title: JW-40533-bethanechol-BR4-TR2

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description:
Library name: Sample 32
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCh38
Supplementary files format and content: Tab-delimited files contains raw counts for each sample

source_name: sorted Lgr5+ cells

growth_protocol: Intestinal crypts were generated from the proximal colon of age- and sex-matched Lgr5-EGFP-IRES-CreERT2 mice. Crypt suspensions were pelleted and resuspended in Corning Matrigel Growth Factor Reduced Basement Membrane Matrix. Droplets of 50 µl were plated on 24-well plates (Corning), overlayed with L-WRN medium and incubated at 37 °C, 5% CO2. Colonic organoids were maintained on L-WRN medium overnight.

extract_protocol:
Qiagen RNAeasy Plus Micro Kit according to the manufacturer’s instructions.
cDNA was generated with Maxima RT polymerase (Thermo Fisher) and amplified with Terra PCR Direct Polymerase (Takara). Library preparation was carried out with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB)

treatment_protocol: Growth medium was replenished daily with fresh Bch-containing medium (250 nM) for 4 days.

value: sorted Lgr5+ cells

value: bethanechol

tag: biological replicate

tag: number sorted_cells

tag: technical replicate


title: Lung,CC024,mouse21,GEX

status: Public on Feb 28 2025

type: SRA

city: Worcester

first: Christopher

last: Sassetti

address: 368 Plantation Street

country: USA

institute: UMass Chan Medical School

library_source: transcriptomic

data_processing:
FASTQ files were uploaded to the 10x Genomics Cloud Analysis application for alignment, filtering, barcode counting and UMI counting using CellRanger count pipeline (cellranger-6.1.2). C57BL/6 was aligned to the GRCm38 reference. Custom references and annotations for PWK/PhJ, CC011, and CC024 were built using cellranger mkref from pseudogenomes generated by g2gtools (v0.2.7). References for the pseudogenomes were the GRCm38 primary assembly, GENCODE vM25 annotations, and variant calls from Srivastava et al (PMID  28592495).
The resulting feature-barcode matrices were imported to Seurat (v5.0.3) using R (v4.2.2) and Rstudio (2022.12.0+353).  Cells were filtered for high mitochondrial content (<10%), empty cells (nFeature_RNA>200) and high feature counts (nFeature_RNA<4000). Doublets were called by DoubletFinderv2 (v2.0.3) and excluded. Gene expression data was normalized using SCTransform followed by dimensionality reduction for the top 30 PCs and clustering via UMAP (resolution=0.5). The antibody derived tag library (ADT) was normalized using the centered log-ratio (CLR) method followed by centering and scaling.Datasets were then integrated and dimensionality reduction and clustering were re-run. Clusters were annotated using SingleR, existing scRNAseq datasets, and expression of canonical markers in the ADT dataset.
Assembly: GRCm38
Supplementary files format and content: an RDS file of the integrated Seurat object containing all GEX and ADT data
Supplementary files format and content: a csv file containing the antibodies and barcodes in the ADT pool
Library strategy: CITE-seq

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
C57BL/6, CC011, PWK/PhJ, and CC024 mice were infected by low-dose aerosol with Mtb. At 4wks post-infection, 4 mice per strain were humanely euthanized and lungs were perfused with DMEM (Gibco) containing 10% FBS. The right Lung lobes were harvested into R10 media (RPMI 1640 plus L-glutamine (Gibco), 10% FBS (Sigma), HEPES (Gibco), and penicillin-streptomycin (Gibco)), treated with collagenase (Gibco) and dissociated using a GentleMacs (Miltenyi). After incubation at 37C for 30 minutes, tissues were subject to another dissociation and passed through a 70um filter. Red blood cells were then lysed (eBioscience RBC Lysis buffer, Thermo Fisher), then cells were washed, and passed through a 40um filter. Dead cells were removed using the Dead Cell Removal Kit (Milentyi Biotec) according to manufacturer’s instructions. Cell suspensions were counted and 1.25x105 cells/sample were transferred to round-bottom polystyrene tubes, treated with TruStain FcX PLUS (Biolegend) to block non-specific antibody binding, and stained with TotalSeq-A universal mouse antibody panel, (Biolegend, pre-catalog version #99833) according to the manufacturer’s instructions. Cells were counted and 10,000 cells/sample were run through the 10x Genomics Chromium Controller using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 as indicated by the manufacturer.
Gene expression (GEX) and antibody derived (ADT) libraries were constructed following the 10x Genomics User Guide #206 and Biolegend TotalSeq-A manufacturer instructions. Libraries were pooled at a ratio of 80% GEX to 20% ADT and sequenced on a NovaSeq6000 sequencer (Illumina) targeting 50,000 paired-end reads/cell.

tag: tissue

value: Lung

tag: cell line

value: primary

tag: cell type

value: lung cells

tag: genotype

tag: library type

value: gene expression

tag: treatment

value: 4wks post-infection


title: JW-40533-untreated-BR4-TR2

description:
Library name: Sample 31
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

tag: Sex

value: male

value: untreated


title: JW-40527-bethanechol-BR3-TR2

description:
Library name: Sample 30
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Lung,CC011,mouse20,GEX


title: JW-40527-untreated-BR3-TR2

description:
Library name: Sample 29
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: glass_DL1_rep1

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Library name: Sample 3

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with edgeR software
Assembly: GCF_000007985.2
Supplementary files format and content: tab-delimited text file include the differential expression results of edgeR and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

growth_protocol: G. sulfurreducens biofilms grown on glass supports were grown in NBAF medium at 25 oC for 48 hours. The planktonic cells were separated from the biofilm that grew at the bottom of the culture tube. On the other hand, biofilms of G. sulfurreducens grown on graphite electrodes were separated from microbial fuel cells poised  operated for 2 weeks. In the MFC, to grow G. sulfurreducens, FWAF medium was used.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's instructions, and residual DNA was removed by DNaseI treatment (Thermo Scientific). RNA samples were quantified using the NanoDrop 200c (Thermo Scientific) and examined with an Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the TruSeq Stranded mRNA kit (Illumina) following the manufacturer´s protocol. The cDNA libraries were purified with the Zymoclean Gel DNA Recovery Kit (Zymo Research).

treatment_protocol: The cells present in the biofilms were resuspended in 1 mL of NBAF and incubated with 100 uL of RNAlater. Cells were pelleted by centrifugation and frozen at -70 oC until use.

value: DL1 wild type strain

value: Biofilm grown on glass support in NBAF medium for 48 h at 25 oC


title: Donor B-HDR-0.50

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-4

data_processing:
Initial quality assessment was performed using negative controls (water only) and reference standards (human universal reference RNA and human brain total RNA) included on every TempO-Seq plate. We confirmed very little signal (< 0.3%) from samples with no cells/RNA. The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.42. The FASTQ files were processed using the “pete. star. Script_v3.0” (BioSpyder). The script uses star v.2.5 and the qCount function from QuasR to align the reads and to extract the feature counts specified in a Gene Transfer Format (GTF) file from the aligned reads, respectively. Using R 3.4.1, the read counts of all samples were normalized as counts per million (CPM) (Law et al. 2014).
Assembly: hg38
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe
Library strategy: TempO-Seq

organism: Homo sapiens

source_name: Blood

growth_protocol: Lymphocytes were maintained in RPMI culture medium supplemented with antibiotics and FBS

extract_protocol:
Cells were lysed and RNA were extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 individual libraries were pooled to create a single pool for sequencing on the NextSeq 500 (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.

treatment_protocol: Isolated white blood cells (mainly lymphocytes and NK) were exposed

value: Blood

value: Primary Cell

value: Lymphocyte

value: HDR

tag: dose rate

value: 1 Gy/min

tag: dose

tag: individual

value: Donor B

tag: age


title: Donor B-HDR-0.25

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-3


title: glass_csrA_rep2

description: Library name: Sample 2

value: DL1 with csrA-deletion


title: Lung,B6,mouse24,GEX


title: JW-40478-bethanechol-BR1-TR2

description:
Library name: Sample 26
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: sorted Lgr5+ cells

value: bethanechol


title: JW-40511-bethanechol-BR2-TR2

description:
Library name: Sample 28
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40478-untreated-BR1-TR2

description:
Library name: Sample 25
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Lung,CC011,mouse19,GEX

value: Lung

value: primary


title: Donor B-HDR-0

description:
Cells were brought to the exposure chamber, but never exposed.
SP0254-B-HDR-0

value: 0 Gy


title: Lung,PWK,mouse18,GEX

value: lung cells

value: PWK

value: gene expression

value: 4wks post-infection


title: JW-40511-untreated-BR2--TR2

description:
Library name: Sample 27
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: male

value: untreated


title: JW-40533-bethanechol-BR4-TR1

description:
Library name: Sample 24
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Lung,PWK,mouse17,GEX


title: Donor B-HDR-0.10

description:
Cells were exposed according to the dose and dose rate
SP0254-B-HDR-2

value: Blood

value: Primary Cell


title: STING-MSC 5

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
Raw data were filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores > 30
Filtered reads were then aligned with STAR 2.7.3a using GRCm39 Genome Reference.
Aligned reads were annotated and counted using HT-seq with Ensembl 108. Differentially expressed genes were identified using DEseq2
Biological interpretations included gene ontology and gene set enrichment analysis (GSEA), which were performed using GSEA
Assembly: GRCm39
Supplementary files format and content: txt files with median ration normalized counts for each sample

molecule: polyA RNA

source_name: Joint

growth_protocol: Mouse stifle tissues (n=5 biological replicates per treatment group of 10 mice) were removed immediately following euthanasia, minced, and stored in RLT lysis buffer (Qiagen) at -80C

extract_protocol:
RNA was extracted from lysed cells by first using TRIzol Reagent (Invitrogen, Waltham, MA) following manufactures instructions, with a 1:3 RLT lysis buffer to TRIzol ratio. RNA precipitate pellet was then cleaned and concentrated using RNeasy MinElute Cleanup Kit
mRNA was enriched using oligo (dT) beads, followed by cDNA library generation using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA).

treatment_protocol: Intra-articular injections of MSC were performed at weeks three and five following DMM operation

value: Joint

value: STING


title: JW-40527-untreated-BR3-TR1

description:
Library name: Sample 21
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40527-bethanechol-BR3-TR1

description:
Library name: Sample 22
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40511-bethanechol-BR2-TR1

description:
Library name: Sample 20
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: STING-MSC 4


title: JW-40533-untreated-BR4-TR1

description:
Library name: Sample 23
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40511-untreated-BR2--TR1

description:
Library name: Sample 19
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: glass_DL1_rep2

description: Library name: Sample 4

value: DL1 wild type strain

value: Biofilm grown on glass support in NBAF medium for 48 h at 25 oC


title: LEC IL1b-2

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

country: France

institute: Inserm

description:
Library name: Sample B8
Column name in all-gene-Fpkm.txt : B8

data_processing:
Transcript quantification was performed with featureCounts, and differential analysis, including normalization of the original readcount, was performed with DESeq2 bioconductor package.
Statistical test (DESeq2 Wald test) was conducted on the expression matrix after standardization.
Assembly: Reads were aligned to the human genome.
Supplementary files format and content: all-gene-Fpkm.txt
Supplementary files format and content: all-gene-Fpkm.csv

source_name: HMVEC-dLy

growth_protocol: Human LECs (PromoCell, HDLEC-c, C-12216) were seeded in 6-well plates (3×105/well) and grown to confluence in complete Endothelial Cell Basal Medium-2 (PromoCell, ECGM-MV2, CC-22121), including 5% FCS with VEGF, IGF, EGF, and FGF supplement, according to recommendations of the supplier.

extract_protocol:
Cells were recovered and RNA extracted (Single Cell RNA Purification Kit, Norgen, 51800) for mRNAseq by Biomarker Technologies (BMK) company (Munster, GE) for identification of differentially expressed genes
BMK generated libraries prior to poly-A mRNA-seq sequencing  using Illumina NovaSeq (PE150)

treatment_protocol: Cells were serum-starved (1% FCS, ECM w/o VEGF, ECGF, EGF) overnight, and exposed to 20 ng/mL recombinant human IL-1β (200-01B, PeproTech) in 2 mL per well of serum-starvation media for 24h.

value: HMVEC-dLy

value: Lymphatic endothelial cell

value: wt

value: 20 ng/mL IL1beta


title: LEC IL1b-1

description:
Library name: Sample B7
Column name in all-gene-Fpkm.txt : B7


title: STING-MSC 3


title: JW-40478-bethanechol-BR1-TR1

description:
Library name: Sample 18
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: sorted Lgr5+ cells

value: bethanechol


title: LEC ctrl 3

description:
Library name: Sample A3
Column name in all-gene-Fpkm.txt : A3

value: Ctrl


title: JW-40478-untreated-BR1-TR1

description:
Library name: Sample 17
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: glass_csrA_rep1

description: Library name: Sample 1

value: DL1 with csrA-deletion


title: STING-MSC 2


title: LEC ctrl 2

description:
Library name: Sample A2
Column name in all-gene-Fpkm.txt : A2


title: conditional knockout kidney-4

city: BOSTON

first: Satya keerthi

last: Kota

state: MA

address: 188 LONGWOOD AVE HSDM REB 406

institute: HARVARD UNIV

description: Library name: KKO-4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Raw counts file in .csv format containing Ensembl gene ids and count data for each control and knockout kidney samples. Processed count files for each sample is in .txt format.

source_name: Kidney

extract_protocol:
Total RNA was extracted from wild type and conditional knockout frozen kidney tissue samples using Qiagen RNeasy plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina, following the manufacturer's protocol (NEB, Ipswich, MA, USA) after enrichement for messenger RNAs using Oligo d(T) beads.

value: Kidney

value: Conditional Knockout


title: LEC IL1b-3

description:
Library name: Sample B9
Column name in all-gene-Fpkm.txt : B9


title: STING-MSC 1


title: LEC ctrl 1

description:
Library name: Sample A1
Column name in all-gene-Fpkm.txt : A1


title: conditional knockout kidney-2

description: Library name: KKO-2


title: conditional knockout kidney-3

description: Library name: KKO-3


title: TLR-MSC 5

value: TLR


title: TLR-MSC 4


title: conditional knockout kidney-1

description: Library name: KKO-1


title: Batch2_Capture_g, ADT

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: Library name: g_adt

data_processing:
Seven Bridges Bioinformatics Platform Filtering, Alignment, run locally in a server
Use default settings of: BD Rhapsody™ WTA Analysis Pipeline run
Assembly: GRCh38-PhiX-gencodev29
Supplementary files format and content: gz, Gene/Cell count matrix
Supplementary files format and content: gz, sample tags
Supplementary files format and content: xlsx, Sample metadata

source_name: Periphery blood

extract_protocol:
Cells were captured with beads in microwell plate, followed by cell lysis, bead retrieval, cDNA synthesis, template switching, and Klenow extension.
Full-length cDNA along with cell barcode identifiers were PCR-amplified and multiple types of libraries, including whole transcriptome, TCR, BCR, Sample Tags, and AbSeq, were prepared and normalized using the BD Rhapsody WTA amplification kit (Cat. #633801) and BD Rhapsody TCR/BCR amplification kit, (Cat. #665345) following manufacturer’s instruction.

value: Periphery blood

value: Primary cells

value: PBMCs


title: JW-40635-untreated-BR9-TR2

description:
Library name: Sample 13
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

source_name: colonic organoids

extract_protocol:
Qiagen RNAeasy Mini Kit according to the manufacturer’s instructions.
cDNA was generated with Maxima RT polymerase (Thermo Fisher) and amplified with Terra PCR Direct Polymerase (Takara). Library preparation was carried out with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB)

value: colonic organoids

value: untreated


title: JW-40614-bethanechol-BR8-TR2

description:
Library name: Sample 12
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Control kidney-4

description: Library name: KWT-4

value: Control


title: JW-40681-untreated-BR10-TR2

description:
Library name: Sample 15
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: TLR-MSC 3

value: Joint


title: Batch2_Capture_f, ADT

description: Library name: f_adt


title: JW-40635-bethanechol-BR9-TR2

description:
Library name: Sample 14
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Batch2_Capture_g, GEX

description: Library name: g_gex

library_source: transcriptomic single cell


title: JW-40681-bethanechol-BR10-TR2

description:
Library name: Sample 16
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40614-untreated-BR8-TR2

description:
Library name: Sample 11
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Batch2_Capture_f, GEX

description: Library name: f_gex


title: TLR-MSC 2


title: Control kidney-3

description: Library name: KWT-3


title: JW-40543-bethanechol-BR7-TR2

description:
Library name: Sample 10
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: TLR-MSC 1


title: Batch1_Capture_e, ADT

description: Library name: e_adt


title: Control kidney-2

description: Library name: KWT-2


title: JW-40543-untreated-BR7-TR2

description:
Library name: Sample 9
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: MSC 5

value: MSC


title: MSC 4


title: Control kidney-1

description: Library name: KWT-1


title: Batch1_Capture_e, GEX

description: Library name: e_gex


title: JW-40681-bethanechol-BR10-TR1

description:
Library name: Sample 8
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Batch1_Capture_d, ADT

description: Library name: d_adt


title: intestinal epithelial cells, rotavirus infection

city: St. Louis

first: Gaopeng

last: Hou

state: MO

address: McDonnell Pediatric Research Building, Rm 9220

department: molecular microbiology

institute: Washinton University inSt. Louis

description: Library name: Sample 2

data_processing:
10X 3' v3 Gene Expression Library
Single-Cell 3'
2x101 HiSeq with Index
Paired End with Index
Assembly: Mouse (mm9)
Supplementary files format and content: cloupe

source_name: small intestine

extract_protocol:
Intestinal epithelial cells were isolated from mock infected and rotavirus infected mice seperately by EDTA-dithiothreitol extraction method.
10X 3' v3 Gene Expression Library kit was used for library construction

treatment_protocol: Rotavirus infection

value: small intestine

value: intestinal epithelial cell

value: rotavirus infection


title: MSC 3


title: MSC 2


title: MSC 1


title: Ctrl 5

value: CTRL


title: Ctrl 4


title: JW-40614-untreated-BR8-TR1

description:
Library name: Sample 3
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40635-bethanechol-BR9-TR1

description:
Library name: Sample 6
R1 fastq file: cDNA; R2 fastq file: barcode/UMI

value: bethanechol


title: Batch1_Capture_b, GEX

description: Library name: b_gex


title: Batch1_Capture_c, ADT

description: Library name: c_adt


title: Batch1_Capture_d, GEX

description: Library name: d_gex


title: intestinal epithelial cells, uninfected mock

description: Library name: Sample 1

value: control


title: Batch1_Capture_b, ADT

description: Library name: b_adt


title: JW-40614-bethanechol-BR8-TR1

description:
Library name: Sample 4
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Batch1_Capture_c, GEX

description: Library name: c_gex


title: [RNA-Seq] MCF10A-SATB1-BaP-3d-4 (replica 4)

city: San Francisco

first: Terumi

last: Kohwi-Shigematsu

address: 513 Parnassus Ave (HSW810)

department: Department of Orofacial Sciences

institute: UCSF

description: Library name: Sample48

data_processing:
For RNA-seq: raw reads were de-multiplexed, trimmed of any adapter sequences and mapped to the GRCh38 human genome using the software program STAR (available at https://code.google.com/p/rna-star) which uses information from an annotated transcriptome provided by Ensembl. For differential expression testing, the genomic alignments were restricted to those that map uniquely to the set of known Ensembl IDs (this includes the exons of all protein coding mRNAs as well as many other coding and noncoding RNAs). STAR aggregates this subset of mappings on a per gene basis as raw input for the program DESeq. DESeq normalizes by each library by size factor (reads per sample) as well 22 as by library complexity and then utilizes a Fischer’s Exact Test (FET) type statistic to assess differential expression. The FET employs a negative-binomial model of dispersion, consistent with the type of variance seen in RNAseq datasets, to assess differential expression.
Assembly: GRCh38
Supplementary files format and content: xlsx file includes GRO-seq and RNA-seq differential gene expression

growth_protocol: MCF10A-1 cells were maintained in DMEM/F12 medium supplemented with 10% fetal bovine serum, instead of horse serum,  epidermal growth factor (20ng/ml), hydrocortisone (0.5µg/ml), insulin (10µg/ml), cholera toxin (100ng/ml), and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 C.

extract_protocol:
For RNA-seq: Total RNA was purified by TRI reagent (Sigma) and followed by the RNeasy kit (Qiagen).
For RNA-seq: One microgram of total RNA from each sample was reverse transcribed using the QuantiTect Rev Transcription kit (Qiagen). The quality of total RNA was confirmed by 2100 bioanalyzer (Agilent Technologies, Inc.) and high-quality RNA samples (RIN>8) were further processed at QB3-Berkeley Genetics Core Facilities (University of California, Berkeley). After mRNA capture using Oligo(dT)25 magnetic beads (ThermoFisher), the library for sequencing was prepared on Apollo 324TM with PrepXTM RNA-Seq Library Preparation Kits (WaferGen Biosystems, Fremont, CA) according to the manufacturer’s recommendation.

treatment_protocol: B[a]P treatment was performed by culturing cells in the presence of 4 uM B[a]P for either 72 hours or 3 days.  SATB1-expressing MCF10A--1 cells were prepared as described in Ordinario et al., 2012 (PLoSONE 7(12): e51786. doi:10.1371/journal.pone.0051786)

value: malignancy of breast epithelial cells

tag: time

value: 3 days

value: B[a]P


title: Ctrl 3


title: Batch1_Capture_a, ADT

description: Library name: a_adt

value: Periphery blood


title: JW-40543-bethanechol-BR7-TR1

description:
Library name: Sample 2
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: JW-40635-untreated-BR9-TR1

description:
Library name: Sample 5
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Ctrl 2


title: [RNA-Seq] MCF10A-SATB1-BaP-3hr-3 (replica 3)

description: Library name: Sample43

value: 3 hours


title: [RNA-Seq] MCF10A-SATB1-BaP-3d-2 (replica 2)

description: Library name: Sample46


title: [RNA-Seq] MCF10A-SATB1-BaP-3hr-4 (replica 4)

description: Library name: Sample44


title: JW-40681-untreated-BR10-TR1

description:
Library name: Sample 7
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: [RNA-Seq] MCF10A-SATB1-BaP-3d-3 (replica 3)

description: Library name: Sample47


title: [RNA-Seq] MCF10A-SATB1-BaP-3d-1 (replica 1)

description: Library name: Sample45


title: JW-40543-untreated-BR7-TR1

description:
Library name: Sample 1
R1 fastq file: cDNA; R2 fastq file: barcode/UMI


title: Batch1_Capture_a, GEX

description: Library name: a_gex

value: Primary cells

value: PBMCs


title: DT SD 10WPA rep4

city: BErgen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
CLC Genomics Workbench 24.0
Trimming
Alignment
Assembly: mm10
Supplementary files format and content: Tab separated file with Raw counts per sample

source_name: Pancreatic islet

extract_protocol:
Qiagen RNEasy Mini kit
QIAseq  stranded mRNA kit Qiagen

value: Pancreatic islet

value: RIP-DTR   HTZ

value: DT


title: Ctrl 1

value: Joint


title: [RNA-Seq] MCF10A-SATB1-BaP-3hr-2 (replica 2)

description: Library name: Sample42


title: DT SD 10WPA rep3


title: [RNA-Seq] MCF10A-SATB1-BaP-3hr-1 (replica 1)

description: Library name: Sample41


title: DT SD 10WPA rep1


title: DT SD 10WPA rep2


title: GM12878, No SDS-prodecure, Cell 34

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description: No SDS-procedure

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy for each sample. hic and mcool files included contact matrices for each sample.
Supplementary files format and content: .3dg files of single-cell 3D genome structures

molecule: genomic DNA

source_name: blood

growth_protocol: GM12878 lymphoblastoid cells were grown in RPMI1640 medium (Gibco, Thermo Fisher Scientific, Cat. # 11875093) media supplemented with 15% FBS and 1% Pen/Strep. GM12878 were cultured at 37° C with 5% CO2 at recommended density.

extract_protocol:
1 million cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.
Single cells were amplified with the state-of-art transposase-based WGA (Multiplexed End Tagging Amplification), barcoded in 96-well plate, then pooled for library preparation.

value: blood

value: lymphoblastoid

value: WT


title: GM12878, No SDS-prodecure, Cell 36

description: No SDS-procedure


title: Dux-LOF-embryo12

first: Clara

last: Hermant

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells (IES)

institute: Helmholtz Zentrum Munich

description: 2x150bp reads

data_processing:
A custom Python Script (available on GitHub) was used to sort between 5' transcript ends and internal transcript fragments according to their adaptor sequence
Reads were mapped to GRCm38 with STAR (v2.7.11a)
BAM files were modified to keep only the Read2 (in case of 5' analysis) using custom Perl script available on Github
TE and genes were quantified using TEcount from TE transcript
for more information see (gitlab link)
Assembly: GRCm38
Supplementary files format and content: Count table from TECount using the second read of the 5' fragments ("five_2nd")
Supplementary files format and content: Count table from TECount using both reads of the internal fragments ("internal")

source_name: Late 2 cell embryo

growth_protocol: Zygotes were collected at 24h post-hCG, microinjected and cultured in KSOM until 48h post-hCG (late 2-cell stage), and collected for RNA-sequencing

extract_protocol:
Single embryos were used for single embryo RNA-seq (Smart-seq+5), for more information see methods of accompanying paper
An adapted version of Smart-seq2 (called Smart-seq+5') enabling to capture both the 5' transcript information in addition to internal fragment (see methods of the accompanying paper for more information)
Smart-seq+5'

treatment_protocol: Embryos were microinjected with either DUX antisense oligonucleotides (DUX_ASO; DUX-LOF), the mRNA for the SRF dominant negative (SRF-DN; SRF-LOF) construct, or the two in combination (SRF-DN+DUX_ASO; DOUBLE-LOF). Control embryos were microinjected with scramble antisense oligo (SCR_ASO; CTRL) (See methods of the accompanying paper for more information).

value: Late 2 cell embryo


title: [RNA-Seq] MCF10A-SATB1-Negative-3 (replica 3)

description: Library name: Sample39

treatment_protocol: no treatment


title: GM12878, No SDS-prodecure, Cell 35

description: No SDS-procedure


title: [RNA-Seq] MCF10A-SATB1-Negative-4 (replica 4)

description: Library name: Sample40


title: Dux-LOF-embryo10

description: 2x150bp reads


title: [RNA-Seq] MCF10A-SATB1-Negative-2 (replica 2)

description: Library name: Sample38


title: Dux-LOF-embryo8

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 32

description: No SDS-procedure


title: DT HFD 10WPA rep3


title: DT HFD 10WPA rep2


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3d-4 (replica 4)

description: Library name: Sample36


title: DT HFD 10WPA rep1


title: Dux-LOF-embryo6

description: 2x150bp reads


title: [RNA-Seq] MCF10A-SATB1-Negative-1 (replica 1)

description: Library name: Sample37


title: GM12878, No SDS-prodecure, Cell 31

description: No SDS-procedure


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3d-3 (replica 3)

description: Library name: Sample35


title: GM12878, No SDS-prodecure, Cell 33

description: No SDS-procedure


title: Dux-LOF-embryo7

description: 2x150bp reads


title: CTRL SD 10W rep3


title: GM12878, No SDS-prodecure, Cell 30

description: No SDS-procedure


title: Double-LOF-embryo10

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 29

description: No SDS-procedure


title: Dux-LOF-embryo11

description: 2x150bp reads


title: CTRL SD 10W rep2


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3d-2 (replica 2)

description: Library name: Sample34


title: Ctrl-embryo10

description: 2x150bp reads


title: CTRL SD 10W rep1


title: GM12878, No SDS-prodecure, Cell 28

description: No SDS-procedure


title: Double-LOF-embryo9

description: 2x150bp reads


title: Dux-LOF-embryo5

description: 2x150bp reads


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3d-1 (replica 1)

description: Library name: Sample33


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3hr-4 (replica 4)

description: Library name: Sample32


title: CTRL HFD 10W rep5


title: GM12878, No SDS-prodecure, Cell 26

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 27

description: No SDS-procedure


title: Srf-LOF-embryo9

description: 2x150bp reads


title: Double-LOF-embryo8

description: 2x150bp reads


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3hr-2 (replica 2)

description: Library name: Sample30


title: CTRL HFD 10W rep2


title: CTRL HFD 10W rep4


title: GM12878, No SDS-prodecure, Cell 24

description: No SDS-procedure


title: DT 30 DPA rep4


title: CTRL HFD 10W rep3


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3hr-1 (replica 1)

description: Library name: Sample29


title: [RNA-Seq] MCF10A-ctrlvector-Negative-4 (replica 4)

description: Library name: Sample28


title: GM12878, No SDS-prodecure, Cell 25

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 23

description: No SDS-procedure


title: Srf-LOF-embryo8

description: 2x150bp reads


title: Ctrl-embryo9

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 22

description: No SDS-procedure


title: DT 30 DPA rep3


title: Ctrl-embryo8

description: 2x150bp reads


title: DT 30 DPA rep2


title: [RNA-Seq] MCF10A-ctrlvector-Negative-3 (replica 3)

description: Library name: Sample27


title: GM12878, No SDS-prodecure, Cell 21

description: No SDS-procedure


title: [RNA-Seq] MCF10A-ctrlvector-Negative-2 (replica 2)

description: Library name: Sample26


title: GM12878, No SDS-prodecure, Cell 20

description: No SDS-procedure


title: Double-LOF-embryo7

description: 2x150bp reads


title: Srf-LOF-embryo7

description: 2x150bp reads


title: [RNA-Seq] MCF10A-ctrlvector-Negative-1 (replica 1)

description: Library name: Sample25


title: [RNA-Seq] MCF10A-ctrlvector-BaP-3hr-3 (replica 3)

description: Library name: Sample31


title: GM12878, No SDS-prodecure, Cell 19

description: No SDS-procedure


title: DT 30 DPA rep1


title: [GRO-Seq] MCF10A-SATB1-Bap-3d-28 (replica 4)

description: Library name: Sample24

data_processing:
For GRO-seq: raw sequence reads were cleaned using HTStream (https://github.com/s4hts/HTStream), a suite of preprocessing tools. This removed technical features such as Illumina adapters, polyAT sequences, PhiX contamination, and reads less than 21 bp in length. Once cleaned, reads were aligned to the GRCh38 human genome using the MEM algorithm in BWA (v0.7.16a), allowing a counts table to be generated using featureCounts and the corresponding genome annotation (GENCODE v40). Differential expression analysis was then performed using R [https://www.R-project.org/] and the limma voom pipeline, consisting of normalization, statistical testing, and multiple testing correction via the Benjamini-Hochberg procedure. Both RNA-seq and GRO-seq analyses were performed by University of California Davis, Bioinformatics Core.
Assembly: GRCh38
Supplementary files format and content: xlsx file includes GRO-seq and RNA-seq differential gene expression
Library strategy: GRO-Seq

extract_protocol:
For GRO-seq: nuclei were isolated from tissue culture cells, counted the number, washed and frozen (1 x 10^6 of nuclei in 10 ul of freezing buffer) at -80C until ready for in vitro Nuclear Run-on (NRO) transcription reaction. When the Gro-seq preparation was ready, 100 ul of nuclei stock were mixed with 100 ul of 2x NRO buffer (containing, ATP, GTP, BrUTP and CTP) and incubated at 37C for 7 min. The reaction was stopped by adding TRI-LS reagent (Sigma) and purified RNA in 20 ul of water with RNase inhibitor (1U/ul). The collected RNAs were further treated with DNase I (Turbo DNA-free kit, Bio-Rad), RNA fragmentation by RNA fragmentation kit (Ambion), purified by Micro-Bio-Spin P-30, incubated with T4 polynucletide kinase (PNK) at 37C for 60 min, and inactivated the PNK at 75C for 5 min. The final Br-UTP incorporated RNAs were immunoprecipitated with beads (anti-BrdU antibody conjugated agarose; Santa Cruz; sc-32323 AC), washed beads, and eluted by 100 ul of 0.25M EDTA-TE for 4 times. The eluted RNAs were purified by EtOH precipitation, and the final RNAs were dissolved in 15 ul of water.
For GRO-seq: performed by Takara SMATer smRNA library kit as manufactured suggested (polyadenylation, cDNA synthesis, PCR and clean up).


title: CTRL HFD 10W rep1


title: Srf-LOF-embryo6

description: 2x150bp reads


title: DT 5 DPA rep4


title: DT 5 DPA rep3


title: Srf-LOF-embryo5

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-Bap-3d-26 (replica 2)

description: Library name: Sample22


title: [GRO-Seq] MCF10A-SATB1-Bap-3d-27 (replica 3)

description: Library name: Sample23


title: GM12878, No SDS-prodecure, Cell 17

description: No SDS-procedure


title: DT 5 DPA rep2


title: GM12878, No SDS-prodecure, Cell 18

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 15

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 16

description: No SDS-procedure


title: DT 5 DPA rep1


title: Double-LOF-embryo6

description: 2x150bp reads


title: Srf-LOF-embryo4

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-Bap-3d-25 (replica 1)

description: Library name: Sample21


title: Double-LOF-embryo5

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-Bap-3hr-18 (replica 4)

description: Library name: Sample20


title: Double-LOF-embryo4

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-Bap-3hr-17 (replica 3)

description: Library name: Sample19


title: CTRL, rep2


title: GM12878, No SDS-prodecure, Cell 13

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 14

description: No SDS-procedure


title: [GRO-Seq] MCF10A-SATB1-Bap-3hr-16 (replica 2)

description: Library name: Sample18


title: Double-LOF-embryo3

description: 2x150bp reads


title: STZ 75mg/kg SD 10WPA rep4

value: STZ 75mg/kg


title: Double-LOF-embryo2

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-0hr-8 (replica 4)

description: Library name: Sample16


title: Ctrl-embryo5

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 10

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 7

description: No SDS-procedure


title: [GRO-Seq] MCF10A-SATB1-0hr-7 (replica 3)

description: Library name: Sample15


title: [GRO-Seq] MCF10A-SATB1-0hr-5 (replica 1)

description: Library name: Sample13


title: CTRL, rep3


title: STZ 75mg/kg SD 10WPA rep1


title: STZ 75mg/kg HFD 10WPA rep4


title: Ctrl-embryo4

description: 2x150bp reads


title: Srf-LOF-embryo3

description: 2x150bp reads


title: [GRO-Seq] MCF10A-SATB1-0hr-6 (replica 2)

description: Library name: Sample14


title: STZ 75mg/kg SD 10WPA rep3


title: [GRO-Seq] MCF10A-SATB1-Bap-3hr-15 (replica 1)

description: Library name: Sample17


title: [GRO-Seq] MCF10A-vec-Bap-3d-24 (replica 4)

description: Library name: Sample12


title: STZ 75mg/kg HFD 10WPA rep3


title: Double-LOF-embryo1

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 5

description: No SDS-procedure


title: CTRL, rep1


title: Ctrl-embryo3

description: 2x150bp reads


title: [GRO-Seq] MCF10A-vec-Bap-3d-22 (replica 2)

description: Library name: Sample10


title: [GRO-Seq] MCF10A-vec-Bap-3d-23 (replica 3)

description: Library name: Sample11


title: [GRO-Seq] MCF10A-vec-Bap-3d-21 (replica 1)

description: Library name: Sample9


title: STZ 75mg/kg HFD 10WPA rep2


title: Dux-LOF-embryo4

description: 2x150bp reads


title: [GRO-Seq] MCF10A-vec-Bap-3hr-14 (replica 4)

description: Library name: Sample8


title: STZ 75mg/kg HFD 10WPA rep1


title: GM12878, No SDS-prodecure, Cell 4

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 2

description: No SDS-procedure


title: Ctrl-embryo1

description: 2x150bp reads


title: [GRO-Seq] MCF10A-vec-Bap-3hr-13 (replica 3)

description: Library name: Sample7


title: Ctrl-embryo2

description: 2x150bp reads


title: WT#1

city: Melbourne

first: Cyril

last: Seillet

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description: 10x genomics

data_processing:
Reads were processed by 10X Cell Ranger v.7 using the mm10 reference genome. scRNAseq data were further processed and analysed using R v.4.2.0 and the Seurat package v. 4.0.6113. Demultiplex step was performed with DemuxMix v0.9.9.6 to determine the identity of each sample based on Hashtag number
Genes with counts per million (CPM) larger than 0.5 in at least one group of samples were kept, and genes related to immunoglobulins (Igh, Igkv) were filtered out.
Differential gene expression was performed in R studio with Bioconductor package DESeq2 (version 1.34.0).
Regularized log transformation (base 2) was conducted in significantly differentially expressed genes (log2 fold change > 1 and adjusted p value < 0.1) for heatmap visualization.
Assembly: mm10
Supplementary files format and content: RDS object
Supplementary files format and content: matrix files and tab-separated value files

source_name: Small intestine

extract_protocol:
Small intestine were digested and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted .
After sorting the samples were labelled with hashtags and TotalSeq-A universal antibody panel (Biolegend protocol) then captured on 2x 3'HT lanes and processed according to the 10X Chromium NextGEM Single Cell 3'-HT protocol

value: Small intestine

tag: strain

value: Female

value: 6-8 week old


title: GM12878, No SDS-prodecure, Cell 1

description: No SDS-procedure


title: Ctrl-embryo6

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 3

description: No SDS-procedure


title: Dux-LOF-embryo3

description: 2x150bp reads


title: GM12878, No SDS-prodecure, Cell 8

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 12

description: No SDS-procedure


title: GM12878, No SDS-prodecure, Cell 6

description: No SDS-procedure


title: STZ 75mg/kg SD 10WPA rep2


title: WT#2

description: 10x genomics


title: GM12878, No SDS-prodecure, Cell 11

description: No SDS-procedure


title: SFK3 miRNA

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description: Library name: Sample18

data_processing:
RNA-seq data is applied quality control and adapter trimming by Trim Galore v0.6.4_dev and mapped to the reference genome using STAR v2.7.2d. And we performed reads summarization for genomic features via featureCounts v2.0.0. The raw read counts normalization and differential expression were determined by DESeq2 v1.34.0. The number of reads matched to an expressed gene was standardized as fragments per kilobase of exon per million mapped fragments (FPKM) values. The genes that exhibited |log2(fold change)| ≥ 2 and adjusted P ≤ 0.05 in the comparisons between fat-tailed/fat-rumped and thin-tailed individuals were considered as differentially expressed genes. GO enrichment analysis used the enrichGO function provided within the R package clusterProfiler v4.2.2.
Assembly: Ovis4.0, Oar_v4.0, GCA_000298735.2, oviAri4
Supplementary files format and content: xlsx format and they are lncRNA transcripts readcount and miRNA readcount

organism: Ovis aries

source_name: tail tissues

extract_protocol:
RNA was extracted from tail tissues, and the samples underwent stringent quality control based on the following criteria. First, agarose gel electrophoresis was used to assess RNA integrity and detect potential DNA contamination. Second, RNA concentration and purity were preliminarily quantified. Finally, the integrity of RNA was accurately measured.
For library construction, strand-specific libraries were prepared using a ribosomal RNA (rRNA) depletion method. Total RNA was first treated to remove rRNA, and the remaining RNA was fragmented into short segments of 250–300 bp. These fragments served as templates for first-strand cDNA synthesis using random oligonucleotide primers. The second-strand cDNA was then synthesized using dNTPs as substrates. The double-stranded cDNA was purified, end-repaired, A-tailed, and ligated with sequencing adapters. The second strand of cDNA was degraded using the USER enzyme, and the remaining cDNA was amplified by PCR to obtain the final strand-specific library. To ensure library quality, a Qubit fluorometer was used for preliminary quantification, diluting the library to 1 ng/µL. The Agilent 2100 Bioanalyzer was then employed to assess the insert fragment size, which was expected to range from 250 to 300 bp. After confirming the expected insert size, qPCR was conducted for precise quantification of the library's effective concentration, which was required to exceed 2 nM to ensure high-quality samples.  Finally, libraries that passed quality control were pooled based on their effective concentration and sequencing data requirements for Illumina PE150 sequencing. In paired-end sequencing (PE150), each end of the cDNA insert is sequenced to a length of 150 bp, with the insert fragment serving as the sequencing unit. Paired-end sequencing not only provides sequence information from both ends of the insert fragment but also offers insights into the length between the two ends, facilitating downstream assembly and alignment.

value: tail tissues

value: fat cell

tag: batch

value: SFK


title: GM12878, No SDS-prodecure, Cell 9

description: No SDS-procedure


title: Heart, TAC, 8 weeks, HEP_FGF21, rep5

city: Cincinnati

first: Georgios

last: Siokatas

state: OH

address: 231 ALBERT SABIN WAY

department: Pharmacology and Systems Physiology

institute: University of Cincinnati

data_processing:
A quality control check on the fastq files was performed using FastQC. Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic1 [Version 0.33]. The trimmed reads were then mapped to a reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat22 [Version 2.0.5]. In the next step, transcript/gene abundance was determined using kallisto3 [Version 0.43.1]. We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and transcript per million (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: Csv file containing: transcript IDs, Gene IDs and raw counts of each sample.

source_name: Heart

extract_protocol:
Total RNA extraction from frozen heart tissue was performed using TRIzol reagent according to the manufacturer's instructions
Libraries were  created for all samples using 1 ng of cDNA. Specifically, the Illumina protocol, the Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool. The concentration of the pool was optimized to acquire at least 30 million reads per sample by using Paired-End 100 bp Reads, so for sequencing a NovaSeq SP (200 cycles) v1.5 flow cell was used. Libraries were sequenced on the Illumina NovaSeq 6000 system following the manufacturer's protocol.

value: Heart


title: SFK2 miRNA

description: Library name: Sample17


title: [GRO-Seq] MCF10A-vec-Bap-3hr-12 (replica 2)

description: Library name: Sample6

value: malignancy of breast epithelial cells

value: 3 hours

value: B[a]P


title: Heart, TAC, 8 weeks, HEP_FGF21, rep4


title: [GRO-Seq] MCF10A-vec-Bap-3h-11 (replica 1)

description: Library name: Sample5


title: Heart, TAC, 8 weeks, HEP_FGF21, rep3


title: [GRO-Seq] MCF10A-vec-0hr-4 (replica 4)

description: Library name: Sample4


title: SFK1 miRNA

description: Library name: Sample16


title: [GRO-Seq] MCF10A-vec-0hr-2 (replica 2)

description: Library name: Sample2


title: HUS3 miRNA

description: Library name: Sample15

value: HUS


title: [GRO-Seq] MCF10A-vec-0hr-3 (replica 3)

description: Library name: Sample3


title: Heart, TAC, 8 weeks, HEP_FGF21, rep1


title: HUS2 miRNA

description: Library name: Sample14


title: CSH3 miRNA

description: Library name: Sample12

value: CSH


title: GM12878, SDS-procedure, Cell 31

description: SDS-procedure

value: blood

value: SDS


title: HUS1 miRNA

description: Library name: Sample13


title: GM12878, SDS-procedure, Cell 34

description: SDS-procedure

value: lymphoblastoid

value: WT


title: Heart, TAC, 8 weeks, CM_FGF21, rep4


title: Heart, TAC, 8 weeks, CM_FGF21, rep3


title: Heart, TAC, 8 weeks, CM_FGF21, rep5


title: GM12878, SDS-procedure, Cell 30

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 33

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 29

description: SDS-procedure


title: Heart, TAC, 8 weeks, HEP_FGF21, rep2


title: Heart, TAC, 8 weeks, CM_FGF21, rep2


title: GM12878, SDS-procedure, Cell 28

description: SDS-procedure


title: Embryo, PCB0.8, 2

city: Stockholm

first: Linus

last: Wiklund

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description:
Library name: PCB0_8b
PCB0_8b

data_processing:
Raw data QC, e.g. remove reads with: adapter contamination, more than 10% uncertain nucleotides, or base quality lower than 5 for more than 50% of reads.
Alignment against reference genome with HISAT2 v2.0.5 and quantification with featureCounts v1.5.0-p3
Removal of genes with fewer than 5 reads or that were detected in fewer than 3 replicates.
Normalization of data with TPM
Assembly: Danio rerio GRCz11 GCA_000002035
Supplementary files format and content: comma-separated text file containing raw counts for all samples
Supplementary files format and content: comma-separated text file containing TPM normalized counts for all samples

organism: Danio rerio

source_name: whole-organism

growth_protocol: Zebrafish embryos were kept in petri-dishes containing E3 medium in an incubator at 28.5 °C.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Zebrafish embryos were treated with three doses each of cadmium or PCB126 from 1 day post fertilization (dpf) to 5 dpf.

value: whole-organism

value: WT, AB strain


title: [GRO-Seq] MCF10A-vec-0hr-1 (replica 1)

description: Library name: Sample1


title: CSH3

description: Library name: Sample9


title: Embryo, PCB0.8, 1

description:
Library name: PCB0_8a
PCB0_8a


title: CSH2

description: Library name: Sample8


title: Heart, TAC, 8 weeks, CM_FGF21, rep1


title: GM12878, SDS-procedure, Cell 35

description: SDS-procedure


title: Heart, TAC, 8 weeks, Ctrl, rep3


title: Embryo, PCB0.4, 3

description:
Library name: PCB0_4c
PCB0_4c


title: GM12878, SDS-procedure, Cell 27

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 32

description: SDS-procedure


title: Embryo, PCB0.8, 3

description:
Library name: PCB0_8c
PCB0_8c


title: CSH1

description: Library name: Sample7


title: HUS3

description: Library name: Sample6


title: Heart, TAC, 8 weeks, Ctrl, rep2


title: Heart, TAC, 8 weeks, Ctrl, rep4


title: Embryo, PCB0.4, 2

description:
Library name: PCB0_4b
PCB0_4b


title: Embryo, PCB0.4, 4

description:
Library name: PCB0_4d
PCB0_4d


title: CSH2 miRNA

description: Library name: Sample11


title: HUS2

description: Library name: Sample5


title: Embryo, PCB0.8, 4

description:
Library name: PCB0_8d
PCB0_8d


title: CSH1 miRNA

description: Library name: Sample10


title: GM12878, SDS-procedure, Cell 25

description: SDS-procedure


title: Heart, TAC, 8 weeks, Ctrl, rep1


title: GM12878, SDS-procedure, Cell 26

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 24

description: SDS-procedure


title: Embryo, PCB0.4, 1

description:
Library name: PCB0_4a
PCB0_4a


title: HUS1

description: Library name: Sample4


title: Heart, TAC, 8 weeks, rep5


title: Embryo, PCB0.08, 4

description:
Library name: PCB0_08d
PCB0_08d


title: GM12878, SDS-procedure, Cell 23

description: SDS-procedure


title: SFK2

description: Library name: Sample2


title: Heart, TAC, 8 weeks, rep3


title: Heart, TAC, 8 weeks, rep4


title: Embryo, PCB0.08, 3

description:
Library name: PCB0_08c
PCB0_08c


title: SFK1

description: Library name: Sample1


title: Heart, TAC, 8 weeks, rep2


title: Embryo, PCB0.08, 1

description:
Library name: PCB0_08a
PCB0_08a


title: Embryo, Cd24, 4

description:
Library name: Cd24d
Cd24d

value: Cd 24 ug/L


title: GM12878, SDS-procedure, Cell 21

description: SDS-procedure


title: Heart, TAC, 8 weeks, rep1


title: GM12878_Micro-C_Rep1

data_processing:
Bulk Micro-C datasets were processed using distiller-nf pipeline.
Assembly: hg38
Supplementary files format and content: Contact matrices (hic and mcool files) for each sample.
Library strategy: Micro-C

extract_protocol: For Micro-C, cells were permeabilized with 100 μL Micro-C buffer1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% IGEPAL CA630, 1 x PIC), incubate on ice for 20 min.

value: no treatment


title: Heart, Sham, 8 weeks, rep5


title: GM12878_Micro-C_Rep2


title: GM12878, SDS-procedure, Cell 22

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 20

description: SDS-procedure


title: Heart, Sham, 8 weeks, rep4


title: mnase_200U_Rep3


title: GM12878, SDS-procedure, Cell 19

description: SDS-procedure


title: Embryo, Cd24, 3

description:
Library name: Cd24c
Cd24c


title: Embryo, Cd24, 2

description:
Library name: Cd24b
Cd24b


title: GM12878, SDS-procedure, Cell 17

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 16

description: SDS-procedure


title: SFK3

description: Library name: Sample3

value: tail tissues


title: Embryo, Cd24, 1

description:
Library name: Cd24a
Cd24a


title: Heart, Sham, 8 weeks, rep3


title: GM12878, SDS-procedure, Cell 15

description: SDS-procedure


title: Embryo, Cd12, 4

description:
Library name: Cd12d
Cd12d

value: Cd 12 ug/L


title: GM12878, SDS-procedure, Cell 14

description: SDS-procedure


title: Embryo, Cd12, 3

description:
Library name: Cd12c
Cd12c


title: Heart, Sham, 8 weeks, rep1


title: Heart, TAC, 2 weeks, rep5

data_processing:
A quality control check on the fastq files was performed using FastQC. Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic1 [Version 0.33]. The trimmed reads were then mapped to a reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat22 [Version 2.0.5]. In the next step, transcript/gene abundance was determined using kallisto3 [Version 0.43.1]. We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and transcript per million (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: Csv file containing: transcript IDs, Gene IDs and TPM (Trancript per million) of each sample.

value: TAC

tag: time point

value: 2 weeks


title: GM12878, SDS-procedure, Cell 18

description: SDS-procedure


title: Embryo, PCB0.08, 2

description:
Library name: PCB0_08b
PCB0_08b


title: mnase_175U_Rep4


title: Heart, TAC, 2 weeks, rep4

value: Heart


title: Embryo, Cd12, 2

description:
Library name: Cd12b
Cd12b


title: mnase_175U_Rep3


title: GM12878, SDS-procedure, Cell 12

description: SDS-procedure


title: Embryo, Cd12, 1

description:
Library name: Cd12a
Cd12a


title: Heart, TAC, 2 weeks, rep3


title: mnase_200U_Rep2


title: GM12878, SDS-procedure, Cell 11

description: SDS-procedure


title: mnase_175U_Rep2


title: Embryo, Cd2.4, 3

description:
Library name: Cd2_4c
Cd2_4c

value: Cd 2.4 ug/L


title: Embryo, Cd2.4, 4

description:
Library name: Cd2_4d
Cd2_4d


title: mnase_175U_Rep1


title: GM12878, SDS-procedure, Cell 9

description: SDS-procedure


title: Heart, TAC, 2 weeks, rep1


title: mnase_175U_Rep5


title: mnase_150U_Rep5


title: GM12878, SDS-procedure, Cell 8

description: SDS-procedure


title: Heart, Sham, 2 weeks, rep5

value: Sham


title: Embryo, Cd2.4, 1

description:
Library name: Cd2_4a
Cd2_4a


title: Heart, TAC, 2 weeks, rep2


title: GM12878, SDS-procedure, Cell 13

description: SDS-procedure


title: mnase_150U_Rep4


title: Heart, Sham, 8 weeks, rep2


title: Heart, Sham, 2 weeks, rep4


title: GM12878, SDS-procedure, Cell 7

description: SDS-procedure


title: mnase_150U_Rep3


title: GM12878, SDS-procedure, Cell 10

description: SDS-procedure


title: Embryo, control, 4

description:
Library name: Cd0d
Cd0d

value: Control


title: Heart, Sham, 2 weeks, rep3


title: mnase_150U_Rep2


title: Heart, Sham, 2 weeks, rep2


title: Embryo, control, 3

description:
Library name: Cd0c
Cd0c


title: mnase_150U_Rep1


title: GM12878, SDS-procedure, Cell 6

description: SDS-procedure


title: Embryo, control, 2

description:
Library name: Cd0b
Cd0b


title: Heart, Sham, 2 weeks, rep1


title: GM12878, SDS-procedure, Cell 3

description: SDS-procedure


title: Embryo, control, 1

description:
Library name: Cd0a
Cd0a


title: GM12878, SDS-procedure, Cell 5

description: SDS-procedure


title: GM12878, SDS-procedure, Cell 4

description: SDS-procedure


title: mnase_100U_Rep3


title: Heart, TAC, 3 days, rep5

value: 3 days


title: GM12878, SDS-procedure, Cell 2

description: SDS-procedure

value: blood


title: Heart, TAC, 3 days, rep4


title: myc2/3/4, methyl jasmonate, rep4

city: Krakow

first: Kenji

last: Yamada

state: Malopolska

address: Gronostajowa 7A

department: Malopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

description: Library name: mycTKOJA

data_processing:
Raw sequence reads (~40 million per sample) were pre-processed using fastqc (v0.11.8), with default settings for paired-end reads.
The trimgalore (v0.6.5) pipeline was used to remove the adaptor sequences, and the clean reads were pseudo-aligned to the Arabidopsis thaliana Col-0 transcriptome reference (TAIR10) using the salmon (v1.1.0) pipeline.
After the removal of low-abundance transcripts not present within replicates under each condition, the count data were imported using the tximport (v1.12.3) package.
Assembly: Arabidopsis TAIR10
Supplementary files format and content: csv file include TPM values of each samples

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were germinated aseptically at 22°C under continuous light (~100 μE·s-1·m-2) on plates filled with half-strength Murashige and Skoog (1/2 MS) medium (Fujifilm Wako Chemical, Japan) containing 0.4% (w/v) gellan gum (Fujifilm Wako Chemical), 0.5% (w/v) 2-(N-morpholino) ethanesulfonic acid (MES)-KOH (pH 5.7), and 1% (w/v) sucrose.

extract_protocol:
Total RNA was isolated from 50 mg of Arabidopsis leaves using the MagMAX Plant RNA Isolation Kit (Thermo-Fisher) and then treated with DNase I (Sigma-Aldrich) to remove traces of contaminating DNA.
Construction of the RNA-seq libraries and next-generation sequencing were performed by Macrogen (Seoul, South Korea). Standard libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: The primary and secondary leaves of 2-week-old Arabidopsis plants were harvested and floated on the water containing 50 µM of methyl-JA (MeJA; Sigma-Aldrich, St. Louis, USA). The JA treatment lasted for 40–48 h at 22°C under continuous light.

value: leaves

value: myc2myc3myc4 mutant

value: methyl jasmonate

value: replicate 4


title: myc2/3/4, mock, rep4

description: Library name: mycTKODW

value: mock


title: mnase_100U_Rep1

value: lymphoblastoid

value: WT


title: GM12878, 200U, Cell 96

description:
200U MNase
GM-200U_096.allValidPairs.gz
GM-200U_096.hic
GM-200U_096.mcool
GM-200U_096.clean.smooth.bw
GM-200U_096_20kb_1.3dg.gz
GM-200U_096_20kb_2.3dg.gz
GM-200U_096_20kb_3.3dg.gz
GM-200U_096_20kb_4.3dg.gz
GM-200U_096_20kb_5.3dg.gz
GM-200U_096_10kb_1.3dg.gz
GM-200U_096_10kb_2.3dg.gz
GM-200U_096_10kb_3.3dg.gz
GM-200U_096_10kb_4.3dg.gz
GM-200U_096_10kb_5.3dg.gz
GM-200U_096_5kb_1.3dg.gz
GM-200U_096_5kb_2.3dg.gz
GM-200U_096_5kb_3.3dg.gz
GM-200U_096_5kb_4.3dg.gz
GM-200U_096_5kb_5.3dg.gz
GM-200U_096_20kb_1.clean.3dg.gz
GM-200U_096_20kb_2.clean.3dg.gz
GM-200U_096_20kb_3.clean.3dg.gz
GM-200U_096_20kb_4.clean.3dg.gz
GM-200U_096_20kb_5.clean.3dg.gz
GM-200U_096_10kb_1.clean.3dg.gz
GM-200U_096_10kb_2.clean.3dg.gz
GM-200U_096_10kb_3.clean.3dg.gz
GM-200U_096_10kb_4.clean.3dg.gz
GM-200U_096_10kb_5.clean.3dg.gz
GM-200U_096_5kb_1.clean.3dg.gz
GM-200U_096_5kb_2.clean.3dg.gz
GM-200U_096_5kb_3.clean.3dg.gz
GM-200U_096_5kb_4.clean.3dg.gz
GM-200U_096_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 95

description:
200U MNase
GM-200U_095.allValidPairs.gz
GM-200U_095.hic
GM-200U_095.mcool
GM-200U_095.clean.smooth.bw
GM-200U_095_20kb_1.3dg.gz
GM-200U_095_20kb_2.3dg.gz
GM-200U_095_20kb_3.3dg.gz
GM-200U_095_20kb_5.3dg.gz
GM-200U_095_10kb_1.3dg.gz
GM-200U_095_10kb_2.3dg.gz
GM-200U_095_10kb_3.3dg.gz
GM-200U_095_10kb_5.3dg.gz
GM-200U_095_5kb_1.3dg.gz
GM-200U_095_5kb_2.3dg.gz
GM-200U_095_5kb_3.3dg.gz
GM-200U_095_5kb_5.3dg.gz
GM-200U_095_20kb_1.clean.3dg.gz
GM-200U_095_20kb_2.clean.3dg.gz
GM-200U_095_20kb_3.clean.3dg.gz
GM-200U_095_20kb_5.clean.3dg.gz
GM-200U_095_10kb_1.clean.3dg.gz
GM-200U_095_10kb_2.clean.3dg.gz
GM-200U_095_10kb_3.clean.3dg.gz
GM-200U_095_10kb_5.clean.3dg.gz
GM-200U_095_5kb_1.clean.3dg.gz
GM-200U_095_5kb_2.clean.3dg.gz
GM-200U_095_5kb_3.clean.3dg.gz
GM-200U_095_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 94

description:
200U MNase
GM-200U_094.allValidPairs.gz
GM-200U_094.hic
GM-200U_094.mcool
GM-200U_094.clean.smooth.bw
GM-200U_094_20kb_1.3dg.gz
GM-200U_094_20kb_2.3dg.gz
GM-200U_094_20kb_3.3dg.gz
GM-200U_094_20kb_4.3dg.gz
GM-200U_094_20kb_5.3dg.gz
GM-200U_094_10kb_1.3dg.gz
GM-200U_094_10kb_2.3dg.gz
GM-200U_094_10kb_3.3dg.gz
GM-200U_094_10kb_4.3dg.gz
GM-200U_094_10kb_5.3dg.gz
GM-200U_094_5kb_1.3dg.gz
GM-200U_094_5kb_2.3dg.gz
GM-200U_094_5kb_3.3dg.gz
GM-200U_094_5kb_4.3dg.gz
GM-200U_094_5kb_5.3dg.gz
GM-200U_094_20kb_1.clean.3dg.gz
GM-200U_094_20kb_2.clean.3dg.gz
GM-200U_094_20kb_3.clean.3dg.gz
GM-200U_094_20kb_4.clean.3dg.gz
GM-200U_094_20kb_5.clean.3dg.gz
GM-200U_094_10kb_1.clean.3dg.gz
GM-200U_094_10kb_2.clean.3dg.gz
GM-200U_094_10kb_3.clean.3dg.gz
GM-200U_094_10kb_4.clean.3dg.gz
GM-200U_094_10kb_5.clean.3dg.gz
GM-200U_094_5kb_1.clean.3dg.gz
GM-200U_094_5kb_2.clean.3dg.gz
GM-200U_094_5kb_3.clean.3dg.gz
GM-200U_094_5kb_4.clean.3dg.gz
GM-200U_094_5kb_5.clean.3dg.gz


title: GM12878, SDS-procedure, Cell 1

description: SDS-procedure

value: SDS


title: myb47/95, mock, rep4

description: Library name: myb47_95DW

value: myb47myb95 mutant


title: Heart, TAC, 3 days, rep2

value: TAC


title: cell_355

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz

data_processing:
Raw sequencing reads were mapped to the reference genome with BWA mem (0.7.17-r1188) with parameters -5SP. Single-cell contacts were generated with the dip-c and hickit (v0.1.1) packages with default parameters.
PCR duplicates were removed from raw SAM files with samblaster (0.1.26) package with parameters --ignoreUnmated -r. Subsequently, nucleosome occupancy signals were calculated with the DANPOS2 package with paramter -a 5 -count 1000000.
Chromatin loop calling was performed with SnapHiC and Chromosight package with default parameters.
Single-cell 3D genome structures were generated with the hickit v0.1.1 package with parameters  -M and -Sr1m -c1 -r10m -c2 -b4m -b1m -b200k -D5 -b50k -D5 -b20k -D5 -b10k -D5 -b5k.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include contacts for each sample. bigWig files include nucleosome occupancy and ligation junction signals for each sample. hic and mcool files included contact matrices for each sample.


title: cell_354


title: Heart, TAC, 3 days, rep1


title: wild type, methyl jasmonate, rep4

description: Library name: WTJA


title: GM12878, 200U, Cell 93

description:
200U MNase
GM-200U_093.allValidPairs.gz
GM-200U_093.hic
GM-200U_093.mcool
GM-200U_093.clean.smooth.bw
GM-200U_093_20kb_1.3dg.gz
GM-200U_093_20kb_2.3dg.gz
GM-200U_093_20kb_3.3dg.gz
GM-200U_093_20kb_4.3dg.gz
GM-200U_093_20kb_5.3dg.gz
GM-200U_093_10kb_1.3dg.gz
GM-200U_093_10kb_2.3dg.gz
GM-200U_093_10kb_3.3dg.gz
GM-200U_093_10kb_4.3dg.gz
GM-200U_093_10kb_5.3dg.gz
GM-200U_093_5kb_1.3dg.gz
GM-200U_093_5kb_2.3dg.gz
GM-200U_093_5kb_3.3dg.gz
GM-200U_093_5kb_4.3dg.gz
GM-200U_093_5kb_5.3dg.gz
GM-200U_093_20kb_1.clean.3dg.gz
GM-200U_093_20kb_2.clean.3dg.gz
GM-200U_093_20kb_3.clean.3dg.gz
GM-200U_093_20kb_4.clean.3dg.gz
GM-200U_093_20kb_5.clean.3dg.gz
GM-200U_093_10kb_1.clean.3dg.gz
GM-200U_093_10kb_2.clean.3dg.gz
GM-200U_093_10kb_3.clean.3dg.gz
GM-200U_093_10kb_4.clean.3dg.gz
GM-200U_093_10kb_5.clean.3dg.gz
GM-200U_093_5kb_1.clean.3dg.gz
GM-200U_093_5kb_2.clean.3dg.gz
GM-200U_093_5kb_3.clean.3dg.gz
GM-200U_093_5kb_4.clean.3dg.gz
GM-200U_093_5kb_5.clean.3dg.gz


title: cell_353


title: Heart, Sham, 3 days, rep5


title: cell_352


title: wild type, mock, rep4

description: Library name: WTDW


title: Heart, Sham, 3 days, rep4


title: GM12878, 200U, Cell 92

description:
200U MNase
GM-200U_092.allValidPairs.gz
GM-200U_092.hic
GM-200U_092.mcool
GM-200U_092.clean.smooth.bw
GM-200U_092_20kb_1.3dg.gz
GM-200U_092_20kb_2.3dg.gz
GM-200U_092_20kb_4.3dg.gz
GM-200U_092_20kb_5.3dg.gz
GM-200U_092_10kb_1.3dg.gz
GM-200U_092_10kb_2.3dg.gz
GM-200U_092_10kb_4.3dg.gz
GM-200U_092_10kb_5.3dg.gz
GM-200U_092_5kb_1.3dg.gz
GM-200U_092_5kb_2.3dg.gz
GM-200U_092_5kb_4.3dg.gz
GM-200U_092_5kb_5.3dg.gz
GM-200U_092_20kb_1.clean.3dg.gz
GM-200U_092_20kb_2.clean.3dg.gz
GM-200U_092_20kb_4.clean.3dg.gz
GM-200U_092_20kb_5.clean.3dg.gz
GM-200U_092_10kb_1.clean.3dg.gz
GM-200U_092_10kb_2.clean.3dg.gz
GM-200U_092_10kb_4.clean.3dg.gz
GM-200U_092_10kb_5.clean.3dg.gz
GM-200U_092_5kb_1.clean.3dg.gz
GM-200U_092_5kb_2.clean.3dg.gz
GM-200U_092_5kb_4.clean.3dg.gz
GM-200U_092_5kb_5.clean.3dg.gz


title: mnase_100U_Rep2

value: no treatment


title: GM12878, 200U, Cell 91

description:
200U MNase
GM-200U_091.allValidPairs.gz
GM-200U_091.hic
GM-200U_091.mcool
GM-200U_091.clean.smooth.bw
GM-200U_091_20kb_1.3dg.gz
GM-200U_091_20kb_2.3dg.gz
GM-200U_091_20kb_3.3dg.gz
GM-200U_091_20kb_4.3dg.gz
GM-200U_091_20kb_5.3dg.gz
GM-200U_091_10kb_1.3dg.gz
GM-200U_091_10kb_2.3dg.gz
GM-200U_091_10kb_3.3dg.gz
GM-200U_091_10kb_4.3dg.gz
GM-200U_091_10kb_5.3dg.gz
GM-200U_091_5kb_1.3dg.gz
GM-200U_091_5kb_2.3dg.gz
GM-200U_091_5kb_3.3dg.gz
GM-200U_091_5kb_4.3dg.gz
GM-200U_091_5kb_5.3dg.gz
GM-200U_091_20kb_1.clean.3dg.gz
GM-200U_091_20kb_2.clean.3dg.gz
GM-200U_091_20kb_3.clean.3dg.gz
GM-200U_091_20kb_4.clean.3dg.gz
GM-200U_091_20kb_5.clean.3dg.gz
GM-200U_091_10kb_1.clean.3dg.gz
GM-200U_091_10kb_2.clean.3dg.gz
GM-200U_091_10kb_3.clean.3dg.gz
GM-200U_091_10kb_4.clean.3dg.gz
GM-200U_091_10kb_5.clean.3dg.gz
GM-200U_091_5kb_1.clean.3dg.gz
GM-200U_091_5kb_2.clean.3dg.gz
GM-200U_091_5kb_3.clean.3dg.gz
GM-200U_091_5kb_4.clean.3dg.gz
GM-200U_091_5kb_5.clean.3dg.gz


title: myc2/3/4, methyl jasmonate, rep3

description: Library name: mycTKO_JA_15

value: replicate 3


title: Heart, TAC, 3 days, rep3

value: Heart


title: Heart, Sham, 3 days, rep3

value: Sham


title: myc2/3/4, methyl jasmonate, rep2

description: Library name: mycTKO_JA_14

value: replicate 2


title: GM12878, 200U, Cell 90

description:
200U MNase
GM-200U_090.allValidPairs.gz
GM-200U_090.hic
GM-200U_090.mcool
GM-200U_090.clean.smooth.bw
GM-200U_090_20kb_2.3dg.gz
GM-200U_090_20kb_3.3dg.gz
GM-200U_090_20kb_4.3dg.gz
GM-200U_090_10kb_2.3dg.gz
GM-200U_090_10kb_3.3dg.gz
GM-200U_090_10kb_4.3dg.gz
GM-200U_090_5kb_2.3dg.gz
GM-200U_090_5kb_3.3dg.gz
GM-200U_090_5kb_4.3dg.gz
GM-200U_090_20kb_2.clean.3dg.gz
GM-200U_090_20kb_3.clean.3dg.gz
GM-200U_090_20kb_4.clean.3dg.gz
GM-200U_090_10kb_2.clean.3dg.gz
GM-200U_090_10kb_3.clean.3dg.gz
GM-200U_090_10kb_4.clean.3dg.gz
GM-200U_090_5kb_2.clean.3dg.gz
GM-200U_090_5kb_3.clean.3dg.gz
GM-200U_090_5kb_4.clean.3dg.gz


title: cell_351


title: myb47/95, methyl jasmonate, rep4

description: Library name: myb47_95JA


title: Heart, Sham, 3 days, rep2

value: 3 days


title: cell_350

value: blood


title: myc2/3/4, methyl jasmonate, rep1

description: Library name: mycTKO_JA_13

value: leaves

value: replicate 1


title: Heart, Sham, 3 days, rep1


title: myc2/3/4, mock, rep3

description: Library name: mycTKO_DW_6_20

value: myc2myc3myc4 mutant


title: GM12878, 200U, Cell 88

description:
200U MNase
GM-200U_088.allValidPairs.gz
GM-200U_088.hic
GM-200U_088.mcool
GM-200U_088.clean.smooth.bw
GM-200U_088_20kb_1.3dg.gz
GM-200U_088_20kb_2.3dg.gz
GM-200U_088_20kb_3.3dg.gz
GM-200U_088_20kb_4.3dg.gz
GM-200U_088_20kb_5.3dg.gz
GM-200U_088_10kb_1.3dg.gz
GM-200U_088_10kb_2.3dg.gz
GM-200U_088_10kb_3.3dg.gz
GM-200U_088_10kb_4.3dg.gz
GM-200U_088_10kb_5.3dg.gz
GM-200U_088_5kb_1.3dg.gz
GM-200U_088_5kb_2.3dg.gz
GM-200U_088_5kb_3.3dg.gz
GM-200U_088_5kb_4.3dg.gz
GM-200U_088_5kb_5.3dg.gz
GM-200U_088_20kb_1.clean.3dg.gz
GM-200U_088_20kb_2.clean.3dg.gz
GM-200U_088_20kb_3.clean.3dg.gz
GM-200U_088_20kb_4.clean.3dg.gz
GM-200U_088_20kb_5.clean.3dg.gz
GM-200U_088_10kb_1.clean.3dg.gz
GM-200U_088_10kb_2.clean.3dg.gz
GM-200U_088_10kb_3.clean.3dg.gz
GM-200U_088_10kb_4.clean.3dg.gz
GM-200U_088_10kb_5.clean.3dg.gz
GM-200U_088_5kb_1.clean.3dg.gz
GM-200U_088_5kb_2.clean.3dg.gz
GM-200U_088_5kb_3.clean.3dg.gz
GM-200U_088_5kb_4.clean.3dg.gz
GM-200U_088_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 89

description:
200U MNase
GM-200U_089.allValidPairs.gz
GM-200U_089.hic
GM-200U_089.mcool
GM-200U_089.clean.smooth.bw
GM-200U_089_20kb_1.3dg.gz
GM-200U_089_20kb_2.3dg.gz
GM-200U_089_20kb_3.3dg.gz
GM-200U_089_20kb_4.3dg.gz
GM-200U_089_20kb_5.3dg.gz
GM-200U_089_10kb_1.3dg.gz
GM-200U_089_10kb_2.3dg.gz
GM-200U_089_10kb_3.3dg.gz
GM-200U_089_10kb_4.3dg.gz
GM-200U_089_10kb_5.3dg.gz
GM-200U_089_5kb_1.3dg.gz
GM-200U_089_5kb_2.3dg.gz
GM-200U_089_5kb_3.3dg.gz
GM-200U_089_5kb_4.3dg.gz
GM-200U_089_5kb_5.3dg.gz
GM-200U_089_20kb_1.clean.3dg.gz
GM-200U_089_20kb_2.clean.3dg.gz
GM-200U_089_20kb_3.clean.3dg.gz
GM-200U_089_20kb_4.clean.3dg.gz
GM-200U_089_20kb_5.clean.3dg.gz
GM-200U_089_10kb_1.clean.3dg.gz
GM-200U_089_10kb_2.clean.3dg.gz
GM-200U_089_10kb_3.clean.3dg.gz
GM-200U_089_10kb_4.clean.3dg.gz
GM-200U_089_10kb_5.clean.3dg.gz
GM-200U_089_5kb_1.clean.3dg.gz
GM-200U_089_5kb_2.clean.3dg.gz
GM-200U_089_5kb_3.clean.3dg.gz
GM-200U_089_5kb_4.clean.3dg.gz
GM-200U_089_5kb_5.clean.3dg.gz


title: cell_348


title: C_1459

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

institute: Indiana University School of Medicine

data_processing:
Barcodes and sequencing adapters were trimmed using TrimGalore
Reads were aligned to Human reference genome mm39 (ENSEMBL) using HISAT2 aligner
Mapped reads were assigned to annotated genomic features of GRCh38 using featureCounts
Differential expression analysis was carried out using DESeq2 package
Assembly: mm39
Supplementary files format and content: comma-separated values (csv) file shows the number of reads (unnormalized counts) mapped to each gene (shown as Ensembl ID) for all the samples

source_name: B6MyC-CaP tumor

growth_protocol: B6MyC CaP cell line was derived from the Hi-MYC transgenic mouse model on a C57BL/6 background (B6MYC), which we previously establisehd by backcrossing FVB Hi-MYC mice with C57BL/6N mice. B6MyC-CaP cells were implanted subcutaneously into 6-week-old male C57BL/6 mice.

extract_protocol:
Total RNA was extracted using RNeasy Plus Kit (Qiagen) according to the manufacturer’s instructions.
RNA quality control, library preparation, and NGS paired-end sequencing on the Illumina NovaSeq platform were performed by the University at Buffalo Genomics and Bioinformatics core.

treatment_protocol: Once tumors were established, mice were randomized into four treatment groups: vehicle, enzalutamide (ENZ), alternate-day fasting (ADF), or ADF + ENZ. ENZ and ADF + ENZ groups were treated with 20mg/kg Enzalutamide by oral gavage once a day. Mice in the Vehicle and ENZ groups were fed normal chow ad libitum. Mice in the ADF and ADF + ENZ groups were fasted for 24 hours and fed ad libitum for 24 hours.

value: B6MyC-CaP tumor

value: Prostate Cancer

value: ADF + ENZ


title: GM12878, 200U, Cell 87

description:
200U MNase
GM-200U_087.allValidPairs.gz
GM-200U_087.hic
GM-200U_087.mcool
GM-200U_087.clean.smooth.bw
GM-200U_087_20kb_1.3dg.gz
GM-200U_087_20kb_2.3dg.gz
GM-200U_087_20kb_3.3dg.gz
GM-200U_087_20kb_4.3dg.gz
GM-200U_087_20kb_5.3dg.gz
GM-200U_087_10kb_1.3dg.gz
GM-200U_087_10kb_2.3dg.gz
GM-200U_087_10kb_3.3dg.gz
GM-200U_087_10kb_4.3dg.gz
GM-200U_087_10kb_5.3dg.gz
GM-200U_087_5kb_1.3dg.gz
GM-200U_087_5kb_2.3dg.gz
GM-200U_087_5kb_3.3dg.gz
GM-200U_087_5kb_4.3dg.gz
GM-200U_087_5kb_5.3dg.gz
GM-200U_087_20kb_1.clean.3dg.gz
GM-200U_087_20kb_2.clean.3dg.gz
GM-200U_087_20kb_3.clean.3dg.gz
GM-200U_087_20kb_4.clean.3dg.gz
GM-200U_087_20kb_5.clean.3dg.gz
GM-200U_087_10kb_1.clean.3dg.gz
GM-200U_087_10kb_2.clean.3dg.gz
GM-200U_087_10kb_3.clean.3dg.gz
GM-200U_087_10kb_4.clean.3dg.gz
GM-200U_087_10kb_5.clean.3dg.gz
GM-200U_087_5kb_1.clean.3dg.gz
GM-200U_087_5kb_2.clean.3dg.gz
GM-200U_087_5kb_3.clean.3dg.gz
GM-200U_087_5kb_4.clean.3dg.gz
GM-200U_087_5kb_5.clean.3dg.gz

value: lymphoblastoid

value: WT


title: myc2/3/4, mock, rep2

description: Library name: mycTKO_DW_5

value: mock


title: cell_349


title: C_1441


title: C_1440


title: GM12878, 200U, Cell 86

description:
200U MNase
GM-200U_086.allValidPairs.gz
GM-200U_086.hic
GM-200U_086.mcool
GM-200U_086.clean.smooth.bw
GM-200U_086_20kb_1.3dg.gz
GM-200U_086_20kb_2.3dg.gz
GM-200U_086_20kb_3.3dg.gz
GM-200U_086_20kb_4.3dg.gz
GM-200U_086_20kb_5.3dg.gz
GM-200U_086_10kb_1.3dg.gz
GM-200U_086_10kb_2.3dg.gz
GM-200U_086_10kb_3.3dg.gz
GM-200U_086_10kb_4.3dg.gz
GM-200U_086_10kb_5.3dg.gz
GM-200U_086_5kb_1.3dg.gz
GM-200U_086_5kb_2.3dg.gz
GM-200U_086_5kb_3.3dg.gz
GM-200U_086_5kb_4.3dg.gz
GM-200U_086_5kb_5.3dg.gz
GM-200U_086_20kb_1.clean.3dg.gz
GM-200U_086_20kb_2.clean.3dg.gz
GM-200U_086_20kb_3.clean.3dg.gz
GM-200U_086_20kb_4.clean.3dg.gz
GM-200U_086_20kb_5.clean.3dg.gz
GM-200U_086_10kb_1.clean.3dg.gz
GM-200U_086_10kb_2.clean.3dg.gz
GM-200U_086_10kb_3.clean.3dg.gz
GM-200U_086_10kb_4.clean.3dg.gz
GM-200U_086_10kb_5.clean.3dg.gz
GM-200U_086_5kb_1.clean.3dg.gz
GM-200U_086_5kb_2.clean.3dg.gz
GM-200U_086_5kb_3.clean.3dg.gz
GM-200U_086_5kb_4.clean.3dg.gz
GM-200U_086_5kb_5.clean.3dg.gz


title: cell_346


title: cell_347


title: myb47/95, methyl jasmonate, rep3

description: Library name: myb47_95JA9_24

value: myb47myb95 mutant

value: methyl jasmonate


title: GM12878, 200U, Cell 85

description:
200U MNase
GM-200U_085.allValidPairs.gz
GM-200U_085.hic
GM-200U_085.mcool
GM-200U_085.clean.smooth.bw
GM-200U_085_20kb_1.3dg.gz
GM-200U_085_20kb_2.3dg.gz
GM-200U_085_20kb_3.3dg.gz
GM-200U_085_20kb_4.3dg.gz
GM-200U_085_10kb_1.3dg.gz
GM-200U_085_10kb_2.3dg.gz
GM-200U_085_10kb_3.3dg.gz
GM-200U_085_10kb_4.3dg.gz
GM-200U_085_5kb_1.3dg.gz
GM-200U_085_5kb_2.3dg.gz
GM-200U_085_5kb_3.3dg.gz
GM-200U_085_5kb_4.3dg.gz
GM-200U_085_20kb_1.clean.3dg.gz
GM-200U_085_20kb_2.clean.3dg.gz
GM-200U_085_20kb_3.clean.3dg.gz
GM-200U_085_20kb_4.clean.3dg.gz
GM-200U_085_10kb_1.clean.3dg.gz
GM-200U_085_10kb_2.clean.3dg.gz
GM-200U_085_10kb_3.clean.3dg.gz
GM-200U_085_10kb_4.clean.3dg.gz
GM-200U_085_5kb_1.clean.3dg.gz
GM-200U_085_5kb_2.clean.3dg.gz
GM-200U_085_5kb_3.clean.3dg.gz
GM-200U_085_5kb_4.clean.3dg.gz


title: cell_345


title: myb47/95, methyl jasmonate, rep2

description: Library name: myb47_95JA7_32


title: C_1401


title: F_1499

value: ADF


title: cell_344


title: GM12878, 200U, Cell 84

description:
200U MNase
GM-200U_084.allValidPairs.gz
GM-200U_084.hic
GM-200U_084.mcool
GM-200U_084.clean.smooth.bw
GM-200U_084_20kb_1.3dg.gz
GM-200U_084_20kb_2.3dg.gz
GM-200U_084_20kb_3.3dg.gz
GM-200U_084_20kb_4.3dg.gz
GM-200U_084_20kb_5.3dg.gz
GM-200U_084_10kb_1.3dg.gz
GM-200U_084_10kb_2.3dg.gz
GM-200U_084_10kb_3.3dg.gz
GM-200U_084_10kb_4.3dg.gz
GM-200U_084_10kb_5.3dg.gz
GM-200U_084_5kb_1.3dg.gz
GM-200U_084_5kb_2.3dg.gz
GM-200U_084_5kb_3.3dg.gz
GM-200U_084_5kb_4.3dg.gz
GM-200U_084_5kb_5.3dg.gz
GM-200U_084_20kb_1.clean.3dg.gz
GM-200U_084_20kb_2.clean.3dg.gz
GM-200U_084_20kb_3.clean.3dg.gz
GM-200U_084_20kb_4.clean.3dg.gz
GM-200U_084_20kb_5.clean.3dg.gz
GM-200U_084_10kb_1.clean.3dg.gz
GM-200U_084_10kb_2.clean.3dg.gz
GM-200U_084_10kb_3.clean.3dg.gz
GM-200U_084_10kb_4.clean.3dg.gz
GM-200U_084_10kb_5.clean.3dg.gz
GM-200U_084_5kb_1.clean.3dg.gz
GM-200U_084_5kb_2.clean.3dg.gz
GM-200U_084_5kb_3.clean.3dg.gz
GM-200U_084_5kb_4.clean.3dg.gz
GM-200U_084_5kb_5.clean.3dg.gz


title: myb47/95, methyl jasmonate, rep1

description: Library name: myb47_95JA6_31


title: GM12878, 200U, Cell 83

description:
200U MNase
GM-200U_083.allValidPairs.gz
GM-200U_083.hic
GM-200U_083.mcool
GM-200U_083.clean.smooth.bw
GM-200U_083_20kb_1.3dg.gz
GM-200U_083_20kb_2.3dg.gz
GM-200U_083_20kb_3.3dg.gz
GM-200U_083_20kb_4.3dg.gz
GM-200U_083_20kb_5.3dg.gz
GM-200U_083_10kb_1.3dg.gz
GM-200U_083_10kb_2.3dg.gz
GM-200U_083_10kb_3.3dg.gz
GM-200U_083_10kb_4.3dg.gz
GM-200U_083_10kb_5.3dg.gz
GM-200U_083_5kb_1.3dg.gz
GM-200U_083_5kb_2.3dg.gz
GM-200U_083_5kb_3.3dg.gz
GM-200U_083_5kb_4.3dg.gz
GM-200U_083_5kb_5.3dg.gz
GM-200U_083_20kb_1.clean.3dg.gz
GM-200U_083_20kb_2.clean.3dg.gz
GM-200U_083_20kb_3.clean.3dg.gz
GM-200U_083_20kb_4.clean.3dg.gz
GM-200U_083_20kb_5.clean.3dg.gz
GM-200U_083_10kb_1.clean.3dg.gz
GM-200U_083_10kb_2.clean.3dg.gz
GM-200U_083_10kb_3.clean.3dg.gz
GM-200U_083_10kb_4.clean.3dg.gz
GM-200U_083_10kb_5.clean.3dg.gz
GM-200U_083_5kb_1.clean.3dg.gz
GM-200U_083_5kb_2.clean.3dg.gz
GM-200U_083_5kb_3.clean.3dg.gz
GM-200U_083_5kb_4.clean.3dg.gz
GM-200U_083_5kb_5.clean.3dg.gz


title: F_1471


title: cell_343


title: myb47/95, mock, rep3

description: Library name: myb47_95_DW__7

value: replicate 3


title: F_1461


title: GM12878, 200U, Cell 82

description:
200U MNase
GM-200U_082.allValidPairs.gz
GM-200U_082.hic
GM-200U_082.mcool
GM-200U_082.clean.smooth.bw
GM-200U_082_20kb_1.3dg.gz
GM-200U_082_20kb_2.3dg.gz
GM-200U_082_20kb_3.3dg.gz
GM-200U_082_20kb_4.3dg.gz
GM-200U_082_20kb_5.3dg.gz
GM-200U_082_10kb_1.3dg.gz
GM-200U_082_10kb_2.3dg.gz
GM-200U_082_10kb_3.3dg.gz
GM-200U_082_10kb_4.3dg.gz
GM-200U_082_10kb_5.3dg.gz
GM-200U_082_5kb_1.3dg.gz
GM-200U_082_5kb_2.3dg.gz
GM-200U_082_5kb_3.3dg.gz
GM-200U_082_5kb_4.3dg.gz
GM-200U_082_5kb_5.3dg.gz
GM-200U_082_20kb_1.clean.3dg.gz
GM-200U_082_20kb_2.clean.3dg.gz
GM-200U_082_20kb_3.clean.3dg.gz
GM-200U_082_20kb_4.clean.3dg.gz
GM-200U_082_20kb_5.clean.3dg.gz
GM-200U_082_10kb_1.clean.3dg.gz
GM-200U_082_10kb_2.clean.3dg.gz
GM-200U_082_10kb_3.clean.3dg.gz
GM-200U_082_10kb_4.clean.3dg.gz
GM-200U_082_10kb_5.clean.3dg.gz
GM-200U_082_5kb_1.clean.3dg.gz
GM-200U_082_5kb_2.clean.3dg.gz
GM-200U_082_5kb_3.clean.3dg.gz
GM-200U_082_5kb_4.clean.3dg.gz
GM-200U_082_5kb_5.clean.3dg.gz


title: myc2/3/4, mock, rep1

description: Library name: mycTKO_DW_4


title: cell_342


title: myb47/95, mock, rep2

description: Library name: myb47_95DW6_21


title: GM12878, 200U, Cell 81

description:
200U MNase
GM-200U_081.allValidPairs.gz
GM-200U_081.hic
GM-200U_081.mcool
GM-200U_081.clean.smooth.bw
GM-200U_081_20kb_1.3dg.gz
GM-200U_081_20kb_2.3dg.gz
GM-200U_081_20kb_3.3dg.gz
GM-200U_081_20kb_4.3dg.gz
GM-200U_081_20kb_5.3dg.gz
GM-200U_081_10kb_1.3dg.gz
GM-200U_081_10kb_2.3dg.gz
GM-200U_081_10kb_3.3dg.gz
GM-200U_081_10kb_4.3dg.gz
GM-200U_081_10kb_5.3dg.gz
GM-200U_081_5kb_1.3dg.gz
GM-200U_081_5kb_2.3dg.gz
GM-200U_081_5kb_3.3dg.gz
GM-200U_081_5kb_4.3dg.gz
GM-200U_081_5kb_5.3dg.gz
GM-200U_081_20kb_1.clean.3dg.gz
GM-200U_081_20kb_2.clean.3dg.gz
GM-200U_081_20kb_3.clean.3dg.gz
GM-200U_081_20kb_4.clean.3dg.gz
GM-200U_081_20kb_5.clean.3dg.gz
GM-200U_081_10kb_1.clean.3dg.gz
GM-200U_081_10kb_2.clean.3dg.gz
GM-200U_081_10kb_3.clean.3dg.gz
GM-200U_081_10kb_4.clean.3dg.gz
GM-200U_081_10kb_5.clean.3dg.gz
GM-200U_081_5kb_1.clean.3dg.gz
GM-200U_081_5kb_2.clean.3dg.gz
GM-200U_081_5kb_3.clean.3dg.gz
GM-200U_081_5kb_4.clean.3dg.gz
GM-200U_081_5kb_5.clean.3dg.gz


title: cell_341


title: myb47/95, mock, rep1

description: Library name: myb47_95_DW5_27


title: F_1449


title: GM12878, 200U, Cell 80

description:
200U MNase
GM-200U_080.allValidPairs.gz
GM-200U_080.hic
GM-200U_080.mcool
GM-200U_080.clean.smooth.bw
GM-200U_080_20kb_1.3dg.gz
GM-200U_080_20kb_2.3dg.gz
GM-200U_080_20kb_3.3dg.gz
GM-200U_080_20kb_4.3dg.gz
GM-200U_080_20kb_5.3dg.gz
GM-200U_080_10kb_1.3dg.gz
GM-200U_080_10kb_2.3dg.gz
GM-200U_080_10kb_3.3dg.gz
GM-200U_080_10kb_4.3dg.gz
GM-200U_080_10kb_5.3dg.gz
GM-200U_080_5kb_1.3dg.gz
GM-200U_080_5kb_2.3dg.gz
GM-200U_080_5kb_3.3dg.gz
GM-200U_080_5kb_4.3dg.gz
GM-200U_080_5kb_5.3dg.gz
GM-200U_080_20kb_1.clean.3dg.gz
GM-200U_080_20kb_2.clean.3dg.gz
GM-200U_080_20kb_3.clean.3dg.gz
GM-200U_080_20kb_4.clean.3dg.gz
GM-200U_080_20kb_5.clean.3dg.gz
GM-200U_080_10kb_1.clean.3dg.gz
GM-200U_080_10kb_2.clean.3dg.gz
GM-200U_080_10kb_3.clean.3dg.gz
GM-200U_080_10kb_4.clean.3dg.gz
GM-200U_080_10kb_5.clean.3dg.gz
GM-200U_080_5kb_1.clean.3dg.gz
GM-200U_080_5kb_2.clean.3dg.gz
GM-200U_080_5kb_3.clean.3dg.gz
GM-200U_080_5kb_4.clean.3dg.gz
GM-200U_080_5kb_5.clean.3dg.gz


title: E_1438

value: ENZ


title: GM12878, 200U, Cell 79

description:
200U MNase
GM-200U_079.allValidPairs.gz
GM-200U_079.hic
GM-200U_079.mcool
GM-200U_079.clean.smooth.bw
GM-200U_079_20kb_1.3dg.gz
GM-200U_079_20kb_2.3dg.gz
GM-200U_079_20kb_3.3dg.gz
GM-200U_079_20kb_4.3dg.gz
GM-200U_079_10kb_1.3dg.gz
GM-200U_079_10kb_2.3dg.gz
GM-200U_079_10kb_3.3dg.gz
GM-200U_079_10kb_4.3dg.gz
GM-200U_079_5kb_1.3dg.gz
GM-200U_079_5kb_2.3dg.gz
GM-200U_079_5kb_3.3dg.gz
GM-200U_079_5kb_4.3dg.gz
GM-200U_079_20kb_1.clean.3dg.gz
GM-200U_079_20kb_2.clean.3dg.gz
GM-200U_079_20kb_3.clean.3dg.gz
GM-200U_079_20kb_4.clean.3dg.gz
GM-200U_079_10kb_1.clean.3dg.gz
GM-200U_079_10kb_2.clean.3dg.gz
GM-200U_079_10kb_3.clean.3dg.gz
GM-200U_079_10kb_4.clean.3dg.gz
GM-200U_079_5kb_1.clean.3dg.gz
GM-200U_079_5kb_2.clean.3dg.gz
GM-200U_079_5kb_3.clean.3dg.gz
GM-200U_079_5kb_4.clean.3dg.gz


title: wild type, methyl jasmonate, rep2

description: Library name: WT_JA__10

value: replicate 2


title: wild type, methyl jasmonate, rep3

description: Library name: WT_JA__11


title: cell_339


title: GM12878, 200U, Cell 78

description:
200U MNase
GM-200U_078.allValidPairs.gz
GM-200U_078.hic
GM-200U_078.mcool
GM-200U_078.clean.smooth.bw
GM-200U_078_20kb_1.3dg.gz
GM-200U_078_20kb_2.3dg.gz
GM-200U_078_20kb_3.3dg.gz
GM-200U_078_20kb_4.3dg.gz
GM-200U_078_20kb_5.3dg.gz
GM-200U_078_10kb_1.3dg.gz
GM-200U_078_10kb_2.3dg.gz
GM-200U_078_10kb_3.3dg.gz
GM-200U_078_10kb_4.3dg.gz
GM-200U_078_10kb_5.3dg.gz
GM-200U_078_5kb_1.3dg.gz
GM-200U_078_5kb_2.3dg.gz
GM-200U_078_5kb_3.3dg.gz
GM-200U_078_5kb_4.3dg.gz
GM-200U_078_5kb_5.3dg.gz
GM-200U_078_20kb_1.clean.3dg.gz
GM-200U_078_20kb_2.clean.3dg.gz
GM-200U_078_20kb_3.clean.3dg.gz
GM-200U_078_20kb_4.clean.3dg.gz
GM-200U_078_20kb_5.clean.3dg.gz
GM-200U_078_10kb_1.clean.3dg.gz
GM-200U_078_10kb_2.clean.3dg.gz
GM-200U_078_10kb_3.clean.3dg.gz
GM-200U_078_10kb_4.clean.3dg.gz
GM-200U_078_10kb_5.clean.3dg.gz
GM-200U_078_5kb_1.clean.3dg.gz
GM-200U_078_5kb_2.clean.3dg.gz
GM-200U_078_5kb_3.clean.3dg.gz
GM-200U_078_5kb_4.clean.3dg.gz
GM-200U_078_5kb_5.clean.3dg.gz


title: E_1420


title: cell_338

description:
gm12878_pooled.allValidPairs.gz
gm12878_pooled.hic
gm12878_pooled.mcool
gm12878_pooled.ligation_junctions.bed
scmicroc_gm12878.snaphic.10kb.postprocessed.summits.bedpe
gm12878.RELA.peaks.con.txt.gz
gm12878.RELA.top5k.peaks.con.txt.gz


title: E_1414


title: cell_337


title: wild type, methyl jasmonate, rep1

description: Library name: WT_JA_4_28


title: cell_340


title: wild type, mock, rep3

description: Library name: WT_DW_3


title: GM12878, 200U, Cell 76

description:
200U MNase
GM-200U_076.allValidPairs.gz
GM-200U_076.hic
GM-200U_076.mcool
GM-200U_076.clean.smooth.bw
GM-200U_076_20kb_1.3dg.gz
GM-200U_076_20kb_2.3dg.gz
GM-200U_076_20kb_3.3dg.gz
GM-200U_076_20kb_4.3dg.gz
GM-200U_076_20kb_5.3dg.gz
GM-200U_076_10kb_1.3dg.gz
GM-200U_076_10kb_2.3dg.gz
GM-200U_076_10kb_3.3dg.gz
GM-200U_076_10kb_4.3dg.gz
GM-200U_076_10kb_5.3dg.gz
GM-200U_076_5kb_1.3dg.gz
GM-200U_076_5kb_2.3dg.gz
GM-200U_076_5kb_3.3dg.gz
GM-200U_076_5kb_4.3dg.gz
GM-200U_076_5kb_5.3dg.gz
GM-200U_076_20kb_1.clean.3dg.gz
GM-200U_076_20kb_2.clean.3dg.gz
GM-200U_076_20kb_3.clean.3dg.gz
GM-200U_076_20kb_4.clean.3dg.gz
GM-200U_076_20kb_5.clean.3dg.gz
GM-200U_076_10kb_1.clean.3dg.gz
GM-200U_076_10kb_2.clean.3dg.gz
GM-200U_076_10kb_3.clean.3dg.gz
GM-200U_076_10kb_4.clean.3dg.gz
GM-200U_076_10kb_5.clean.3dg.gz
GM-200U_076_5kb_1.clean.3dg.gz
GM-200U_076_5kb_2.clean.3dg.gz
GM-200U_076_5kb_3.clean.3dg.gz
GM-200U_076_5kb_4.clean.3dg.gz
GM-200U_076_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 77

description:
200U MNase
GM-200U_077.allValidPairs.gz
GM-200U_077.hic
GM-200U_077.mcool
GM-200U_077.clean.smooth.bw
GM-200U_077_20kb_1.3dg.gz
GM-200U_077_20kb_2.3dg.gz
GM-200U_077_20kb_3.3dg.gz
GM-200U_077_20kb_4.3dg.gz
GM-200U_077_20kb_5.3dg.gz
GM-200U_077_10kb_1.3dg.gz
GM-200U_077_10kb_2.3dg.gz
GM-200U_077_10kb_3.3dg.gz
GM-200U_077_10kb_4.3dg.gz
GM-200U_077_10kb_5.3dg.gz
GM-200U_077_5kb_1.3dg.gz
GM-200U_077_5kb_2.3dg.gz
GM-200U_077_5kb_3.3dg.gz
GM-200U_077_5kb_4.3dg.gz
GM-200U_077_5kb_5.3dg.gz
GM-200U_077_20kb_1.clean.3dg.gz
GM-200U_077_20kb_2.clean.3dg.gz
GM-200U_077_20kb_3.clean.3dg.gz
GM-200U_077_20kb_4.clean.3dg.gz
GM-200U_077_20kb_5.clean.3dg.gz
GM-200U_077_10kb_1.clean.3dg.gz
GM-200U_077_10kb_2.clean.3dg.gz
GM-200U_077_10kb_3.clean.3dg.gz
GM-200U_077_10kb_4.clean.3dg.gz
GM-200U_077_10kb_5.clean.3dg.gz
GM-200U_077_5kb_1.clean.3dg.gz
GM-200U_077_5kb_2.clean.3dg.gz
GM-200U_077_5kb_3.clean.3dg.gz
GM-200U_077_5kb_4.clean.3dg.gz
GM-200U_077_5kb_5.clean.3dg.gz


title: V_1458

value: Vehicle


title: V_1453


title: GM12878, 200U, Cell 75

description:
200U MNase
GM-200U_075.allValidPairs.gz
GM-200U_075.hic
GM-200U_075.mcool
GM-200U_075.clean.smooth.bw
GM-200U_075_20kb_3.3dg.gz
GM-200U_075_20kb_4.3dg.gz
GM-200U_075_20kb_5.3dg.gz
GM-200U_075_10kb_3.3dg.gz
GM-200U_075_10kb_4.3dg.gz
GM-200U_075_10kb_5.3dg.gz
GM-200U_075_5kb_3.3dg.gz
GM-200U_075_5kb_4.3dg.gz
GM-200U_075_5kb_5.3dg.gz
GM-200U_075_20kb_3.clean.3dg.gz
GM-200U_075_20kb_4.clean.3dg.gz
GM-200U_075_20kb_5.clean.3dg.gz
GM-200U_075_10kb_3.clean.3dg.gz
GM-200U_075_10kb_4.clean.3dg.gz
GM-200U_075_10kb_5.clean.3dg.gz
GM-200U_075_5kb_3.clean.3dg.gz
GM-200U_075_5kb_4.clean.3dg.gz
GM-200U_075_5kb_5.clean.3dg.gz

value: blood


title: cell_335


title: cell_336


title: wild type, mock, rep2

description: Library name: WT_DW_2

value: leaves


title: wild type, mock, rep1

description: Library name: WT_DW_1

value: replicate 1


title: cell_334


title: IP_HDIP1-del-DBD_FLAG_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

description: Library name: Sample 6

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis thaliana

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates or soil with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis thaliana

value: Arabidopsis seedlings

tag: chip antibody

value: SIGMA, F1804

value: 1305-HDIP1-{delta}DBD-FLAG transformed plants (in Col-0)


title: V_1409

value: B6MyC-CaP tumor

value: Prostate Cancer


title: GM12878, 200U, Cell 74

description:
200U MNase
GM-200U_074.allValidPairs.gz
GM-200U_074.hic
GM-200U_074.mcool
GM-200U_074.clean.smooth.bw
GM-200U_074_20kb_1.3dg.gz
GM-200U_074_20kb_2.3dg.gz
GM-200U_074_20kb_3.3dg.gz
GM-200U_074_20kb_5.3dg.gz
GM-200U_074_10kb_1.3dg.gz
GM-200U_074_10kb_2.3dg.gz
GM-200U_074_10kb_3.3dg.gz
GM-200U_074_10kb_5.3dg.gz
GM-200U_074_5kb_1.3dg.gz
GM-200U_074_5kb_2.3dg.gz
GM-200U_074_5kb_3.3dg.gz
GM-200U_074_5kb_5.3dg.gz
GM-200U_074_20kb_1.clean.3dg.gz
GM-200U_074_20kb_2.clean.3dg.gz
GM-200U_074_20kb_3.clean.3dg.gz
GM-200U_074_20kb_5.clean.3dg.gz
GM-200U_074_10kb_1.clean.3dg.gz
GM-200U_074_10kb_2.clean.3dg.gz
GM-200U_074_10kb_3.clean.3dg.gz
GM-200U_074_10kb_5.clean.3dg.gz
GM-200U_074_5kb_1.clean.3dg.gz
GM-200U_074_5kb_2.clean.3dg.gz
GM-200U_074_5kb_3.clean.3dg.gz
GM-200U_074_5kb_5.clean.3dg.gz

value: lymphoblastoid

value: WT


title: GM12878, 200U, Cell 73

description:
200U MNase
GM-200U_073.allValidPairs.gz
GM-200U_073.hic
GM-200U_073.mcool
GM-200U_073.clean.smooth.bw
GM-200U_073_20kb_1.3dg.gz
GM-200U_073_20kb_2.3dg.gz
GM-200U_073_20kb_3.3dg.gz
GM-200U_073_20kb_4.3dg.gz
GM-200U_073_20kb_5.3dg.gz
GM-200U_073_10kb_1.3dg.gz
GM-200U_073_10kb_2.3dg.gz
GM-200U_073_10kb_3.3dg.gz
GM-200U_073_10kb_4.3dg.gz
GM-200U_073_10kb_5.3dg.gz
GM-200U_073_5kb_1.3dg.gz
GM-200U_073_5kb_2.3dg.gz
GM-200U_073_5kb_3.3dg.gz
GM-200U_073_5kb_4.3dg.gz
GM-200U_073_5kb_5.3dg.gz
GM-200U_073_20kb_1.clean.3dg.gz
GM-200U_073_20kb_2.clean.3dg.gz
GM-200U_073_20kb_3.clean.3dg.gz
GM-200U_073_20kb_4.clean.3dg.gz
GM-200U_073_20kb_5.clean.3dg.gz
GM-200U_073_10kb_1.clean.3dg.gz
GM-200U_073_10kb_2.clean.3dg.gz
GM-200U_073_10kb_3.clean.3dg.gz
GM-200U_073_10kb_4.clean.3dg.gz
GM-200U_073_10kb_5.clean.3dg.gz
GM-200U_073_5kb_1.clean.3dg.gz
GM-200U_073_5kb_2.clean.3dg.gz
GM-200U_073_5kb_3.clean.3dg.gz
GM-200U_073_5kb_4.clean.3dg.gz
GM-200U_073_5kb_5.clean.3dg.gz


title: V_1407


title: IP_HDIP1-del-DBD_FLAG_rep1

description: Library name: Sample 5


title: cell_332


title: IL15 CTL, Pim1/2 dKO, bio rep 3

city: Dundee

first: Laura

last: Spinelli

address: Dow Street

department: Cell Signalling and Immunology

country: United Kingdom

institute: University of Dundee

description: Illumina TruSeq Stranded mRNA

data_processing:
bcl2fastq2 conversion software (NovaSeq 6000) for base calling and automatic adapter trimming.
Trimmed sequence reads were mapper to GRCm38.p6 using STAR (version 2.7.1a) with ‘outFilterType BySJout’ option switched on to reduce spurious junctions. STAR quantMode GeneCounts option was used to map aligned reads to genes to generate a gene counts matrix, using the annotation file GRCm38.101.
Low count genes reduced using filterByExpr function in EdgeR.
Count matrix was normalised using Trimmed Mean of M-values (TMM) method in EdgeR.
CalculateTPM function from Scater was used on TMM-normalised counts to calculate TPM values, with total exon length calculated using GenomicRanges as the sum of the non-overlapping exonic regions for a gene.
Assembly: GRCm38p6
Supplementary files format and content: Comma-separated values file containing raw counts for each sample.
Supplementary files format and content: Comma-separated values file containing TPM values for each sample.

source_name: lymph node

growth_protocol: Lymph node cell suspension from Pim1/Pim2 WT (WT) and Pim1/Pim2 double knockout (Pim dKO) mice were stimulated for 2 days with anti-CD3/anti-CD28 (0.5 µg/mL) + h-IL2 (20 ng/mL) or h-IL15 (20 ng/mL) in RPMI 1640 containing glutamine, 10%FBS, pen/strep, 50 µM 2-mercaptoethanol. Cells were washed out of activation media then split daily into fresh media and IL2 or IL15 at a density of 0.3 million live cells/mL or 0.5 million live cells/mL respectively. On day 3 of culture (1 day after removal form activation media) CD4 T cells were magnetically depleted.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen). 2 µg of total RNA was submitted per sample for library prep.
300 ng of total RNA was used for library preparation using the Illumina TruSeq Stranded mRNA sample preparation kit (15031047) as per manufacturer instructions.

treatment_protocol: On day 6 of culture CD8 T cell were cultured in fresh warm media + IL2 (20 ng/mL) or IL15 (20 ng/mL) for 2 hours prior to harvesting pellets for transcriptomic analysis.

value: lymph node

value: male

value: CD8 T cell

value: Pim1/2 dKO

value: IL15 differentiated memory T cells


title: GM12878, 200U, Cell 71

description:
200U MNase
GM-200U_071.allValidPairs.gz
GM-200U_071.hic
GM-200U_071.mcool
GM-200U_071.clean.smooth.bw
GM-200U_071_20kb_1.3dg.gz
GM-200U_071_20kb_2.3dg.gz
GM-200U_071_20kb_3.3dg.gz
GM-200U_071_20kb_4.3dg.gz
GM-200U_071_20kb_5.3dg.gz
GM-200U_071_10kb_1.3dg.gz
GM-200U_071_10kb_2.3dg.gz
GM-200U_071_10kb_3.3dg.gz
GM-200U_071_10kb_4.3dg.gz
GM-200U_071_10kb_5.3dg.gz
GM-200U_071_5kb_1.3dg.gz
GM-200U_071_5kb_2.3dg.gz
GM-200U_071_5kb_3.3dg.gz
GM-200U_071_5kb_4.3dg.gz
GM-200U_071_5kb_5.3dg.gz
GM-200U_071_20kb_1.clean.3dg.gz
GM-200U_071_20kb_2.clean.3dg.gz
GM-200U_071_20kb_3.clean.3dg.gz
GM-200U_071_20kb_4.clean.3dg.gz
GM-200U_071_20kb_5.clean.3dg.gz
GM-200U_071_10kb_1.clean.3dg.gz
GM-200U_071_10kb_2.clean.3dg.gz
GM-200U_071_10kb_3.clean.3dg.gz
GM-200U_071_10kb_4.clean.3dg.gz
GM-200U_071_10kb_5.clean.3dg.gz
GM-200U_071_5kb_1.clean.3dg.gz
GM-200U_071_5kb_2.clean.3dg.gz
GM-200U_071_5kb_3.clean.3dg.gz
GM-200U_071_5kb_4.clean.3dg.gz
GM-200U_071_5kb_5.clean.3dg.gz


title: GM12878, 200U, Cell 72

description:
200U MNase
GM-200U_072.allValidPairs.gz
GM-200U_072.hic
GM-200U_072.mcool
GM-200U_072.clean.smooth.bw
GM-200U_072_20kb_1.3dg.gz
GM-200U_072_20kb_2.3dg.gz
GM-200U_072_20kb_4.3dg.gz
GM-200U_072_20kb_5.3dg.gz
GM-200U_072_10kb_1.3dg.gz
GM-200U_072_10kb_2.3dg.gz
GM-200U_072_10kb_4.3dg.gz
GM-200U_072_10kb_5.3dg.gz
GM-200U_072_5kb_1.3dg.gz
GM-200U_072_5kb_2.3dg.gz
GM-200U_072_5kb_4.3dg.gz
GM-200U_072_5kb_5.3dg.gz
GM-200U_072_20kb_1.clean.3dg.gz
GM-200U_072_20kb_2.clean.3dg.gz
GM-200U_072_20kb_4.clean.3dg.gz
GM-200U_072_20kb_5.clean.3dg.gz
GM-200U_072_10kb_1.clean.3dg.gz
GM-200U_072_10kb_2.clean.3dg.gz
GM-200U_072_10kb_4.clean.3dg.gz
GM-200U_072_10kb_5.clean.3dg.gz
GM-200U_072_5kb_1.clean.3dg.gz
GM-200U_072_5kb_2.clean.3dg.gz
GM-200U_072_5kb_4.clean.3dg.gz
GM-200U_072_5kb_5.clean.3dg.gz


title: cell_331


title: IP_HDIP1-WT_FLAG_rep2

description: Library name: Sample 3

value: 1305-HDIP1-FLAG transformed plants (in Col-0)


title: Input_HDIP1-del-DBD_FLAG

description: Library name: Sample 4


title: IL15 CTL, Pim1/2 dKO, bio rep 2

description: Illumina TruSeq Stranded mRNA


title: cell_333

value: blood


title: cell_330


title: IL15 CTL, Pim1/2 dKO, bio rep 1

description: Illumina TruSeq Stranded mRNA


title: IL15 CTL, WT, bio rep 3

description: Illumina TruSeq Stranded mRNA


title: GM12878, 200U, Cell 69

description:
200U MNase
GM-200U_069.allValidPairs.gz
GM-200U_069.hic
GM-200U_069.mcool
GM-200U_069.clean.smooth.bw
GM-200U_069_20kb_1.3dg.gz
GM-200U_069_20kb_2.3dg.gz
GM-200U_069_20kb_3.3dg.gz
GM-200U_069_20kb_5.3dg.gz
GM-200U_069_10kb_1.3dg.gz
GM-200U_069_10kb_2.3dg.gz
GM-200U_069_10kb_3.3dg.gz
GM-200U_069_10kb_5.3dg.gz
GM-200U_069_5kb_1.3dg.gz
GM-200U_069_5kb_2.3dg.gz
GM-200U_069_5kb_3.3dg.gz
GM-200U_069_5kb_5.3dg.gz
GM-200U_069_20kb_1.clean.3dg.gz
GM-200U_069_20kb_2.clean.3dg.gz
GM-200U_069_20kb_3.clean.3dg.gz
GM-200U_069_20kb_5.clean.3dg.gz
GM-200U_069_10kb_1.clean.3dg.gz
GM-200U_069_10kb_2.clean.3dg.gz
GM-200U_069_10kb_3.clean.3dg.gz
GM-200U_069_10kb_5.clean.3dg.gz
GM-200U_069_5kb_1.clean.3dg.gz
GM-200U_069_5kb_2.clean.3dg.gz
GM-200U_069_5kb_3.clean.3dg.gz
GM-200U_069_5kb_5.clean.3dg.gz


title: cell_329


title: IP_HDIP1-WT_FLAG_rep1

description: Library name: Sample 2


title: cell_328


title: mnase_175U_Rep6

value: no treatment


title: GM12878, 200U, Cell 67

description:
200U MNase
GM-200U_067.allValidPairs.gz
GM-200U_067.hic
GM-200U_067.mcool
GM-200U_067.clean.smooth.bw
GM-200U_067_20kb_2.3dg.gz
GM-200U_067_20kb_3.3dg.gz
GM-200U_067_20kb_4.3dg.gz
GM-200U_067_20kb_5.3dg.gz
GM-200U_067_10kb_2.3dg.gz
GM-200U_067_10kb_3.3dg.gz
GM-200U_067_10kb_4.3dg.gz
GM-200U_067_10kb_5.3dg.gz
GM-200U_067_5kb_2.3dg.gz
GM-200U_067_5kb_3.3dg.gz
GM-200U_067_5kb_4.3dg.gz
GM-200U_067_5kb_5.3dg.gz
GM-200U_067_20kb_2.clean.3dg.gz
GM-200U_067_20kb_3.clean.3dg.gz
GM-200U_067_20kb_4.clean.3dg.gz
GM-200U_067_20kb_5.clean.3dg.gz
GM-200U_067_10kb_2.clean.3dg.gz
GM-200U_067_10kb_3.clean.3dg.gz
GM-200U_067_10kb_4.clean.3dg.gz
GM-200U_067_10kb_5.clean.3dg.gz
GM-200U_067_5kb_2.clean.3dg.gz
GM-200U_067_5kb_3.clean.3dg.gz
GM-200U_067_5kb_4.clean.3dg.gz
GM-200U_067_5kb_5.clean.3dg.gz


title: mnase_200U_Rep1


title: IL15 CTL, WT, bio rep 1

description: Illumina TruSeq Stranded mRNA