method as described earlier (Khodosevich et al, 2007). RNA was purified using RNeasy MinElute Cleanup kit (Qiagen, Hilden, Germany). Total RNA was eluted with 14 µl of ribonuclease-free water, and then stored at -80°C. The quality of RNA was measured with Bioanalyzer.

tag: Sex

value: female

value: adult

value: hypothalamus


title: GnRH_female_biological rep5


title: Endometrial_Tissue_Fertile_UIF_7


title: Mut1_D3_H3K27ac_HiChIP

description: 1609110_SNP235_D3_H3K27ac_HiChIP_S2_L002_R1_001.fastq.gz

data_processing:
library strategy: HiChIP
The sequencing reads were mapped to hg19 using HiC-pro (Servant et al., 2015). The output were further processed using Hichipper (Lareau and Aryee, 2018) to identify significant loops
Genome_build: hg19

source_name: HUDEP-2 cell line

treatment_protocol: For HUDEP-2 cell differentiation, cells were cultured at 0.7-1.4 million cells/ml of IMDM medium supplemented with 2% FBS, 3% human serum albumin, 3 IU/mL EPO, 10 µg/mL insulin, 1000 µg/mL holo-transferrin, 3 units/mL heparin and 1 µg/mL doxycycline

value: 3 days


title: GnRH_male_biological rep6

description: Gene expression data from GnRH neurons of GnRH-GFP transgenic male mice

value: male


title: Endometrial_Tissue_Fertile_UIF_8

value: patient with UIF


title: GnRH_female_biological rep3


title: GnRH_female_biological rep6


title: GnRH_male_biological rep4


title: Endometrial_Tissue_Fertile_UIF_9

value: Endometrial tissue


title: GnRH_male_biological rep5


title: GnRH_female_biological rep1


title: Endometrial_Tissue_Fertile_UIF_4


title: HUDEP2_D3_H3K27ac_HiChIP

description: 1482819_1512832_Hudep2_D3_H3K27AC_HiChIP


title: GnRH_female_biological rep2


title: Endometrial_Tissue_Fertile_UIF_5


title: ChIP-seq_CTCF, wildtype, rep 3

description: ChIP-seq library

data_processing:
Reads were aligned against Drosophila melanogaster genome assembly release 6 (dm6) using MicMap (v2.20200223)
Samtools v1.10 was used to identify duplicate reads
Coverage (in reads per million) was evaluated after truncating each paired end read to the 50nt region centered on the its midpoint, ignoring duplicate reads.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files were generated using R package rtracklayer v1.42.2. Score represent coverage in reads per million.

extract_protocol:
60 third-instar larval CNSs per biological replicate (two biological replicates per sample) were dissected in ice-cold PBS. Chromatin was prepared as described in (Gambetta, Oktaba and Müller, 2009) with the following modifications: inverted larval cuticles were cross-linked for 15 minutes at room temperature in 1.8% (v/v) paraformaldehyde, and dissected brains were sonicated in 120 µl of previously described RIPA140 buffer in AFA microtubes in a Covaris S220 sonicator (Covaris) for 5 minutes with a peak incident power of 140W, a duty cycle of 5% and 200 cycles per burst. Sonicated chromatin was centrifuged to pellet insoluble material and snap-frozen.  ChIP was performed with rabbit polyclonal antibody crude sera against CTCF1-293 and Cp1901-1096 generated for this study. ChIP was performed as previously described in (Gambetta, Oktaba and Müller, 2009) except that Protein A and G Dynabeads were used. ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina. An equimolar pool of multiplexed ChIP-seq libraries at 4 nM was sequenced on the Illumina HiSeq4000 (150 bp paired-end).
Standard ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep kit for Illumina.

treatment_protocol: animals were not subjected to a particular treatment

value: central nervous system

value: third instar larva

value: Wildtype

tag: replicate

value: CTCF rabbit polyclonal (this sudy)


title: Endometrial_Tissue_Fertile_UIF_6


title: GnRH_male_biological rep2


title: ZR-75-1 ER ChIP Veh consensus

data_processing:
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control. A cut-off of p<0.005 was used to call peaks.
Peaks found in 2 out of the 3 replicates (as determined using BEDTools (Quinlan & Hall, 2010)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two of three replicate experiments. An average enrichment signal from all replicates was generated by merging mapped reads for a given condition (Picard Toolkit, 2018), followed by subsequent conversion to bigwig format using deepTools (Ramirez et al. 2016).

extract_protocol:
ZR-75-1 cells were fixed by 1% formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5µg of antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: ZR-75-1 cells were treated for 6h with either a vehicle, 1 nM E2, 1 µM Bicalutamide, 1 nM E2 + 1 µM Bicalutamide, or 1 nM E2 + 1 nM DHT. Bicalutamide was added 1h prior to any hormone addition.

tag: cell line

value: 14-16 (where replicates represent sequential passages)

value: ER (Millipore 06-935)

value: Veh


title: ZR-75-1 ER ChIP Bic consensus

tag: treatment

value: Bic


title: ZR-75-1 pooled input (Bicalutamide study)

value: Input DNA


title: ChIP-seq_CTCF, wildtype, rep 2

description: ChIP-seq library

tag: strain


title: ZR-75-1, SRC-3 ChIP Veh Consensus

value: Breast cancer cell line ZR-75-1

value: SRC-3 (Cell Signaling Technology #2126S)

value: Vehicle


title: Endometrial_Tissue_Fertile_UIF_3

tag: tissue


title: CD34_Day12_ATAC_Rep2

data_processing:
The adaptor sequencing were trimmed by skewer,and then  mapped to hg19 using BWA (version 0.7.1).Reads mapped to mitochondrial DNA were removed.
ATAC-seq peaks were called using MACS2 with the following parameters macs2 callpeak --nomodel --shift -100 --extsize 200
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: Frozen CD34+ cells were thawed and used directly for experiment

extract_protocol:
ATAC-seq libraries on 50,000 cells per sample were constructed according to the published omni-ATAC protocol(Corces et al., 2017)
libraries were constructed according to the published omni-ATAC protocol(Corces et al., 2017)

treatment_protocol: For CD34+ cell differentiation, in days 0-7, cells were cultured at a density of 1-8 x105 cells/mL in IMDM medium with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 µg/mL insulin, 200 µg/mL holo-transferrin, 1 IU/ml of EPO, 10 ng/mL human SCF, and 1 ng/mL IL-3. In days8-12, IL-3 was omitted from the medium.

value: Hematopoietic stem/progenitor cells

tag: cell subtype

value: erythroblast

value: 12 days


title: Endometrial_Tissue_Fertile_UIF_2

value: patient with UIF


title: CD34_Day0_ATAC_Rep1

value: Human CD34+ Hematopoietic stem/progenitor cells

value: No


title: GnRH_male_biological rep3

value: male

value: adult

value: hypothalamus


title: GnRH_male_biological rep1


title: Endometrial_Tissue_Fertile_UIF_1

value: Endometrial tissue


title: Endometrial_Tissue_Fertile_RPL_24

description: Gene expression in the endometrium of RPL patient during the window of implantation

value: patient with RPL


title: RNA-seq_Cp190KO, rep2

description: strand-specific RNA library

value: central nervous system

value: third instar larva

value: Cp190[KO] mutant


title: HUDEP2_Day3_input_ChIP

description: 1102839_Hudep2_D3_input_R1_R1_trim_50bp_n

data_processing:
The sequencing reads were mapped to hg19 using BWA (0.7.15-r1140) with the default setting (bwa mem), reads that could not be uniquely mapped to the human genome were removed by samtools (Version: 1.3.1, samtools view -q 1).
ChIP-seq peaks were called using MACS2,and peaks identified by two biological replicates were kept. Peaks overlapped with the blacklist regions defined by ENCODE were further removed.
Genome_build: hg19
Supplementary_files_format_and_content: peak files

treatment_protocol: For CD34+ cell differentiation, in days 0-7, cells were cultured at a density of 1-8 x105 cells/mL in IMDM medium with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 µg/mL insulin, 200 µg/mL holo-transferrin, 1 IU/ml of EPO, 10 ng/mL human SCF, and 1 ng/mL IL-3. In days 8-12, IL-3 was omitted from the medium.  For HUDEP-2 cell differentiation, cells were cultured at 0.7-1.4 million cells/ml of IMDM medium supplemented with 2% FBS, 3% human serum albumin, 3 IU/mL EPO, 10 µg/mL insulin, 1000 µg/mL holo-transferrin, 3 units/mL heparin and 1 µg/mL doxycycline

value: HUDEP-2 cell line

value: 3 days


title: ZR-75-1 ER ChIP E2+Bic consensus

value: 14-16 (where replicates represent sequential passages)

value: ER (Millipore 06-935)


title: RNA-seq_Cp190KO, rep1

description: strand-specific RNA library


title: CD34_Day12_ATAC_Rep1

value: Hematopoietic stem/progenitor cells

value: erythroblast


title: ZR-75-1 ER ChIP E2 consensus


title: ZR-75-1 Pooled input (p300)

extract_protocol:
ZR-75-1 cells were fixed with 2mM disuccinimidyl glutarate for 20m followed by 1% formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5µg of p300 antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the KAPA HyperPrep Kit.
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: ZR-75-1 cells were treated for 6h with either a vehicle (ethanol), 10 nM E2 or 10 nM E2 + 10nM DHT

value: 18-21 (where replicates represent sequential passages)

value: Input DNA


title: RNA-seq_Wildtype control for Cp190KO, rep3

description: strand-specific RNA library

value: Wildtype


title: Mut1_Day3_CTCF_ChIP

description: 1512846_SNP235_C10_D3_CTCF_ChIP_R1_trim_50bp_n

value: HUDEP-2 deleleting a CTCF motif

value: CTCF(Millipore, 07-729)


title: CD34_Day0_ATAC_Rep2

value: Human CD34+ Hematopoietic stem/progenitor cells

value: No


title: RNA-seq_Wildtype control for Cp190KO, rep2

description: strand-specific RNA library


title: RNA-seq_Cp190KO, rep3

description: strand-specific RNA library


title: Mut1_Day3_H3K27ac_ChIP

description: 1579747_SNP235_C10_D3_H3K27AC_ChIP_R1_trim_50bp_n

value: H3K27ac (Abcam, ab4729)


title: HUDEP2_Day3_H3K27ac_ChIP_rep2


title: Endometrial_Tissue_Fertile_RPL_22

value: patient with RPL

value: Endometrial tissue


title: ZR-75-1 p300 ChIP E2 Consensus

value: p300 (Santa Cruz SC-585X)


title: Endometrial_Tissue_Fertile_RPL_20


title: ZR-75-1 p300 ChIP Veh Consensus

value: Veh


title: HUDEP2_Day3_H3K27ac_ChIP_rep1

value: HUDEP-2 cell line

value: 3 days


title: Endometrial_Tissue_Fertile_RPL_19


title: Endometrial_Tissue_Fertile_RPL_21


title: Hi-C_CTCF0 mutant larval CNSs, rep2

description: Hi-C library

data_processing:
The FASTQ read pairs were analyzed with a Perl script to locate and separate fusion sites using the patterns /GATCGATC/, /TTATAA/, /GATCTAA/ and /TTAGATC/.
The maximal length of each read was trimmed at 60 nucleotides, then reads were mapped to the dm6 genome using MicMap (v2.20200223) and matched to the genomic region (fragment) defined by the nearest upstream and downstream restriction sites.
Read pairs were discarded if they (1) mapped to non-unique positions in the reference genome, (2) had indels or >2 mismatches per read, (3) represented fusion of 2 oppositely oriented reads within 2 kb of each other, which may have not resulted from ligation of 2 digested fragments (these fragments were used to estimate local copy number status of the underpinning genomic region), (4) were likely additional copies of a given read pair, i.e. likely PCR duplicates.
Genome_build: dm6
Supplementary_files_format_and_content: Number of read pairs between pairs of fragments in bedpe file format (tab-delimited with columns chrom1, start1, end1, chrom2, start2, end2, number of read pairs). Supplementary file fragments.bed.gz contains a list of all possible genomic restriction fragments resulting from double digestion of genomic DNA with MboI and MseI enzymes in bed file format (tab-delimited with columns chromosome, start, end)

extract_protocol:
60 larval central nervous systems or 1 whole-bodied fly per replicate were homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting sequentially with MboI and MseI restriction enzymes.
Illumina sequencing libraries were prepared with a standard protocol.

value: central nervous system

value: third instar larva

value: CTCF[0] mutant


title: Hi-C_CTCF0 mutant larval CNSs, rep4

description: Hi-C library


title: HCI-005_H3K27ac_DHT

source_name: Breast cancer PDX HCI-005 tumour

growth_protocol: A single patient-derived tumour tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet. Tumours were allowed to grow until reaching ~200mm3 size.

extract_protocol:
Tumours were cut into 30µm slices on a cryostat and fixed with 2mM disuccinimidyl glutarate for 25m followed by 1%formaldehyde for 20m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 5.5 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5µg AR, 5µg ER, or 2µg H3K27ac antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, DHT, or enobosarm. Enobosarm (10mg/kg/day) was dissolved in 10% Tween80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumours were excised and snap-frozen.

value: PDX model HCI-005

tag: time point

value: Short-term (5 days treatment)

value: H3K27ac (Abcam Ab4729)

value: DHT


title: Endometrial_Tissue_Fertile_RPL_18


title: Endometrial_Tissue_Fertile_RPL_23


title: ZR-75-1 p300 ChIP E2+DHT Consensus

value: 18-21 (where replicates represent sequential passages)


title: Hi-C_Wildtype larval CNSs, rep4

description: Hi-C library

tag: age

value: Wildtype


title: HUDEP2_Day3_GATA1_ChIP

description: 1102833_Hudep2_D3_GATA1_R1_R1_trim_50bp_n

value: GATA1 (Abcam, ab11852)


title: HUDEP2_Day3_CTCF_ChIP

description: 1227501_Hudep2_D3_CTCF_R2_R1_trim_50bp_n

value: CTCF(Millipore, 07-729)


title: Mut1_Day3_GATA1_ChIP

description: 1471548_SNP235_C10_D3_GATA1_ChIP_R1_trim_50bp_n

value: HUDEP-2 deleleting a CTCF motif


title: CD34_day12_input_ChIP

description: 1111620_CD34_D12_input_50bp_R1_trim_50bp_n

value: Hematopoietic stem/progenitor cells

value: erythroblast

value: 12 days


title: RNA-seq_Wildtype control for Cp190KO, rep1

description: strand-specific RNA library

tag: genotype


title: HCI-005_H3K27ac_Veh

value: Vehicle


title: HCI-005_AR_DHT

extract_protocol:
Tumours were cut into 30µm slices on a cryostat and fixed with 2mM disuccinimidyl glutarate for 25m followed by 1%formaldehyde for 20m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 5.5 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 5µg AR, 5µg ER, or 2µg H3K27Ac antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

value: AR (Abcam Ab74272)


title: ZR-75-1 ER ChIP E2+DHT consensus

value: 14-16 (where replicates represent sequential passages)

value: ER (Millipore 06-935)


title: CD34_day0_input_ChIP

description: 1111618_CD34_D0_input_50bp_R1_trim_50bp_n

value: Human CD34+ Hematopoietic stem/progenitor cells

value: No


title: HCI-005_AR_SARM

value: PDX model HCI-005

value: Short-term (5 days treatment)

value: Enobosarm


title: CD34_Day12_GATA1_ChIP_Rep2

description: 1227500_CD34_D12_GATA1_R2_50bp_R1_trim_50bp_n


title: ChIP-seq_Cp190, CTCF[0] mutant, rep 2

description: ChIP-seq library

value: central nervous system

value: third instar larva

value: CTCF[0] mutant

value: Cp190 rabbit polyclonal (this study)


title: Hi-C_Wildtype larval CNSs, rep2

description: Hi-C library

value: Wildtype


title: ChIP-seq_Cp190, Cp190[KO] mutant, rep 1

description: ChIP-seq library

value: Cp190[KO] mutant


title: ChIP-seq_Cp190, Cp190[KO] mutant, rep 2

description: ChIP-seq library


title: HCI-005_H3K27ac_SARM

value: H3K27ac (Abcam Ab4729)


title: CD34_Day12_GATA1_ChIP_Rep1

description: 1227499_CD34_D12_GATA1_R1_50bp_R1_trim_50bp_n

value: Hematopoietic stem/progenitor cells

value: erythroblast

value: 12 days

value: GATA1 (Abcam, ab11852)


title: Endometrial_Tissue_Fertile_RPL_17

value: patient with RPL

value: Endometrial tissue


title: Endometrial_Tissue_Fertile_RPL_16


title: ChIP-seq_Cp190, CTCF[0] mutant, rep 1

description: ChIP-seq library


title: HCI-005_Input

value: Pooled input


title: CD34_Day12_H3K27me3_ChIP_Rep2

value: H3K27me3 (Abcam, ab6002)


title: ChIP-seq_Cp190, wildtype, rep 2

description: ChIP-seq library


title: Endometrial_Tissue_Fertile_RPL_14


title: Endometrial_Tissue_Fertile_RPL_15


title: CD34_Day12_H3K27me3_ChIP_Rep1


title: Endometrial_Tissue_Fertile_RPL_11


title: Endometrial_Tissue_Fertile_RPL_13


title: HCI-005_ER_DHT

value: PDX model HCI-005

value: Short-term (5 days treatment)

value: ERα (HC-20)X (Santa Cruz SC-543X)

value: DHT


title: ChIP-seq_Cp190, wildtype, rep 1

description: ChIP-seq library

value: central nervous system

value: third instar larva


title: HCI-005_ER_SARM

value: Enobosarm


title: CD34_Day12_H3K27ac_ChIP_Rep2

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq_CTCF, Cp190[KO] mutant, rep2

description: ChIP-seq library

value: Cp190[KO] mutant

value: CTCF rabbit polyclonal (this sudy)


title: HCI-005_ER_Veh

value: Vehicle


title: CD34_Day12_H3K27ac_ChIP_Rep1

value: Hematopoietic stem/progenitor cells

value: erythroblast

value: 12 days


title: ChIP-seq_CTCF, Cp190[KO] mutant, rep1

description: ChIP-seq library


title: T-47D pooled input

data_processing:
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control.
Peaks found in a minimum of 2 replicates (as determined using BEDTools (Quinlan & Hall, 2010)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two of three replicate experiments. An average enrichment signal from all replicates was generated by merging mapped reads for a given condition (Picard Toolkit, 2018), followed by subsequent conversion to bigwig format using deepTools (Ramirez et al. 2016).

growth_protocol: T-47D cells were grown in hormone-deplete conditions (phenol red-free RPMI-1640 + 5% dextran-coated charcoal-stripped FBS) for 72h

extract_protocol:
T-47D cells were fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 10µg of AR or ERα antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: T-47D cells were treated for 4 h with either 10 nM E2 or 10 nM E2 + 10 nM DHT

value: 14-16 (where replicates represent sequential passages)


title: ChIP-seq_CTCF, CTCF[0] mutant, rep 2

description: ChIP-seq library

value: CTCF[0] mutant


title: T-47D ER ChIP E2+DHT Consensus


title: HCI-005_AR_Veh

value: AR (Abcam Ab74272)


title: CD34_Day12_CTCF_ChIP_Rep1

description: 1151784_CD34_D12_CTCF_R1_trim_50bp_trim_50bp_n

value: CTCF(Millipore, 07-729)


title: ChIP-seq_CTCF, wildtype, rep 1

description: ChIP-seq library

value: Wildtype


title: T-47D ER ChIP E2 Consensus

value: ERα (HC-20)X (Santa Cruz SC-543X)


title: CD34_Day0_CTCF_ChIP_Rep2

description: 1151783_CD34_D0_CTCF_R2_trim_50bp_trim_50bp_n

value: Human CD34+ Hematopoietic stem/progenitor cells

value: No


title: ChIP-seq_CTCF, CTCF[0] mutant, rep 1

description: ChIP-seq library

value: central nervous system

value: third instar larva


title: T-47D AR ChIP E2+DHT Consensus

value: AR (N-20) (Santa Cruz SC-816)


title: CD34_Day0_CTCF_ChIP_Rep1

description: 1151782_CD34_D0_CTCF_R1_trim_50bp_trim_50bp_n


title: Endometrial_Tissue_Fertile_RPL_12

value: patient with RPL

value: Endometrial tissue


title: Endometrial_Tissue_Fertile_RPL_9


title: T-47D AR ChIP E2 Consensus


title: Endometrial_Tissue_Fertile_RPL_8


title: Endometrial_Tissue_Fertile_RPL_6


title: Endometrial_Tissue_Fertile_RPL_7


title: Endometrial_Tissue_Fertile_RPL_5


title: Endometrial_Tissue_Fertile_RPL_10


title: Hi-C_CTCF0 mutant whole-fly, rep1

description: Hi-C library

source_name: whole-bodied female pharate adult

value: whole fly

value: pharate adult


title: AK034F: A549 RNase L KO,  0.25 µg/ml poly I:C, 4.5 h

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: Biological replicate of AK018F

data_processing:
Library strategy: ribosome profiling
Samples were sequenced on the HiSeq2500 or HiSeq3000. Reads in samples starting with "AK" are demultiplexed and trimmed but contain UMIs (Unique Molecular Identifier). Reads in samples starting with "GJ" have linker sequences but no UMIs (samples prepared as in Ingolia et al., 2009) .
Reads were aligned to a library of human non-coding RNA genes (rRNAs and tRNAs) with bowtie 1 and those not matching were retained.
Samples had PCR duplicates removed (except "GJ" files).
Reads were then aligned to hg38 human transcriptome tophat.  The aligned reads  were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were created by Plastid. All reads are 5' end aligned.

source_name: whole cell

growth_protocol: cell line appropriate media + 10% FBS, 37˚C, 5% CO2

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose cushion. RNA was then extracted using trizol and footprints of the specified size were retained by gel purification.
Samples starting with "GJ" were prepared accoring to Ingolia et al, 2009. Samples starting with "AK" were prepared using the protocol published in McGlincy and Ingolia, 2017. Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. rRNA was subtracted using Ribo-Zero Illumina kit after ligation. cDNAs were then circularized and PCR amplified.

treatment_protocol: 2-5A and poly I:C were transfected by Lipofectamine 3000. Transfection controls were only treated with Lipofectamine 3000. Cells were washed with ice cold DPBS and flash frozen in liquid nitrogen. Then cells were lysed in lysis buffer.

value: 0.25 µg/ml poly I:C, 4.5 h

value: RNASEL KO

tag: molecule subtype

value: 80S ribosome protected RNA (25-34 nt)


title: Endometrial_Tissue_Fertile_RPL_2


title: Hi-C_Wildtype whole-fly, rep1

description: Hi-C library

source_name: whole-bodied female young adult

value: young adult


title: AK029_30F: A549 wt, 1 µM trimer 2-5A. 4.5 h

description: Biological replicate of AK006F and AK021_22F, consists of two technical replicates AK029F and AK030F

value: 1 µM trimer 2-5A, 4.5 h

value: wild type


title: Endometrial_Tissue_Fertile_RPL_3


title: Hi-C_CTCF0 mutant larval CNSs, rep1

description: Hi-C library

value: CTCF[0] mutant


title: AK028F: A549 RNase L KO, WT RNAse L electro, 0.25 µg/ml poly I:C, 4.5 h

value: RNASEL KO,wild type RNAse L transently transfected


title: ZR-75-1_Rep3_E2+DHT

data_processing:
Basecalls performed using Illumina software.
hg19 alignment was performed using CLC Genomics Workbench 11 (QIAGEN) using the following mapping parameters: Mismatch cost 2; Insertion cost 3; Deletion cost 3; Length fraction 0.8; Similarity fraction 0.8.
Multiple mapped reads from a given sample were merged post-mapping.
Differential gene expression was performed using a Generalised Linear Model with FDR correction based on Negative Binomial Distribution.
Expression was measured based on the total counts of mapped short reads and normalised based on RPKM (CLC Genomics Workbench).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data presented as RPKM

extract_protocol:
Total RNA was extracted using Zymo Direct-Zol RNA kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded Total RNA HT Library Prep Kit
RNA-Seq; Illumina NextSeq 500 v4 paired-end 100bp reads

treatment_protocol: ZR-75-1 cells were treated for 4h with either 10nM E2 or 10nM E2 + 10nM DHT

tag: cell type

value: Breast cancer cell line


title: AK027F: A549 RNase L KO, WT RNAse L electro, 1 µM trimer 2-5A. 4.5 h


title: ZR-75-1_Rep2_E2+DHT


title: CD34_Day12_CTCF_ChIP_Rep2

description: 1151785_CD34_D12_CTCF_R2_trim_50bp_trim_50bp_n

value: Hematopoietic stem/progenitor cells

value: erythroblast

value: 12 days

value: CTCF(Millipore, 07-729)


title: ZR-75-1_Rep1_E2+DHT


title: Endometrial_Tissue_Fertile_RPL_4

value: patient with RPL


title: BER6_4

city: Shanghai

first: Minhang

last: Yuan

address: Fenglin

department: Shanghai Institute of Plant Physiology and Ecology

country: China

institute: Chinese Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through CASAVA version 1.4 In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
TPM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: bbc_Pst DC3000 D36E(avrRpt2)_6hpi

growth_protocol: Plants  were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.

extract_protocol:
Total mRNA was extracted from leaves using Trizol reagent. Total RNA was treated with DNase I to remove DNA, and purified RNA was recovered with RNeasy® MinElute™ Cleanup kit. A total amount of 1 μg RNA per sample was used as input material for library preparation and Illumina sequencing.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®  following manufacturer’s recommendations and sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Four-week-old Arabidopsis plant leaves were infiltrated with Sterile water (Mock) or different Pst strains at OD600=0.04, and then harvested at indicated time points. Two leaves from different plants were collected as one sample and in total 4 samples were collected for each treatment.

tag: ecotype background

tag: genotype/variation

value: bbc

value: Four-week-old

value: Pst DC3000 D36E(avrRpt2)

value: leaf


title: Endometrial_Tissue_Fertile_Control_24

description: Gene expression in the endometrium of fertile control during the window of implantation

tag: subject status/group

value: Control

value: Endometrial tissue


title: AK025F: A549 RNase L KO, H672N RNAse L electro,  1 µM trimer 2-5A. 4.5 h

value: RNASEL KO,H672N RNAse L transently transfected

value: 80S ribosome protected RNA (25-34 nt)


title: Endometrial_Tissue_Fertile_RPL_1

description: Gene expression in the endometrium of RPL patient during the window of implantation


title: ZR-75-1_Rep4_E2+DHT

tag: passages


title: ZR-75-1_Rep4_E2


title: ZR-75-1_Rep3_E2


title: ZR-75-1_Rep2_E2


title: BER6_2


title: Endometrial_Tissue_Fertile_Control_23


title: BER6_1


title: Endometrial_Tissue_Fertile_Control_22


title: Endometrial_Tissue_Fertile_Control_21


title: AK021_22F: A549 wt, 1 µM trimer 2-5A, 4.5 h

description: Biological replicate of AK006F and AK029_30F, consists of two technical replicates AK021F and AK022F

value: 1 µM trimer 2-5A, 4.5 h

value: wild type


title: ZR-75-1_Rep1_E2


title: Endometrial_Tissue_Fertile_Control_20


title: Hi-C_Wildtype larval CNSs, rep1

description: Hi-C library

value: central nervous system

value: third instar larva

value: Wildtype


title: AK026F: A549 RNase L KO, H672N RNAse L electro,  0.25 µg/ml poly I:C, 4.5 h

value: 0.25 µg/ml poly I:C, 4.5 h


title: CER6_4

source_name: wild type_Pst DC3000 D36E(avrRpt2)_6hpi


title: ZR-75-1 pooled input

data_processing:
Basecalls performed in BaseSpace.
Trimmed FASTQ files were aligned to the hg19 genome assembly using Bowtie2 (Langmead & Salzberg, 2012).
Mapped reads with a minimum MAPQ <10 and duplicate reads were removed using SAMtools (Li et al., 2009).
Peaks were called using MACS2 (Zhang et al., 2008 & Feng et al., 2012) with a pooled input sample as the control.
Peaks found in 2 out of the 3 replicates (as determined using BEDTools (Quinlan & Hall, 2010)) were kept for the consensus peakset.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two of three replicate experiments. Bigwig files, representing an average enrichment signal from all replicates, were created using HOMER (Heinz et al. 2010).

extract_protocol:
ZR-75-1 cells were fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Plus for 10 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with 10µg of AR or ERα antibody, or 2µg H3K27ac antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions accompanying the Qiagen Ultralow Input Library Kit (Part# 180495).
ChIP-Seq; Illumina NextSeq500 (High Output v2) single-end 75 bp reads.

treatment_protocol: ZR-75-1 cells were treated for 4h with either 10 nM E2 or 10 nM E2 + 10 nM DHT

value: Breast cancer cell line

value: 14-17 (where replicates represent sequential passages)

tag: chip antibody

value: Input DNA


title: CER6_3


title: Endometrial_Tissue_Fertile_Control_19


title: AK024F: A549 RNase L KO, H672N RNAse L electro, transfection control, 4.5 h

value: untreated

value: RNASEL KO, H672N RNAse L transently transfected


title: BER6_3

value: bbc

value: Four-week-old

value: Pst DC3000 D36E(avrRpt2)


title: CER6_2

value: leaf


title: ZR-75-1 H3K27ac ChIP E2 Consensus

value: H3K27ac (Abcam Ab4729)


title: AK018F: A549 RNase L KO, 0.25 µg/ml poly I:C, 4.5 h

description: Biological replicate of AK034F

value: RNASEL KO

value: 80S ribosome protected RNA (25-34 nt)


title: ZR-75-1 H3K27ac ChIP E2+DHT Consensus


title: Endometrial_Tissue_Fertile_Control_17

value: Control

value: Endometrial tissue


title: AK023F: A549 RNase L KO, wtRNAse L electro, transfection control, 4.5 h

value: RNASEL KO, wild type RNAse L transently transfected


title: AK017F: A549 RNase L KO, 1 µM trimer 2-5A. 4.5 h

description: Biological replicate of AK008F

value: 1 µM trimer 2-5A, 4.5 h


title: Endometrial_Tissue_Fertile_Control_16


title: ZR-75-1 ER ChIP E2+DHT Consensus

value: ERα (HC-20)X (Santa Cruz SC-543X)


title: AK019_20F: A549 wt, 0.25 µg/ml poly I:C, 4.5 h

description: Biological replicate of AK012F , consists of two technical replicates AK019F and AK020F

value: 0.25 µg/ml poly I:C, 4.5 h

value: wild type


title: BE6_4

source_name: bbc_Pst DC3000 D36E_6hpi

value: Pst DC3000 D36E


title: Endometrial_Tissue_Fertile_Control_18


title: ZR-75-1 ER ChIP E2 Consensus

value: Breast cancer cell line

value: 14-17 (where replicates represent sequential passages)


title: AK015F: A549 wt, 1 µM dimer 2-5A, 4.5 h

value: 1 µM dimer 2-5A


title: AK016F: A549 RNase L KO, transfection control, 4.5 h

description: Biological replicate of AK007F

value: untreated


title: BE6_3

value: bbc

value: Four-week-old


title: Endometrial_Tissue_Fertile_Control_14


title: Endometrial_Tissue_Fertile_Control_15


title: ZR-75-1 AR ChIP E2+DHT Consensus

value: AR (N-20) (Santa Cruz SC-816)


title: AK014F: A549 wt, transfection control, 4.5 h

description: Biological replicate of AK006F


title: ZR-75-1 AR ChIP E2 Consensus


title: AK013F: A549 wt, 1 µM trimer 2-5A,, 2.25 h

value: 1 µM trimer 2-5A, 2.25 h


title: BE6_2

value: leaf


title: BE6_1


title: ZR-75-1_xeno_Input_Sarm

data_processing:
FASTQ files were aligned to hg19 using bwa (v0.7.15; default parameters) (Li & Durbin, 2009).
Mapped reads were filtered using a minimum MAPQ quality score of 15.
Mapped reads with a minimum MAPQ <15 were removed using SAMtools and peaks were called using MACS2 (default settings).
Consensus peaksets were obtained through DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: Consensus bed files were generated corresponding to shared peaks found within any two replicate experiments. Bigwig files, representing an average enrichment signal from all replicates, were created using HOMER (Heinz et al. 2010).

source_name: ZR-75-1 cell line xenograft tumour

growth_protocol: Athymic nude mice were subcutaneously implanted with an E2 pellet and injected with 5x10^6 (20µl) ZR-75-1 cells into the fourth inguinal mammary fat pad. Tumours were allowed to grow until reaching ~200mm3 size before beginning treatment.

extract_protocol:
Tumours were cut into 30µm slices on a cryostat and fixed with formaldehyde for 10m prior to quenching. Chromatin was prepared and subsequently sheared by the Diagenode BioRuptor Pico for 8 cycles (30 sec on, 30 sec off) on ice. Sheared chromatin was immunoprecipitated with AR or ERα antibody overnight, after coupling to Protein A Dynabeads (10002D). DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
Libraries were prepared according to manufacturer's instructions.
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

value: ZR-75-1 cell line xenograft tumour

value: Enobosarm

value: Short-term (5 days treatment)

value: Pooled input


title: ZR-75-1_xeno_Input_DHT

value: DHT


title: AK012F: A549 wt, 0.25 µg/ml poly I:C, 4.5 h

description: Biological replicate of AK019_20F

value: 0.25 µg/ml poly I:C, 4.5 h

value: 80S ribosome protected RNA (25-34 nt)


title: CE6_4

source_name: wild type_Pst DC3000 D36E_6hpi

value: wild type

value: Pst DC3000 D36E


title: CE6_3


title: AK010F: A549 wt, 1 µM trimer 2-5A, 4.5 h

description: Biological replicate of AK021_22F and AK029_30F

value: 1 µM trimer 2-5A, 4.5 h


title: AK009F: A549 wt, 0.1 µM trimer 2-5A, 4.5 h

value: 0.1 µM trimer 2-5A, 4.5 h


title: CE6_1


title: ZR-75-1_xeno_AR_Sarm

value: AR (N-20)X (Santa Cruz SC-816X)


title: CE6_2


title: ZR-75-1_xeno_AR_DHT


title: AK008F: A549 RNase L KO, 1 µM trimer 2-5A. 4.5 h

description: Biological replicate of AK017F

value: RNASEL KO


title: Endometrial_Tissue_Fertile_Control_10

extract_protocol: Total RNA were extracted from the endometrium tissues samples; as 24 RPL patients, 24 UIF and 24 controls, under cold chain conditions with QIAGEN RNeasy Plus Mini Isolation Kit according to the manufacturer’s instructions. The quantity and quality of obtained total RNA were firstly measured by NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific) and secondly by the Agilent RNA Nano Chip kit on Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).

value: Control

value: Endometrial tissue


title: AK007F: A549 RNase L KO,transfection control, 4.5 h

description: Biological replicate of AK016F

value: untreated


title: BM6_4

value: bbc

value: Four-week-old

value: leaf


title: AK011F: A549 wt, 10 µM trimer 2-5A, 4.5 h

value: 10 µM trimer 2-5A, 4.5 h


title: Endometrial_Tissue_Fertile_Control_9


title: AK006F: A549 wt, transfection control, 4.5 h

description: Biological replicate of AK014F


title: ZR-75-1_xeno_AR_Veh

value: ZR-75-1 cell line xenograft tumour

value: Vehicle

value: Short-term (5 days treatment)


title: BM6_3


title: ZR-75-1_xeno_ER_Sarm

value: Enobosarm

value: ERα (HC-20)X (Santa Cruz SC-543X)


title: Endometrial_Tissue_Fertile_Control_13


title: BM6_2


title: ZR-75-1_xeno_Input_Veh

value: Pooled input


title: Endometrial_Tissue_Fertile_Control_11


title: Endometrial_Tissue_Fertile_Control_8


title: ZR-75-1_xeno_ER_DHT

value: DHT


title: Endometrial_Tissue_Fertile_Control_12


title: Endometrial_Tissue_Fertile_Control_7


title: cold7_4

city: Boston

first: Yu-Hua

last: Tseng

state: MA

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

data_processing:
Sample demultiplexing, STAR alignment to the mm10 transcriptome, filtering, and UMI counting were achieved using Cell Ranger 3.0.1 (10X Genomics)44. The Cell Ranger cellcalling algorithm for filtering barcodes was not employed; instead, the top 14,000 cell 39 barcodes with the highest number of UMIs for each of the 16 samples were output for custom quality control (QC) analysis.
Genome_build: mm10
Supplementary_files_format_and_content: filtered_raw_counts_all_clusters.tar.gz - sparses matrix table in MatrixMarket format with raw gene counts for every gene for filtered cells used for clustering analysis.  Also, includes the genes (row names) and cell IDs (column names) for the matrix.
Supplementary_files_format_and_content: filtered_raw_counts_for_pseudotime_and_pseudobulk_DGE.tar.gz - sparses matrix table in MatrixMarket format with raw gene counts for the subset of cells used for the DE and pseudotime analyses.  Also, includes the genes (row names) and cell IDs (column names) for the matrix.
Supplementary_files_format_and_content: metadata_all_clusters.csv.gz - metadata for all filtered cells and the corresponding cluster identities determined during the analysis
Supplementary_files_format_and_content: metadata_for_pseudotime_and_pseudobulk_DGE.csv.gz  - metadata for the subset of filtered cells used for the DE and pseudotime analyses and the corresponding cluster identities determined during the analysis

source_name: SVF-BAT cells

extract_protocol:
Interscapular BAT was dissected, minced, and digested with a cocktail containing type 1 Collagenase (1.5 mg/mL; Worthington Biochemical), Dispase II (2.5 U/mL; STEMCELL Technologies), fatty acid free bovine serum albumin (2%; Gemini Bio Products) in Hanks’ balanced salt’s solution (Corning® Hank's Balanced Salt Solution, 1X with calcium and magnesium) for 45 minutes at 37°C with gentle shaking. Dissociated tissue was centrifuged at 500 g at 4°C for 10 minutes. The top adipocyte layer and the supernatant were gently removed, the SVF pellet was resuspended in 10 ml of 10% Fetal Bovine Serum (FBS) in DMEM, filtered through a 100 µm cell strainer into a fresh 50 ml tube, 38 and centrifuged at 500 g for 7 minutes. The red blood cell lysis was performed by resuspending the pellet in 2 ml sterile ACK (Ammonium-Chloride-Potassium) lysis buffer (ACK Lysing Buffer, Lonza) and incubating on ice for 5 minutes. The cells were then filtered through a 40 µm cell strainer, washed with 20 ml 10% FBS in DMEM, and centrifuged at 500 g for 7 minutes. The pellet was resuspended in 1 ml of 1.5% BSA in PBS. The dead cell removal was performed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer’s instructions. The cells were finally resuspended in 50- 100 µl of 1.5% BSA in PBS and kept on ice before immediately proceeding to single cell isolation.
Single-cell RNA-seq libraries were obtained following the 10x Genomics recommended protocol, using the reagents included in the Chromium Single Cell 3′ v3 Reagent Kit.

treatment_protocol: For experiments involving cold exposure, C57BL6J mice were housed at 5°C for 2 or 7 days, 22°C (room temperature) for 1 week, or 30°C (thermoneutral)  in a controlled environmental diurnal chamber (Caron Products & Services Inc., Marietta, OH) with free access to food and water.

value: stromal vascular fraction of BAT

tag: temperature


title: BM6_1


title: cold7_3


title: cold2_4


title: Endometrial_Tissue_Fertile_Control_6

data_processing: Hybridization signals were extracted using the Agilent Feature Extraction software, version 11.0.1.1. Background correction and quantile normalization was performed using the R package limma.


title: Endometrial_Tissue_Fertile_Control_4


title: CM6_4

source_name: wild type_Mock_6hpi

value: wild type


title: HCI-005 SARM tumor 3

description:
processed data file:
HCI-005_Veh_Sarm_DHT.edgeR.fc.txt
HCI-005_Veh_Sarm_DHT.matrix.txt

data_processing:
Transcripts were aligned to hg38 using STAR v2.5 (Dobin et al. 2013), and marked for duplicates using Picard tools v1.138.
Read counts were computed in R v3.4.3 using Rsubread 1.28.0 (Liao et al., 2013).
Gene expression analysis was conducted using edgeR 3.20.1 (Robinson et al., 2010, McCarthy et al., 2012) and limma 3.34.1 (Ritchie et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression analysis of vehicle, DHT, and enobosarm-treated PDX tumors.

source_name: HCI-005 SARM tumor

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet. Tumors were allowed to grow until reaching ~200mm3 size.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit
RNA-Seq; Illumina NextSeq 500 (High Output v2) 75 bp single-end reads

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, DHT, or enobosarm. Enobosarm (10 mg/kg/day) was dissolved in 10% Tween 80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumors were excised and snap-frozen.

value: Breast cancer PDX model HCI-005 tumor

tag: replicate


title: HCI-005 SARM tumor 2


title: Mut1_Day0_cHiC_RBM38pro

description: Capture-C

data_processing:
Library strategy: Capture Hi-C
Capture Hi-C data was processed with CCanalyser3 (Davies et al., 2016)
Genome_build: hg19
Supplementary_files_format_and_content: wig

extract_protocol:
Capture Hi-C libraries were constructed according to the published protocol (Davies et al., 2016). 20 million cells per sample were used to construct the 3C libraries. Biotinylated bait DNA targeting RBM38 promoter region were designed to target both end of DpnII restriction fragment using CapSequm software (Hughes et al., 2014).
2ug of the 3C DNA were used for capture. Libraries were paired-end 75bp sequenced using an Illumina Nextseq550.

tag: cell line

value: HUDEP-2 deleleting a CTCF motif

tag: erythropoiesis

value: No

tag: bait

value: RBM38 promoter


title: Endometrial_Tissue_Fertile_Control_3

value: Control

tag: tissue

value: Endometrial tissue


title: CM6_3

value: Four-week-old

tag: treatment

value: leaf


title: CM6_2

tag: time point


title: cold2_3

tag: strain


title: Endometrial_Tissue_Fertile_Control_1


title: Mut1_Day3_cHiC_RBM38pro

description: Capture-C


title: Endometrial_Tissue_Fertile_Control_5


title: HUDEP2_Day3_cHiC_RBM38pro

description: Capture-C

value: 3 days


title: HCI-005 SARM tumor 1


title: Endometrial_Tissue_Fertile_Control_2


title: CM6_1

tag: age


title: HCI-005 DHT 2

source_name: HCI-005 DHT tumor


title: HCI-005 DHT 3

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit
RNA-Seq; Illumina NextSeq 500 (High Output v2) 75 bp single-end reads
s


title: HUDEP2_Day0_cHiC_RBM38pro

description: Capture-C


title: RT_3

value: RT


title: BER3_4

source_name: bbc_Pst DC3000 D36E(avrRpt2)_3hpi

value: bbc

value: Pst DC3000 D36E(avrRpt2)


title: ZR-75-1_xeno_ER_Veh

value: ZR-75-1 cell line xenograft tumour

value: Vehicle

value: Short-term (5 days treatment)

value: ERα (HC-20)X (Santa Cruz SC-543X)


title: TN_4

value: stromal vascular fraction of BAT

value: TN


title: Ustilago maydis growing in MM with ethanol

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

data_processing:
These reads were evaluated for quality with a phred score greater than 32
The fastq files were trimmed for the presence of TruSeq adapters and the barcodes removed using trimmotic Trimmomatic-v0.36
The mapping of the clean reads to the Ustilago maydis 521 genome (https://mycocosm.jgi.doe.gov/Ustma2_2/Ustma2_2.home.html) was performed with Kallisto.

organism: Mycosarcoma maydis

source_name: Micelium growing in liquid media

growth_protocol: grown for 24 h in liquid CM containing 1% glucose as the carbon source

extract_protocol: Total RNA was extracted from frozen and ground fungal tissue using the PureLink RNA Mini Kit (Invitrogen, Carlsbad, California, USA) method, according to the manufacturer’s protocol.

treatment_protocol: Cell suspensions (1 x 106 cells ml-1) were used to inoculate synthetic MM medium containing 1% ethanol or 1% glucose as carbon source maintained at 30 °C. The cultures were then incubated at 28 °C on a shaker (200 r.p.m.), and at intervals growth was measured by its optical density (OD) at 600 nm. After 14 h of growth, cells were recovered from the media by centrifugation

value: Ethanol as a carbon source


title: RT_4


title: HCI-005 DHT 1

treatment_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet. Tumors were allowed to grow until reaching ~200mm3 size.

value: Breast cancer PDX model HCI-005 tumor

value: DHT


title: Ustilago maydis growing in MM with glucose

value: Glucose as a carbon source


title: BER3_1


title: HCI-005 Veh 4

source_name: HCI-005 Veh tumor


title: cold7_2


title: CER3_4

source_name: wild type_Pst DC3000 D36E(avrRpt2)_3hpi

value: wild type


title: HCI-005 Veh 2


title: cold2_1


title: HCI-005 Veh 1

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet. Tumors were allowed to grow until reaching ~200mm3 size.A single patient-derived tumour tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet. Tumours were allowed to grow until reaching ~200mm3 size.


title: CER3_1

value: Four-week-old


title: HCI-005 Veh 3


title: BER3_2

value: leaf


title: RT_2


title: cold2_2


title: BE3_4

source_name: bbc_Pst DC3000 D36E_3hpi

value: Pst DC3000 D36E


title: BE3_3


title: CER3_2


title: GAR15-13 SARM 5

description:
processed data file:
Gar15-13_Veh_Sarm_DHT.edgeR.fc.txt
Gar15-13_Veh_Sarm_DHT.matrix.txt

source_name: GAR15-13 SARM tumor

value: Breast cancer PDX model GAR15-13

value: Enobosarm


title: TN_3


title: RT_1

value: RT


title: GAR15-13 SARM 4


title: GAR15-13 SARM 3


title: TN_2


title: BE3_1

value: bbc


title: TN_1


title: HCoEC-biological_rep1

city: Atlanta

first: Michael

last: Koval

state: GA

address: 205 Whitehead Bldg, 615 Michael St

department: Pulmonary Medicine

institute: Emory University School of Medicine

description: Gene expression data from cultured cells

hyb_protocol: Following fragmentation,  cRNAs were hybridized on Affymetrix Human Gene 1.0 ST Arrays [HuGene-1_0-st-v1] according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000

data_processing: Probe sets in the top 5%  with a fold difference greater than 1.5 were analyzed. Probe sets with an absolute difference less than 100 expression units relative to control were removed for all Affymetrix array analyses. This filtering allowed for identification of genes well above background levels. Absent calls were also excluded.

source_name: Human coronary arterial endothelial cells

label_protocol: Double-stranded cDNAs were synthesized from total RNA by using the cDNA  Synthesis  System  (Invitrogen,  Carlsbad,  CA).  Biotin-labeled  cRNA  was  generated  and  used  to  probe  Affymetrix  arrays  according  to  the  manufacturer’s  recommendations (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary human endothelial cells were cultured in Microvascular Endothelial Cell Growth Medium-2 (complete medium, EGM-2MV, Lonza) until confluent.

extract_protocol: Cytoplasmic RNA was isolated by using an RNAeasy kit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity.

treatment_protocol: Cultured cells were used for RNA extraction and hybridization on Affymetrix microarrays.

value: coronary artery

value: Cultured primary endothelial cells


title: GAR15-13 SARM 2

value: Short-term (5 days treatment)


title: HAoEC-biological_rep3

source_name: Human aortic endothelial cells

value: aorta


title: HCoEC-biological_rep2


title: CE3_4

source_name: wild type_Pst DC3000 D36E_3hpi


title: HAoEC-biological_rep2


title: HCoEC-biological_rep3


title: GAR15-13 SARM 1


title: HAoEC-biological_rep1


title: GAR15-13 DHT 4

source_name: GAR15-13 DHT tumor


title: P7 mice -ST

first: Jia

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: Wild-type mice cerebellum

extract_protocol:
For scRNA-seq,cerebellar tissues were obtained from mice and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, WT cerebellar tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I) and GFP-positive and DsRed-positive cells were sorted by FACs, and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol. For ST,cerebellar tissues were embedded in Tissue-Tek (OCT) and snap-frozen using an isopentane/dry ice slurry. Cerebellar tissues were cryosectioned at 10-μm thickness while keeping the samples frozen. Samples were placed within the frame of Capture Areas on the Visium Spatial Gene Expression.

value: cerebellum


title: HSaVEC-biological_rep3

source_name: Human saphenous vein endothelial cells

value: saphenous vein


title: GAR15-13 DHT 3


title: cold7_1

value: stromal vascular fraction of BAT


title: Patched+/- MB-2 -scRNA

source_name: SHH medulloblastoma

value: Patched+/-

value: SHH medulloblastoma


title: Patched+/- MB-3 -scRNA


title: CE3_3

value: wild type


title: CE3_2

value: Four-week-old


title: CE3_1

value: leaf


title: GAR15-13 DHT 2

value: DHT


title: Patched+/- MB-1 -scRNA


title: BE3_2

value: Pst DC3000 D36E


title: P11 mice -scRNA


title: BM3_3


title: BM3_4


title: GAR15-13 Veh 5

source_name: GAR15-13 Veh tumor

value: Breast cancer PDX model GAR15-13

value: Vehicle


title: BM3_2

value: bbc


title: HSaVEC-biological_rep1


title: GAR15-13 Veh 4

data_processing:
Transcripts were aligned to hg38 using STAR v2.5 (Dobin et al. 2013), and marked for duplicates using Picard tools v1.138.
Read counts were computed in R v3.4.3 using Rsubread 1.28.0 (Liao et al., 2013).
Gene expression analysis was conducted using edgeR 3.20.1 (Robinson et al., 2010, McCarthy et al., 2012) and limma 3.34.1 (Ritchie et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression analysis of vehicle, DHT, and enobosarm-treated PDX tumors.
Supplementary_files_format_and_content: Differential expression analysis of vehicle, DHT, and enobosarm-treated PDX tumours.


title: P7 mice -scRNA


title: HUVEC-biological_rep3

source_name: Human umbilical vein endothelial cells

value: umbilical vein


title: P11 Dcx-DsRed mice-scRNA

description: P11 DCX_S1

source_name: Dcx-DsRed mice cerebellum

value: Dcx-DsRed

value: DsRed-positive cells


title: BM3_1


title: LNCaP-DHT-3

city: New York

first: Xuanrong

last: Chen

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Mapping: Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20. The clean reads were then aligned to hg38_UCSC_2013 genome using the star program.
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 ((version 1.18.1)) Bioconductor package. Padj of genes were setted <0.05 to detect differential expressed ones.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LNCaP

growth_protocol: LNCaP cells (obtained from ATCC) were grown in RPMI1640 mediun supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double- stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA- tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor- ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
The libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.

treatment_protocol: LNCaP cells were perfused with charcoal-dextran stripped fetal bovine serum (CD-FBS) for 3 days, and then treated with dimethyl sulfoxide (DMSO) or 10 nM dihydrotestosterone (DHT) for 24 hours.

value: Prostate cancer cell line

value: LNCaP

tag: castration condition


title: HUVEC-biological_rep1

tag: cell type

value: Cultured primary endothelial cells


title: GAR15-13 Veh 3

value: Short-term (5 days treatment)


title: LNCaP-DHT-2

value: 10 nM dihydrotestosterone (DHT) for 24 hours

value: charcoal-dextran stripped fetal bovine serum (CD-FBS) for 3 days


title: P7 Dcx-DsRed mice-scRNA

description: P7 DCX_S1

value: cerebellum


title: GAR15-13 Veh 2

data_processing:
Transcripts were aligned to hg38 using STAR v2.5 (Dobin et al. 2013), and marked for duplicates using Picard tools v1.138.
Read counts were computed in R v3.4.3 using Rsubread 1.28.0 (Liao et al., 2013).
Gene expression analysis was conducted using edgeR 3.20.1 (Robinson et al., 2010, McCarthy et al., 2012) and limma 3.34.1 (Ritchie et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression analysis of vehicle, DHT, and enobosarm-treated PDX tumours.


title: P11 Math1-GFP mice-scRNA

description: P11 math1_S1

source_name: Math1-GFP mice cerebellum

value: GFP-positive cells


title: LNCaP-DMSO-2

value: dimethyl sulfoxide (DMSO) for 24 hrs


title: CM3_4

source_name: wild type_Mock_3hpi

tag: ecotype background

value: wild type

value: Four-week-old

value: leaf


title: LNCaP-DMSO-3


title: HUVEC-biological_rep2


title: CM3_3

tag: genotype/variation


title: P7 Math1-GFP mice-scRNA

description: P7 math1_S1


title: GAR15-13 DHT 1

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle, DHT, or enobosarm. Enobosarm (10 mg/kg/day) was dissolved in 10% Tween 80 and delivered daily by oral gavage. DHT pellets were surgically implanted subcutaneously. After 5 days, tumors were excised and snap-frozen

value: Breast cancer PDX model GAR15-13

value: DHT


title: CER6_1

source_name: wild type_Pst DC3000 D36E(avrRpt2)_6hpi

value: Pst DC3000 D36E(avrRpt2)


title: GAR15-13 Veh 1

value: Vehicle


title: CM3_1


title: LNCaP-DMSO-1


title: CD11+Gr1+

status: Public on Jan 17 2021

city: Guagzhou

first: Shouheng

last: Lin

address: 190 Kaiyuan Avenue, Science Park, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent  signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were  read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform  combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis  Sequencing Method.
All the generated raw sequencing reads were filtered to remove reads with adaptors, reads in which unknown bases are more than 10%, and low quality reads. Clean reads were then obtained and stored as FASTQ format. HISAT was used to map clean reads to genome of PDL-0 (HISAT parameters for PE reads: HISAT was used to map clean reads to reference genome (-p 8 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000).
Gene expression levels were quantified by the software package RSEM. The DEGseq method was used to screen differentially expressed genes between groups (cutoff criteria: fold change absolute value of log2-Ratio ≥1 and a false discovery rate (FDR) ≤ 0.001).
Genome_build: NCBI_GRCh38.p11
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample; tab-delimited text files include RPKM values for each Sample

source_name: myeloid cell

extract_protocol:
RNA was isolated from cell pellets using TRIzol™ Reagent (Invitrogen), and RNA quality was determined using the Bioanalyzer 2100 (Agilent). 23S and 16S rRNAs were depleted using a MicrobExpress kit (Ambion). Genomic DNA was removed with two digestions using amplification-grade DNase 1 (Invitrogen). The processed RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction
RNase H was used to remove the rRNA, DNase I was used to digest double-stranded and single-stranded DNA in total RNA. Purified RNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Master Mix by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments were amplified with adapters by PCR, and the products was purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR product from previous step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China).

value: myeloid cell


title: Liver-MDSC


title: Spleen-MDSC


title: Tumor-MDSC


title: LNCaP-DHT-1

value: Prostate cancer cell line


title: Sh-CCR3_3

source_name: lung carcinoma cell

value: cell line

value: lung carcinoma cell

tag: cell line name

tag: genotype

value: CCR3 Knockdown


title: CCL11_3


title: Sh-CCR3_2


title: CCL11_1


title: CCL11_2


title: Con_3


title: Con_2


title: LC123

source_name: lung carcinoma

value: tumor

tag: engraftment success

value: no


title: LC58


title: Con_1


title: LC65


title: LC63


title: LC56


title: LC57


title: LC48


title: LC36


title: LC61


title: LC27


title: LC54


title: Sh-CCR3_1


title: LC25


title: LC29


title: LC52


title: LC62


title: LC50


title: LC51


title: LC66


title: LC31


title: LC67


title: LC44


title: LC55


title: LC39


title: LC47


title: LC49


title: LC60


title: LC45


title: LC30


title: LC94


title: LC96


title: LC46


title: LC24


title: LC59


title: LC26


title: LC71


title: LC73


title: LC70


title: LC106


title: LC43


title: LC23

value: yes


title: LC69


title: LC18


title: LC22


title: LC11


title: LC15


title: LC17


title: LC9


title: LC33


title: LC19


title: LC20


title: LC10


title: LC16


title: LC2


title: LC92


title: LC12


title: LC91


title: LC90


title: LC89


title: LC82


title: LC83


title: LC84


title: LC88


title: LC68


title: LC81


title: LC87


title: LC80


title: LC79


title: LC86


title: LC78


title: LC76


title: LC77


title: LC85


title: LC75


title: LC5


title: LC74


title: Mkp-1 KO CS

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

data_processing:
HTSeq v0.6.1 software used
All statistical analyses were carried out with HTSeq v0.6.1; after removing transcriptionally inactive genes (read count per million < 1) from raw RNA sequencing gene counts, we obtained high confidence gene counts
For gene expression analysis, the matched reads were calculated and then normalized to reads per kilobase of exon model per million mapped reads (FPKM)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: distal colonic epithelial tissue

growth_protocol: mice were maintained under standard conditions of ventilation, temperatures (22± 30 C), and lighting (light/dark: 13 h/11 h) and kept under observation for one week prior to experimentation. Drinking water and standard pellets diet were provided ad libitum throughout the study.

extract_protocol:
total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacture’s instruction
Illumina RNA-Seq libraries were subsequently performed  using the SMARTer Stranded RNA-Seq Kit (Clontech, Mountain View, CA) according to the manufacturer's instructions

treatment_protocol: The protocol for the induction of adenoma stage (AS) is illustrated in Fig 1. Briefly, 5–6-week-old male BALB/c mice were injected with AOM (10 mg/kg i.p.) once per week for the first 3 weeks. During this period, mice were exposed to drinking water containing 1.5% DSS and were left to drink normal water for 3 weeks. For the carcinoma stage (CS), 5–6-week-old-old male mice were also injected with AOM (10 mg/kg i.p.), exposed to drinking water containing 2% DSS for 1 week, and then left to drink normal water for 2 weeks. This treatment was repeated for three additional cycles. Finally, the mice were left to drink water containing 2% DSS for 1 week, followed by normal water for 9 weeks.

tag: background strain

value: AOM/DSS treatment

tag: sample label

tag: subgroups

value: Mkp-1 KO CS

value: distal colonic epithelial tissue


title: Mkp-1 KO for AS

value: untreated

value: Mkp-1 KO


title: WT-AS

value: wild-type

value: WT-AS


title: WT-CS

value: WT-CS


title: Mkp-1 KO AS

value: Mkp-1 KO AS


title: HSaVEC-biological_rep2

value: saphenous vein

value: Cultured primary endothelial cells


title: Slpi_rep 3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Slpi-overexpressing MC3T3-E1 cells

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: For in vitro MC3T3-E1 cell analysis, subconfluent cells were digested in QIAZOL (Qiagen) to extract total RNA, in accordance with the manufacturer’s instructions.

tag: cell line

value: MC3T3-E1 cells

value: Slpi-overexpressing


title: WT-C for CS

value: WT-C


title: WT-C for AS


title: Slpi_rep 2


title: Mock_rep 3

source_name: mock-overexpressing MC3T3-E1 cells

value: mock-overexpressing


title: Slpi_rep 1


title: Mock_rep 1


title: Tf2_Hippocampus_4_P3

city: Milan

first: Beatrice

last: Bodega

address: Via Francesco Sforza 35

country: Italy

institute: INGM Istituto Nazionale Genetica Molecolare

description: Bisulfite conversion based methylation analysis of L1MdTf

data_processing:
Reads were trimmed for low quality using Trimmomatic (parameters:  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15  MINLEN:75)
Paired reads were aligned to IAP and L1 consensus sequences using Bismark (parameters: --local -N 1 -L 15 --non_directional)
DNA methylation data was called was called using MethylDackel
Genome_build: Custom (IAPLTR1a_Mm and L1MdTf Mus musculus consensus sequences)
Supplementary_files_format_and_content: Per-base CpG metrics are provided in a standard bedGraph format with 4th column being the methylation percentage at a given position, 5th column the number of read pairs reporting methylated bases and 6th column the number of read pairs reporting unmethylated bases.

source_name: Brain

extract_protocol:
Brains were excised and cerebellum, cortex and hippocampus were isolated. Genomic DNA was extracted with phenol/chloroform. 500ng of genomic DNA were bisulfite-converted using MethylEdge Bisulfite Conversion Kit (Promega).
Targetted Bisultite-seq. Library was prepared as follows: briefly genomic DNA was bisulfite-converted and the amplified using specific primers: each organ in each developmental stage was associated to a distinct couple of Forw and Rev primers 5’-end tagged,  in order to be unambiguously identified in the sequencing analysis step. All the L1MdTf and IAPLTR1a amplicons were then pooled in equimolar quantities to obtain a final pooling concentration of 2 ng/μL. Library for DNA sequencing was produced on the pooled PCR products.

value: Hippocampus

value: Post natal day 3


title: Tf2_Hippocampus_4_E15.5

value: Embryonic day 15.5


title: Tf2_Hippocampus_4_P0

value: Post natal day 0


title: Tf2_Hippocampus_4_P14

value: Post natal day 14


title: Tf2_Hippocampus_4_E18.5

value: Embryonic day 18.5