title: BORpos

city: Montreal

first: Sanne

middle: Marlijn

last: Janssen

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

department: Pathology

institute: Lady Davis Institute for Medical Research

description:
processed data file:
HTSeq_count.xlsx
edgeR_exactTest_DEG_BOR_NEG_VS_BOR_POS_cpm0.5.csv

data_processing:
FastQ files were aligned using STAR-2.6.0c RNA-seq aligner with default parameters
each BAM file was indexed and name sorted with SAMtools-1.7
'HTSeq' framework, version 0.6.0,  was used to count the number of reads that mapped to each gene, with the following command; python -m HTSeq.scripts.count -f bam -r name -s no -i gene_name gencode.v28.annotation.gtf
edgeR version 3.24.3 was used to select a CPM cutoff and perform Differential Gene Expression analysis according to the protocol
Genome_build: hg38 (GRCh38.p12 )
Supplementary_files_format_and_content: excel tables in xlsx and csv format

growth_protocol: MM057 cells were infected with the lentiviral vector pI20-EV or pI20-BORIS and selected by addition of 150μg/ml G418/Neomycin (Wisent, 450-130-QL). Upon selection, cell lines were maintained in the presence of 50μg/ml G418. For the RNA-seq experiments, cells were cultured in a treated 100mm tissue culture dish for five days either in the absence or presence of 50ng/ml doxycycline (Clontech, 631311). Doxycycline was refreshed every 48 hours. Cell culture medium: Ham’s F10 medium (Wisent, 318-050-CL) supplemented with 8% heat-inactivated fetal bovine serum (Wisent, 080- 450), 1% penicillin-streptomycin (Wisent, 450-201-EL), 1% GlutaPlus (Wisent, 609-066-EL) and 50μg/ml G418.

extract_protocol:
Cells were detached from the culture dish with citric saline (270mM KCl, 30mM sodium citrate), passed through a 40um filter and counted using a hemocytometer to collect 500.000 cells. Total RNA was extracted using the Nucleospin RNA kit (Macherey Nagel, 740955.5) according to manufacturer’s instructions. DNase treatment was used to exclude genomic DNA.
Libraries were constructed by the Centre for Applied Genomics in Toronto (ON, Canada). RNA-seq libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) to enrich for poly(A) mRNA and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7420), according to manufacturers’ specifications. Libraries were indexed using the NEBNext Multiplex Oligos 1-8 for Illumina (Index Primers Set 1; New England Biolabs, E7335), according to manufacturers’ specifications.

value: melanoma cell line

tag: genotype/variation

tag: passages

value: 50ng/ml doxycycline


title: Mouse 1 Skin Nfil3(GFP)posKlrg1pos Treg

status: Public on Jan 01 2020

type: SRA

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Skin tisTregST2 (mouse1)

library_source: transcriptomic

data_processing:
Fastq files were processed using Cell Ranger (version 2.2.0) based on 10xGenomics provided mm10 reference genome (refdata-cellranger-vdj-GRCm38-alts-ensembl-2.2.0). Clones were matched by TRA and TRB sequence and clonal diversity was estimated using the inverse Simpson index. Samples from each mouse were compared in a pairwise fashion using the Jaccard index. Clonal abundance pie charts were generated using ggplot2 (version 2.2.1) and R (version 3.4.2). R1 fastq is technical, R2 fastq biological. R1 is built with partial Illumina Read 1 sequence (22nucleotides) followed by 10x barcode (16 nucleotides) followed by UMI (10 nucleotides) and switch oligo (13 nucleotides).
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: skin

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol: Samples for scTCR-seq were loaded on the Chromium Single cell Controller using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics #1000014) and the Single Cell V(D)J Enrichment Kit, Mouse T Cell (10x Genomics #1000071). TCR samples were sequenced on an Illumina NextSeq 500 with 300 cycles paired-end sequencing.

treatment_protocol: For scTCR-seq, we sorted 15000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1-Nfil3(GFP)- Treg, 15000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1-Nfil3(GFP)+ Treg, 8000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1+Nfil3(GFP)+ Treg, 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg, 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg, and 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg. Samples were sorted from single male Nfil3(GFP) animals.

tag: tissue

value: Skin

tag: cell type

value: Nfil3(GFP)positive Klrg1positive


title: EVpos

country: Canada

description:
processed data file:
HTSeq_count.xlsx
edgeR_exactTest_DEG_EV_NEG_VS_EV_POS_cpm0.5.csv

organism: Homo sapiens

tag: cell line

tag: treatment


title: AB5222 scRNA-seq

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Note: Second read contained only cell and molecule barcodes and was not submitted. This information was instead appended to the fastq entry header of the first read (forward/R1 file)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata.txt :Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Lymph node

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
CFP+ Ag-specific CD4 T cells were transfered into PA-GFP mice, which were then infected in the footpad with either rVSV or rLCMV viruses. Two days upon infection, draining popliteal lymph nodes (LN) were photoactivated in areas containing Ag-specific CD4+ T cell clusters. LN were processed and photoactivated GFP+ cells were single-cell sorted for single-cell RNA-seq
Mice were sacrified by CO2

tag: strain

value: C57BL/6 PA-GFP

value: Lymph node

tag: selection marker

value: PA-GFP+

tag: infection

value: LCMV

tag: replicate id

tag: age

value: 9 weeks


title: AB5221 scRNA-seq

value: VSV


title: EVneg


title: MCF10A_HER2_plastic_siAS

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Raw reads were aligned using STAR (Dobin et al., 2013) version 2.5.3a to build version hg19 of the human genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package (Liao et al., 2014).
Normalization and differential analysis were carried out using edgeR package (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix of raw counts for each sample

source_name: MCF10A human breast epithelial cell line

growth_protocol: Cells were cultured in DMEM/F12 (Gibco) with 5% horse serum, glutamine and antibiotics, freshly supplemented with insulin (Sigma-Aldrich), EGF (Peprotech), hydrocortisone (Sigma-Aldrich) and cholera toxin (Sigma-Aldrich).

extract_protocol:
Cells were harvested by the RNeasy Mini Kit (Qiagen) for total RNA extraction and contaminant DNA was removed by the RNase-Free DNase Set (Qiagen).
RNA-seq libraries for deep-sequencing were prepared with the Illumina TruSeq Standard Total RNA with Ribo-Zero GOLD kit.

treatment_protocol: MCF10A cells were  transducted with retroviral constructs (pBABEpuro-HER2-CAV659E or pBABEpuro). siRNA transfections were done with Lipofectamine RNAi-MAX (Thermo Fisher Scientific) in antibiotics-free medium according to the manufacturer’s instructions.

tag: transduction

tag: substrate

value: plastic

tag: transfection

value: Control siRNA


title: MCF10A_empty_plastic_siYT3

value: empty

value: YAP/TAZ siRNA #3


title: 4414_mix-MLXKO_0mM3_S9_L004_R1_001

city: Boston

first: Niklas

last: Mejhert

address: 655 Huntington Avenue

country: USA

institute: Harvard TH Chan School of Public Health

data_processing:
The raw sequence data were converted to FASTQ format using bcl2fastq software (Illumina).
Transcript abundance was quantified using Salmon (Patro et al., 2017).
Results were imported into RStudio using tximport (Soneson et al., 2015).
Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts from tximport

source_name: SUM159 cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit. Complete lysis was ensured using QIAshredder and DNA digested with RNase-Free DNase Set
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Library Prep kit. In brief, mRNAs were enriched with polyA selection. The enriched mRNAs were then chemically fragmented, followed by double strand cDNA synthesis, A-tailing, adaptor ligation size selection and finally PCR amplified. The resulting libraries were individually quantified using a Fragment Analyzer, mixed (equal molar) into a library pool, loaded on a cBot for clustering onto a flow cell, and sequenced on a HiSeq 2500 using V4 chemistry.

tag: genotype

value: MLX KO

tag: glucose

value: 0 mM


title: 4414_mix-MLXKO_25mM2_S11_L004_R1_001

value: 25 mM


title: Mouse 2 Spleen Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen tisTregST2 (mouse2)

source_name: spleen

value: Spleen


title: AB5218 scRNA-seq


title: 4414_mix-MLXKO_25mM3_S12_L004_R1_001


title: AB5220 scRNA-seq


title: AB5219 scRNA-seq


title: 4414_mix-MLXKO_0mM1_S7_L004_R1_001


title: AB5217 scRNA-seq


title: 4414_mix-MLXKO_0mM2_S8_L004_R1_001


title: 4414_mix-MLXKO_25mM1_S10_L004_R1_001


title: AB5121 scRNA-seq


title: 4414_mix-WT_25mM_2_S5_L004_R1_001

value: wild type


title: AB5120 scRNA-seq


title: 4414_mix-WT_25mM_3_S6_L004_R1_001


title: BORneg

value: melanoma cell line


title: 4414_mix-WT_25mM_1_S4_L004_R1_001


title: Mouse 1 Spleen Nfil3(GFP)negKlrg1neg Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen DN Treg (mouse1)

value: Nfil3(GFP)negative Klrg1negative


title: AB5119 scRNA-seq

value: C57BL/6 PA-GFP


title: 4414_mix-WT_0mM_2_S2_L004_R1_001


title: 4414_mix-WT_0mM_3_S3_L004_R1_001


title: 24h_In_vitro_activated_B_cells_3

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: 24h_In_vitro_activated_B_cells_Spleen_Rep3

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.5).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.3) (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.0c) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts package by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: Spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit . Cluster generation and 75bp paired-read dual-indexed sequencing was performed on Illumina NextSeq500

treatment_protocol: Cells were bead purified and surfaced stained using antibodies and BD FacsAria sorted as decribed in supplemental materials

value: Balb/c


title: 4414_mix-WT_0mM_1_S1_L004_R1_001


title: 24h_In_vitro_activated_B_cells_2

description: 24h_In_vitro_activated_B_cells_Spleen_Rep2


title: 24h_In_vitro_activated_B_cells_1

description: 24h_In_vitro_activated_B_cells_Spleen_Rep1


title: 12h_In_vitro_activated_B_cells_3

description: 12h_In_vitro_activated_B_cells_Spleen_Rep3


title: 4907_mix-MLXKO_25mM_2_S11_L001_R1_001

source_name: THP-1 macrophages

tag: differentiation

value: THP-1 cells were differentiated for two days and then transfected with siRNAs (RISC-free non-targeting control or siMLX)

tag: sirna

value: siMLX


title: 4907_mix-MLXKO_25mM_3_S12_L001_R1_001


title: AB5122 scRNA-seq

value: Lymph node

value: PA-GFP+

value: LCMV

value: 9 weeks


title: 4907_mix-MLXKO_25mM_1_S10_L001_R1_001


title: 12h_In_vitro_activated_B_cells_2

description: 12h_In_vitro_activated_B_cells_Spleen_Rep2


title: 4907_mix-MLXKO_0mM_3_S9_L001_R1_001


title: 12h_In_vitro_activated_B_cells_1

description: 12h_In_vitro_activated_B_cells_Spleen_Rep1


title: 4h_In_vitro_activated_B_cells_2

description: 4h_In_vitro_activated_B_cells_Spleen_Rep2


title: 4907_mix-MLXKO_0mM_2_S8_L001_R1_001


title: 4h_In_vitro_activated_B_cells_1

description: 4h_In_vitro_activated_B_cells_Spleen_Rep1


title: 4907_mix-MLXKO_0mM_1_S7_L001_R1_001


title: Naive_2

value: Naive


title: 4h_In_vitro_activated_B_cells_3

description: 4h_In_vitro_activated_B_cells_Spleen_Rep3


title: 4907_mix-RISC_free_25mM_1_S4_L001_R1_001

value: RISC-free


title: In_vivo_activated_B_cells_3


title: Naive_3


title: 4907_mix-RISC_free_25mM_2_S5_L001_R1_001


title: 4907_mix-RISC_free_0mM_2_S2_L001_R1_001


title: 4907_mix-RISC_free_25mM_3_S6_L001_R1_001


title: Naive_1


title: In_vivo_activated_B_cells_2


title: With_LDL_2_CTTGTA_L007_all

value: THP-1 cells were differentiated for one day using 50 nM phorbol 12-myristate 13-acetate

tag: acldl incubation

value: with acLDL (50 ug/mL) for two days


title: No_LDL_2_ACAGTG_L007_all

value: without acLDL


title: No_LDL_1_TGACCA_L007_all


title: With_LDL_1_GCCAAT_L007_all


title: Hi-C_seq_CTCF_siRNA_LNCaP_Rep2.1

city: Darlinghurst

first: Amanda

last: Khoury

state: NSW

address: 384 Victoria St.

country: Australia

institute: Garvan Institute

description:
LNCaP_CTCF_KD_40kb_domains_sorted.bed
LNCaP_CTCF_KD_40kb.contact_counts.bed.gz

library_source: genomic

data_processing:
All Hi-C libraries were processed through the NGSane framework v0.5.2, using the "fastqc", "hicup" and "fithicaggregate" modules.
Quality check of sequence libraries was performed with FastQC v0.11.2. Raw fastq files were then pre-processed, mapped with bowtie v1.1.0 and assessed for artifact levels through HiCuP v0.5.2 supplying genome assembly (hg19) and the BglII restriction enzyme cut site. Aligned read files in BAM format were sorted with Samtools v1.2 and duplicates were tagged using MarkDuplicates from Picard tools v1.121. Replicates were pooled using bespoke Python scripts (provided within NGSane) leveraging the sparse matrices formats in the SciPy librarie.
Contact counts for a 40kb resolution were created using a custom adaptation of fit-hi-c (provided within NGSane) supplying iteratively corrected bias offsets calculated through HiCorrector v1.1 as well as genome mappability tracks from ENCODE.
Contact matrices were processed through the “Hi-C Domain Caller” pipeline previously described by Ren’s Lab to identify topologically associating domains with a 40kb resolution.
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: LNCaP Prostate Cancer Cells

growth_protocol: LNCaP were cultured under ATCC recommended conditions at 37°C and 5% CO2.

extract_protocol:
Cells were cross-linked with formaldehyde, lysed and the nuclei were permeabilized. DNA was then cut with BglII restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads. Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing was performed using the NEBNext DNA Master Mix kit and the ligation of universal adapters was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
Libraries were prepared using TruSeq ChIP sample Preparation Kit (Catalog # IP-202-900).

treatment_protocol: LNCaP cells were transfected with 20nM of Dhamacon ON-TARGET plus pooled Non-targeting siRNA or 20nM of Dhamacon ON-TARGET plus pooled CTCF siRNA (containing sequences GAUGAAGACUGAAGUAAUG, GGAGAAAGAAGAAGAGUA, GAAGAUGCCUGCCACUUAC, GAACAGCCCAUAAACAUAG) according to the manufacturer-supplied protocol. Following 72hrs of transfection, cells were split and reverse transfected for a further 72hrs (144hrs).

tag: tissue

value: prostate

value: LNCaP Prostate Cancer Cells

value: 20nM CTCF siRNA pool

tag: restriction enzyme

value: BglII


title: Late_GC_2

value: Spleen

tag: cell type


title: Peak_GC_1

value: Balb/c


title: Hi-C_seq_CTCF_siRNA_LNCaP_Rep2

tag: cell line

tag: treatment


title: 4907_mix-RISC_free_0mM_3_S3_L001_R1_001

value: THP-1 cells were differentiated for two days and then transfected with siRNAs (RISC-free non-targeting control or siMLX)

value: 0 mM


title: Early_GC_2

tag: strain


title: LFD_RNAseq_replicate4

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

description: RNAseq_TPM_per_gene_DEseq2.txt.gz, RNAseq_counts_per_gene.txt.gz

data_processing:
ChIP-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered reads were mapped to mm9 via Bowtie (v0.12.8) with parameters -m 1 -X 2000 --chunkmbs 1024.
Duplicate read pairs were removed via MarkDuplicates.jar from the Picard tools suite v1.110.
Uniquely-mapped non-duplicate reads were downsampled to 10 million prior to peak-calling with SICER. SICER parameters were window size 200, gap size 200, FDR 0.001 for H3K27ac.
For HNF4a and C/EBPa, peak calls was done by Homer with  "- factor"
Mapped read depth files were generated by BEDtools genomeCoverageBed then by UCSC utility bedGraphToBigWig, after read pairs were converted to a single fragment by filling in region between read ends with Ns. Mapped depths are normalized to 10M uniquely-mapped non-duplicate read pairs per sample.
RNA-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered read pairs were mapped to mm9 via STAR v2.5 with the following paramters: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000.
For each sample, counts per gene were extracted by subread featureCounts v1.5.0-p1 with parameters -s2 -Sfr -p.
HiC and capture HiC reads were processed by HiCUP (v0.6.1) to generate genomic alignments.
HiCExplorer was used to generate contact matrices (hicBuildMatrix with parameters --binSize 10000 --restrictionSequence AAGCTT --inputBufferSize 100000; then hicSumMatrices to combine replicates), normalize (hicCorrectMatrix), and call TADs (hicFindTADs).
CHiCAGO (v1.2.0) was used to process the capture HiC data and generate interaction calls; filtering was applied to require a minimum score of a 5 and maximum distance of 1Mb.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq normalized mapped read depth in bigWig format.
Supplementary_files_format_and_content: ChIP-seq peak calls in BED or txt format.
Supplementary_files_format_and_content: RNA-seq raw counts per gene per sample in tab-delimited text format.
Supplementary_files_format_and_content: HiC TADs in tab-delimited text format.
Supplementary_files_format_and_content: PCHiC interactions in tab-delimited text format.

source_name: liver tissue

extract_protocol: Chip-seq libraries were prepared by Bioo NEXTflex Rapid DNA-seq Kit (cat# 514402).

treatment_protocol: liver tissue was isolated from mice on the low fat diet and high fat diet

tag: Sex

value: male

tag: library type

value: RNA-seq,ribozero

tag: diet

value: low fat diet


title: 4907_mix-RISC_free_0mM_1_S1_L001_R1_001


title: Hi-C_seq_CTCF_siRNA_LNCaP_Rep1.1


title: Peak_GC_3


title: In_vivo_activated_B_cells_1


title: Late_GC_1


title: Peak_GC_2


title: LFD_RNAseq_replicate2


title: Late_GC_3


title: LFD_RNAseq_replicate5


title: Hi-C_seq_NonTarget_siRNA_LNCaP_Rep2

description:
LNCaP_NT_40kb_domains_sorted.bed
LNCaP_CTCF_NT_40kb.contact_counts.bed.gz

value: 20nM Non-Target siRNA pool


title: Hi-C_seq_NonTarget_siRNA_LNCaP_Rep1


title: N1_RNAseq

city: Harbin

first: Xishan

last: Wang

address: Xue Fu Road 246

country: China

institute: The Second Affiliated Hospital of Harbin Medical University

data_processing:
The raw reads were quality controlled using FastQC and then reads were aligned to human GCRh37 / hg19 reference genome using Tophat2.
The  mapped  reads  were assembled into transcripts guided by Ensembl gene models using Cufflinks.
The  expression  level  of  all  transcripts  were  then normalized  by  Cuffnorm  with  default  normalization  method.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: normal breast tissue

extract_protocol:
Tissues were ground in liquid nitrogen, and total RNAs were extracted and checked for quality.
The RNA libraries were quantified using Qubit Instruments after PCR enrichment and cluster generated using a Start cBot instrument, and then were sequenced using Hiseq2500 platform.

value: normal breast tissue


title: Early_GC_3


title: P6_RNAseq

source_name: breast tumor

value: breast tumor

tag: tissue location

value: 6 o'clock of tumor periphery


title: A1_RNAseq

source_name: adjacent tumor

value: adjacent tumor


title: P12_RNAseq

value: 12 o'clock of tumor periphery


title: LFD_RNAseq_replicate3


title: Early_GC_1

description: Early_GC _Spleen_Rep1


title: HFD_RNAseq_replicate5

value: high fat diet


title: P3_RNAseq

value: 3 o'clock of tumor periphery


title: C1_RNAseq

value: tumor center


title: P9_RNAseq

value: 9 o'clock of tumor periphery


title: LFD_RNAseq_replicate1


title: HFD_RNAseq_replicate4


title: Hi-C_seq_CTCF_siRNA_LNCaP_Rep1

value: prostate

value: LNCaP Prostate Cancer Cells

value: 20nM CTCF siRNA pool

value: BglII


title: HFD_RNAseq_replicate1

value: male


title: HFD_RNAseq_replicate3

value: RNA-seq,ribozero


title: HFD_RNAseq_replicate2


title: P6_RRBS

data_processing:
Using Trim Galore to remove reads with poor quality and 5 '/ 3' end adapter sequences.
The remaining reads were then aligned to the human GCRh37 / hg19 reference genome using the Bismark and only the reads with unique alignments were analyzed.
The mapped file with sam format for each sample was subsequently used for identifying epialleles by epialleJS software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include information of epialleles identified from each sample.

extract_protocol:
DNA was extracted from frozen tissue sections. The DNA was first fragmented using NEB4 buffer and MspI enzyme, and the QIAquick PCR Purification Kit was used to purify the digested product according to the manufacturer’s recommendations. RNA-seq:Tissues were ground in liquid nitrogen, and total RNAs were extracted and checked for quality.
The DNA libraries were quantified using Qubit Instruments after PCR enrichment, and then were sequenced using a Hiseq2500 platform.


title: N1_RRBS


title: P12_RRBS


title: P3_RRBS


title: P9_RRBS


title: LFD_C/EBPa_ChIPSeq_replicate1_input

value: low fat diet


title: LFD_C/EBPa_ChIPSeq_replicate2_input


title: HFD_C/EBPa_ChIPSeq_replicate2_input


title: LFD_C/EBPa_ChIPSeq_replicate2

value: ChiP-seq:C/EBPa (Abcam, ab40764)


title: HFD_C/EBPa_ChIPSeq_replicate1_input


title: NC8_Ctrl_CD31_d14

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
Reads mapping to human rRNA transcripts were removed using bwa/0.7.12 alignment and samtools/1.3.1. Remaining reads were aligned to human genome hg38 using TopHat v2.1.1 (GTF annotation file hg38, RefSeq from UCSC, 2015/01; library-type fr-unstranded). Reads in genes were counted with htseq-count v0.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: differentiated endothelial cell

growth_protocol: Vascular organoids were cultured in DMEM:F12 (incl. Glutamax and NEAA) with 20%KOSR, 15%FBS, 100ng/ml VEGF and 100ng/mL FGF-2.

extract_protocol: cDNA synthesis and amplification were performed from total RNA using SMARTer RNA Kit (Clontech) according to the manufacturers instructions.

treatment_protocol: For RNA purification, vascular organoids were treated for 1h with 3U/mL Dispase1 on ice and FACS sorted for CD31 and CD140b.

value: iPSC line NC8

value: differentiated endothelial cell

tag: gender

tag: day

value: d14 (vascular organoids)


title: HFE145, HNF4α (overexpressing) Input

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

description: A control library for HNF4α ChIP-seq in HFE145 cells

data_processing:
Reads from ChIP-seq were mapped to the hg19 reference genome using BWA, retaining reads with MAPQ>=10, removing PCR duplicates by using samtools. Transcription bindings were predicted using MACS2 with -q 0.01 --extsize 250; Histone ChIP-seq regions were predicted using CCAT.
RNA-seq reads were processed using the star-rsem pipeline published at https://github.com/gis-rpd/pipelines
Genome_build: hg19
Supplementary_files_format_and_content: Please refer to the self-explanatory header of each file.

source_name: Normal gastric epithelial cells

extract_protocol: ChIP-seq libraries were prepared following manufacturer protocols (New England Biolabs). RNAseq libraries were prepared using Illumina Tru-Seq RNA Sample Preparation v2 protocol, according to the manufacturer’s instructions.

value: Normal gastric epithelial cells


title: LFD_C/EBPa_ChIPSeq_replicate1


title: LFD_HNF4a_ChIPSeq_replicate2_input


title: IM95 H3K4me1 ChIP

description: H3K4me1 ChIP-seq in IM95 cells

source_name: Gastric Cancer Line

value: Gastric Cancer Line


title: HFD_HNF4a_ChIPSeq_replicate2_input

value: high fat diet


title: NC8_Ctrl_CD140_d14

source_name: differentiated pericyte

value: differentiated pericyte


title: NC8_Ctrl_CD140_d10

value: d10 (early formed vascular network)


title: HFD_C/EBPa_ChIPSeq_replicate2


title: A1_RRBS

value: adjacent tumor


title: HFD_HNF4a_ChIPSeq_replicate1_input


title: NC8_Ctrl_CD31_d10


title: HFD_C/EBPa_ChIPSeq_replicate1


title: HFE145, HNF4α (overexpressing) ChIP

description: HNF4α ChIP-seq in HFE145 after overexpressing HNF4α (002)


title: H9_ESC

source_name: ESC

value: ESC

value: female


title: LFD_HNF4a_ChIPSeq_replicate1

value: ChiP-seq:HNF4a (Abcam, ab41900


title: HFD_HNF4a_ChIPSeq_replicate2

value: ChiP-seq:HNF4a (Abcam, ab41899


title: LFD_HNF4a_ChIPSeq_replicate2

value: male

value: ChiP-seq:HNF4a (Abcam, ab41901


title: HFD_HNF4a_ChIPSeq_replicate1

value: ChiP-seq:HNF4a (Abcam, ab41898


title: ARVC patients' heart RV7

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-ended reads were mapped to human hg19 genome using Tophat V2.1.1, along with the human reference annotation file from RefSeq.
Cufflinks V2.2.1 was used to assemble the transcriptome and cuffcompare was used to annotate the transcripts. DESeq2 was used to normalize the raw read counts.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 output normalized reads counts

source_name: heart RV tissue

extract_protocol:
ARVC patients' heart RV tissue frozen in liquid nitrigen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart RV tissue


title: ARVC patients' heart RV9


title: ARVC patients' heart RV8


title: C1_RRBS

value: breast tumor

value: tumor center


title: LFD_H3K27ac_ChIPSeq_replicate3_input

value: low fat diet


title: LFD_H3K27ac_ChIPSeq_replicate2_input


title: ARVC patients' heart RV6


title: NC8_iPSC

source_name: iPSC

value: iPSC line NC8

value: iPSC


title: ARVC patients' heart RV4


title: LFD_HNF4a_ChIPSeq_replicate1_input


title: ARVC patients' heart RV5


title: LFD_H3K27ac_ChIPSeq_replicate1_input


title: ARVC patients' heart RV3


title: ARVC-LV6

source_name: ARVC patients' heart LV

extract_protocol:
ARVC patients' heart LV tissue frozen in liquid nitrigen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: Arrhythmogenic right ventricular cardiomyopathy (ARVC) patient

value: heart left ventricular (LV)


title: LFD_H3K27ac_ChIPSeq_replicate3

value: ChiP-seq:H3K27ac (Abcam, ab4729)


title: HFD_H3K27ac_ChIPSeq_replicate3

value: high fat diet


title: HFD_H3K27ac_ChIPSeq_replicate1_input


title: ARVC-LV3


title: LFD_H3K27ac_ChIPSeq_replicate2


title: HFD_H3K27ac_ChIPSeq_replicate2


title: LFD_H3K27ac_ChIPSeq_replicate1


title: ARVC patients' heart RV2


title: ARVC-LV2


title: ARVC-LV4


title: ARVC-LV5


title: ARVC-LV1


title: HFD_H3K27ac_ChIPSeq_replicate1


title: LUNC.ct-654

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

institute: UCSD

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

tag: sample type

value: cell-free DNA


title: Vegfa;Shh Mutant_A

city: Chicago

first: Lisandra

last: Vila Ellis

state: IL

address: 303 E Superior

department: Cell and Developmental Biology

institute: Northwestern University

data_processing:
The libraries were bar-coded (New England BioLabs, E7335S) and sequenced on a NextSeq 500 at the UT MD Anderson Sequencing and Microarray Facility to obtain 20−30 million 76 nucleotide pair-end reads for each sample.
Alignment to the mm10 genome using a tophat2 v2.0.14 /bowtie2 v2.2.3 pipeline followed by normalization with cufflinks v2.2.1 pipeline
Pairwise comparisons made using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with all control and mutant samples, their FPKM, fold change and p value.

source_name: Vegfa;Shh Mutant

extract_protocol:
QIAgen RNeasy Mini  100~200 ng total RNA was used to prepare an RNAseq library using an mRNA isolation kit (New England BioLabs, E7490) and a NEBNext Ultra RNA library prep kit (New England BioLabs, E7530S) with a final double (0.65 x -1 x bead volume) size selection step using a SPRIselect reagent kit (Beckman Coulter, B23318).
Seventy-six nucleotide pair-end reads were generated for each sample and aligned to the UCSC mm10 reference genome using tophat2 and bowtie2 in R

tag: strain background

value: mixed

tag: age

value: Postnatal day 7

tag: genotype/variation

value: mutant

value: Lung endothelial cells


title: LUNC.ct-653


title: Vegfa;Shh Mutant_B


title: LUNC.ct-652


title: Vegfa;Shh Mutant_C


title: Vegfa;Shh Control_C

source_name: Vegfa;Shh Control

value: control


title: LUNC.ct-651


title: HFD_H3K27ac_ChIPSeq_replicate3_input

value: male


title: HFD_H3K27ac_ChIPSeq_replicate2_input


title: LUNC.ct-650


title: Vegfa;Shh Control_A


title: Vegfa;Shh Control_B


title: LUNC.ct-648


title: ARVC patients' heart RV1

tag: tissue

value: heart RV tissue


title: LUNC.ct-649


title: LUNC.ct-647


title: LUNC.ct-646


title: LUNC.ct-645


title: MEFs_WT_S3

city: Philadelphia

first: Donita

middle: Colette

last: Brady

address: 421 Curie Blvd. BRBII/III Room 612

department: Cancer Biology

institute: University of Pennsylvania

description:
WT_S3_S3
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv

data_processing:
Read quality was checked for each sample usign FastQC.
Fastq files containing raw sequencing and quality scores were mapped to the mouse genome (GRCm38) using the STAR aligner.
Salmon was used to quantify alignments against the mouse version M17 transcripts from Gencode.
Transcript counts were summarized to the gene level using tximport.  Raw and normalized counts were exported from DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts and scaled count values for each sample

source_name: Embryonic Fibroblasts

growth_protocol: MEFs were routinely propagated by re-plating every 3 days (typically 0.5 × 106 cells into a 10cm plate) on uncoated plastic in DMEM media (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
MEFs were scraped from the dish and RNA was harvested using  Nucleospin RNA kit (Takara Bio). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEFs were treated with 500μM BCS for 48 hours

value: Fibroblast

tag: immortalized

value: T/t antigen

tag: genotype

value: wild type


title: MEFs_WT_S1

description:
WT_S1_S1
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: MEFs_WT_S2

description:
WT_S2_S2
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: MEFs_FloxedCtr1_S3

description:
FloxedCtr1_S3_S6
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: LUNC.ct-644


title: LUNC.ct-642


title: LUNC.ct-641


title: LUNC.ct-640


title: LUNC.ct-643


title: LUNC.ct-639


title: MEFs_FloxedCtr1_BCS_S2

description:
FloxedCtr1_BCS_S2_S8
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv

value: bathocuproine disulfonic acid (BCS), 500μM, 48 hours


title: MEFs_FloxedCtr1_S1

description:
FloxedCtr1_S1_S4
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: LUNC.ct-637


title: MEFs_FloxedCtr1_BCS_S3

description:
FloxedCtr1_BCS_S3_S9
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: LUNC.ct-635


title: LUNC.ct-636


title: b3_7FD4_c95

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts and transcripts per million(TPM)  were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: Mouse ESCs (mESCs) and iPS cell lines were cultured on feeder layers with mESC medium (high glucose DMEM, 15%FBS, NEAA, GlutaMAX, LIF) plus 2i (1 m PD0325901, 3 m CHIR99021). MEF cells were maintained in 10% FBS medium (high glucose DMEM supplemented with 10% FBS, GlutaMAX and NEAA).  The reprogramming cells at different days were cultured in iCD1 medium.

extract_protocol:
For bulk cells, total RNAs were extracted by chloroform-isopropanol method; for single cell, following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)


title: MEFs_FloxedCtr1_BCS_S1

description:
FloxedCtr1_BCS_S1_S7
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: b3_7FD4_c91


title: LUNC.ct-633


title: LUNC.ct-634


title: b3_7FD4_c90


title: LUNC.ct-632


title: b3_7FD4_c88


title: LUNC.ct-631


title: LUNC.ct-630


title: b3_7FD4_c78


title: LUNC.ct-628


title: LUNC.ct-629


title: b3_7FD4_c77


title: MEFs_FloxedCtr1_S2

description:
FloxedCtr1_S2_S5
9samp_scaled_salmonTxi.csv
9samp_counts_salmonTxi.csv


title: LUNC.ct-626


title: b3_7FD4_c69


title: b3_7FD4_c76


title: LUNC.ct-638


title: b3_7FD4_c70


title: LUNC.ct-625


title: LUNC.ct-627


title: b3_7FD4_c68


title: b3_7FD4_c66


title: b3_7FD4_c67


title: LUNC.ct-624


title: LUNC.ct-622


title: LUNC.ct-621


title: b3_7FD4_c64


title: b3_7FD4_c81


title: LUNC.ct-620


title: LUNC.ct-619


title: b3_7FD4_c62


title: b3_7FD4_c60


title: LUNC.ct-618


title: LUNC.ct-616


title: LUNC.ct-617


title: b3_7FD4_c59


title: b3_7FD4_c58


title: LUNC.ct-615


title: LUNC.ct-623


title: LUNC.ct-613


title: LUNC.ct-614


title: b3_7FD4_c57


title: LUNC.ct-612


title: b3_7FD4_c55


title: b3_7FD4_c65


title: b3_7FD4_c52


title: LUNC.ct-611


title: LUNC.ct-610


title: LUNC.ct-609


title: LUNC.ct-607


title: b3_7FD4_c63


title: LUNC.ct-608


title: b3_7FD4_c48


title: b3_7FD4_c50


title: b3_7FD4_c51


title: LUNC.ct-606


title: b3_7FD4_c44


title: LUNC.ct-605


title: b3_7FD4_c47


title: b3_7FD4_c43


title: b3_7FD4_c56


title: LUNC.ct-604


title: b3_7FD4_c40


title: b3_7FD4_c42


title: LUNC.ct-601


title: LUNC.ct-602


title: LUNC.ct-603


title: b3_7FD4_c39


title: b3_7FD4_c37


title: b3_7FD4_c38


title: LUNC.ct-597


title: LUNC.ct-598


title: b3_7FD4_c33


title: LUNC.ct-600


title: LUNC.ct-596


title: LUNC.ct-599


title: b3_7FD4_c29


title: LUNC.ct-595


title: LUNC.ct-594


title: LUNC.ct-593


title: b3_7FD4_c31


title: LUNC.ct-592


title: b3_7FD4_c26


title: LUNC.ct-591


title: b3_7FD4_c25


title: b3_7FD4_c24


title: b3_7FD4_c36


title: LUNC.ct-590


title: b3_7FD4_c32


title: b3_7FD4_c21


title: LUNC.ct-587


title: LUNC.ct-588


title: LUNC.ct-589


title: LUNC.ct-584


title: b3_7FD4_c16


title: b3_7FD4_c17


title: LUNC.ct-585


title: b3_7FD4_c13


title: b3_7FD4_c28


title: b3_7FD4_c08


title: b3_7FD4_c09


title: b3_7FD4_c07


title: b3_7FD4_c06


title: LUNC.ct-582


title: LUNC.ct-581


title: LUNC.ct-580


title: b3_7FD4_c19


title: b3_7FD4_c04


title: b3_7FD4_c05


title: b3_7FD4_c03


title: b3_7FD4_c02


title: LUNC.ct-576


title: LUNC.ct-579


title: b3_7FD4_c01


title: b2_7FD7_c96


title: LUNC.ct-575


title: LUNC.ct-577


title: LUNC.ct-583


title: LUNC.ct-586


title: b2_7FD7_c95


title: b2_7FD7_c93


title: b3_7FD4_c54


title: b2_7FD7_c88


title: b2_7FD7_c89


title: b2_7FD7_c90


title: LUNC.ct-574


title: b2_7FD7_c85


title: LUNC.ct-572


title: LUNC.ct-570


title: LUNC.ct-569


title: LUNC.ct-571


title: LUNC.ct-578


title: LUNC.ct-567


title: b2_7FD7_c84


title: LUNC.ct-568


title: LUNC.ct-566


title: b2_7FD7_c79


title: b2_7FD7_c81


title: b2_7FD7_c77


title: LUNC.ct-564


title: LUNC.ct-573


title: LUNC.ct-565


title: LUNC.ct-562


title: b2_7FD7_c72


title: LUNC.ct-561


title: b2_7FD7_c76


title: b2_7FD7_c70


title: b2_7FD7_c69


title: b2_7FD7_c65


title: LUNC.ct-556


title: LUNC.ct-557


title: LUNC.ct-558


title: b2_7FD7_c67


title: b2_7FD7_c82


title: LUNC.ct-559


title: LUNC.ct-554


title: LUNC.ct-555


title: LUNC.ct-553


title: LUNC.ct-563


title: b2_7FD7_c60


title: b2_7FD7_c73


title: b2_7FD7_c57


title: b2_7FD7_c56


title: b2_7FD7_c59


title: LUNC.ct-551


title: LUNC.ct-552


title: LUNC.ct-560


title: LUNC.ct-550


title: b2_7FD7_c54


title: LUNC.ct-549


title: b2_7FD7_c68


title: b2_7FD7_c49


title: b2_7FD7_c47


title: b2_7FD7_c45


title: b2_7FD7_c44


title: LUNC.ct-547


title: LUNC.ct-546


title: b2_7FD7_c53


title: b2_7FD7_c43


title: LUNC.ct-548


title: b2_7FD7_c41


title: LUNC.ct-543


title: LUNC.ct-544


title: b2_7FD7_c38


title: b2_7FD7_c39


title: LUNC.ct-545


title: b2_7FD7_c40


title: LUNC.ct-541


title: LUNC.ct-539


title: b2_7FD7_c36


title: LUNC.ct-538


title: b2_7FD7_c35


title: LUNC.ct-537


title: LUNC.ct-540


title: b2_7FD7_c33


title: LUNC.ct-542


title: b2_7FD7_c34


title: LUNC.ct-535


title: b2_7FD7_c30


title: b2_7FD7_c29


title: b2_7FD7_c42


title: LUNC.ct-534


title: b2_7FD7_c26


title: LUNC.ct-531


title: LUNC.ct-533


title: LUNC.ct-530


title: LUNC.ct-532


title: b2_7FD7_c27


title: b2_7FD7_c25


title: LUNC.ct-528


title: LUNC.ct-527


title: b2_7FD7_c32


title: b2_7FD7_c23


title: b2_7FD7_c22


title: b2_7FD7_c19


title: b2_7FD7_c21


title: b2_7FD7_c28


title: LUNC.ct-526


title: LUNC.ct-525


title: LUNC.ct-524


title: b2_7FD7_c20


title: LUNC.ct-536


title: LUNC.ct-523


title: LUNC.ct-522


title: b2_7FD7_c17


title: LUNC.ct-521


title: LUNC.ct-520


title: b2_7FD7_c15


title: b2_7FD7_c13


title: b2_7FD7_c11


title: b2_7FD7_c12


title: LUNC.ct-518


title: LUNC.ct-519


title: b2_7FD7_c10


title: b2_7FD7_c16


title: LUNC.ct-516


title: LUNC.ct-529


title: b2_7FD7_c06


title: b2_7FD7_c04


title: LUNC.ct-513


title: b2_7FD7_c05


title: LUNC.ct-514


title: LUNC.ct-515


title: LUNC.ct-511


title: LUNC.ct-512


title: b2_7FD5_c94


title: b2_7FD5_c92


title: b2_7FD5_c93


title: LUNC.ct-509


title: LUNC.ct-508


title: b2_7FD5_c91


title: LUNC.ct-517


title: b2_7FD5_c90


title: LUNC.ct-506


title: LUNC.ct-507


title: LUNC.ct-505


title: b2_7FD5_c89


title: b2_7FD5_c87


title: LUNC.ct-504


title: LUNC.ct-503


title: b2_7FD5_c85


title: LUNC.ct-502


title: b2_7FD7_c02


title: b2_7FD5_c82


title: b2_7FD7_c03


title: LUNC.ct-501


title: LUNC.ct-498


title: LUNC.ct-499


title: LUNC.ct-500


title: b2_7FD5_c80


title: b2_7FD5_c79


title: b2_7FD5_c78


title: b2_7FD5_c75


title: LUNC.ct-497


title: b2_7FD5_c86


title: b2_7FD5_c77


title: b2_7FD5_c76


title: LUNC.ct-496


title: LUNC.ct-494


title: LUNC.ct-492


title: b2_7FD5_c73


title: b2_7FD5_c72


title: LUNC.ct-491


title: b2_7FD5_c74


title: b2_7FD5_c71


title: b2_7FD5_c84


title: b2_7FD5_c70


title: LUNC.ct-490


title: LUNC.ct-488


title: b2_7FD5_c68


title: LUNC.ct-487


title: LUNC.ct-495


title: LUNC.ct-489


title: LUNC.ct-486


title: b2_7FD5_c67


title: b2_7FD5_c65


title: b2_7FD5_c64


title: LUNC.ct-510


title: b2_7FD5_c69


title: b2_7FD7_c24


title: LUNC.ct-485


title: LUNC.ct-482


title: b2_7FD5_c63


title: LUNC.ct-480


title: b2_7FD5_c60


title: LUNC.ct-483


title: b2_7FD5_c59


title: LUNC.ct-481


title: LUNC.ct-484


title: b2_7FD5_c61


title: LUNC.ct-478


title: b2_7FD5_c56


title: LUNC.ct-479


title: b2_7FD5_c57


title: LUNC.ct-477


title: LUNC.ct-476


title: b2_7FD5_c53


title: b2_7FD5_c51


title: LUNC.ct-474


title: b2_7FD5_c49


title: b2_7FD5_c62


title: LUNC.ct-475


title: b2_7FD5_c52


title: LUNC.ct-472


title: b2_7FD5_c45


title: LUNC.ct-471


title: LUNC.ct-470


title: b2_7FD5_c46


title: b2_7FD5_c55


title: LUNC.ct-473


title: LUNC.ct-468


title: LUNC.ct-465


title: b2_7FD5_c41


title: LUNC.ct-467


title: b2_7FD5_c42


title: LUNC.ct-464


title: b2_7FD5_c43


title: LUNC.ct-466


title: b2_7FD5_c40


title: b2_7FD5_c38


title: LUNC.ct-463


title: LUNC.ct-462


title: b2_7FD5_c37


title: b2_7FD5_c50


title: b2_7FD5_c36


title: b2_7FD5_c35


title: LUNC.ct-460


title: LUNC.ct-459


title: b2_7FD5_c44


title: LUNC.ct-458


title: LUNC.ct-469


title: LUNC.ct-493


title: LUNC.ct-461


title: b2_7FD5_c32


title: b2_7FD5_c33


title: LUNC.ct-457


title: LUNC.ct-455


title: b2_7FD5_c30


title: b2_7FD5_c28


title: LUNC.ct-454


title: LUNC.ct-456


title: b2_7FD5_c27


title: b2_7FD5_c26


title: LUNC.ct-451


title: b2_7FD5_c29


title: b2_7FD5_c25


title: b2_7FD5_c24


title: LUNC.ct-452


title: b2_7FD5_c34


title: LUNC.ct-450


title: LUNC.ct-449


title: b2_7FD5_c22


title: LUNC.ct-448


title: b2_7FD5_c20


title: b2_7FD5_c21


title: LUNC.ct-447


title: b2_7FD5_c18


title: b2_7FD5_c17


title: b2_7FD5_c15


title: LUNC.ct-444


title: LUNC.ct-443


title: b2_7FD5_c16


title: LUNC.ct-445


title: LUNC.ct-446


title: LUNC.ct-453


title: LUNC.ct-441


title: LUNC.ct-442


title: b2_7FD5_c10


title: b2_7FD5_c13


title: b2_7FD5_c11


title: b2_7FD5_c12


title: b2_7FD5_c09


title: LUNC.ct-439


title: LUNC.ct-440


title: LUNC.ct-437


title: LUNC.ct-438


title: LUNC.ct-436


title: b2_7FD5_c08


title: b2_7FD5_c05


title: b2_7FD5_c04


title: LUNC.ct-435


title: b2_7FD5_c02


title: LUNC.ct-433


title: b2_7FD5_c01


title: b2_7FD5_c14


title: LUNC.ct-432


title: LUNC.ct-431


title: LUNC.ct-430


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title: b2_7FD3_c85


title: LUNC.ct-429


title: b2_7FD3_c86


title: LUNC.ct-428


title: LUNC.ct-427


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title: LUNC.ct-426


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title: b2_7FD3_c75


title: LUNC.ct-425


title: LUNC.ct-434


title: LUNC.ct-422


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title: b2_7FD3_c70


title: LUNC.ct-420


title: LUNC.ct-421


title: LUNC.ct-419


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title: b2_7FD3_c68


title: LUNC.ct-418


title: b2_7FD3_c66


title: LUNC.ct-417


title: b2_7FD3_c65


title: b2_7FD3_c64


title: b2_7FD3_c69


title: LUNC.ct-415


title: b2_7FD3_c80


title: b2_7FD3_c62


title: LUNC.ct-414


title: LUNC.ct-423


title: LUNC.ct-424


title: b2_7FD3_c72


title: LUNC.ct-413


title: LUNC.ct-412


title: b2_7FD3_c58


title: LUNC.ct-411


title: LUNC.ct-416


title: LUNC.ct-410


title: b2_7FD3_c56


title: LUNC.ct-409


title: LUNC.ct-408


title: b2_7FD3_c53


title: LUNC.ct-407


title: b2_7FD3_c52


title: LUNC.ct-406


title: LUNC.ct-405


title: b2_7FD3_c51


title: b2_7FD3_c61


title: b2_7FD3_c60


title: b2_7FD3_c40


title: LUNC.ct-403


title: LUNC.ct-402


title: LUNC.ct-401


title: b2_7FD3_c57


title: b2_7FD3_c34


title: b2_7FD3_c39


title: b2_7FD3_c38


title: LUNC.ct-397


title: b2_7FD3_c41


title: b2_7FD3_c37


title: b2_7FD3_c54


title: b2_7FD3_c32


title: LUNC.ct-396


title: LUNC.ct-398


title: b2_7FD3_c31


title: LUNC.ct-400


title: b2_7FD3_c33


title: LUNC.ct-395


title: b2_7FD3_c30


title: b2_7FD3_c49


title: LUNC.ct-394


title: LUNC.ct-393


title: b2_7FD3_c29


title: LUNC.ct-404


title: b2_7FD3_c26


title: LUNC.ct-399


title: LUNC.ct-392


title: b2_7FD3_c28


title: b2_7FD3_c21


title: LUNC.ct-391


title: LUNC.ct-389


title: b2_7FD3_c24


title: b2_7FD3_c19


title: LUNC.ct-385


title: b2_7FD3_c17


title: b2_7FD3_c20


title: LUNC.ct-387


title: LUNC.ct-386


title: LUNC.ct-388


title: b2_7FD3_c18


title: b2_7FD3_c13


title: LUNC.ct-382


title: b2_7FD3_c14


title: LUNC.ct-381


title: b2_7FD3_c09


title: LUNC.ct-383


title: LUNC.ct-384


title: b2_7FD3_c08


title: b2_7FD3_c11


title: b2_7FD3_c06


title: b2_7FD3_c07


title: LUNC.ct-390


title: b2_7FD3_c05


title: LUNC.ct-378


title: LUNC.ct-377


title: LUNC.ct-379


title: b2_7FD3_c04


title: LUNC.ct-376


title: b2_7FD3_c03


title: LUNC.ct-375


title: b2_7FD3_c02


title: LUNC.ct-374


title: LUNC.ct-372


title: b2_7FD1_c92


title: b2_7FD1_c93


title: LUNC.ct-371


title: LUNC.ct-373


title: LUNC.ct-370


title: LUNC.ct-369


title: b2_7FD1_c89


title: b2_7FD1_c95


title: LUNC.ct-368


title: b2_7FD1_c88


title: LUNC.ct-366


title: LUNC.ct-367


title: b2_7FD1_c86


title: b2_7FD1_c82


title: b2_7FD1_c83


title: LUNC.ct-365


title: b2_7FD1_c81


title: b2_7FD1_c75


title: b2_7FD1_c76


title: b2_7FD1_c74


title: LUNC.ct-363


title: LUNC.ct-364


title: LUNC.ct-362


title: LUNC.ct-361


title: LUNC.ct-360


title: b2_7FD1_c73


title: b2_7FD1_c87


title: LUNC.ct-359


title: b2_7FD1_c72


title: b2_7FD1_c71


title: LUNC.ct-357


title: b2_7FD1_c59


title: b2_7FD1_c61


title: LUNC.ct-358


title: b2_7FD1_c57


title: LUNC.ct-356


title: LUNC.ct-355


title: LUNC.ct-353


title: LUNC.ct-352


title: LUNC.ct-380


title: b2_7FD1_c50


title: b2_7FD1_c49


title: b2_7FD1_c48


title: LUNC.ct-351


title: b2_7FD1_c46


title: b2_7FD1_c45


title: LUNC.ct-350


title: b2_7FD1_c44


title: LUNC.ct-348


title: b2_7FD1_c43


title: LUNC.ct-349


title: LUNC.ct-347


title: b2_7FD1_c42


title: b2_7FD1_c41


title: LUNC.ct-346


title: b2_7FD1_c51


title: LUNC.ct-345


title: b2_7FD1_c38


title: LUNC.ct-354


title: LUNC.ct-342


title: LUNC.ct-343


title: LUNC.ct-344


title: b2_7FD1_c35


title: b2_7FD1_c32


title: LUNC.ct-340


title: LUNC.ct-339


title: b2_7FD1_c34


title: LUNC.ct-337


title: b2_7FD1_c31


title: LUNC.ct-336


title: b2_7FD1_c28


title: LUNC.ct-335


title: b2_7FD1_c27


title: b2_7FD1_c26


title: LUNC.ct-333


title: b2_7FD1_c25


title: LUNC.ct-341


title: b2_7FD1_c24


title: b2_7FD1_c36


title: LUNC.ct-332


title: LUNC.ct-331


title: b2_7FD1_c37


title: LUNC.ct-330


title: b2_7FD1_c21


title: b2_7FD1_c23


title: b2_7FD1_c22


title: LUNC.ct-329


title: LUNC.ct-338


title: b2_7FD1_c20


title: b2_7FD1_c29


title: LUNC.ct-328


title: LUNC.ct-327


title: b2_7FD1_c16


title: LUNC.ct-326


title: b2_7FD1_c13


title: b2_7FD1_c14


title: LUNC.ct-334


title: b2_7FD1_c11


title: LUNC.ct-324


title: b2_7FD1_c07


title: b2_7FD1_c10


title: LUNC.ct-323


title: LUNC.ct-322


title: LUNC.ct-321


title: b2_7FD1_c04


title: b2_7FD1_c05


title: LUNC.ct-319


title: b2_7FD1_c02


title: LUNC.ct-320


title: b2_7FD1_c01


title: LUNC.ct-325


title: b2_7FD1_c03


title: LUNC.ct-318


title: b2_7FD0_c95


title: LUNC.ct-315


title: LUNC.ct-316


title: LUNC.ct-314


title: LUNC.ct-313


title: LUNC.ct-312


title: LUNC.ct-311


title: b2_7FD0_c92


title: b2_7FD0_c90


title: b2_7FD0_c89


title: b2_7FD0_c96


title: LUNC.ct-310


title: b2_7FD0_c87


title: b2_7FD0_c88


title: LUNC.ct-309


title: LUNC.ct-308


title: b2_7FD0_c93


title: b2_7FD0_c85


title: b2_7FD1_c39


title: b2_7FD0_c84


title: LUNC.ct-305


title: LUNC.ct-317


title: b2_7FD0_c80


title: LUNC.ct-303


title: b2_7FD0_c78


title: b2_7FD0_c77


title: LUNC.ct-302


title: LUNC.ct-306


title: LUNC.ct-304


title: b2_7FD0_c73


title: LUNC.ct-300


title: LUNC.ct-299


title: LUNC.ct-301


title: b2_7FD0_c81


title: LUNC.ct-307


title: LUNC.ct-298


title: b2_7FD0_c67


title: LUNC.ct-297


title: b2_7FD0_c72


title: b2_7FD0_c70


title: b2_7FD0_c62


title: b2_7FD0_c64


title: b2_7FD0_c61


title: LUNC.ct-296


title: LUNC.ct-295


title: LUNC.ct-293


title: LUNC.ct-290


title: b2_7FD0_c57


title: b2_7FD0_c50


title: LUNC.ct-289


title: b2_7FD0_c52


title: b2_7FD0_c43


title: LUNC.ct-292


title: b2_7FD0_c49


title: b2_7FD0_c51


title: LUNC.ct-287


title: b2_7FD0_c68


title: b2_7FD0_c53


title: b2_7FD0_c38


title: LUNC.ct-285


title: LUNC.ct-286


title: LUNC.ct-288


title: LUNC.ct-283


title: b2_7FD0_c36


title: LUNC.ct-284


title: b2_7FD0_c35


title: LUNC.ct-282


title: b2_7FD0_c33


title: b2_7FD0_c37


title: b2_7FD0_c30


title: b2_7FD0_c29


title: LUNC.ct-280


title: LUNC.ct-279


title: b2_7FD0_c28


title: b2_7FD0_c24


title: b2_7FD0_c26


title: LUNC.ct-277


title: LUNC.ct-276


title: b2_7FD0_c22


title: b2_7FD0_c21


title: LUNC.ct-278


title: LUNC.ct-291


title: b2_7FD0_c34


title: LUNC.ct-273


title: b2_7FD0_c18


title: LUNC.ct-274


title: LUNC.ct-272


title: b2_7FD0_c14


title: b2_7FD0_c17


title: LUNC.ct-271


title: LUNC.ct-275


title: b2_7FD0_c16


title: LUNC.ct-270


title: LUNC.ct-269


title: b2_7FD0_c13


title: LUNC.ct-281


title: b2_7FD0_c06


title: b2_7FD0_c11


title: LUNC.ct-268


title: b2_7FD0_c04


title: LUNC.ct-267


title: LUNC.ct-266


title: LUNC.ct-262


title: b1_7FD7_c96


title: LUNC.ct-264


title: b1_7FD7_c89


title: LUNC.ct-260


title: LUNC.ct-265


title: LUNC.ct-261


title: b1_7FD5_c65


title: LUNC.ct-258


title: LUNC.ct-259


title: b1_7FD5_c61


title: LUNC.ct-256


title: LUNC.ct-257


title: b2_7FD0_c12


title: b1_7FD3_c92


title: LUNC.ct-255


title: b1_7FD5_c70


title: b2_7FD0_c05


title: b2_7FD0_c03


title: b1_7FD3_c91


title: LUNC.ct-253


title: LUNC.ct-263


title: b2_7FD0_c01


title: LUNC.ct-252


title: LUNC.ct-251


title: LUNC.ct-250


title: b1_7FD3_c88


title: b1_7FD5_c25


title: b1_7FD3_c87


title: LUNC.ct-247


title: LUNC.ct-249


title: b1_7FD5_c59


title: b1_7FD3_c84


title: b1_7FD3_c78


title: b1_7FD3_c82


title: LUNC.ct-248


title: b1_7FD3_c75


title: LUNC.ct-246


title: b1_7FD3_c8


title: LUNC.ct-245


title: b1_7FD3_c71


title: LUNC.ct-254


title: LUNC.ct-240


title: b1_7FD3_c70


title: LUNC.ct-244


title: LUNC.ct-243


title: b1_7FD3_c90


title: b1_7FD3_c85


title: b1_7FD3_c7


title: LUNC.ct-239


title: LUNC.ct-242


title: b1_7FD3_c83


title: b1_7FD3_c67


title: LUNC.ct-237


title: LUNC.ct-238


title: LUNC.ct-241


title: b1_7FD3_c76


title: LUNC.ct-236


title: b1_7FD3_c66


title: LUNC.ct-235


title: b1_7FD3_c65


title: LUNC.ct-234


title: b1_7FD3_c64


title: b1_7FD3_c73


title: LUNC.ct-231


title: b1_7FD3_c60


title: LUNC.ct-230


title: b1_7FD3_c6


title: b1_7FD3_c61


title: b1_7FD3_c59


title: LUNC.ct-229


title: b1_7FD3_c58


title: b1_7FD3_c56


title: LUNC.ct-228


title: LUNC.ct-227


title: LUNC.ct-233


title: b1_7FD3_c54


title: LUNC.ct-225


title: LUNC.ct-226


title: LUNC.ct-224


title: b1_7FD3_c52


title: b1_7FD3_c55


title: LUNC.ct-223


title: LUNC.ct-294


title: b1_7FD3_c45


title: b1_7FD3_c43


title: LUNC.ct-222


title: LUNC.ct-221


title: LUNC.ct-220


title: b1_7FD3_c42


title: b1_7FD3_c5


title: b1_7FD3_c41


title: b1_7FD3_c40


title: LUNC.ct-219


title: LUNC.ct-218


title: b1_7FD3_c4


title: b1_7FD3_c37


title: b1_7FD3_c39


title: b1_7FD3_c38


title: LUNC.ct-216


title: b1_7FD3_c63


title: LUNC.ct-214


title: LUNC.ct-215


title: b1_7FD3_c35


title: LUNC.ct-213


title: b1_7FD3_c33


title: b1_7FD3_c32


title: b1_7FD3_c34


title: LUNC.ct-212


title: b1_7FD3_c3


title: LUNC.ct-210


title: LUNC.ct-208


title: LUNC.ct-211


title: LUNC.ct-207


title: b1_7FD3_c24


title: b1_7FD3_c25


title: LUNC.ct-209


title: b1_7FD3_c23


title: LUNC.ct-206


title: b1_7FD3_c22


title: b1_7FD3_c21


title: LUNC.ct-204


title: LUNC.ct-232


title: b1_7FD3_c2


title: LUNC.ct-203


title: LUNC.ct-201


title: LUNC.ct-205


title: LUNC.ct-202


title: b1_7FD3_c18


title: b1_7FD3_c19


title: b1_7FD3_c28


title: LUNC.ct-200


title: b1_7FD3_c16


title: LUNC.ct-199


title: b1_7FD3_c14


title: b1_7FD3_c15


title: LUNC.ct-198


title: b1_7FD3_c11


title: LUNC.ct-197


title: b1_7FD3_c12


title: LUNC.ct-196


title: LUNC.ct-217


title: b1_7FD0_c94


title: b1_7FD3_c1


title: LUNC.ct-195


title: LUNC.ct-193


title: b1_7FD0_c90


title: b1_7FD0_c9


title: LUNC.ct-189


title: b1_7FD0_c87


title: LUNC.ct-190


title: b1_7FD0_c75


title: b1_7FD0_c70


title: b1_7FD0_c60


title: LUNC.ct-187


title: b1_7FD0_c42


title: b1_7FD0_c4


title: LUNC.ct-185


title: b1_7FD0_c53


title: LUNC.ct-184


title: LUNC.ct-194


title: b1_7FD0_c39


title: LUNC.ct-186


title: b1_7FD0_c33


title: b1_7FD0_c37


title: b1_7FD0_c28


title: b1_7FD0_c29


title: LUNC.ct-181


title: LUNC.ct-179


title: LUNC.ct-188


title: LUNC.ct-178


title: b1_7FD0_c26


title: b1_7FD0_c24


title: LUNC.ct-180


title: LUNC.ct-177


title: b1_7FD0_c19


title: LUNC.ct-182


title: LUNC.ct-192


title: LUNC.ct-175


title: b1_7FD0_c15


title: LUNC.ct-172


title: LUNC.ct-173


title: HUtSMC-crCtrl-INPUT-Rep-3

first: Debabrata

last: Chakravarti

address: 303 E Superior St.

data_processing:
ChIP-seq reads were aligned to the GRCh38 human genome assembly obtained from Ensembl (release 90) using bowtie (v1.2.2; settings: --best -m 1).
Peak calling was performed with HOMER (v4.10.3, histone peak calling: -tbp 1 -F 4 -style histone)
Genome_build: GRCh38
Supplementary_files_format_and_content: Reads per genomic content normalization (RPGC, 1x normalization) of BAM files obtained from Bowtie alignments was performed with DeepTools to produce BigWig files.

source_name: Human uterine smooth muscle cells (HUtSMCs)

growth_protocol: Cells were cultured in vascular smooth muscle cell complete media (ATCC, cat #s PCS-100-030, PCS-100-042) and grown at 37°C in a humidified cell culture incubator containing 5% CO2.

extract_protocol:
16% paraformaldehyde was added to full media-containing HUtSM cell plates to a final concentration of 1% paraformaldehyde and incubated at room temperature for 10min and then quenched with 0.125M glycine for 10min at room temperature with rotation. Cross-linked cells were then incubated in ChIP lysis buffer 1 (50mM HEPES-KOH [pH 7.6], 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed by end-over-end rotation at 4°C for 15min and then low speed centrifugation at 4°C. Samples were resuspended in ChIP lysis buffer 2 (10mM Tris-HCl [pH 8.0], 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed again by end-over-end rotation at 4°C for 15min and sample recovery by low speed centrifugation at 4°C. Samples were then resuspended in ChIP lysis buffer 3 (10mM Tris-HCl [pH 7.5], 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% sarkosyl) and sonicated in an ice water bath (Misonix, setting 6 [~6 W power output], 12 cycles of 15sec on and 45sec off). Triton X-100 was added to a final concentration of 1% and samples were centrifuged at 20,000 x g at 4°C for 20min, with recovery of chromatin-containing supernatant. Solubilized chromatin was incubated overnight with antibody at 4°C with end-over-end rotation.
KAPA Hyper Prep kit (Kapa Biosystems, cat # KK8502) was used for end-repair, A-tailing, and adapter ligation with TruSeq index adapters, all according to manufacturer’s instructions. A 0.6X-0.8X AMPure XP bead (Beckman Coulter, cat # A63881) size selection was carried out after adapter ligation to enrich for sub-nucleosomal DNA fragments followed by 12 cycles of PCR amplification.

treatment_protocol: 1.35 x 105 HUtSMCs were combined with crRNA:tracrRNA:cas9:electroporation enhancer mix targeting either non-silencing control or AP-1 (JUN, JUNB, JUND, FOS, and FOSB) and electroporated in a 10μl Neon pipette tip (pulse voltage = 1,500V, pulse width = 10ms, # of pulses = 3) using a Neon electroporation system (ThermoFisher, cat # MPK5000). Fresh smooth muscle cell complete media was then added and cells were allowed to grow to 90% confluence.

value: Myometrium

tag: chip antibody


title: HUtSMC-crCtrl-INPUT-Rep-1


title: HUtSMC-crCtrl-INPUT-Rep-2


title: LUNC.ct-176


title: HUtSMC-crAP-1-INPUT-Rep-2

value: AP-1 depleted


title: HUtSMC-crAP-1-INPUT-Rep-1


title: LUNC.ct-169


title: LUNC.ct-166


title: b1_7FD0_c27


title: LUNC.ct-165


title: LUNC.ct-183


title: HUtSMC-crAP-1-H3K27Ac-Rep-3


title: HUtSMC-crCtrl-H3K27Ac-Rep-1


title: HUtSMC-crCtrl-H3K27Ac-Rep-2


title: HUtSMC-crCtrl-H3K27Ac-Rep-3


title: LUNC.ct-164


title: LUNC.ct-163


title: LUNC.ct-162


title: LUNC.ct-171


title: HUtSMC-crCtrl-Rep-3

data_processing:
RNA sequencing reads were aligned to the GRCh38 human genome assembly using the STAR aligner (v2.5.3a) with default settings.
Counting of reads per gene was performed using featureCounts from the Subread package (v1.5.0; exon count settings: -g gene_id -t exon -p -s 2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw exonic counts of annotated transcripts

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini kit according to manufacturer’s instructions (Qiagen, cat # 217004). After RNA elution, an in-solution DNase treatment was performed to completely digest genomic DNA (Qiagen, cat # 79254). RNA quality was verified using the Bioanalyzer eukaryote total RNA 600 nano kit (Agilent technologies, cat # 5067). Purified RNA samples had a mean RNA integrity number (RIN) of 9.0.
RNA was prepared for sequencing using the KAPA mRNA HyperPrep kit according to the manufacturer’s instructions (Kapa Biosystems, cat # KK8580).

tag: cell type


title: HUtSMC-crAP-1-H3K27Ac-Rep-1


title: LUNC.ct-170


title: HUtSMC-crAP-1-INPUT-Rep-3


title: HUtSMC-crCtrl-Rep-2


title: LUNC.ct-161


title: LUNC.ct-160


title: LUNC.ct-191


title: HUtSMC-crCtrl-Rep-1


title: LUNC.ct-159


title: LUNC.ct-158


title: HUtSMC-crAP-1-Rep-2


title: HUtSMC-crAP-1-Rep-3


title: HUtSMC-crAP-1-Rep-1


title: LUNC.ct-156


title: LUNC.ct-155


title: LUNC.ct-153


title: HUtSMC-crAP-1-H3K27Ac-Rep-2


title: LUNC.ct-154


title: LUNC.ct-150


title: LUNC.ct-152


title: LUNC.ct-151


title: LUNC.ct-148


title: LUNC.ct-145


title: LUNC.ct-144


title: LUNC.ct-143


title: LUNC.ct-147


title: LUNC.ct-141


title: LUNC.ct-142


title: LUNC.ct-157


title: LUNC.ct-146


title: LUNC.ct-137


title: LUNC.ct-139


title: LUNC.ct-138


title: LUNC.ct-135


title: LUNC.ct-136


title: LUNC.ct-132


title: LUNC.ct-130


title: LUNC.ct-129


title: LUNC.ct-149


title: Nalm-6 cells, Wild-type control day 14

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

institute: The Hospital for Sick Children

description: sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Genome_build: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library.
Supplementary_files_format_and_content: tab separated sgRNA read counts for each sample

source_name: Nalm-6 pre-B lymphoid cell line

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA sequences were recovered and fitted with Illumina adaptors by PCR as previously described (Bertomeu et al., 2017, PMID:29038160).

tag: cell line

value: pre-B lymphoid cells

value: Wild-type control

tag: time

value: day 14

tag: infection

value: pooled sgRNA library


title: LUNC.ct-131

value: cell-free DNA


title: LUNC.ct-127


title: LUNC.ct-128


title: LUNC.ct-126


title: Nalm-6 cells, Wild-type control day 0

description: sgRNAs PCR-amplified from genomic DNA

value: day 0


title: MAIT cells 3

city: Albany

first: Qi

last: Yang

address: 43 New Scotland Avenue

institute: Albany Medical College

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Text file for processed data file
Supplementary_files_format_and_content: Normalized abundance measurements

source_name: peripheral blood

extract_protocol:
PBMCs were extracted, CD4+ T cells and MAIT cells were FACS sorted based on the following surface expression: CD45+ CD4+ or CD45+ CD3+ MR1 5-OP-RU tetramer+. Cells were pooled per sample and were sorted into Trizol LS
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: donor

value: healthy donor

value: MAIT cells


title: LUNC.ct-124


title: LUNC.ct-123


title: LUNC.ct-167


title: MAIT cells 2


title: MAIT cells 1


title: CD4 T cells 3

value: CD4 T cells


title: LUNC.ct-133


title: LUNC.ct-122


title: Ribosome profiling from 27wt/72Lmax/27min (pilot experiment)

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
Ribosome profiling (Ribo-seq)
RPallreads_Exp1_counts_combined_CDS_filt.txt.gz
RPallreads_Exp1_fpkm_CDS.txt.gz
RPlength29_Exp1_counts_combined_CDS_filt.txt.gz
RPlength29_Exp1_fpkm_CDS.txt.gz

data_processing:
Library strategy: Ribo-seq
Sequencing reads were demultiplexed and adapter-trimmed using flexbar (Dodt et al., 2012) and mapped to the hg19 version of the human genome using tophat2 (Kim et al., 2013) or to the NA construct sequences using bowtie2 (Langmead and Salzberg, 2012).
Only reads with mapping quality 24 or higher were kept, which also filtered out reads mapping to the constant regions at the beginning and end of the NA constructs. Non-coding genes and Histones were filtered out.
For ribosome profiling experiments, read lenghtes with high periodicity (21nt, 29nt, 30nt) were also counted separately. Sequencing reads per gene as annotated in the refSeq database were counted using quasR (Gaidatzis et al., 2015).
Translation efficiencies from readcounts were calculated using RiboDiff (Zhong et al., 2017)
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values

source_name: Transfected HEK 293T cells

growth_protocol: HEK293T cells were grown in DMEM + 10%FCS

extract_protocol:
Cells were lysed in mammalian polysome buffer, digested with RNase I, loaded on a MicroSpin S-400 HR colum (GE Healthcare) and RNA was extracted using Trizol LS as described in Calviello et al. 2016 (doi:10.1038/nmeth.3688)
libraries were constructed as described in Calviello et al. 2016 (doi:10.1038/nmeth.3688)

treatment_protocol: Expression plasmids containing recoded neuraminidase genes have been transfected into HEK 293T cells for 24h

tag: na constructs

value: 27wt, 72Lmax and 27min


title: LUNC.ct-120


title: CD4 T cells 2


title: LUNC.ct-119


title: CD4 T cells 1


title: LUNC.ct-121


title: input

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

data_processing:
Fastq files were trimmed usinf TrimGalore for Q>30
Mapping with BWA
Narrow peaks were called with MACS2 (2.1.1.20160309) against input
BigWig were obtained using bamcoverage with RPGC normalization
Genome_build: hg19
Supplementary_files_format_and_content: standard MACS2 output in bed format

source_name: input

growth_protocol: For maintainance, cells were cultured in DMEM/F-12 supplemented with 10% (v/v) charcoal-stripped fetal bovine serum, 1% nonessential amino acids, sodium pyruvate and penicillin/streptomycin and with a daily addition of 10nM E2 in 0.1% DMSO

extract_protocol:
5 million cells were formaldehyde-fixed at 1% for 8 minutes, sonicated 14x in BioRuptor Pico and the ChIP against H3K27ac (ab4729, Abcam) was done with the iDeal ChIP-seq kit for histones as per the manufacturer’s protocol (Diagenode)
Libraries were prepared using the TruSeq ChIP Sample Prep kit and we performed paired-end sequencing with the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) (Illumina)

treatment_protocol: 10nM 17β-estradiol in 0.1% DMSO (CTR and ReSt) or only 0.1% DMSO (E2D)

value: MCF-7 HTB22 (ATCC)

tag: treatment

value: CTR

tag: time point


title: LUNC.ct-118


title: ReSt d14 rep2

source_name: ReSt d14 rep2

value: ReSt


title: LUNC.ct-125


title: LUNC.ct-116


title: ReSt d14 rep1

source_name: ReSt d14 rep1


title: LUNC.ct-117


title: E2D d14 rep1

source_name: E2D d14 rep1


title: LUNC.ct-115


title: E2D d14 rep2

source_name: E2D d14 rep2


title: LUNC.ct-114


title: CTR d14 rep1

source_name: CTR d14 rep1


title: CTR d14 rep2

source_name: CTR d14 rep2


title: LUNC.ct-110


title: LUNC.ct-113


title: LUNC.ct-111


title: LUNC.ct-168


title: LUNC.ct-108


title: LUNC.ct-109


title: LUNC.ct-107


title: LUNC.ct-112


title: LUNC.ct-106


title: LUNC.ct-104


title: LUNC.ct-105


title: LUNC.ct-101


title: LUNC.ct-100


title: LUNC.ct-103


title: LUNC.ct-102


title: LUNC.ct-97


title: LUNC.ct-95


title: LUNC.ct-98


title: LUNC.ct-96


title: LUNC.ct-94


title: LUNC.ct-93


title: LUNC.ct-92


title: LUNC.ct-88


title: LUNC.ct-89


title: LUNC.ct-91


title: LUNC.ct-87


title: LUNC.ct-86


title: LUNC.ct-84


title: LUNC.ct-83


title: LUNC.ct-81


title: LUNC.ct-82


title: LUNC.ct-80


title: LUNC.ct-78


title: LUNC.ct-79


title: LUNC.ct-73


title: LUNC.ct-99


title: LUNC.ct-77


title: LUNC.ct-75


title: LUNC.ct-71


title: LUNC.ct-72


title: LUNC.ct-90


title: LUNC.ct-68


title: LUNC.ct-69


title: LUNC.ct-67


title: LUNC.ct-85


title: LUNC.ct-65


title: LUNC.ct-63


title: LUNC.ct-66


title: LUNC.ct-62


title: LUNC.ct-60


title: LUNC.ct-61


title: LUNC.ct-76


title: LUNC.ct-74


title: LUNC.ct-57


title: LUNC.ct-59


title: LUNC.ct-58


title: LUNC.ct-53


title: LUNC.ct-52


title: LUNC.ct-70


title: LUNC.ct-47


title: LUNC.ct-49


title: LUNC.ct-48


title: LUNC.ct-64


title: LUNC.ct-45


title: LUNC.ct-43


title: LUNC.ct-44


title: LUNC.ct-51


title: LUNC.ct-42


title: LUNC.ct-56


title: LUNC.ct-40


title: LUNC.ct-39


title: LUNC.ct-140


title: LUNC.ct-55


title: LUNC.ct-38


title: LUNC.ct-36


title: LUNC.ct-54


title: LUNC.ct-35


title: LUNC.ct-33


title: LUNC.ct-32


title: LUNC.ct-37


title: LUNC.ct-174


title: LUNC.ct-34


title: LUNC.ct-30


title: LUNC.ct-50


title: LUNC.ct-29


title: LUNC.ct-46


title: LUNC.ct-28


title: LUNC.ct-25


title: LUNC.ct-41


title: LUNC.ct-26


title: LUNC.ct-24


title: LUNC.ct-23


title: LUNC.ct-22


title: LUNC.ct-27


title: LUNC.ct-21


title: LUNC.ct-18


title: LUNC.ct-19


title: LUNC.ct-16


title: LUNC.ct-17


title: LUNC.ct-14


title: LUNC.ct-11


title: LUNC.ct-9


title: LUNC.ct-20


title: LUNC.ct-31


title: LUNC.ct-15


title: LUNC.ct-10


title: LUNC.ct-13


title: LUNC.ct-6


title: LUNC.ct-4


title: LUNC.ct-8


title: LUNC.ct-3


title: LUNC.ct-2


title: LUNC.ct-12


title: LUNC.ct-1


title: COAD.ct-773


title: LUNC.ct-5


title: COAD.ct-771


title: COAD.ct-772


title: COAD.ct-770


title: COAD.ct-769


title: COAD.ct-767


title: COAD.ct-768


title: COAD.ct-762


title: LUNC.ct-7


title: COAD.ct-765


title: COAD.ct-764


title: COAD.ct-760


title: COAD.ct-761


title: COAD.ct-759


title: COAD.ct-755


title: COAD.ct-756


title: COAD.ct-758


title: COAD.ct-753


title: COAD.ct-754


title: MYO-PT1151-shMAMMX

source_name: Myometrium primary cells

growth_protocol: Cells were cultured in smooth muscle cell culture media (SmGM-2 smooth muscle cell growth medium BulletKit [cat # CC-3182], 1% Penicillin-Streptomycin) and grown at 37°C in a humidified cell culture incubator containing 5% CO2.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini kit according to manufacturer’s instructions (Qiagen, cat # 217004). After RNA elution, an in-solution DNase treatment was performed to completely digest genomic DNA (Qiagen, cat # 79254). RNA quality was verified using the Bioanalyzer eukaryote total RNA 600 nano kit (Agilent technologies, cat # 5067). Purified RNA samples had a mean RNA integrity number (RIN) of 8.0.
RNA was prepared for sequencing using the KAPA Stranded RNA-seq with RiboErase kit according to the manufacturer’s instructions (Kapa Biosystems, cat # KK8483).

treatment_protocol: 1.0 x 106 myometrium primary cells collected from two patients were transduced with either non-silencing control or AP-1 gene silencing concentrated lentiviral particles and 6mg/ml of polybrene for 18 hours. Fresh SmGM-2 muscle cell media was then added and cells were allowed to grow for 3-4 days.

tag: transduction

value: shMAMMX


title: COAD.ct-752

source_name: blood serum

tag: sample type


title: COAD.ct-751


title: MYO-PT1119-shMAMMX


title: MYO-PT1151-shAP1


title: COAD.ct-750


title: MYO-PT1119-shAP1


title: LUNC.ct-134


title: LEIO-PT1063 [capture Hi-C]

data_processing:
Library strategy: HiC-Seq
Promoter capture Hi-C sequencing reads were processed using the Hi-C User Pipeline (HiCUP, v0.5.10), with the bowtie aligner (v1.2.2) being used to align the reads to the GRCh38 human genome assembly.
Processed BAM files were passed as input files for the capture Hi-C analysis of genomic organization package (CHiCAGO) pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: .chinput text files of CHiCAGO prepared counts of bait-otherEnd interactions processed from HiCUP aligned BAM files.

source_name: Uterine tumor

extract_protocol:
Myometrium and leiomyoma tissue samples were cryopulverized into a fine powder and immediately formaldehyde cross-linked with 1% formaldehyde for 10min at room temperature with rotation and then quenched with 0.15M glycine for 10min at room temperature with rotation. In-situ Hi-C protocol was used performed on cross-linked tissue samples with HindIII digestion of chromatin_x000B_for 12-16hrs at 37°C. Labeling of DNA ends was carried out with 28.4μM D-Desthiobiotin-7-dATP and ends were proximity ligated with T4 DNA ligase. Labeled and proximity ligated DNA was isolated by phenol-chloroform extraction and sheared to a size of 300-500bp using a Covaris S2 focused ultrasonicator followed by a 0.5X-0.9X AMPure XP bead size selection. Biotin was removed from unligated ends with T4 DNA polymerase followed by streptavidin bead-based biotin pulldown. DNA was eluted off the beads with 10mM biotin, followed by a 1X AMPure XP bead cleanup.
KAPA Hyper Prep kit (Kapa Biosystems, cat # KK8502) was used for end-repair, A-tailing, adapter ligation with TruSeq index adapters, and 12 cycles of PCR amplification, all according to manufacturer’s instructions. Previously described custom-designed biotinylated 120-mer RNA baits targeting Ensembl promoters of protein coding and non-coding transcripts were used to capture promoter associated biotinylated and adapter ligated Hi-C DNA from myometrium and leiomyoma samples.

tag: tissue type

value: Leiomyoma


title: COAD.ct-749


title: COAD.ct-766


title: COAD.ct-748


title: LEIO-PT886 [capture Hi-C]


title: LEIO-PT916 [capture Hi-C]


title: LEIO-PT967 [capture Hi-C]


title: COAD.ct-747


title: COAD.ct-763


title: LEIO-PT848 [capture Hi-C]


title: COAD.ct-745


title: COAD.ct-746


title: COAD.ct-744


title: MYO-PT967 [capture Hi-C]

source_name: Uterine muscle tissue

value: Myometrium


title: MYO-PT1063 [capture Hi-C]


title: COAD.ct-743


title: MYO-PT848 [capture Hi-C]


title: COAD.ct-742


title: COAD.ct-741


title: MYO-PT916 [capture Hi-C]


title: PT1063-LEIO-INPUT

data_processing:
ChIP-seq reads were first adapter trimmed using cutadapt (v1.15). Reads were then aligned to the GRCh38 human genome assembly obtained from Ensembl (release 90) using bowtie (v1.2.2; settings: --best -m 1).
Peak calling was performed with HOMER (v4.10.3, histone peak calling: -tbp 1 -F 4 -style histone, transcription factor/ cofactor peak calling: -tbp 1 -F 3 -style factor)
Genome_build: GRCh38
Supplementary_files_format_and_content: Reads per genomic content normalization (RPGC, 1x normalization) of BAM files obtained from Bowtie alignments was performed with DeepTools to produce BigWig files.

extract_protocol:
Myometrium and leiomyoma tissue samples were cryopulverized into a fine powder and immediately formaldehyde cross-linked with 1% formaldehyde for 10min at room temperature with rotation and then quenched with 0.15M glycine for 10min at room temperature with rotation. Cross-linked tissue samples were dounce homogenized in ChIP lysis buffer 1 (50mM HEPES-KOH [pH 7.6], 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed by end-over-end rotation at 4°C for 15min and then low speed centrifugation at 4°C. Samples were resuspended in ChIP lysis buffer 2 (10mM Tris-HCl [pH 8.0], 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X Protease inhibitor cocktail [Roche, cat # 4693132001]) followed again by end-over-end rotation at 4°C for 15min and sample recovery by low speed centrifugation at 4°C. Samples were then resuspended in MNase digestion buffer (20mM Tris-HCl [pH 8.0], 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS, 125U MNase [Worthington, cat # LS004798]) and incubated at 37°C until 75% mononucleosomal chromatin profile is observable by gel electrophoresis of purified MNase digested DNA. Digestion was quenched with MNase quenching buffer (10mM EDTA, 20mM EGTA) after which samples were briefly sonicated (Misonix, setting 6 [~6 W power output], 3 cycles of 15sec on and 45sec off). Collagen and cell debris was removed by centrifugation at 20,000 x g at 4°C for 20min. Solubilized chromatin was incubated overnight with antibody at 4°C with end-over-end rotation.
KAPA Hyper Prep kit (Kapa Biosystems, cat # KK8502) was used for end-repair, A-tailing, and adapter ligation with TruSeq index adapters, all according to manufacturer’s instructions. A 1.1X-1.8X AMPure XP bead (Beckman Coulter, cat # A63881) size selection was carried out after adapter ligation to enrich for sub-nucleosomal DNA fragments followed by 10-12 cycles of PCR amplification. For H3K27Ac ChIP, a 0.6X-1.0X AMPure XP bead size selection was performed to enrich for mono-nucleosomal DNA fragments.


title: COAD.ct-739


title: COAD.ct-738


title: COAD.ct-737


title: COAD.ct-740


title: COAD.ct-736


title: COAD.ct-735


title: PT1063-MYO-INPUT


title: PT967-LEIO-INPUT


title: PT848-LEIO-INPUT


title: PT916-LEIO-INPUT


title: PT886-LEIO-INPUT


title: COAD.ct-733


title: PT967-MYO-INPUT


title: COAD.ct-732


title: PT916-MYO-INPUT


title: PT848-MYO-INPUT


title: COAD.ct-731


title: PT886-MYO-INPUT


title: COAD.ct-730


title: PT1063-LEIO-MED12

value: MED12 (Bethyl, cat # A300-774A)


title: COAD.ct-729


title: PT967-LEIO-MED12


title: COAD.ct-728


title: COAD.ct-727


title: PT916-LEIO-MED12


title: COAD.ct-757


title: COAD.ct-726


title: COAD.ct-725


title: COAD.ct-734


title: PT848-LEIO-MED12


title: PT886-LEIO-MED12


title: PT1063-MYO-MED12


title: COAD.ct-723


title: PT967-MYO-MED12


title: COAD.ct-721


title: COAD.ct-722


title: COAD.ct-720


title: COAD.ct-719


title: PT886-MYO-MED12


title: COAD.ct-717


title: PT1063-LEIO-CDK8

value: CDK8 (Bethyl, cat # A302-500A)


title: PT916-LEIO-CDK8


title: COAD.ct-716


title: PT1063-MYO-CDK8


title: PT886-LEIO-CDK8


title: PT848-LEIO-CDK8


title: MYO-PT886 [capture Hi-C]


title: COAD.ct-715


title: COAD.ct-724


title: COAD.ct-714


title: PT848-MYO-MED12


title: PT967-MYO-CDK8


title: PT916-MYO-MED12


title: PT886-MYO-CDK8


title: COAD.ct-711


title: PT916-MYO-CDK8


title: PT848-MYO-CDK8


title: PT1063-LEIO-JUN

value: JUN (abcam, cat # ab31419)


title: COAD.ct-713


title: COAD.ct-718


title: COAD.ct-708


title: COAD.ct-709


title: COAD.ct-707


title: PT916-LEIO-JUN


title: PT967-LEIO-JUN


title: PT967-LEIO-CDK8


title: PT886-LEIO-JUN


title: PT848-LEIO-JUN


title: COAD.ct-706


title: COAD.ct-704


title: COAD.ct-712


title: PT967-MYO-JUN


title: COAD.ct-703


title: COAD.ct-701


title: PT886-MYO-JUN


title: PT848-MYO-JUN


title: COAD.ct-700


title: PT1063-LEIO-FOS

value: FOS (Millipore, cat # 06-341)


title: COAD.ct-699


title: PT967-LEIO-FOS


title: PT916-LEIO-FOS


title: COAD.ct-697


title: COAD.ct-696


title: PT886-LEIO-FOS


title: COAD.ct-698


title: COAD.ct-705


title: COAD.ct-695


title: PT848-LEIO-FOS


title: PT1063-MYO-JUN


title: PT1063-MYO-FOS


title: COAD.ct-694


title: PT916-MYO-FOS


title: COAD.ct-693


title: PT916-MYO-JUN


title: PT967-MYO-FOS


title: PT886-MYO-FOS


title: COAD.ct-692


title: COAD.ct-691


title: COAD.ct-702


title: PT848-MYO-FOS


title: PT1063-LEIO-RNAPII

value: RNAPII (Millipore, cat # 05-952, clone 8WG16, lot # 2839641)


title: COAD.ct-690

value: cell-free DNA


title: COAD.ct-687


title: COAD.ct-689


title: PT916-LEIO-RNAPII


title: COAD.ct-686


title: COAD.ct-685


title: COAD.ct-684


title: COAD.ct-688


title: PT886-LEIO-RNAPII


title: PT967-LEIO-RNAPII


title: PT916-MYO-RNAPII


title: PT1063-MYO-RNAPII


title: COAD.ct-683


title: PT967-MYO-RNAPII


title: PT886-MYO-RNAPII


title: COAD.ct-681


title: COAD.ct-682


title: PT1063-LEIO-INPUT-Histone


title: PT848-MYO-RNAPII


title: COAD.ct-679


title: COAD.ct-677


title: COAD.ct-678


title: PT967-LEIO-INPUT-Histone


title: PT1063-LEIO-H3K27Ac


title: PT967-LEIO-H3K27Ac


title: COAD.ct-676


title: COAD.ct-710


title: COAD.ct-675


title: PT916-LEIO-INPUT-Histone


title: PT848-LEIO-RNAPII


title: PT916-LEIO-H3K27Ac


title: PT886-LEIO-H3K27Ac


title: PT886-LEIO-INPUT-Histone


title: COAD.ct-673


title: COAD.ct-674


title: COAD.ct-672


title: COAD.ct-671


title: COAD.ct-669


title: COAD.ct-680


title: COAD.ct-670


title: PT848-LEIO-H3K27Ac


title: PT1063-MYO-INPUT-Histone


title: COAD.ct-668


title: PT967-MYO-INPUT-Histone


title: PT967-MYO-H3K27Ac


title: COAD.ct-667


title: PT1063-MYO-H3K27Ac


title: PT916-MYO-INPUT-Histone


title: PT848-LEIO-INPUT-Histone


title: PT916-MYO-H3K27Ac


title: COAD.ct-666


title: COAD.ct-664


title: COAD.ct-663


title: PT886-MYO-H3K27Ac


title: COAD.ct-665


title: PT886-MYO-INPUT-Histone


title: PT848-MYO-INPUT-Histone


title: COAD.ct-661


title: COAD.ct-662


title: COAD.ct-660


title: PT848-MYO-H3K27Ac


title: COAD.ct-658


title: LEIO-PT1123

extract_protocol:
Total RNA was isolated using Qiagen miRNeasy Mini kit according to manufacturer’s instructions (Qiagen, cat # 217004). After RNA elution, an in-solution DNase treatment was performed to completely digest genomic DNA (Qiagen, cat # 79254). RNA quality was verified using the Bioanalyzer eukaryote total RNA 600 nano kit (Agilent technologies, cat # 5067). Purified RNA samples had a mean RNA integrity number (RIN) of 8.0.
RNA was prepared for sequencing using the KAPA Stranded RNA-seq with RiboErase kit according to the manufacturer’s instructions (Kapa Biosystems, cat # KK8483).


title: COAD.ct-659


title: LEIO-PTc57


title: LEIO-PT1151


title: LEIO-PT1119


title: COAD.ct-656


title: COAD.ct-657


title: COAD.ct-655


title: COAD.ct-654


title: COAD.ct-653


title: LEIO-PT967


title: LEIO-PT1063


title: LEIO-PT886


title: LEIO-PT848


title: LEIO_PT758


title: COAD.ct-652


title: COAD.ct-651


title: COAD.ct-649


title: COAD.ct-650


title: LEIO-PT916


title: LEIO_PT728


title: COAD.ct-646


title: LEIO-PT563


title: LEIO-PT354


title: COAD.ct-645


title: LEIO-PT1113


title: MYO-PTc57


title: MYO-PT1151


title: COAD.ct-644


title: COAD.ct-642


title: COAD.ct-643


title: MYO-PT1123


title: COAD.ct-641


title: COAD.ct-640


title: COAD.ct-648


title: MYO-PT967


title: LEIO-PT845


title: COAD.ct-639


title: MYO-PT1063


title: MYO-PT1113


title: COAD.ct-638


title: COAD.ct-637


title: COAD.ct-636


title: MYO-PT916


title: COAD.ct-647


title: MYO-PT1119


title: MYO-PT848


title: COAD.ct-635


title: MYO-PT845


title: COAD.ct-632


title: MYO_PT758


title: MYO_PT728


title: COAD.ct-630


title: COAD.ct-629


title: MYO-PT563


title: COAD.ct-628


title: USP36#5-1

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_11 was used.
Clean read sequences were aligned with STAR version 2.6.1c.
Read counting for exonic regions was performed with subread featureCounts version 1.6.3.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

source_name: HeLa cervical carcinoma cells

growth_protocol: parental human cervix carcinoma HeLa cells were routinely grown in DMEM supplemented with 10% FBS without antibiotics

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen, Germany) following the manufacturer's instructions and 600 ng of RNA were reverse transcribed using the Transcriptor High Fidelity cDNA Synthesis Kit (Roche, Switzerland)  following the manufacturer's instructions
Sequencing libraries have been prepared with Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer's handbook.

treatment_protocol: HeLa cells were transfected with 10nM control or USP36 siRNA on three consecutive days, with media change after every 24h, and RNA was extracted 24h after the last siRNA treatment

value: parental epithelial HeLa cells

tag: passages

value: low passage number <8

tag: sirna treatment


title: USP36#3-1


title: COAD.ct-626


title: MYO-PT886


title: USP36#1-2


title: COAD.ct-633


title: COAD.ct-624


title: COAD.ct-634


title: COAD.ct-623


title: Control#4-1

value: control


title: COAD.ct-627


title: COAD.ct-625


title: Control#3-1


title: COAD.ct-622


title: Control#1-2


title: COAD.ct-621


title: Control#5-1


title: Beige_D21_FSK_Rep1

city: Athens

first: Liang

state: GA

address: 325 Riverbend Road

department: Biochemistry and Molecular Biology, Center for Molecular Medicine

institute: University of Georgia

data_processing:
Constructed libraries were sequenced in illumina NextSeq 500 platform and basecalling was perfomed in Real-Time Analysis (RTA) System V2 (illumina).
Sequence data (fastq) were mapped to hg19 using STAR (V2.6.1.C) on default setting with "-quantMode GeneCounts" to obtain read count of each sample.
Raw readcount of each samples were collected and analyzed in R Studio (Version 1.0.143) with RNA-Seq analysis package "limma_3.32.10 ","edgeR_3.18.1" and "DESeq2_1.16.1" following published analytic pipelines (Law, Charity W et al. 2016; Love, Michael et al. 2014) .
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw read counts for each sample.

source_name: Human Primary Mesenchymal stem cells

growth_protocol: ADSCs were grown in ADSC-growth medium 10% fetal bovine serum in DMEM-F12 with glutamine, Non-Essential amino acid supplement and antibiotic-antimyotics.

extract_protocol:
Total RNA were extracted using E.Z.N.A. Total RNA kit I (Omega, R6834), according to manufacture's protocol.
RNA samples with RNA Integrity number above 8.0 were seleced for library preparation in Geogia Genomic and Bioinformatic Core (https://dna.uga.edu/). KAPA Stranded mRNA-Seq Kit  for Illumina® Platforms (KR0960-v5.17) were used for library constructions of all RNA-Seq samples included in this study.
Pair-end stranded libraries were construced and then sequenced in NextSeq platform with read length 75 bp. Each sample has more than 30 millions read per end.

treatment_protocol: Beige adipocyte differentiation of ADSCs were performed using B-8 medium, which consisted of the addition of a cocktail of 8 growth factors or inhibitors added to a chemically-defined based medium. To perform beige differentiations, ADSCs were passaged and seeded at a density of 5000 cell/cm2 and were grown to confluency, ~5 days.  B-8 medium was subsequently added and medium was changed every other day for 3 weeks.

tag: commerical source

value: Thermo Fisher (R7788110)

tag: cell identity

value: In Vitro differentiated Beige Adipocytes

tag: differentiation method

value: Beige differentiation using B-8 media described in the protocol section.

tag: forskolin treatment

value: YES


title: COAD.ct-631


title: Beige_D21_CTR_Rep2

source_name: ASC52telo, hTERT immortalized adipose derived Mesenchymal stem cells

value: ATCC SCRC-4000

value: NO


title: White_D28_CTR

value: In Vitro differentiated White Adipocytes

value: White adipocytes differentiation was perfomed using StemPro adipogenesis differentiation kit (ThermoFisher, A10070-01).  Media was changed every two days for 3 weeks.


title: MYO-PT354

tag: cell type

value: Myometrium


title: USP36#4-1


title: COAD.ct-618


title: Beige_D21_CTR_Rep1


title: COAD.ct-617


title: ADSC_Rep2

value: mesenchymal stem cells


title: COAD.ct-616


title: ADSC_Rep1


title: COAD.ct-614


title: COAD.ct-615


title: Beige_D21_FSK_Rep2


title: COAD.ct-620


title: COAD.ct-613


title: COAD.ct-611


title: RPE-Cas9-p53KD_KO6-d27

city: Baltimore

first: Daniel

last: Ardeljan

address: 733 N Broadway, MRB 432

institute: Johns Hopkins University School of Medicine

description:
sgRNA DNA library
KDscreen_MAGeCK_NTCnorm_counts.txt

data_processing:
Library strategy: CRISPR KO screen
CRISPR KO reads aligned to Brunello Index using Bowtie.
CRISPR KO counts processed with MAGeCK.
RNAseq reads aligned with STAR (hg38), counted with HTSeq, and differential expression was performed with DESeq2.
Genome_build: hg38 or Brunello Index (https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/). Brunello citation PMID: 26780180
Supplementary_files_format_and_content: All are .txt files. The DESeq2 file contains differential expression data for cells expressing LINE-1 vs. Luciferase that is standard output from the DESeq2 program. The 'htseq_output_with_stat_summary.txt' file includes the RNA-seq differential expression analysis table to accompany the reads. The MAGeCK files contain screen count data normalized to non-target-controls, as generated by the MAGeCK program.

growth_protocol: RPE cell lines are grown in DMEM/F12 supplemented with sodium bicarbonate and 10% FBS at 37C and 5% CO2. Tet-Free FBS is used in Tet-On expression systems. Tet-On expression systems also require 400 ug/ml G418 and Cas9-expressing cells require 10 ug/ml Blasticidin.

extract_protocol: genomic DNA was collected by lysing in SDS and treating with proteinase K and RNase A. gDNA was purified with Ethanol precipitation. CRISPR sequencing libraries were created using primers to amplify the sgRNA sequences. The primers encoded adaptors P5 and P7 for use in Illumina sequencing machines.

tag: expression method

value: Tet-On Luciferase

value: cells were transduced with the Brunello Knockout Library and doxycycline was added to induce expression of LINE-1 or Luciferase


title: RPE-Cas9-p53KD_KO4-d27


title: RPE-Cas9-p53KD_KO2-d27

value: Tet-On LINE-1


title: RPE-Cas9-p53KD_KO3-d27


title: RPE-Cas9-p53KD_KO1-d27


title: COAD.ct-619

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

value: cell-free DNA


title: RPE-Cas9-p53KD_KO5-d27


title: RPE-Cas9-p53KD_KO6-d22


title: COAD.ct-612


title: COAD.ct-608


title: COAD.ct-610


title: COAD.ct-607


title: COAD.ct-606


title: RPE-Cas9-p53KD_KO4-d22


title: RPE-Cas9-p53KD_KO5-d22


title: COAD.ct-605


title: RPE-Cas9-p53KD_KO2-d22


title: COAD.ct-603


title: RPE-Cas9-p53KD_KO6-d17


title: RPE-Cas9-p53KD_KO1-d22


title: COAD.ct-602


title: COAD.ct-609


title: COAD.ct-601


title: RPE-Cas9-p53KD_KO5-d17


title: RPE-Cas9-p53KD_KO4-d17


title: COAD.ct-599


title: COAD.ct-596


title: RPE-Cas9-p53KD_KO2-d17


title: RPE-Cas9-p53KD_KO1-d17


title: COAD.ct-600


title: RPE-Cas9-p53KD_KO4-d13


title: RPE-Cas9-p53KD_KO5-d13


title: RPE-Cas9-p53KD_KO6-d13


title: COAD.ct-595


title: COAD.ct-598


title: COAD.ct-597


title: COAD.ct-592


title: COAD.ct-593


title: RPE-Cas9-p53KD_KO2-d13


title: RPE-Cas9-p53KD_KO1-d13


title: COAD.ct-591


title: RPE-Cas9-p53KD_KO3-d13


title: COAD.ct-604


title: RPE-Cas9-p53KD_KO5-d8


title: RPE-Cas9-p53KD_KO4-d8


title: COAD.ct-589


title: COAD.ct-594


title: RPE-Cas9-p53KD_KO2-d8


title: RPE-Cas9-p53KD_KO3-d8


title: COAD.ct-587


title: COAD.ct-590


title: COAD.ct-586


title: RPE-Cas9-p53KD_KO1-d8


title: COAD.ct-585


title: COAD.ct-584


title: COAD.ct-588


title: RPE-Cas9-p53KD_KO6-d4


title: RPE-Cas9-p53KD_KO6-d8


title: COAD.ct-582


title: RPE-Cas9-p53KD_KO3-d17


title: COAD.ct-583


title: RPE-Cas9-p53KD_KO4-d4


title: RPE-Cas9-p53KD_KO3-d4


title: RPE-Cas9-p53KD_KO1-d4


title: COAD.ct-579


title: RPE-Cas9-p53KD_KO2-d4


title: COAD.ct-581


title: COAD.ct-580


title: COAD.ct-578


title: RPE-Cas9_LINE1 screen B

description:
sgRNA DNA library
WTscreen_MAGeCK_NTCnorm_counts.txt

value: plasmid LINE-1

value: cells were transduced with the Brunello Knockout Library and then transfected with eGFP or LINE-1 plasmids


title: COAD.ct-577


title: RPE-Cas9_LINE1 screen D


title: RPE-Cas9_eGFP screen C

value: plasmid eGFP


title: COAD.ct-576


title: COAD.ct-575


title: COAD.ct-574


title: COAD.ct-573


title: COAD.ct-572


title: HD_16F2_LP3

city: Jerusalem

first: Matan

last: Sorek

address: Edmond J. Safra Campus

department: Genetics

institute: The Hebrew University of Jerusalem

description:
human embryonic stem cells- and induced pluripotenet stem cells-derived striatal GABAergic neurons
all_raw_counts.txt
all_normalized_RPM_counts.txt

data_processing:
Raw reads that passed the quality controls were aligned to human genome assembly hg19 using STAR (Dobin et al. ,2013, Bioinformatics) with parameters alignIntronMax=1000 and alignMatesGapMax=1000.
unmapped and low quality read were removed
multiple reads that were mapped to the same location in the genome with the same UMI in the same sample were removed
Filtered reads were passed to the End Sequence Analysis Toolkit (ESAT, Derr et al., 2016, Genome Research)  with parameters wLen=400, wOlap=50, wExt=2000 and sigTest=0.05.
Reads Per Megabase of library size (RPM) were calculated, and further normalized according to DE-Seq (Anders et al., 2010, Genome Biology). In short, each sample is normalized by a factor which corresponds to the median ratio of expression of genes in the sample and the geometric mean of genes in all samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPM values for each sample

source_name: striatal GABAergic neurons

growth_protocol: hESCs (Bradley et al., 2011), and hiPSCs were cultured as described (Takahashi et al., 2007). For neuronal induction, hiPSC colonies were induced for neuronal lineage differentiation using dual SMAD inhibition by blocking BMP and TGF. hiPSC colonies were separated and seeded on Matrigel as single cells and incubated with human induction media [DMEM/F12, Neurobasal, N2, B27] supplemented with 2 SMADi (20 M SB, 100 nM LDN) and 1 μM XAV-939 for 10 days. From day 10 to 20 of differentiation, cells were incubated with neural induction media supplemented with 50 nM SAG and 1 μM XAV-939, inducing the cells to become neural progenitor cells (NPCs). For terminal differentiation, the cells were re-seeded on PLO/laminin coated plates at 75,000 cells/cm2, and exposed to neural terminal differentiation medium supplemented with 20 ng/ml BDNF, 0.5 mM dbcAMP, and 0.5 mM Valpromide.

extract_protocol:
RNA was extracted from neurons using Qiagene 96-well kit according to the manufacturer's instructions.
library construction was carried out as published (Soumillion et al., 2014)

treatment_protocol: For progerin induced samples, HEK293T cells were transduced with the target lentiviral vector (either lenti-GFP- LMNA or lenti-GFP-progerin) and packaging vectors deltaR8.9 and VSV- G (2th generation) using TransIT-LT1 (Mirus) transfection reagent. Before transfection, HEK293T medium was replaced with neural medium (w/o neuro-factors). 24 and 48-hours post transfection, Polybrene (8 μg/ml) and neurofactors were added to filtered-medium containing-virions. From each well containing neurons, 2/3 of the volume was replaced with media containing virions. For the drugs GSK-J4 and UNC1999, they were added in day 39 of the differentiation protocol, in concentrations of 10 μM and  5 μM, respectively.

value: striatal GABAergic neurons

tag: derived from hesc or ipsc

value: iPSC

tag: genotype

value: HD

tag: progerin

value: Yes


title: HD_16F2_LP1


title: RPE-Cas9_eGFP screen A


title: HD_14F2_LP2


title: HD_14F2_LP1


title: COAD.ct-570


title: COAD.ct-569


title: COAD.ct-568


title: HD_10F2_LP3


title: HD_10F2_LP4


title: HD_10F2_LP2


title: HD_10F2_LP1


title: COAD.ct-571


title: COAD.ct-567


title: COAD.ct-565


title: WT_12F2_LP4

value: WT


title: COAD.ct-564


title: WT_12F2_LP3


title: WT_12F2_LP2