title: 3564_ileum_NI

tag: disease status

tag: biopsy location

value: ileum


title: 124_ileum_NI

status: Public on Apr 15 2020

type: SRA

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

department: Genetics

country: USA

institute: University of North Carolina, Chapel Hill

description:
intestinal bacteria 16S rRNA
WashU_abundance_genera.txt
WashU_abundance_species.txt

library_source: genomic

data_processing:
Library strategy: 16s rRNA seq
Illumina MiSeq software used for basecalling
Barcodes removed with in-house script
Data filtered and trimmed using DADA2
Paired reads merged using DADA2
Chimeric sequences removed using DADA2
Taxonomy assigned using RDP bacterial genome database.
Genome_build: None
Supplementary_files_format_and_content: Amplicon sequence variant (ASV) count table

molecule: genomic DNA

organism: Homo sapiens

source_name: mucosal biopsy

extract_protocol:
PCR products were normalized using a SequalPrepTM kit (Invitrogen, Carlsbad, CA), pooled, lyophilized, purified and concentrated using a DNA Clean and Concentrator Kit (Zymo, Irvine, CA). Pooled amplicons were quantified using Qubit Fluorometer 2.0 (Invitrogen, Carlsbad, CA). The pool was diluted to 4nM and denatured with 0.2 N NaOH at room temperature. The denatured DNA was diluted to 15pM and spiked with 25% of the Illumina PhiX control DNA prior to loading the sequencer
Amplicon libraries were prepared for sequencing using standard Illumina protocols

value: CD

tag: inflammation status

value: NI

tag: rutgeerts score

tag: institution

value: WashU

tag: sequence batch


title: B3-PF1

city: Stanford

first: Natalina

last: Quarto

state: CA

address: 257 Campus Drive

department: Surgery - Plastic and Reconstructive Surgery

institute: Stanford University School of Medicine

description: PF SSCs from Plate 1

library_source: transcriptomic

data_processing:
RNA-Seq alignment to the reference was performed using STAR v2.5.3a using default conditions as described in Dobin et al., Bioinformatics, 2013.
Gene counts were tabulated from STAR v2.5.3a by mapping against mouse mm9 reference and used as input to Seurat. The counts coincide with those produced by htseq-count with default parameters.
The R package Seurat v2.3.0 was used for QC, analysis, and exploration of single-cell RNA-Seq data using R v3.4.4.
Genes expressed in at least 3 cells and cells with at least 200 expressed genes were retained for further analysis. Gene expression measurements for each cell were normalized by their total expression, scaled by 10,000, and log-transformed. Following normalization, genes that varied between single cells were identified.
PCA was performed on genes to output a set of genes that most strongly defined a set of principal components. Seurat’s graph-based clustering approach was used to cluster the cells. Seurat was further used to perform tSNE clustering which placed cells with similar local neighborhoods in high-dimensional space together in low-dimensional space. Positive and negative markers in each cluster were identified by comparing genes in cells of one cluster against genes in all other cells. Only genes that were detected in at least 25% of cells in either of the two populations were tested. Violin plots were used to visualize expression of top markers in each cluster. Finally, a heatmap of the top 20 marker genes across all cells in the 4 clusters was plotted.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Cranial Posterior Frontal Suture

extract_protocol:
Total single cell RNA profiles of SSCs isolated post-natal day 3 posterior frontal (PF), sagittal (SAG), coronal (COR) sutures and the growth plate (GP) of the tibial long bone from CD-1, wild-type mice were purified using Qiagen MiRNeasy Kit (Cat #217084) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina single cell RNA seq protocols.

tag: strain

tag: tissue

value: Suture complex:bone/mesenchyme

tag: age

value: post natal day 3

tag: genotype

value: wild type

tag: cell type

value: Skeletal Stem Cell


title: Sample085

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Reads were mapped to the human genome (GrCh37) with hisat2
aligned reads were transformed with SAMtools to quantify number of reads at the gene level with HTSeq-0.6.1 using default “union” mode
counts were normalized using TMM normalization with edgeR
confounding effects were adjusted with SVA and SNM
Genome_build: GrCh37
Supplementary_files_format_and_content: tab-delimited text file include normalized read counts at the gene level for each sample

extract_protocol:
Ileal biopsy specimens were obtained via pinch endoscopy forceps. Biopsies were stored in RNAlater, and RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing (RNA-seq) libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced by the Molecular Evolution Core at GT on the Illumina NextSeq single-end 150-bp or 75-bp reads.

tag: gender

value: Female

tag: age at diagnosis

tag: ancestry

value: White

tag: diagnosis

value: Control

value: Ileum


title: 1122_ileum_NI


title: B2-PF1

description: PF SSCs from Plate 1


title: Sample084

source_name: Ulcerative Colitis_Ileum

value: Asian

value: Ulcerative Colitis


title: B12-PF1

description: PF SSCs from Plate 1


title: RNA_NTDUrea_replicate 1

city: Buffalo

first: Sarah

middle: E.

last: Walker

state: New York

address: 534 Cooke Hall, North Campus

department: Biological Sciences

institute: University at Buffalo, SUNY

data_processing:
Linker sequences (3' adapter sequence: CTGTAGGCACCATCAAT) were trimmed in the raw reads of both the ribosome footprint and RNA-seq using the Cutadapt program (version 1.1.a).
The trimmed sequences were aligned to the S. cerevisiae ribosomal database using Bowtie (version 1.1.a; (11)).
The non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae transcriptome using Bowtie (version 0.1.3.) Only uniquely mapped reads from the alignment were used for subsequent analyses. Read counts were measured using Ribocount (version 0.3.1.)
Statistical analysis of differences in ribosome footprint or RNAseq read counts, or TE values, between WT and mutant samples, urea-treated and un-treated samples was conducted using DESeq2.
Genome_build: sacCer3
Supplementary_files_format_and_content: comma-separated values (*.csv) file includes summary of riboseq and rnaseq read counts, summary of difference in Translation efficiency (TE), RNAseq, and Riboseq

organism: Saccharomyces cerevisiae

source_name: Yeast WCE

growth_protocol: Yeast were grown directly from -80 stocks on solid (2% agar) Synthetic Drop-out (SD) media (20 g/L glucose, 1.71 g/L yeast nitrogen base without amino acids, 5 g/L ammonium sulfate) at 30°C for 2-4 days, then directly cultured overnight at 30°C shaking in an overnight liquid SD culture that was used to inoculate a 500 ml culture in SD (with or without urea treatment) to 0.05 OD. This culture was harvested at 0.8 OD600 U for ribosome profiling analysis.

extract_protocol:
At an OD600 of approximately 0.8 yeast were rapidly harvested by vacuum filtering at room temperature and scraping the slurry directly into liquid nitrogen. Frozen cell pellets were then lysed in a freezer mill with added lysis buffer (20 mM Tris at pH 8, 140 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 100 µg/ml cycloheximide), treated with RNAse I, and cycloheximide-stabilized ribosome footprints purified and size-selected from the monosome peak on sucrose gradients by SDS/hot acid phenol/chlorofom and gel purification. For RNA-seq library preparation, total RNA  was isolated from the same cell extracts used for footprint library generation using the SDS/hot acid phenol and chloroform RNA extraction procedure followed by fragmentation and size selection on a denaturing gel.
Monosomes of RNase treated samples were isolated from 10-50% sucrose gradients. Ribosome-protected mRNA fragments (footprints) were purified with SDS/hot acid phenol and chloroform. Purified RNA footprints were extracted from a 15% denaturing PAGE gel, dephosphorylated and ligated to a pre-adenylated universal linker (5’-/5Phos/CTG TAG GCA CCA TCA AT/3ddC) using T4 RNA Ligase 2, truncated. rRNA was depleted using the Ribo-Zero Gold rRNA removal kit, first strand synthesis was performed with Superscript III (Life Technologies, USA) using reverse transcription primer NINI9 (5’-/5Phos/ AGA TCG GAA GAG CGT CGT GTA G GGA AAG AGT GTA GAT CTC GGT GGT CGC /SpacerC18/ CAC TCA /SpacerC18/ TTC AGA CGT GTG CTC TTC CGA TCT ATT GAT GGT GCC TAC AG), followed by circular ligation with CircLigase (Epicentre) and PCR amplification of the cDNA library using primer NINI2 (AAT GAT ACG GCG ACC ACC GAG ATC TAC AC) and primer with barcode (CAA GCA GAA GAC GGC ATA CGA GAT XXX XXX GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG), where XXXXXX denotes a six-nucleotide-barcode used to distinguish samples run in the same lane. For RNA-seq, total RNA was isolated from the same cell extracts using SDS/hot acid phenol/chloroform extraction. The Ribo-Zero Gold Yeast kit was used to remove rRNA, and total RNA was randomly fragmented by incubating for 20 minutes at 95°C in fragmentation buffer ([pH 9.2] 10 mM sodium carbonate, 90 mM sodium bicarbonate, 2 mM EDTA). RNA was then precipitated and fragments of 40–60 nt were purified from a denaturing PAGE gel, and library generation carried out as above. Ribo-Seq and RNA-Seq were performed for two independent cultures for each condition (WT and ∆ntd cells grown in SD both with and without 3% Urea), and the 16 indexed libraries sequenced in 2 lanes on an Illumina HiSeq instrument by Genewiz.

treatment_protocol: For assays with urea treatment, yeast cells from an overnight culture in SD media were diluted to an OD600 of 0.05 in SD media or SD media supplemented with 3% urea, and allowed to grow to mid-log phase with vigorous shaking at 30°C, unless otherwise noted.

value: tif3{delta}ntd strain

value: mutant

tag: treatment

value: 3% Urea


title: RNA_NTDSD_replicate 1

value: No treatment


title: Sample083

value: Male


title: 93_ileum_NI

description:
intestinal bacteria 16S rRNA
UNC_abundance_genera.txt
UNC_abundance_species.txt

value: CD

value: ileum

value: NI

value: UNC


title: RNA_NTDSD_replicate 2


title: C10-PF1

description: PF SSCs from Plate 1

value: Suture complex:bone/mesenchyme

value: post natal day 3

value: wild type


title: RNA_WTUrea_replicate 2


title: 77_ileum_NI


title: Sample082

source_name: Crohn's Disease_Ileum

value: Female

value: White

value: Crohn's Disease


title: 76_ileum_NI


title: Sample081

value: Asian

value: Ileum


title: DMSO replicate 1

first: Ian

middle: Daniel

last: Ferguson

address: 265 Campus Dr

department: Cancer Biology PhD program

institute: Stanford University

data_processing:
HISAT v2.0.4
Bowtie v2.2.5
RSEM v1.2.12
Supplementary_files_format_and_content: TPM (transcripts per million) values for Samples 1-4 with gene names and NCBI Reference Sequence IDs

growth_protocol: MM.1S cells were grown in RPMI-1640 medium supplemented with 10% FBS, PenStrep, and 2mM glutamine.

extract_protocol:
RNA extraction from flash frozen cell pellets (5e6 cells) was peformed by BGI (Beijing Genomics Institute)
Libraries were constructed by BGI.
BGISEQ-500 platform, RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit

treatment_protocol: Cells were treated with 350nM JG342 or DMSO for 26 hours.

tag: cell line

value: multiple myeloma cell line

value: DMSO


title: RNA_WTUrea_replicate 1

value: 3% Urea


title: 57_ileum_NI

tag: disease status


title: Sample080

value: Hispanic


title: B10-PF1

description: PF SSCs from Plate 1

value: Skeletal Stem Cell


title: Sample086

value: Male

value: Control


title: A7-PF1

description: PF SSCs from Plate 1


title: 51_ileum_NI

value: CD

tag: biopsy location

value: ileum

value: NI


title: RNA_NTDUrea_replicate 2

value: tif3{delta}ntd strain

value: mutant


title: RNA_WTSD_replicate 1

value: wild type

value: No treatment


title: A5-PF1

description: PF SSCs from Plate 1

value: Suture complex:bone/mesenchyme

value: post natal day 3


title: RNA_WTSD_replicate 2


title: Ribo_NTDUrea_replicate 2

description: ribosome footprint

data_processing:
Library strategy: Ribo-seq
Linker sequences (3' adapter sequence: CTGTAGGCACCATCAAT) were trimmed in the raw reads of both the ribosome footprint and RNA-seq using the Cutadapt program (version 1.1.a).
The trimmed sequences were aligned to the S. cerevisiae ribosomal database using Bowtie (version 1.1.a; (11)).
The non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae transcriptome using Bowtie (version 0.1.3.) Only uniquely mapped reads from the alignment were used for subsequent analyses. Read counts were measured using Ribocount (version 0.3.1.)
Statistical analysis of differences in ribosome footprint or RNAseq read counts, or TE values, between WT and mutant samples, urea-treated and un-treated samples was conducted using DESeq2.
Genome_build: sacCer3
Supplementary_files_format_and_content: comma-separated values (*.csv) file includes summary of riboseq and rnaseq read counts, summary of difference in Translation efficiency (TE), RNAseq, and Riboseq


title: B11-PF1

description: PF SSCs from Plate 1


title: 44000_ileum_NI

tag: inflammation status

value: UNC


title: A2-PF1

description: PF SSCs from Plate 1


title: Sample079

value: Asian

value: Ulcerative Colitis

value: Ileum


title: 45_ileum_NI

tag: rutgeerts score


title: Ribo_NTDUrea_replicate 1

description: ribosome footprint

value: 3% Urea


title: Sample077

value: White

value: Crohn's Disease


title: Sample078

value: Male

value: Control


title: A10-PF1

description: PF SSCs from Plate 1

value: Skeletal Stem Cell


title: 43600_ileum_NI

value: CD

value: ileum

value: NI

tag: institution


title: Sample076

value: Female


title: Sagittal (Sag)

data_processing:
RNA-Seq alignment to the reference was performed using STAR v2.5.1b using default conditions as described in Dobin et al., Bioinformatics, 2013.
Normalized transcript abundances (FPKM) were calculated and differential expression analyses for RNA-Seq were performed using the Cuffdiff program from the Cufflinks v2.2.1 suite using default conditions as described in Trapnell et al., Nature Biotechnology, 2013. The bias detection and correction algorithm was used to significantly improve accuracy of transcript abundance estimates as described in Roberts et al., Genome Biology, 2011. The initial estimation procedure was used to more accurately weight reads mapping to multiple locations in the genome.
Exploration, analysis and visualization of Cuffdiff results were performed using the CummeRbund v2.12.1 R package installed in R v3.2.2 as described in Trapnell et al., Nature Protocols, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Cranial Sagittal Suture

extract_protocol:
Total RNA isolated from post-natal day 3 posterior frontal (PF), sagittal (Sag), coronal (Cor) sutures and the growth plate (GP) of the tibial long bone from CD-1, wild-type mice were purified using Qiagen MiRNeasy Kit (Cat #217084) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wild type


title: Ribo_NTDSD_replicate 1

description: ribosome footprint

value: tif3{delta}ntd strain

value: mutant

value: No treatment


title: Sample075


title: 42500_ileum_NI

value: UNC

tag: sequence batch


title: A9-PF1

description: PF SSCs from Plate 1

tag: strain

value: Suture complex:bone/mesenchyme

value: post natal day 3


title: Ribo_WTUrea_replicate 2

description: ribosome footprint

value: 3% Urea


title: Ribo_WTUrea_replicate 1

description: ribosome footprint


title: Growth Plate (GP)

source_name: Tibial Longbone Growth Plate

tag: tissue

value: Bone


title: Coronal (Cor)

source_name: Cranial Coronal Suture

tag: age


title: 42400_ileum_NI


title: 42200_ileum_NI


title: Posterior Frontal (PF)

tag: genotype


title: Sample072

value: White

value: Crohn's Disease

value: Ileum


title: Ribo_WTSD_replicate 2

description: ribosome footprint


title: Ribo_NTDSD_replicate 2

description: ribosome footprint


title: Sample071

value: Male

value: African American


title: Ribo_WTSD_replicate 1

description: ribosome footprint


title: 42100_ileum_NI

value: CD

value: ileum


title: 41700_ileum_NI

value: NI


title: Sample070

value: Female


title: CIC_L_L_Cre_plus_B

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: P1 CIC KO brain

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: mm9
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM value of each gene in each sample

source_name: Mouse brain

growth_protocol: We harvested mouse brains at postnatal day 1.

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: developmental stage

value: Postnatal 1 day

tag: mouse genotype

value: Nes-Cre;CIClox/lox


title: 41400_ileum_NI

value: UNC


title: 42600_ileum_NI


title: CIC_L_L_Cre_minus_B

description: P1 WT brain

value: Nes-Cre;CIC+/+


title: Sample069

tag: gender

tag: age at diagnosis

value: Asian

value: Control


title: Sample074

tag: ancestry

value: Hispanic

tag: diagnosis

value: Ulcerative Colitis


title: 41_ileum_NI


title: CIC_L_L_Cre_minus_A

description: P1 WT brain


title: Sample073

value: Multiracial


title: Sample067

value: White

value: Crohn's Disease

value: Ileum


title: 40100_ileum_NI

value: CD


title: Sample068

value: African American


title: Uninfected sunflower rep3

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Read count per gene were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: Helianthus annuus HanXRQr1.0; Beta vulgaris BETVU1.2.2; Ricinus communis RICCO1.1; Phaseolus vulgaris PVULG_BAT93
Supplementary_files_format_and_content: tab-delimited text files include total count of uniquely mapped reads per gene for each Sample

organism: Helianthus annuus

source_name: ~20mm leaf disk from uninfected plants

growth_protocol: Plants were  grown in Jiffy pots under controlled conditions at 23°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The edge and center of developed mycelial colonies (~20 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

value: XRQ

value: Leaves of 5-week old plants

tag: infection

value: control (uninfected)


title: X080618.Healthy.ppLN.cDC1

city: Philadelphia

first: Jeffrey

middle: Howard

last: Lin

state: PA

address: 3400 Civic Center Blvd

department: Immunology Graduate Group

institute: University of Pennsylvania

data_processing:
Salmon Sailfish v0.7.6 pseudoalignment
Genome_build: mm10
Supplementary_files_format_and_content: sailfish output (sf files)

source_name: Peri-pancreatic lymph node

extract_protocol:
Qiagen Rneasy Plus Micro Kit, 74034
NEBNext Ultra II Directional RNA library prep kit, E7760S

tag: neoplasia stage

value: Healthy


title: X073018.Healthy.ppLN.cDC1


title: 38_ileum_NI

tag: disease status

tag: biopsy location

value: ileum

value: NI


title: Sample065

value: Female


title: 15_ileum_NI

tag: inflammation status

tag: rutgeerts score

value: UNC


title: Sample066

value: Male

value: Control


title: CIC_L_L_Cre_plus_A

description: P1 CIC KO brain

value: Brain

value: Postnatal 1 day

value: Nes-Cre;CIClox/lox


title: Uninfected sunflower rep2


title: X072618.PanIN.ppLN.cDC1

value: PanIN


title: 149_ileum_NI

tag: institution

tag: sequence batch


title: X071718.PanIN.ppLN.cDC1


title: X071618.Tumor.ppLN.cDC1

value: Tumor


title: Sample064

tag: tissue

value: Ileum


title: 145_ileum_NI

value: CD


title: 138_ileum_NI


title: 144_ileum_NI


title: Uninfected common bean rep3

organism: Phaseolus vulgaris

tag: accession


title: Sample063

value: White


title: X062918.PanIN.ppLN.cDC1


title: X062918.Tumor.ppLN.cDC1


title: X070618.Tumor.ppLN.cDC1


title: Uninfected sunflower rep1

tag: genotype

value: XRQ

value: Leaves of 5-week old plants


title: Sample062

value: African American

value: Crohn's Disease


title: 137_ileum_NI

value: ileum

value: NI


title: Uninfected common bean rep2

value: control (uninfected)


title: Sample060

value: Male


title: 092518-NoTumor-NoCD40-iLN-cDC1

data_processing:
Salmon Sailfish 0.7.6 pseudoalignment
Genome_build: mm10
Supplementary_files_format_and_content: sailfish output (sf files)

source_name: Inguinal LN

tag: tumor

value: no

tag: cd40 agonist

tag: group


title: X062918.Healthy.ppLN.cDC1

value: Healthy


title: Sample059

tag: gender

value: Female

tag: age at diagnosis

value: Ulcerative Colitis


title: Uninfected common bean rep1


title: 96_colon_NI

value: colon

value: UNC


title: 091418-Tumor-NoCD40-iLN-cDC1

value: yes


title: 129_ileum_NI

value: CD


title: 92_colon_NI


title: Sample057

tag: ancestry

tag: diagnosis

value: Ileum


title: 90_colon_NI


title: 091418-Tumor-CD40-iLN-cDC1


title: Sample058

value: White


title: Sample061

value: Control


title: 091418-NoTumor-CD40-iLN-cDC1


title: Sample055

value: African American


title: 86_colon_NI


title: 091318-Tumor-NoCD40-iLN-cDC1


title: Sample054

value: Crohn's Disease


title: 091318-Tumor-CD40-iLN-cDC1


title: 81_colon_NI


title: Sample053


title: 51_colon_NI


title: 091318-NoTumor-NoCD40-iLN-cDC1


title: Sample052


title: 091318-NoTumor-CD40-iLN-cDC1


title: 43300_colon_NI


title: Sample051


title: Control EPC-derived endothelial cells - basal - 10

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

description:
Gene expression from control EPC-derived endothelial cells - basal
A42_(HuEx-1_0-st-v2).CEL

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip HumanExon1.0ST and chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were RMA normalized with Bioconductor using Version18 of Brain Array Human Exon1.0 CDF file.

label: Biotin

source_name: EC derived from circulating EPCs_healthy control_basal conditions

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

tag: subject status

value: Healthy control

value: peripheral blood

tag: cell type

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

tag: treatment

value: unstimulated


title: 091218-Tumor-NoCD40-iLN-cDC1

value: no


title: Control EPC-derived endothelial cells - hypoxia - 11

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
A43_(HuEx-1_0-st-v2).CEL

source_name: EC derived from circulating EPCs_healthy control_hypoxic exposure

value: hypoxic exposure


title: Sample050

value: Male


title: Control EPC-derived endothelial cells - hypoxia - 9

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
34h_(HuEx-1_0-st-v2).CEL


title: Control EPC-derived endothelial cells - basal - 11

description:
Gene expression from control EPC-derived endothelial cells - basal
A44_(HuEx-1_0-st-v2).CEL


title: Sample056

value: Female


title: 091218-Tumor-CD40-iLN-cDC1


title: 43100_colon_NI

tag: disease status

tag: biopsy location

value: colon

tag: inflammation status

value: NI


title: Control EPC-derived endothelial cells - basal - 9

description:
Gene expression from control EPC-derived endothelial cells - basal
34_(HuEx-1_0-st-v2).CEL


title: Control EPC-derived endothelial cells - hypoxia - 8

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
21h_(HuEx-1_0-st-v2).CEL


title: 091218-NoTumor-NoCD40-iLN-cDC1


title: Control EPC-derived endothelial cells - hypoxia - 10

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
A41_(HuEx-1_0-st-v2).CEL


title: 40500_colon_NI

tag: institution

value: UNC

tag: sequence batch


title: Sample048

tag: tissue


title: 42900_colon_NI

value: CD


title: 73_colon_NI

tag: rutgeerts score


title: Sample049

value: Ileum


title: Control EPC-derived endothelial cells - hypoxia - 7

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
20_(HuEx-1_0-st-v2).CEL


title: 40200_colon_NI


title: Sample047

value: Ulcerative Colitis


title: Control EPC-derived endothelial cells - basal - 8

description:
Gene expression from control EPC-derived endothelial cells - basal
21_(HuEx-1_0-st-v2).CEL


title: 040618_TdLN_CD40_CD11c

tag: tumor

value: yes

tag: disease state

value: Tumor-Draining LN


title: Control EPC-derived endothelial cells - hypoxia - 6

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
19H_(HuEx-1_0-st-v2).CEL


title: Control EPC-derived endothelial cells - basal - 7

description:
Gene expression from control EPC-derived endothelial cells - basal
20_(HuEx-1_0-st-v2).CEL


title: 040618_TdLN_CD11c

tag: cd40 agonist


title: 21_colon_NI


title: Sample046

tag: gender

value: MULT


title: Sample045

tag: age at diagnosis

value: African American

value: Crohn's Disease


title: 77_ileum_I

value: ileum

value: I


title: 091218-NoTumor-CD40-iLN-cDC1

value: no

tag: group


title: Sample044

tag: ancestry

tag: diagnosis


title: 152_colon_NI


title: Control EPC-derived endothelial cells - basal - 6

description:
Gene expression from control EPC-derived endothelial cells - basal
19_(HuEx-1_0-st-v2).CEL

tag: subject status

value: Healthy control

value: peripheral blood

tag: cell type

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

value: unstimulated


title: 033118_TdLN_CD40_CD11c


title: Sample043

value: Female

value: White

value: Control


title: Sample041

value: Ileum


title: 033118_Healthy_iLN_CD11c

value: Healthy


title: 73_ileum_I

tag: disease status

value: CD

value: UNC


title: 57_ileum_I

tag: biopsy location


title: Sample042

value: Male


title: 033118_TdLN_CD11c

value: yes

value: Tumor-Draining LN


title: 51_ileum_I

value: ileum

tag: inflammation status


title: 040618_Healthy_iLN_CD11c


title: 032418_TdLN_CD40_CD11c


title: Control EPC-derived endothelial cells - basal - 5

description:
Gene expression from control EPC-derived endothelial cells - basal
YA5.CEL

tag: treatment


title: Control EPC-derived endothelial cells - basal - 4

description:
Gene expression from control EPC-derived endothelial cells - basal
YA4.CEL


title: 032418_TdLN_CD11c


title: Control EPC-derived endothelial cells - hypoxia - 5

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
YA5H.CEL

value: hypoxic exposure


title: 44000_ileum_I

value: I

tag: institution

tag: sequence batch


title: Control EPC-derived endothelial cells - hypoxia - 4

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
YA4H.CEL

value: Healthy control

tag: tissue


title: Control EPC-derived endothelial cells - hypoxia - 3

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
YA3H.CEL

value: peripheral blood


title: Sample039

value: African American

value: Crohn's Disease


title: 032418_Healthy_iLN_CD11c

tag: tumor

value: no


title: 031618_TdLN_CD40_CD11c

tag: disease state


title: 43300_ileum_I

description:
intestinal bacteria 16S rRNA
UNC_abundance_genera.txt
UNC_abundance_species.txt

tag: rutgeerts score


title: Control EPC-derived endothelial cells - basal - 3

description:
Gene expression from control EPC-derived endothelial cells - basal
YA3.CEL

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

value: unstimulated


title: Sample037

tag: gender

value: Female

value: Ileum


title: 42600_ileum_I

value: CD


title: Sample038

tag: age at diagnosis

value: White

value: Control


title: 42400_ileum_I

value: UNC


title: Sample036


title: 031618_TdLN_CD11c

value: yes

tag: cd40 agonist

value: Tumor-Draining LN


title: 42200_ileum_I

value: ileum


title: Control EPC-derived endothelial cells - hypoxia - 2

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
YA2H.CEL

value: hypoxic exposure


title: 031618_Healthy_iLN_CD11c

value: Healthy


title: Sample040

value: Male

tag: ancestry


title: 29_colon_NI

value: colon

value: NI


title: Control EPC-derived endothelial cells - hypoxia - 1

description:
Gene expression from control EPC-derived endothelial cells - hypoxia
YA1H.CEL

value: Healthy control

value: peripheral blood


title: Sample035

value: African American

tag: diagnosis

value: Ulcerative Colitis


title: Nudt21+/- 3

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Raw reads were trimmed using fastp.
PolyA tails were trimmed using hts_PolyATTrim.
Trimmed reads were aligned to the reference genome using bowtie2.
Samtools were used to sort, convert and index alignment files.
Deeptools were used to generate bigwig files.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: left hippocampus

growth_protocol: We housed the mice in an AAALAS-certified level three facility on a 14-hour light cycle with ad libitum access to standard chow and water.

extract_protocol:
We dissected the left hippocampuses of 46-week-old Nudt21+/- mice and their wild-type littermates. We immediately flash froze the tissue in liquid nitrogen and stored it temporarily at -80°C. We later homogenized the tissue in TRIzol Reagent (ThermoFisher Scientific) with the Polytron PT 10-35 GT (Kinematica). Lastly, we isolated the RNA by chloroform phase separation, precipitated it with 2-propanol, and washed it with 75% ethanol. We eluted the purified RNA in water.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: We generated C57BL/6J Nudt21flox/flox mice by inserting loxP sites flanking exons 2 and 3 of Nudt21 by homologous recombination in embryonic stem cells (Ozgene). We then crossed male Nudt21flox/flox mice with female C57BL/6J Sox2-Cre hemizygous mice (B6.Cg-Edil3Tg(Sox2-cre)1Amc/J) to obtain Nudt21+/- mice. All oocytes from Sox2-Cre hemizygous females have Cre and can induce cre/lox recombination, even those haploid oocytes that do not have the Cre transgene. We confirmed successful cre/lox recombination by Sanger sequencing. To eliminate potential confounding from recombination mosaicism, we first crossed the Nudt21+/- F1 generation with wild-type C57BL/6J mice (Jackson Lab) before establishing mating pairs with F2s to generate experimental cohorts.

tag: strain/background

tag: genotype

tag: age

value: 46 weeks

value: left hippocampus


title: Sample034

value: Female

value: Crohn's Disease

value: Ileum


title: 42100_ileum_I

tag: disease status

value: CD

tag: biopsy location

value: I

value: UNC


title: Sample033


title: Nudt21+/- 2


title: Control EPC-derived endothelial cells - basal - 1

description:
Gene expression from control EPC-derived endothelial cells - basal
YA1.CEL

tag: subject status

tag: cell type

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

tag: treatment

value: unstimulated


title: Nudt21+/- 1

tag: tissue


title: 41700_ileum_I

value: ileum

tag: inflammation status

tag: institution

tag: sequence batch


title: Sample032

tag: gender

value: Male

value: White

value: IBS


title: Wild type 3

value: Wild type


title: RA EPC-derived endothelial cells - hypoxia - 18

description:
Gene expression from RA-derived endothelial cells - hypoxia
139_(HuEx-1_0-st-v2).CEL

source_name: EC derived from circulating EPCs_RA_hypoxic exposure

value: Rheumatoid arthritis

value: peripheral blood

value: hypoxic exposure


title: RA EPC-derived endothelial cells - basal - 18

description:
Gene expression from RA-derived endothelial cells -basal
A40_(HuEx-1_0-st-v2).CEL

source_name: EC derived from circulating EPCs_RA_basal conditions


title: 41_ileum_I

source_name: mucosal biopsy

tag: rutgeerts score


title: Sample031

tag: age at diagnosis


title: Control EPC-derived endothelial cells - basal - 2

description:
Gene expression from control EPC-derived endothelial cells - basal
YA2.CEL

value: Healthy control


title: Sample029

value: Female

tag: ancestry

value: Control


title: Sample030

value: African American

tag: diagnosis

value: Crohn's Disease

value: Ileum


title: Wild type 1

tag: strain/background

value: 46 weeks

value: left hippocampus


title: RA EPC-derived endothelial cells - hypoxia - 17

description:
Gene expression from RA-derived endothelial cells - hypoxia
A37_(HuEx-1_0-st-v2).CEL

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)


title: 29_ileum_I

value: CD

value: ileum

value: I

value: UNC


title: Wild type 2

tag: genotype

value: Wild type


title: RA EPC-derived endothelial cells - basal - 17

description:
Gene expression from RA-derived endothelial cells -basal
A38_(HuEx-1_0-st-v2).CEL

value: Rheumatoid arthritis

value: unstimulated


title: Injury_6

city: Edinburgh

first: Leah

last: Herrgen

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: This sample and two others showed a high duplication and low mapping rate during bioinformatics QC. The high level of variation in these three samples would have caused signal from the remaining samples to be overwhelmed. They were therefore excluded from downstream analysis.

data_processing:
Reads were trimmed using Cutadapt (version cutadapt-1.9.dev2). Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit (AGATCGGAAGAGC). Reads after trimming were required to have a minimum length of 35.
The reference used for mapping was the Danio rerio (GRCz10) genome from Ensembl. The annotation used for counting was the standard GTF-format annotation for that reference (annotation version 84).
Reads were aligned to the reference genome using STAR (version 2.5.2b) specifying paired-end reads and the option --outSAMtype BAM Unsorted. All other parameters were left at default.
Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene_id in the reference genome using featureCounts (version 1.5.1). Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices.
The raw counts table was filtered to remove genes consisting predominantly of near-zero counts, filtering on counts per million (CPM) to avoid artefacts due to library depth. Specifically, a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples, corresponding to the smallest sample group as defined by Group, once any samples were removed (where applicable).
Reads were normalised using the weighted trimmed mean of M-values method, passing ‘TMM’ as the method to the calcNormFactors method of edgeR.
A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data, while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples (Injury_3, Injury_5 and Injury_6) were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed, and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury_3, Injury_5 and Injury_6 were removed, and filtering and normalisation re-performed, prior to generation of subsequent plots and downstream analysis.
Differential analysis was carried out with edgeR (version 3.20.1). Fold changes were estimated as per the default behaviour of edgeR, to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi-likelihood (QL) F-test.
Genome_build: GRCz10
Supplementary_files_format_and_content: A comma-separated value file of normalised gene-wise counts, gene-wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.

organism: Danio rerio

source_name: Macrophage-lineage cells

extract_protocol:
RNA was extracted from sorted cells using a RNeasy Plus Micro kit (Qiagen). RNA was reverse transcribed and amplified using an Ovation RNA-Seq System V2 (NuGEN) with an input of at least 500 ng RNA per sample.
Libraries were prepared using a manual TruSeq DNA Nano gel free library kit (Illumina).

treatment_protocol: Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 hours post injury (hpi), sham and injured larvae were anaesthesised, larval heads were transected, the tissue was homogenised, and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.

tag: age

value: 4 days post fertilisation


title: Sample028

value: Male


title: RA EPC-derived endothelial cells - basal - 16

description:
Gene expression from RA-derived endothelial cells -basal
A36_(HuEx-1_0-st-v2).CEL

value: peripheral blood


title: 41800_ileum_I

tag: disease status


title: RA EPC-derived endothelial cells - hypoxia - 16

description:
Gene expression from RA-derived endothelial cells - hypoxia
A35_(HuEx-1_0-st-v2).CEL

value: hypoxic exposure


title: Injury_5


title: Sample027

value: Female

value: White

value: Control


title: 15_ileum_I

tag: biopsy location


title: RA EPC-derived endothelial cells - basal - 15

description:
Gene expression from RA-derived endothelial cells -basal
A34_(HuEx-1_0-st-v2).CEL

tag: subject status


title: Injury_4


title: 147_ileum_I


title: 40100_ileum_I


title: Sample025

source_name: Ulcerative Colitis_Ileum

value: African American

value: Ulcerative Colitis

value: Ileum


title: 144_ileum_I

value: CD


title: Injury_2


title: 143_ileum_I

value: ileum


title: 138_ileum_I

value: I


title: 21_ileum_I

value: UNC


title: Injury_1


title: Injury_3


title: Sham_6


title: Sample023

value: Crohn's Disease


title: 137_ileum_I


title: Sample022


title: Sham_5


title: RA EPC-derived endothelial cells - hypoxia - 13

description:
Gene expression from RA-derived endothelial cells - hypoxia
A29 (HuEx-1_0-st-v2).CEL

value: Rheumatoid arthritis

tag: cell type

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)


title: RA EPC-derived endothelial cells - basal - 13

description:
Gene expression from RA-derived endothelial cells -basal
A30_(HuEx-1_0-st-v2).CEL

tag: treatment

value: unstimulated


title: Sample021

tag: tissue


title: RA EPC-derived endothelial cells - hypoxia - 15

description:
Gene expression from RA-derived endothelial cells - hypoxia
A33_(HuEx-1_0-st-v2).CEL


title: Sample024


title: Sham_4

value: 4 days post fertilisation


title: RA EPC-derived endothelial cells - basal - 12

description:
Gene expression from RA-derived endothelial cells -basal
A28_(HuEx-1_0-st-v2).CEL

value: peripheral blood


title: RA EPC-derived endothelial cells - hypoxia - 12

description:
Gene expression from RA-derived endothelial cells - hypoxia
A27_(HuEx-1_0-st-v2).CEL

value: hypoxic exposure


title: Sample026

value: Female


title: 129_ileum_I

description:
intestinal bacteria 16S rRNA
UNC_abundance_genera.txt
UNC_abundance_species.txt

tag: inflammation status


title: RA EPC-derived endothelial cells - basal - 14

description:
Gene expression from RA-derived endothelial cells -basal
A32_(HuEx-1_0-st-v2).CEL


title: Sample020

value: White


title: RA EPC-derived endothelial cells - hypoxia - 14

description:
Gene expression from RA-derived endothelial cells - hypoxia
A31_(HuEx-1_0-st-v2).CEL


title: Sample019

value: Hispanic

value: Control


title: 42900_colon_I

value: colon

tag: institution


title: Sham_2


title: 40200_colon_I

tag: sequence batch


title: RA EPC-derived endothelial cells - basal - 11

description:
Gene expression from RA-derived endothelial cells -basal
A26_(HuEx-1_0-st-v2).CEL


title: RA EPC-derived endothelial cells - basal - 10

description:
Gene expression from RA-derived endothelial cells -basal
A24_(HuEx-1_0-st-v2).CEL


title: 135_ileum_I


title: Sample018

tag: gender

value: Male

value: African American

value: Ileum


title: RA EPC-derived endothelial cells - hypoxia - 11

description:
Gene expression from RA-derived endothelial cells - hypoxia
A25_(HuEx-1_0-st-v2).CEL


title: Sham_1


title: 79_colon_I

value: CD

value: I


title: RA EPC-derived endothelial cells - hypoxia - 10

description:
Gene expression from RA-derived endothelial cells - hypoxia
A23_(HuEx-1_0-st-v2).CEL


title: 76_colon_I

tag: rutgeerts score

value: UNC


title: 41400_colon_I


title: Sample015

tag: age at diagnosis

value: Crohn's Disease


title: RA EPC-derived endothelial cells - hypoxia - 9

description:
Gene expression from RA-derived endothelial cells - hypoxia
A19_(HuEx-1_0-st-v2).CEL

value: Rheumatoid arthritis

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)


title: Sample016

tag: ancestry

value: Ulcerative Colitis


title: Sham_3

value: 4 days post fertilisation


title: 41300_colon_I


title: Sample014

tag: diagnosis


title: RA EPC-derived endothelial cells - basal - 9

description:
Gene expression from RA-derived endothelial cells -basal
A20_(HuEx-1_0-st-v2).CEL

value: peripheral blood

value: unstimulated


title: ∆eed_EPR-1 N7539 DAM-ID-seq

city: Eugene

first: Elizabeth

middle: Toomey

last: Wiles

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

description: CTCTGGAT_N7539_eed_NCU07505-DAM_122018_S61_L008_R1_001

data_processing:
Library strategy: DamID-seq
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy {Afgan:2018gf} were used to map mRNA-sequencing reads (intron size < 1kb) {Dobin:2012fg} against the corrected N. crassa OR74A (NC12) genome {Galazka:2016cm}, count the number of reads per gene {Dobin:2012fg} and determine differentially expressed genes with DESeq2 {Love:2014ka}.
DamID-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type, ∆set-7 (both from Klocko et al. 2016; GSE82222) and ∆epr-1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: DamID-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Preparation of N6-methyladenine-containing DNA for sequencing was performed using a previously reported procedure {Bernstein:2012wx} with the following modifications: 5 μg of genomic DNA from N. crassa strains expressing a Dam fusion was digested with 1 μL of DpnI (NEB, 20 units/μL); ligation to primer 5050 was carried out overnight at 16 °C; amplification reactions of ligated DNA with primer 5051 were performed in triplicate, contained 5 μL dNTPs, and an additional PCR cycle was added to the 2nd and 3rd phase of the PCR protocol (4 and 18 cycles respectively); 3 μg of pooled, amplified DNA was sheared using a Bioruptor (Diagenode) twice on high for 10 minutes (30 seconds on/off) at 4 °C; biotinylated DNA was purified using 250 μL slurry of streptavidin-agarose beads (Sigma).


title: ∆eed_EPR-1 N7938 DAM-ID-seq

description: GCTACTCT_N7538_eed_NCU07505-DAM_122018_S60_L008_R1_001


title: EPR-1PHD N7900 DAM-ID-seq

description: AGATCGTC_N7900_WT_NCU07505_W292A-DAM_122018_S62_L008_R1_001

value: mat a; epr-1W292A::10xGly::Dam::nat-1


title: EPR-1PHD N7901 DAM-ID-seq

description: GCTCAGTT_N7901_WT_NCU07505_W292A-DAM_122018_S63_L008_R1_001


title: RA EPC-derived endothelial cells - hypoxia - 8

description:
Gene expression from RA-derived endothelial cells - hypoxia
A17_(HuEx-1_0-st-v2).CEL

value: hypoxic exposure


title: Sample013

source_name: Crohn's Disease_Ileum


title: 40500_colon_I


title: RA EPC-derived endothelial cells - basal - 7

description:
Gene expression from RA-derived endothelial cells -basal
A16_(HuEx-1_0-st-v2).CEL


title: RA EPC-derived endothelial cells - basal - 8

description:
Gene expression from RA-derived endothelial cells -basal
A18_(HuEx-1_0-st-v2).CEL


title: Sample012

value: White


title: Sample017


title: 38_colon_I

value: colon


title: 140_colon_I


title: Sample011

value: Female


title: EPR-1 N7526 DAM-ID-seq

description: AGAGTCCA_N7526_WT_NCU07505-DAM_122018_S59_L008_R1_001

value: mat a; epr-1WT::10xGly::Dam::nat-1


title: EPR-1 N7525 DAM-ID-seq

description: GTAGCGTA_N7525_WT_NCU07505-DAM_122018_S58_L008_R1_001

value: mat A; epr-1WT::10xGly::Dam::nat-1


title: RA EPC-derived endothelial cells - hypoxia - 7

description:
Gene expression from RA-derived endothelial cells - hypoxia
A15_(HuEx-1_0-st-v2).CEL


title: 42_ileum_NI

description:
intestinal bacteria 16S rRNA
UNC_abundance_genera.txt
UNC_abundance_species.txt

value: nonIBD

value: ileum

value: NI


title: ∆epr-1 N7479 RNA-seq

description: ACCTCAGT_7479_deltaNCU07505_RNAseq_120117

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy {Afgan:2018gf} were used to map mRNA-sequencing reads (intron size < 1kb) {Dobin:2012fg} against the corrected N. crassa OR74A (NC12) genome {Galazka:2016cm}, count the number of reads per gene {Dobin:2012fg} and determine differentially expressed genes with DESeq2 {Love:2014ka}.
DamID-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type, ∆set-7 (both from Klocko et al. 2016; GSE82222) and ∆epr-1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: DamID-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAseI, amplification grade (Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems).

value: mat A; {delta}epr-1::hph


title: Sample010

source_name: Unclassified IBD_Ileum

value: Male

value: Unclassified IBD

value: Ileum


title: Sample009

value: Ulcerative Colitis


title: Pool of RNA from three clones, serum starved, Dox and auxin treated

city: New York

first: Alan

last: Gerber

address: 1230 York Avenue

institute: The Rockefeller University

description: Gene expression data from 3 clones expressing an auxin-degradable RPB1 serum starved for 20hrs total. After 6 hours starvation, cells were treated for 12 hrs with doxycycline, to induce the plant ubiquitin ligase OsTIR1, and 2 hrs with auxin to degrade the tagged RPB1.

hyb_protocol: Hybridization was performed at 45 degrees Celsius for 16 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The data expressed as CEL files were normalized using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) algorithm with Transcriptome Analysis Console (TAC) 4.0 (Thermofisher)
The .chp files contain Expression (Gene + Exon) analysis results. However, only gene-level data were used for subsequent analysis.
The supplementary file HTA-2_0.na36.hg19.probeset.csv includes the annotation for all probe sets included in the chp files.

label: biotin

source_name: Pool of total RNAs prepared from 3 clones serum starved and treated with Dox (12hrs) and auxin (2hrs)

label_protocol: RNA samples were processed and prepared for whole transcriptome expression analysis using the GeneChip WT PLUS Reagent Kit (Thermofisher 902280)

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and Pen-Strep. For starvation experiments, the culture medium was replaced with DMEM supplemented with Pen-Strep only. For serum stimulation experiments, 20% FCS was directly added to the serum-free culture medium.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated for 12 hrs with water (vehicle, control condition) or doxycycline (Dox) or Dox for 12 hrs and auxin for 2 hrs (DA) in presence of serum or after 6hrs starvation. Stimulation with serum was performed for 60 min with serum starved cells (see samples description).

tag: cell line

value: HEK293-tagged RPB1

value: Dox and auxin starved


title: ∆epr-1 N7491 RNA-seq

description: AACAACCG_7491_deltaNCU07505_RNAseq_120117

tag: genotype

value: mat a; {delta}epr-1::hph


title: Pool of RNA from three clones, serum starved, Dox and auxin treated, stimulated with serum 60 min

description: Gene expression data from 3 clones expressing an auxin-degradable RPB1 serum starved for 20hrs total followed by 1hr stimulation with 20% FCS. After 6 hours starvation, cells were treated for 12 hrs with doxycycline, to induce the plant ubiquitin ligase OsTIR1, and 2 hrs with auxin to degrade the tagged RPB1 and finally stimulated with serum.

source_name: Pool of total RNAs prepared from 3 clones serum starved and treated with Dox (12hrs) and auxin (2hrs) followed by serum for 60 min

value: Dox and auxin stimulated


title: GFP-EPR-1BAH N7752 ChIP-seq

description: GACGTCAT_N7752_WT_GFP-NCU07505_W184A_122018_S54_L008_R1_001

extract_protocol: GFP ChIPs were performed with the same protocol as histone modification ChIP except that cross-linking was done with 1% formaldehyde for 10 minutes, tissue was sonicated with 3x 10 pulses, chromatin was sheared 4x 10 minutes using a Bioruptor, and protein A beads (Sigma) were used for the IP. GFP ChIP-seq libraries were size selected (for fragments 400-800 bp) using Mag-Bind RXNPure Plus Beads (Omega Biotek).

tag: chip antibody


title: Sample008

value: African American

value: Crohn's Disease


title: GFP-EPR-1BAH N7753 ChIP-seq

description: ACGTCCAA_N7753_WT_GFP-NCU07505_W184A_122018_S55_L008_R1_001


title: Pool of RNA from three clones, serum starved, stimulated with serum 60 min

description: Gene expression data from 3 clones expressing an auxin-degradable RPB1 serum starved for 20hrs total followed by 1hr stimulation with 20% FCS. After 6 hours starvation, cells were treated for 12 hrs with vehicle (water) and 2 hrs with auxin and finally stimulated with serum.

source_name: Pool of total RNAs prepared from 3 clones serum starved and treated with vehicle (water) and stimulated with serum for 60 min

value: control stimulated


title: RA EPC-derived endothelial cells - basal - 6

description:
Gene expression from RA-derived endothelial cells -basal
A14_(HuEx-1_0-st-v2).CEL

value: Rheumatoid arthritis

value: peripheral blood

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

value: unstimulated


title: RA EPC-derived endothelial cells - basal - 5

description:
Gene expression from RA-derived endothelial cells -basal
A12_(HuEx-1_0-st-v2).CEL


title: GFP-EPR-1PHD N7754 ChIP-seq

description: GATCCACT_N7754_WT_GFP-NCU07505_W292A_122018_S56_L008_R1_001


title: Pool of RNA from three clones, serum starved, control

description: Gene expression data from 3 clones expressing an auxin-degradable RPB1 serum starved for 20hrs total. After 6 hours starvation, cells were treated for vehicle (water) for 12 hrs followed by auxin for 2hrs.

source_name: Pool of total RNAs prepared from 3 clones serum starved and treated with vehicle (water)

value: control starved


title: Sample006

value: Female


title: GFP-EPR-1PHD N7755 ChIP-seq

description: AGCCTATC_N7755_WT_GFP-NCU07505_W292A_122018_S57_L008_R1_001


title: RA EPC-derived endothelial cells - basal - 4

description:
Gene expression from RA-derived endothelial cells -basal
A10_(HuEx-1_0-st-v2).CEL


title: Sample005

value: Male


title: RA EPC-derived endothelial cells - hypoxia - 6

description:
Gene expression from RA-derived endothelial cells - hypoxia
A13_(HuEx-1_0-st-v2).CEL

value: hypoxic exposure


title: Pool of RNA from three clones, Dox and auxin treated

description:
Gene expression data from 3 clones expressing an auxin-degradable RPB1 treated for 12 hrs with doxycycline, to induce the plant ubiquitin ligase OsTIR1, and 2 hrs with auxin to degrade the tagged RPB1
Pool_DA

hyb_protocol: Hybridization was performed at 45 degrees celcius for 16 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

data_processing:
The data expressed as CEL files were normalized using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) algorithm with Transcriptome Analysis Console (TAC) 4.0 (Thermofisher)
The .chp files contain Expression (Gene + Exon) analysis results.  However, only gene-level data were used for subsequent analysis.
The supplementary file HTA-2_0.na36.hg19.probeset.csv includes the annotation for all probe sets included in the chp files.

source_name: Pool of total RNAs prepared from 3 clones treated with Dox for 12 hrs and auxin 2 hrs

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and Pen-Strep

treatment_protocol: Cells were treated for 12 hrs with water (vehicle, control condition) or doxycycline (Dox) or Dox for 12 hrs and auxin for 2 hrs (DA).

value: Dox and auxin treated


title: RA EPC-derived endothelial cells - hypoxia - 5

description:
Gene expression from RA-derived endothelial cells - hypoxia
A11_(HuEx-1_0-st-v2).CEL


title: Pool of RNA from three clones, Dox treated

description:
Gene expression data from 3 clones expressing an auxin-degradable RPB1 treated for 12 hrs with doxycycline to induce the plant ubiquitin ligase OsTIR1
Pool_Dox

source_name: Pool of total RNAs prepared from 3 clones treated with Dox for 12 hrs

value: Dox treated


title: GFP-EPR-1 N7689 ChIP-seq

description: GTGGTATG_N7689_WT_GFP-NCU07505_122018_S52_L008_R1_001


title: Sample004

value: Hispanic

value: Control

value: Ileum


title: RA EPC-derived endothelial cells - hypoxia - 4

description:
Gene expression from RA-derived endothelial cells - hypoxia
A9_(HuEx-1_0-st-v2).CEL


title: GFP-EPR-1 N7690 ChIP-seq

description: CCAACTTC_N7690_WT_GFP-NCU07505_122018_S53_L008_R1_001


title: Sample003

value: Ulcerative Colitis


title: Sample007

value: White


title: Pool of RNA from three clones, control

description:
Gene expression data from 3 clones expressing an auxin-degradable RPB1 treated with vehicle (water)
Pool_Ctl

source_name: Pool of total RNAs prepared from 3 clones treated with vehicle (water)

value: HEK293-tagged RPB1

value: control


title: Sample002

value: African American


title: ∆epr-1 N7479 H3K27me2/3 ChIP-seq

description: GACCGATA_N7479_deltaNCU07505_H3K27me2me3_120117

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 10 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

value: mat A; {delta}epr-1::hph


title: ∆epr-1 N7491 H3K27me2/3 ChIP-seq

description: CAGACGTT_N7491_deltaNCU07505_H3K27me2me3_120117

value: mat a; {delta}epr-1::hph


title: RA EPC-derived endothelial cells - hypoxia - 3

description:
Gene expression from RA-derived endothelial cells - hypoxia
A7_(HuEx-1_0-st-v2).CEL

value: Rheumatoid arthritis

value: peripheral blood

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)


title: RA EPC-derived endothelial cells - basal - 2

description:
Gene expression from RA-derived endothelial cells -basal
A6_(HuEx-1_0-st-v2).CEL

value: unstimulated


title: RA EPC-derived endothelial cells - basal - 1

description:
Gene expression from RA-derived endothelial cells -basal
A4_(HuEx-1_0-st-v2).CEL


title: Sample001

value: Male


title: Male nonwounded (AGNW_5)

status: Public on Apr 14 2020

city: New Haven

first: Valerie

last: Horsley

state: CT

address: 225 Propsect St

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing:
Pseudoalignment + quantification: Kallisto (Bray et al. Nat. Methods 2016) + Bustools (Melsted et al. Bioinformatics 2019) with GENCODE vM22 annotation.
Data normalization: sctransform (Hafemeister and Satija BioRXiv 2019).
Data integration: Seurat (Stuart et al. Cell 2019).
Genome_build: Genome annotation: GENCODE vM22
Supplementary_files_format_and_content: shook_single_cell_expression_sctransform.csv: Gene expression matrix: batch corrected (csv).
Supplementary_files_format_and_content: shook_single_cell_expression_UMI_counts.csv: Gene expression matrix: raw UMI counts (csv).
Supplementary_files_format_and_content: shook_single_cell_metadata_and_GFP.csv: Experimental design, GFP expression, and cell level metadata (csv).

source_name: uninjured mouse back skin

extract_protocol: 10X Chromium Single Cell 3' v3 Chemistry.

tag: strain

value: AdipoqCre; mT/mG

tag: Sex

tag: age

value: 7 weeks

value: Uninjured skin

value: CD45- and CD31-negative cells


title: ChIP LLC ID R1

first: Nishana

last: Mayilaadumveettil

address: 31st Street & East River DR, Receiving Department BLDG Smilow Floor 03, RM 307 (Jane Skok Laboratory)

institute: NYU Langone health

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Replicate 1 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
rwas counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: LLC ID

growth_protocol: Mouse embryonic stem cells E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin (Sigma ES-006-B) coated dishes (Falcon, 353003) at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM (Thermo Fisher, 11965-118) supplemented with 15% fetal bovine serum (Thermo Fisher, SH30071.03), 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma, P4458), 1 X GlutaMax supplement (Thermo Fisher, 35050-061), 1 mM sodium pyruvate (Thermo Fisher, 11360-070), 1 X MEM non-essential amino-acids (Thermo Fisher, 11140-50), 50 μM b-mercaptoethanol (Sigma, 38171), 104 U/ml leukemia inhibitory factor (Millipore, ESG1107), 3 μM CHIR99021 (Sigma, SML1046) and 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162). The cells were passaged every alternate day by dissociation with TrypLE (Thermo Fisher, 12563011).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104) as per the manufacturer's protocol.
ChIP-seq libraries were constructed using the Illumina Nextera DNA Sample prep kit. RNA seq libraries were prepared using standard Illumina protocols. Hi-C libraries were prepared as per the Arima kit guidelines.

treatment_protocol: For degradation of endogenous CTCF, 500 μM indole-3-acetic acid/IAA (Sigma, I5148) was added to the media. Expression of transgenes were achieved by the addition of doxycycline (Dox, 1 μg/ml) (Sigma, D9891) to the media. The cells were treated with IAA and/or Dox for 2 days for RNA seq and ChIP seq and 4 days for HiC.

value: Mouse embryonic stem cells

tag: parental cell line

value: 129/Ola, XY

tag: genotype/variation

value: CTCF-AID, Tir1, Flag-LLC-mRuby 2 transgene at Tigre

tag: kit

value: Nextera

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)


title: ChIP LLC ID R2

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 48 h. Replicate 2 of 2

tag: tissue


title: ChIP IgG CTCF ID

description: IgG ChIP control

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the GRCm38/mm10 assembly of mouse genome using bowtie2
Reads with quality < 30 and duplicates were removed using Samtools/1.3 for ChIP-seq
Peaks were called using Macs/1.4
raw counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization.

source_name: CTCF ID

value: mouse ES cells E14Tg2a

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre

value: IgG (Abcam ab37415)


title: ChIP IgG CTCF U

description: IgG ChIP control

source_name: CTCF U


title: ChIP CLL ID R2

source_name: CLL ID

value: CTCF-AID, Tir1, Flag-CLL-mRuby 2 transgene at Tigre


title: ChIP CLL ID R1


title: ChIP CLL D R2

description: Flag antibody ChIP seq in cells treated with Dox for 48 h. Replicate 2 of 2

source_name: CLL D


title: ChIP CLL D R1

description: Flag antibody ChIP seq in cells treated with Dox for 48 h. Replicate 1 of 2


title: RA EPC-derived endothelial cells - hypoxia - 1

description:
Gene expression from RA-derived endothelial cells - hypoxia
A3_(HuEx-1_0-st-v2).CEL

source_name: EC derived from circulating EPCs_RA_hypoxic exposure

tag: subject status

value: Rheumatoid arthritis

value: peripheral blood

tag: cell type

tag: treatment

value: hypoxic exposure


title: Human osteoclastoma derived enriched giant osteoclast cells (GCT-OCL)

city: Charleston

first: Sakamuri

middle: V

last: Reddy

state: SC

address: 173 Ashley Avenue

department: DCRI/Pediatrics

institute: Medical University of South Carolinia

description: three pooled samples

hyb_protocol: Code Link bioarrays were hybridized with  the cRNA target and stained with  cy5-streptavidin

scan_protocol: Slides were scanned on an  Axon GenePlx 4000B scanner

data_processing:
Data were analyzed with CodeLink and GeneSpring software
fold changes in expression

source_name: osteoclastoma

label_protocol: Biotynyated cRNA target was prepared from the DNA templates

extract_protocol: Human osteoclatoma bone tumor tissues were enriched by 23C6 antibody positive osteoclast cells

value: osteoclastoma-derived enriched giant osteoclast cells (multinucleated cells)


title: RA EPC-derived endothelial cells - hypoxia - 2

description:
Gene expression from RA-derived endothelial cells - hypoxia
A5_(HuEx-1_0-st-v2).CEL

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)


title: ChIP LLC D R2

source_name: LLC D


title: HK2_vehicle pretreated_16h OGD_rep2

city: Tokyo

first: MARIE

last: ITO

address: 7-3-1 Hongo, Bunkyo

department: Department of Nephrology and Endocrinology

country: Japan

institute: the University of Tokyo

description:
Ctrl_5
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction Software 11.5.1.1(Agilent). Raw data were processed with the R package limma in Bioconductor to perform background correction and data normalization using the quantile normalization method.

source_name: HK2 cell, vehicle pretreated, 16h OGD

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

growth_protocol: HK2, an immortalized human renal proximal tubular cell line, was cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS). Cells were plated in 6 well plates before experiment and exposed to 10 uM enarodustat (Japan Tobacco Inc., Osaka, Japan) or Dimethyl Sulfoxide (DMSO) (Wako Pure Chemicals, Osaka, Japan) for 24 hours.

extract_protocol: Total cellular RNA was isolated using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).

treatment_protocol: As oxygen-glucose deprivation (OGD), the medium was changed to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS, and the cells were put in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 h.

value: vehicle pretreated, 16h OGD


title: HK2_sham_rep2

description:
Sham_2
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to normal medium for 16 hours

source_name: HK2 cell, sham

value: immortalized human renal proximal tubular cell line

value: sham


title: ChIP LLC D R1

value: Mouse embryonic stem cells


title: HK2_sham_rep3

description:
Sham_3
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to normal medium for 16 hours


title: Normal human bone marrow cells (NBM)

description: three pooled samples

source_name: bone marrow cells

value: Normal bone marrow cells (mononuclear cells)


title: HK2_sham_rep1

description:
Sham_1
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to normal medium for 16 hours


title: HK2_enarodustat pretreated_16h OGD_rep3

description:
JTZ951_9
Gene expression of HK2 after pretreatment with 10 uM enarosutat for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours

source_name: HK2 cell, enarodustat pretreated, 16h OGD

value: enarodustat pretreated, 16h OGD


title: HK2_enarodustat pretreated_16h OGD_rep1

description:
JTZ951_7
Gene expression of HK2 after pretreatment with 10 uM enarosutat for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours


title: HK2_vehicle pretreated_16h OGD_rep3

description:
Ctrl_6
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours


title: HK2_enarodustat pretreated_16h OGD_rep2

description:
JTZ951_8
Gene expression of HK2 after pretreatment with 10 uM enarosutat for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours


title: HK2_vehicle pretreated_16h OGD_rep1

description:
Ctrl_4
Gene expression of HK2 after pretreatment with DMSO for 24 hours and exposure to DMEM/Ham's F-12 (No Glucose) with L-glutamine and sodium pyruvate (Nacalai Tesque, Kyoto, Japan) without FBS in an anoxic bag with Anaero Pack (Mitsubishi Gas Chemical Co. Inc., Tokyo, Japan) for 16 hours


title: ChIP IgG CTCF D

description: IgG ChIP control

source_name: CTCF D

value: 129/Ola, XY

value: Nextera


title: Male 5d Wound bed (AG5d_3)

description: Day 5 wound bed.

source_name: mouse skin wound beds

value: AdipoqCre; mT/mG

value: Male

value: 7 weeks

value: Skin wound bed

value: CD45- and CD31-negative cells


title: Female 5d Wound bed (AG5d_9)

description: Day 5 wound bed.

value: Female


title: ChIP IgG CLC D

description: IgG ChIP control

source_name: CLC D

value: mouse ES cells E14Tg2a

value: CTCF-AID, Tir1, Flag-CLC-mRuby 2 transgene at Tigre

value: IgG (Abcam ab37415)


title: ChIP IgG CTCFL ID

description: IgG ChIP control

source_name: CTCFL ID

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre


title: ChIP IgG CTCFL D

description: IgG ChIP control

source_name: CTCFL D


title: ChIP IgG CLC ID

description: IgG ChIP control

source_name: CLC ID


title: RNA seq LCL ID R2

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 2 of 2
BCB-2i-ID_merge-RNA_seq.bw

molecule: polyA RNA

source_name: LCL ID

value: CTCF-AID, Tir1, Flag-LCL-mRuby 2 transgene at Tigre

tag: agent

value: IAA and Dox

tag: time point


title: ChIP IgG CTCF I

description: IgG ChIP control

source_name: CTCF I

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre


title: RNA seq LCL ID R1

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 1 of 2
BCB-2i-ID_merge-RNA_seq.bw


title: ChIP IgG LCL ID

description: IgG ChIP control


title: ChIP IgG LCL D

description: IgG ChIP control

source_name: LCL D


title: RNA seq LCL U R2

description:
RNAseq in untreated cells. Replicate 2 of 2
BCB-2i-UI_merge-RNA_seq.bw

source_name: LCL U

value: untreated cells.


title: RNA seq LCL I R1

description:
RNAseq in cells treated with IAA for 24 h. Replicate 1 of 2
BCB-2i-I_merge-RNA_seq.bw

source_name: LCL I

value: IAA


title: RNA seq LCL I R2

description:
RNAseq in cells treated with IAA for 24 h. Replicate 2 of 2
BCB-2i-I_merge-RNA_seq.bw

value: 129/Ola, XY


title: RNA seq LCL D R1

description:
RNAseq in cells treated with Dox for 24 h. Replicate 1 of 2
BCB-2i-D_merge-RNA_seq.bw

value: Dox


title: RNA seq CLC ID R2

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 2 of 2
CBC-2i-ID_merge-RNA_seq.bw


title: RNA seq CLC D R2

description:
RNAseq in cells treated with Dox for 24 h. Replicate 2 of 2
CBC-2i-D_merge-RNA_seq.bw


title: RNA seq CLC ID R1

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 1 of 2
CBC-2i-ID_merge-RNA_seq.bw


title: FA_Bt2

city: Shanghai

first: Yi

last: Guo

address: 2699 Western Gaoke Road

department: Shanghai First Maternity and Infant Hospital

country: China

institute: Tong ji university

data_processing:
The raw data was handled by R and data quality was checked by FastQC （v0.11.2）.
The number of transcripts in each sample was calculated based on the number of fragments per kilobase of transcript per million fragments mapped (FPKM); Cuffnorm software was used to calculate the FPKM value for each sample, and the values were log2 transformed.
DESeq(v1.22.1) software was used to calculate the differential gene transcripts between different samples.
Genome_build: mm10

source_name: Blastocyst

extract_protocol:
oocytes, cumulus cells, or blastocysts were transferred into the lysis buffer and directly reverse transcribed.
A poly(A) tail was added to the 3′ end of the first-stand cDNA using terminal deoxynucleotidyl transferase. The total cDNA library was used for RNA-seq library construction after 18–20 cyclic amplification. Paired-end 125-bp sequencing was further performed

value: Blastocyst

value: Filtered air group


title: FA_Bt1


title: FA_Bt3


title: CAP_Bt3

value: PM2.5 exposure group


title: CAP_Bt2


title: RNA seq CLC I R2

description: RNAseq in cells treated with IAA for 24 h. Replicate 2 of 2

source_name: CLC I


title: RNA seq LCL D R2

description:
RNAseq in cells treated with Dox for 24 h. Replicate 2 of 2
BCB-2i-D_merge-RNA_seq.bw


title: RNA seq CLC I R1

description: RNAseq in cells treated with IAA for 24 h. Replicate 1 of 2


title: RNA seq CTCFL ID R2

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 2 of 3
B.ID_merge.bw


title: FA_Cs3

source_name: Cumulus cell

value: Cumulus cell


title: FA_Cs2


title: CAP_Bt1


title: RNA seq CLC U R1

description:
RNAseq in untreated cells. Replicate 1 of 2
CBC-2i-UI_merge-RNA_seq.bw

source_name: CLC U


title: FA_Cs1


title: RNA seq CLC U R2

description:
RNAseq in untreated cells. Replicate 2 of 2
CBC-2i-UI_merge-RNA_seq.bw


title: RNA seq CTCFL ID R1

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 1 of 3
B.ID_merge.bw


title: CAP_Cs3


title: CAP_Cs2


title: RNA seq CTCFL D R3

description:
RNAseq in cells treated with Dox for 24 h. Replicate 3 of 3
B.D_merge.bw


title: CAP_Cs1


title: FA_Oe3

source_name: Oocyte

value: Oocyte


title: RNA seq CTCFL D R2

description:
RNAseq in cells treated with Dox for 24 h. Replicate 2 of 3
B.D_merge.bw


title: RNA seq CTCFL I R3

description:
RNAseq in cells treated with IAA for 24 h. Replicate 3 of 3
B.I_merge.bw

source_name: CTCFL I


title: FA_Oe1


title: RNA seq CLC D R1

description:
RNAseq in cells treated with Dox for 24 h. Replicate 1 of 2
CBC-2i-D_merge-RNA_seq.bw


title: RNA seq CTCFL I R2

description:
RNAseq in cells treated with IAA for 24 h. Replicate 2 of 3
B.I_merge.bw


title: FA_Oe2


title: CAP_Oe3


title: CAP_Oe2


title: RNA seq CTCFL U R3

description:
RNAseq in untreated cells. Replicate 3 of 3
B.UI_merge.bw

source_name: CTCFL U


title: RNA seq CTCFL I R1

description:
RNAseq in cells treated with IAA for 24 h. Replicate 1 of 3
B.I_merge.bw


title: CAP_Oe1


title: RNA seq CTCFL U R2

description:
RNAseq in untreated cells. Replicate 2 of 3
B.UI_merge.bw


title: RNA seq CTCFL U R1

description:
RNAseq in untreated cells. Replicate 1 of 3
B.UI_merge.bw


title: RNA seq LCL U R1

description:
RNAseq in untreated cells. Replicate 1 of 2
BCB-2i-UI_merge-RNA_seq.bw


title: CTCF WIZdel Rep 1

first: Jill

last: Dowen

address: 250 Bell Tower Drive, CB 7100 3360 Genome Sciences Building

institute: UNC Chapel Hill

description: CTCF-WIZdel-ChIPseq.bw

data_processing:
Alignment:  reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.2 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.9 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v 2016-02-15) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.26) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Genome_build: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary_files_format_and_content: For each ChIPped factor, a BigWig coverage track of merged replicates is provided for viewing in UCSC genome browser.

source_name: Mouse embryonic stem cells v6.5

growth_protocol: V6.5 murine embryonic stem cells (mESCs) (male) were grown on irradiated murine embryonic fibroblasts under standard conditions, as previously described (Dowen et al, 2014)

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 2 minutes before quenching with 125 mM glycine. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before resuspension in Sonication Buffer 1. Human chromatin (from HEK293T cells) was spiked in (to final 5%) prior to sonication for the indicated experiments. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 8, PIP/W 210, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1,000 base pair size were generated.  Antibody was incubated with 100uL Protein G Dynabeads for 6 hours. Unbound antibody was removed via washing, as detailed above, before incubation of antibody bound beads with chromatin overnight. Beads were then washed with Sonication Buffer 1 and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. Zymo ChIP DNA Clean and Concentrate kit (D5205) was used to purify DNA following Proteinase digestion. Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645S).

value: WIZ deletion

value: mESC v6.5

tag: antibody

value: anti-CTCF; Active Motif 61311


title: RNA seq CTCF ID R3

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 3 of 3
C.ID_merge.bw

source_name: CTCF ID

value: mouse ES cells E14Tg2a


title: RNA seq CTCFL D R1

description:
RNAseq in cells treated with Dox for 24 h. Replicate 1 of 3
B.D_merge.bw

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre


title: RNA seq CTCF ID R2

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 2 of 3
C.ID_merge.bw


title: SMC1A Rep 1

value: Wild Type

value: anti-SMC1A; Bethyl A300-055A


title: WIZ Rep 2

description: WIZ-ChIPseq.bw

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 2 minutes before quenching with 125 mM glycine. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before resuspension in Sonication Buffer 1. Human chromatin (from HEK293T cells) was spiked in (to final 5%) prior to sonication for the indicated experiments. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 8, PIP/W 210, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1,000 base pair size were generated.  Antibody was incubated with 100uL Protein G Dynabeads for 6 hours. Unbound antibody was removed via washing, as detailed above, before incubation of antibody bound beads with chromatin overnight. Beads were then washed with Sonication Buffer 1 and Wash Buffers 1, 2, and 3. Chromatin was eluted. Crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. Zymo ChIP DNA Clean and Concentrate kit (D5205) was used to purify DNA following Proteinase digestion. Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645S).

value: anti-WIZ; Novus NBP1-80586


title: SMC1A Rep 2

description:
This sample has two associated fastq files, because it was sequenced on two different lanes. These fastq files were pooled for analysis.
SMC1A-ChIPseq.bw

extract_protocol: mESCs were crosslinked for 20 minutes in 1% formaldehyde (Sigma-Aldrich, 252549) in DMEM-KO supplemented with 15% FBS, and quenched by adding 125 mM glycine. Cells were lysed using Lysis Buffers 1 and 2, and recovered nuclei were resuspended in Sonication Buffer 1 and sonicated using a Biorupter (Diagenode) water bath sonicator. Insoluble material was then cleared by spinning sonicated lysates for 10 minutes at 21,000 rcf. To perform the IP, 15µg of anti-SMC1A antibody (Bethyl, A300-055A) was incubated with 100µl Dynabeads per IP for 8 hours, after which beads were washed twice with PBS to remove excess antibodies. An estimated 25x106 cell equivalents of chromatin in 550µl then were incubated overnight at 4ºC with the antibody-bound beads while rotating. Beads were collected using a magnet and the unbound fraction removed, followed by washes with Wash Buffers 1, 2, and 3. Crosslinks were reversed and phenol:chloroform extraction was used to collect DNA. Libraries were prepared using a ThruPlex DNAseq kit according to manufacturer’s instructions.


title: RNA seq CTCF D R1

description:
RNAseq in cells treated with Dox for 24 h. Replicate 1 of 3
C.D_merge.bw

source_name: CTCF D

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre


title: CD8_SBRT+IL12_2

city: Rochester

first: Bradley

last: Mills

address: 601 Elmwood Avenue

institute: University of Rochester Medical Center

description:
processed data files:
CD8_deSeq2_SBRT-IL12_vs_unIrr.txt

data_processing:
Illumina HiSeq Control Software used for basecalling.
Sequenced reads were trimmed using Trimmomatic-0.36, quality control was performed using FastQC 0.11.8, and sequences were mapped to GRCm38 + M17 genome using STAR_2.6.0c software.
Reads were mapped using the Subread featureCounts program and Salmon was used to quantify the expression of transcripts.
Genome_build: GRCm38 + M17
Supplementary_files_format_and_content: Tab-delimited text files include base mean, log2(fold change), stat, p-value, and adjusted p-value for each sample.

source_name: Immune cells

growth_protocol: KCKO orthotopic tumors were implanted as follows: 100,000 cells (50 uL) were injected into the pancreatic tail and two 4-mm titanium fiducial markers to assist in SBRT targeting were implanted adjacent to the tumor bubble. For one minute immediately following tumor cell injection, a cotton swab was placed over the injection site to prevent peritoneal leakage.

extract_protocol:
Tissues were mechanically dissociated followed by digestion with 30% collagenase. Homogenates were passed through 40 um filters and cells were resuspended in PAB. Between 2e6 and 4e6 cells from each treatment group were stained for cell surface antigens for 30 minutes at 4° C in the dark. CD8+ T cell, IM, and TAM populations were sorted on a FACSAria II cell sorter using a 100 mm nozzle. Cells were immediately lysed in Buffer RLT (containing b-mercaptoethanol), homogenized with QIAShredder spin columns, and RNA was purified using the RNeasy Micro Kit following manufacturer’s instructions. RNA quality was assessed using an Agilent Bioanalyzer, and all samples analyzed demonstrated RNA integrity values > 5.
CDNA libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit V2 following manufacturer’s instructions, and sequencing was performed on an Illumina high-throughput HiSeq 2500 platform.

treatment_protocol: SBRT was administered to tumor-bearing mice following a schedule of 6 Gy radiation in 4 fractions on days 6-9 post-implantation, yielding a BED of 38.4 for tumor and 72 for normal tissue. Localized delivery was targeted using previously mentioned titanium fiducial markers; markers were visualized with pretreatment CT scans. Lyophilized microspheres were resuspended in PBS (20 uL per mouse) prior to i.t. delivery. Twenty-four hours following the final SBRT fraction (day 10) empty MS control (2 mg beads) or IL-12 MS (2 mg beads containing 0.5 ug recombinant IL-12) were injected i.t. using an 18-guage Hamilton syringe.

value: Tumor-derived CD8 T cells

tag: sort markers


title: RNA seq CTCF D R2

description:
RNAseq in cells treated with Dox for 24 h. Replicate 2 of 3
C.D_merge.bw

value: 129/Ola, XY


title: RNA seq CTCF D R3

description:
RNAseq in cells treated with Dox for 24 h. Replicate 3 of 3
C.D_merge.bw

value: Dox


title: RNA seq CTCF I R2

description:
RNAseq in cells treated with IAA for 24 h. Replicate 2 of 3
C.I_merge.bw

value: IAA


title: CD8_IL12_3

description:
processed data files:
CD8_deSeq2_unIrr-IL12_vs_unIrr


title: RNA seq CTCF I R3

description:
RNAseq in cells treated with IAA for 24 h. Replicate 3 of 3
C.I_merge.bw


title: RNA seq CTCF U R2

description:
RNAseq in untreated cells. Replicate 2 of 2
C.UI_merge.bw

source_name: CTCF U

value: untreated cells.


title: CD8_SBRT+IL12_1


title: RNA seq CTCF I R1

description:
RNAseq in cells treated with IAA for 24 h. Replicate 1 of 3
C.I_merge.bw


title: RNA seq CTCF U R1

description:
RNAseq in untreated cells. Replicate 1 of 2
C.UI_merge.bw


title: CD8_IL12_2


title: CD8_IL12_1


title: Rad21 ChIP LCL ID R1

description: Rad21 antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 1 of 2

source_name: LCL  ID

value: CTCF-AID, Tir1, Flag-LCL-mRuby 2 transgene at Tigre

value: Nextera

value: Anti-Rad21 antibody; abcam (ab992)

value: IAA and Dox


title: CD8_SBRT_2

description:
processed data files:
CD8_deSeq2_SBRT_vs_unIrr.txt


title: Rad21 ChIP LCL ID R2

description: Rad21 antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 2 of 2


title: CD8_SBRT_3


title: CD8_SBRT_1


title: RNA seq CTCF ID R1

description:
RNAseq in cells treated with IAA and Dox for 24 h. Replicate 1 of 3
C.ID_merge.bw


title: Rad21 ChIP LCL D R1

description: Rad21 antibody ChIP seq in cells treated with Dox for 24 h. Replicate 1 of 2


title: CTCF Rep 1

city: Chapel Hill

description: CTCF-ChIPseq.bw

extract_protocol: mESCs were crosslinked in 1% formaldehyde for 2 minutes before quenching with 125 mM glycine. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before resuspension in Sonication Buffer 1. Human chromatin (from HEK293T cells) was spiked in (to final 5%) prior to sonication for the indicated experiments. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 8, PIP/W 210, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1,000 base pair size were generated.  Antibody was incubated with 100uL Protein G Dynabeads for 6 hours. Unbound antibody was removed via washing, before incubation of antibody bound beads with chromatin overnight. Beads were then washed with Sonication Buffer 1 and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. Zymo ChIP DNA Clean and Concentrate kit (D5205) was used to purify DNA following Proteinase digestion. Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645S).

tag: cell line

value: mESC v6.5


title: CD8_SBRT+IL12_3


title: CD8_unIrr_3

description:
processed data files:
CD8_deSeq2_SBRT_vs_unIrr.txt
CD8_deSeq2_unIrr-IL12_vs_unIrr
CD8_deSeq2_SBRT-IL12_vs_unIrr.txt


title: Rad21 ChIP CLC ID R1

source_name: CLC  ID

value: CTCF-AID, Tir1, Flag-CLC-mRuby 2 transgene at Tigre


title: CD8_unIrr_2


title: CD8_unIrr_1


title: Rad21 ChIP LCL D R2

description: Rad21 antibody ChIP seq in cells treated with Dox for 24 h. Replicate 2 of 2

source_name: LCL D

value: mouse ES cells E14Tg2a


title: TAM_SBRT+IL12_2

description:
processed data files:
TAM_deSeq2_SBRT-IL12_vs_unIrr.txt


title: Rad21 ChIP CLC D R2

source_name: CLC D


title: TAM_SBRT+IL12_1


title: Rad21 ChIP CLC ID R2


title: TAM_IL12_3

description:
processed data files:
TAM_deSeq2_unIrr-IL12_vs_unIrr


title: TAM_IL12_2


title: TAM_SBRT_2

description:
processed data files:
TAM_deSeq2_SBRT_vs_unIrr.txt


title: Rad21 ChIP CLC D R1


title: Rad21 ChIP CTCFL ID R1

source_name: CTCFL ID

value: CTCF-AID, Tir1, Flag-CTCFL-mRuby 2 transgene at Tigre


title: Rad21 ChIP CTCFL ID R2


title: Rad21 ChIP CTCFL D R1

source_name: CTCFL D


title: Rad21 ChIP CTCF ID R2


title: TAM_unIrr_2

description:
processed data files:
TAM_deSeq2_SBRT_vs_unIrr.txt
TAM_deSeq2_unIrr-IL12_vs_unIrr
TAM_deSeq2_SBRT-IL12_vs_unIrr.txt


title: TAM_IL12_1


title: TAM_unIrr_1


title: TAM_SBRT_1


title: RA EPC-derived endothelial cells - basal - 3

description:
Gene expression from RA-derived endothelial cells -basal
A8_(HuEx-1_0-st-v2).CEL

source_name: EC derived from circulating EPCs_RA_basal conditions

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

value: Rheumatoid arthritis

value: peripheral blood

value: Endothelial cells (EC) derived from circulating endothelial progenitor cells (EPCs)

value: unstimulated


title: Rad21 ChIP CTCFL D R2


title: Rad21 ChIP CTCF ID R1

value: CTCF-AID, Tir1, Flag-CTCF-mRuby 2 transgene at Tigre


title: Rad21 ChIP CTCF D R1

value: 129/Ola, XY


title: IM_SBRT+IL12_3

description:
processed data files:
IM_deSeq2_SBRT-IL12_vs_unIrr.txt

value: Tumor-derived inflammatory monocytes


title: IM_SBRT+IL12_1


title: Flag ChIP LCL ID R2

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 2 of 2

value: Anti-Flag M2 Magnetic Beads; Sigma (M8823)


title: Flag ChIP LCL ID R1

description: Flag antibody ChIP seq in cells treated with IAA and Dox for 24 h. Replicate 1 of 2


title: IM_SBRT+IL12_2


title: IM_IL12_2

description:
processed data files:
IM_deSeq2_unIrr-IL12_vs_unIrr


title: IM_IL12_3


title: IM_IL12_1


title: Flag ChIP LCL D R2

description: Flag antibody ChIP seq in cells treated with Dox for 24 h. Replicate 2 of 2

value: Dox


title: IM_SBRT_3

description:
processed data files:
IM_deSeq2_SBRT_vs_unIrr.txt


title: Flag ChIP CLC ID R1


title: IM_SBRT_2


title: Flag ChIP LCL D R1

description: Flag antibody ChIP seq in cells treated with Dox for 24 h. Replicate 1 of 2

value: CTCF-AID, Tir1, Flag-LCL-mRuby 2 transgene at Tigre


title: IM_unIrr_3

description:
processed data files:
IM_deSeq2_SBRT_vs_unIrr.txt
IM_deSeq2_unIrr-IL12_vs_unIrr
IM_deSeq2_SBRT-IL12_vs_unIrr.txt


title: Flag ChIP CLC D R1

value: Nextera


title: Rad21 ChIP CTCF D R2

value: Anti-Rad21 antibody; abcam (ab992)


title: IM_unIrr_2


title: Flag ChIP CTCFL ID R1

value: IAA and Dox


title: IM_SBRT_1


title: Flag ChIP CLC D R2


title: Flag ChIP CTCFL D R1


title: Flag ChIP CTCFL D R2


title: Flag ChIP CTCFL ID R2


title: IM_unIrr_1


title: Flag ChIP CTCF D R1