title: Cynomolgus monkey PBMCs treated with LPS (10 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

source_name: The PBMCs cultured under similar conditions without any stimulation served as the negative control, replicate 1


title: PBMC_POST-TX MALIGN_Patient 5

status: Public on Nov 28 2018

type: RNA

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Whole Human Genome Microarray 4x44 K slides, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software.
A p-value cut-off of 0.05 and a fold-change cut-off of 2,5 were applied to identify differentially expressed genes able to discriminate between the study groups.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC_post kidney transplant malignancies

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: Twenty ml of whole blood were harvested from all patients at the time of enrolment. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden). Total RNA was extracted automatically and qualitatively and quantitatively analyzed through Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with good quality characterized by RIN> 8 were used in the microarray experiment.

tag: gender

value: Male

tag: age

tag: treatment

value: Tacrolimus


title: PBMC_POST-TX MALIGN_Patient 4

value: Cyclosporin


title: Signs of BMD

type: SRA

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

description:
Pool of 2 specimens
BUR-

library_source: transcriptomic

data_processing:
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using the Oases software (Schulz et al., 2012) and the Velvet algorithm (Zerbino and Birney, 2008).
Genome_build: Ruditapes_seq.fasta
Supplementary_files_format_and_content: raw counts : comma-separated csv file including count values for each sample / assembly : fasta file

organism: Ruditapes philippinarum

source_name: posterior adductor muscle

extract_protocol:
RNeasy Mini kit (Qiagen) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2

tag: tissue

value: posterior adductor muscle

tag: health

value: BMD-Infected


title: Cynomolgus monkey PBMCs treated with LPS (2 μg.ml-1) replicate 1

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

hyb_protocol: The purified total RNA was amplified and labeled, and the microarray analysis was then performed overnight using Agilent Human and Monkey Whole Genome GeneChips (Agilent, Palo Alto, CA).

scan_protocol: not provided the array data were analyzed using Agilent Feature Extraction software.

data_processing: After normalization of the raw data, probes with intensities <400 were removed from the subsequent analysis using Significance Analysis of Microarray (SAM) software. The differentially expressed genes (DEGs) were identified as those having an adjusted q-value of <0.05 and an average fold-change difference of >1.5.

organism: Macaca fascicularis

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with LPS ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

label_protocol: not provided

growth_protocol: Whole heparinized cynomolgus monkey blood was obtained from 3 apparently healthy 2.5-year-old cynomolgus monkeys. The monkey PBMCs were isolated by Ficoll-Hypaque density centrifugation (Histopaque LTS1079, Sigma, USA). All procedures were performed in accordance with the Guide for the Care and Use of Laboratory Animals of NCSED, China. A relative centrifugal force of 2000 rpm was used for 30 minutes to separate the PBMCs. The PBMCs were washed twice in Hank’s and re-suspended at a final concentration of 1×10^6 cells/ml in culture medium (RPMI1640, GIBCO, USA) supplemented with 10% fetal calf serum. All experiments using the cultured cells were set up in triplicate.

extract_protocol: The total RNA was extracted from the PBMCs using Trizol reagent (Invitrogen Company) according to the manufacturer’s instructions. The purity of the RNA in each sample was assessed spectrophotometerically at 260 and 280 nm (NanoDrop Technologies), and the RNA integrity was assessed using formaldehyde agarose gel electrophoresis.

treatment_protocol: The PBMCs (1×10^6 cells/ml) obtained from the cynomolgus monkeys or the human donors were treated with PHA (2 μg.ml-1 or 10 μg.ml-1) or LPS (2 μg.ml-1 or 10 μg.ml-1) and incubated at 37 °C for 3 days. Cells cultured under similar conditions without any stimulation served as the negative control.

value: peripheral blood

tag: cell type

value: mononuclear

tag: process

value: test

tag: stimulation

value: LPS

value: control


title: Li2

city: Alar

first: Shaowei

last: Qin

state: Xinjiang

address: Hongqiao Road 705

department: College of Life Sciences

institute: Tarim University

description: strand-specific RNA sequencing

data_processing:
The clean reads obtained from sequencing were compared with P. euphratica genome (GCF_000495115.1_ PopEup_1.0_genomic.fna.gz, https://www.ncbi.nlm.nih.gov/genome/13265) by TopHat2
The clean reads were further compared with P. euphratica transcriptome to calculate the expressive abundance of every transcripts by bowtie2 (-k30 -t) and eXpress (---rf-stranded).
The transcripts were rebuilt based on probabilistic model using cufflinks (--no-update-check--library-type fr-firststrand).
All the transcripts were compared with P. euphratica transcriptome to remove known code transcripts and locus. Then these transcripts shorter than 200 bp or exons less than 2 were also removed. Remainder transcripts were analyzed with CPC (default), CNCI (-m pl), Pfam (-e_seq  0.001) and PLEK (default) to remove code transcripts, and lncRNAs of P. euphratica were obtained at last.
The expressive abundance of mRNA and lncRNA were quantified as FPKM (Fragments Per kb Per Million Reads)
Based on the sequencing results, the circRNAs were predicted De Novo with CIRI (command: CIRI_v2.0.1pl-Ialn-pe.sam-O CircRNA.gtf-S 100000-F genome.fa-M Mt-A reference.gtf)
The expressive abundance of circRNA was quantified as RPM (spliced reads per millon).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and RPM for each Sample

organism: Populus euphratica

source_name: juvenile linear leaf

growth_protocol: The juvenile linear,lanceolate,ovate and broad-ovate leaf groups were respectively sampled from 0-3, 4-6, 8-12 and over 20 years old P. euphratica in Alar (81°17′56.52″ E, 40°32′36.90″ N), Xinjiang province, China at April 2017

extract_protocol:
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The strand-specific libraries (dUTP) were constructed using TruSeq Stranded Total RNA LT - (with Ribo-Zero Plant) according to the manufacturer’s instructions

tag: leaf shape

value: linear

tag: tree age

value: 0-3 years


title: Li1

description: strand-specific RNA sequencing


title: Cells_IL23 20ug/ml_ 72hrs, replicate 3

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

description: Gene expression after 3 day in K562 cells

hyb_protocol: Hybridization buffer (Agilent Technologies) was added to the labeled mixture to a final volume of 45 uL. The mixture was heated at 100°C for 5 minutes and immediately cooled to 0°C. Each 45 L sample was hybridized onto an Agilent human miRNA Microarray R21 (Agilent Technologies) at 55°C for 20 hours.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, model G2505C) at 535 nm for Cy3.

data_processing: Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis.

source_name: K562 cells, IL23 20ug/ml, 3 days, replicate 3

label_protocol: Total RNA (0.1 ug) were dephosphorylated and labeled with pCp-Cy3 by Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

growth_protocol: K562 cells culture in RPMI-1640 medium

extract_protocol: The total RNAs of treated K562 cells were isolated by using the QIAamp RNA Blood Mini Kit (QIAGEN GmbH, Germany)

treatment_protocol: K562 cells were cultured in medium with or without the presence of IL-23 (20 ng/mL).

tag: cell line


title: No sign of BMD

description:
Pool of 3 specimens
SURF+

value: Healthy


title: Cells_IL23 20ug/ml_ 72hrs, replicate 2

source_name: K562 cells, IL23 20ug/ml, 3 days, replicate 2


title: Cells_coulture medium_3days, replicate 1

source_name: K562 cells, culture medium only, 3 days, replicate 1


title: Cynomolgus monkey PBMCs treated with PHA (10 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 10 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1

value: PHA


title: PBMC_POST-TX MALIGN_Patient 3


title: PBMC_POST-TX MALIGN_Patient 1


title: Susceptible Male 21

status: Public on Nov 27 2018

type: genomic

city: Nanjing

first: Zhe

last: Ma

state: JS

address: Tonwei Road No.1

institute: nanjing agricultural university

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

molecule: genomic DNA

organism: Mus musculus

source_name: Streptococcus Suis Serotype 2 Susceptible Male mouse

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: A/J and C57BL/6 mice were purchased from Model Animal Research Center of Nanjing University (Nanjing, China). A/J male mice were mated with C57BL/6 female mice to generate an F1 population. For generation of F2 progeny, F1 male mice were mated with inbred F1 female mice

extract_protocol: Blood samples were collected aseptically from susceptible and resistant F2 mice. Genomic DNA was extracted from blood using TIANamp Genomic DNA Kit,

treatment_protocol: The SS2 inoculum for experimental infection was adjusted to a concentration of 1×108 CFU/mL. Seventy male and seventy female F2 mice were injected i.p. with a 1 mL inoculum per mouse. F2 mice surviving for fewer than 3 days following infection were regarded as susceptible (22 males and 22 females), while those surviving for more than 15 days were regarded as resistant (23 males and 21 females).

tag: sample type

value: Survival under infection


title: Cells_IL23 20ug/ml_ 72hrs, replicate 1

source_name: K562 cells, IL23 20ug/ml, 3 days, replicate 1


title: PBMC_POST-TX MALIGN_Patient 2


title: Susceptible Male 23

description: Hybridized to 250K_Sty


title: Susceptible Male 22

description: Hybridized to 250K_Sty


title: Cynomolgus monkey PBMCs without stimulation replicate 1


title: Susceptible Male 20

description: Hybridized to 250K_Sty


title: Susceptible Male 19

description: Hybridized to 250K_Sty


title: Susceptible Male 17

description: Hybridized to 250K_Sty


title: Susceptible Male 12

description: Hybridized to 250K_Sty


title: Susceptible Male 18

description: Hybridized to 250K_Sty


title: Susceptible Male 14

description: Hybridized to 250K_Sty


title: Susceptible Male 13

description: Hybridized to 250K_Sty


title: Susceptible Male 16

description: Hybridized to 250K_Sty


title: Susceptible Male 11

description: Hybridized to 250K_Sty


title: Susceptible Male 09

description: Hybridized to 250K_Sty


title: Susceptible Male 07

description: Hybridized to 250K_Sty


title: Susceptible Male 15

description: Hybridized to 250K_Sty


title: Susceptible Male 06

description: Hybridized to 250K_Sty


title: Susceptible Male 08

description: Hybridized to 250K_Sty


title: Susceptible Male 05

description: Hybridized to 250K_Nsp


title: Susceptible Male 03

description: Hybridized to 250K_Nsp


title: Susceptible Male 04

description: Hybridized to 250K_Nsp


title: Cynomolgus monkey PBMCs treated with PHA (2 μg.ml-1) replicate 1

source_name: The PBMCs (1×106 cells/ml) obtained from the cynomolgus monkeys were treated with PHA ( 2 μg.ml-1 ) and incubated at 37 °C for 3 days, replicate 1


title: Ov2 [miRNA-Seq]

description: small RNA sequencing

data_processing:
The known miRNAs were identified by aligning against miRBase v.21 database (http://www.mirbase.org/,mismatch=0)
Unannotated small RNAs were analyzed by mirdeep2 (-c -j -l 18 -m ) to predict novel miRNAs
miRNAs were quantified and normalized to TPM (transcript per million).
Supplementary_files_format_and_content: tab-delimited text files include TPM values and precursor coordinate of novel miRNAs

source_name: juvenile ovate leaf

extract_protocol:
Total RNA was extracted using the mirVanamiRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The small RNA libraries were constructed using RNA extracted from juvenile linear,lanceolate,ovate and broad-ovate leaves.

value: ovate

value: 8-12 years


title: Susceptible Male 02

description: Hybridized to 250K_Nsp


title: Susceptible Male 01

description: Hybridized to 250K_Nsp


title: Susceptible Female 16

description: Hybridized to 250K_Sty

source_name: Streptococcus Suis Serotype 2 Susceptible Female mouse


title: Susceptible Female 20

description: Hybridized to 250K_Nsp


title: Susceptible Female 21

description: Hybridized to 250K_Nsp


title: Susceptible Male 10

description: Hybridized to 250K_Sty


title: Susceptible Female 17

description: Hybridized to 250K_Nsp


title: Susceptible Female 12

description: Hybridized to 250K_Sty


title: Susceptible Female 11

description: Hybridized to 250K_Sty


title: Susceptible Female 15

description: Hybridized to 250K_Sty


title: Susceptible Female 06

description: Hybridized to 250K_Nsp


title: Susceptible Female 13

description: Hybridized to 250K_Sty


title: Susceptible Female 10

description: Hybridized to 250K_Sty


title: Susceptible Female 07

description: Hybridized to 250K_Sty


title: Susceptible Female 08

description: Hybridized to 250K_Sty


title: Susceptible Female 19

description: Hybridized to 250K_Nsp


title: Susceptible Female 01

description: Hybridized to 250K_Nsp


title: Susceptible Female 05

description: Hybridized to 250K_Nsp


title: Susceptible Female 02

description: Hybridized to 250K_Nsp


title: Susceptible Female 04

description: Hybridized to 250K_Nsp


title: Susceptible Female 03

description: Hybridized to 250K_Nsp


title: Resistance Male 22

description: Hybridized to 250K_Nsp

source_name: Streptococcus Suis Serotype 2 Resistance Male mouse


title: Susceptible Female 18

description: Hybridized to 250K_Nsp


title: Resistance Male 21

description: Hybridized to 250K_Nsp


title: Resistance Male 20

description: Hybridized to 250K_Nsp


title: Susceptible Female 14

description: Hybridized to 250K_Sty


title: Resistance Male 19

description: Hybridized to 250K_Nsp


title: Resistance Male 18

description: Hybridized to 250K_Sty


title: Resistance Male 17

description: Hybridized to 250K_Sty


title: Resistance Male 16

description: Hybridized to 250K_Sty


title: Susceptible Female 09

description: Hybridized to 250K_Sty


title: Resistance Male 15

description: Hybridized to 250K_Sty


title: Bat2_10_I44

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

country: USA

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.

scan_protocol: GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)

data_processing: Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used (Brainarray, Mm430_Mm_ENTREZG).

label: biotin

source_name: nerve

label_protocol: We generated biotinylated cDNA probes from a single round of DNA displacement synthesis amplification of 20ng total RNA (Ovation Biotin RNA Amplification and Labelling System; NuGen) for hybridization to the whole-genome Affymetrix GeneChips using the Affymetrix protocol.

growth_protocol: Nf1fl/fl: mixed background, with mainly C57BL/6 and small percent of 129. DhhCre;Nf1fl/fl: Mixed background, with mainly C57BL/6 and small percent of 129 and FVBN. EGFR/EGFR: mixed background, with mainly C57BL/6 and small portion of FVBN.

extract_protocol: Total RNA was extracted by the phenol/chloroform method and purified using the Qiagen microRNA isolation kit (Qiagen, Inc. Valencia, CA).

treatment_protocol: P30: 30 days of age. P60: 60 days of age.

tag: batch

value: batch 2

value: 1-month nerve

value: nerve

tag: genotype/variation

value: EGFR/EGFR


title: Resistance Male 14

description: Hybridized to 250K_Sty


title: Resistance Male 12

description: Hybridized to 250K_Sty


title: Resistance Male 13

description: Hybridized to 250K_Sty


title: Resistance Male 06

description: Hybridized to 250K_Nsp


title: Resistance Male 07

description: Hybridized to 250K_Nsp


title: Resistance Male 04

description: Hybridized to 250K_Nsp


title: Resistance Male 08

description: Hybridized to 250K_Nsp


title: Resistance Male 11

description: Hybridized to 250K_Sty


title: Resistance Male 10

description: Hybridized to 250K_Sty


title: Resistance Male 05

description: Hybridized to 250K_Nsp


title: Resistance Female 22

description: Hybridized to 250K_Nsp

source_name: Streptococcus Suis Serotype 2 Resistance Female mouse


title: Resistance Female 15

description: Hybridized to 250K_Sty


title: Resistance Female 20

description: Hybridized to 250K_Sty


title: Resistance Female 19

description: Hybridized to 250K_Sty


title: Resistance Female 17

description: Hybridized to 250K_Sty


title: Resistance Female 18

description: Hybridized to 250K_Sty


title: Resistance Female 16

description: Hybridized to 250K_Sty


title: Resistance Female 14

description: Hybridized to 250K_Sty


title: Resistance Male 03

description: Hybridized to 250K_Nsp


title: Resistance Female 13

description: Hybridized to 250K_Sty


title: Resistance Female 11

description: Hybridized to 250K_Sty


title: Resistance Female 07

description: Hybridized to 250K_Nsp


title: Resistance Female 06

description: Hybridized to 250K_Nsp


title: Resistance Female 09

description: Hybridized to 250K_Nsp


title: Resistance Female 10

description: Hybridized to 250K_Nsp


title: Resistance Female 05

description: Hybridized to 250K_Nsp


title: Resistance Female 08

description: Hybridized to 250K_Nsp


title: Resistance Male 09

description: Hybridized to 250K_Sty


title: Resistance Female 04

description: Hybridized to 250K_Nsp


title: Resistance Female 21

description: Hybridized to 250K_Nsp


title: Resistance Female 03

description: Hybridized to 250K_Nsp


title: Resistance Male 02

description: Hybridized to 250K_Nsp


title: Resistance Female 02

description: Hybridized to 250K_Nsp


title: Resistance Female 01

description: Hybridized to 250K_Nsp


title: Resistance Male 01

description: Hybridized to 250K_Nsp


title: Treated: H9c2 cells transfected with beta4 plasmid

city: Mexico

first: Jorge

middle: Alberto

last: Sanchez

state: DF

address: Av. Politecnico 2508

department: Farmacología

country: Mexico

institute: Cinvestav

data_processing:
LCSciences sequencing the libraries using Hiseq 2000, the remainings reads are mappable reads.
Mappable reads were aligned to the rat genome (UCSC rn4) using Tophat_v1.4.1.
Genome_build: UCSC rn4
Supplementary_files_format_and_content: isoform_exp_diff.xls: pairwise differential expression analysis
Supplementary_files_format_and_content: isoform_exp_diff_significant.xls: isoforms showing significant difference (q-value** < 0.05)
Supplementary_files_format_and_content: pathway_analysis.xls: Pathway analysis of isoforms showing significant difference

organism: Rattus norvegicus

source_name: H9c2 cells

extract_protocol:
RNA samples from transfected cells were purified with RNAeasy kit (Qiagen) following the instructions of the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: heart/myocardium

value: H9c2 cells


title: Control: H9c2 cells transfected with empty vector


title: Resistance Female 12

description: Hybridized to 250K_Sty


title: 174_RISK_Rectal_UC

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
10-043-R

data_processing:
Raw reads were quantified by Kallisto, using Gencode v 24 as the reference genome and transcripts per million as the output.
Prior to analyses, data were baselined to the median of the control samples and filtered to include 14085 reasonably-expressed, protein-coding transcripts for analysis.
Statistical significance was defined as fold change >1.5 and FDR<0.05.
Genome_build: Gencode v12
Supplementary_files_format_and_content: text files with gene symbol and transcripts per million

source_name: Rectal biopsy

extract_protocol:
RNA was isolated from rectal biopsies obtained during diagnostic colonoscopy using the Qiagen AllPrep RNA/DNA Mini Kit.
PolyA-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, TruSeq RNA sample library preparation and 75-bp, single end sequencing was performed.

value: rectum

tag: diagnosis

value: UC

tag: location

tag: population

value: pediatric

tag: biopsy location

value: rectal

tag: disease subtype


title: 187_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
27-020-R

tag: tissue


title: 189_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
29-011-R


title: 175_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
11-032-R


title: 182_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-125-R


title: 188_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
27-028-R


title: 170_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
09-004-R


title: 181_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-086-R


title: 179_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-051-R


title: 180_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-084-R


title: 169_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-061-R


title: 171_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
09-054-R


title: 177_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
11-062-R


title: 184_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-172-R


title: 186_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
23-006-R


title: 173_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
09-067-R


title: 185_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
15-008-R


title: 190_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
29-020-R


title: 178_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
12-008-R


title: 183_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
13-135-R


title: 167_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-018-R


title: 166_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-017-R


title: 165_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-008-R


title: 164_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-006-R


title: 162_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
07-049-R


title: 176_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
11-060-R


title: 172_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
09-064-R


title: 168_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
08-021-R


title: 161_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
06-073-R


title: 144_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-005-R

value: Control

value: not IBD


title: 157_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-138-R


title: 145_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-006-R


title: 155_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-101-R


title: 146_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-009-R


title: 151_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-073-R


title: 156_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-112-R


title: 160_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
06-071-R


title: 149_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
03-047-R


title: 153_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-093-R


title: 148_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
01-064-R


title: 138_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-010-R


title: 142_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-001-R


title: 159_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
06-070-R


title: 147_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-037-R


title: 163_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
07-053-R


title: 143_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
27-002-R


title: 140_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-016-R


title: 152_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-076-R


title: 150_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
03-174-Ra


title: 139_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-011-R


title: 137_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-009-R


title: 158_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-142-R


title: 136_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-008-R


title: 134_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
23-009-R


title: 135_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-004-R


title: 133_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
21-020-R


title: 154_RISK_Rectal_UC

description:
Rectal biopsy from a newly-diagnosed, pediatric, UC patient
05-099-R


title: 141_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
24-018-R


title: 131_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
17-003-R


title: 125_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-063-R


title: 121_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-007-R


title: 112_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-082-R


title: 113_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-091-R


title: 110_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-067-R


title: 128_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
11-033-R


title: 126_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
10-023-R


title: 129_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
11-041-R


title: 114_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
07-030-R


title: 130_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
14-015-R


title: 124_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-033-R


title: 127_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
11-028-R


title: 123_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-026-R


title: 118_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-003-R


title: 115_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
07-037-R


title: 117_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
07-051-R


title: 116_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
07-040-R


title: 119_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-004-R


title: 111_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-078-R


title: 122_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-023-R


title: 108_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-063-R


title: 107_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-060-R


title: 106_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-050-R


title: 105_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
05-127-R


title: 104_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
05-108-R


title: 132_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
21-018-R


title: 103_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
05-102-R


title: 120_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
08-005-R


title: 109_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
06-064-R


title: 101_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
05-094-R


title: 102_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
05-100-R


title: 99_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
03-119-R


title: 95_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
03-075-R


title: 92_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
29-035-R

value: CD

value: ileal CD


title: 93_RISK_Rectal_NotIBD

description:
Rectal biopsy from a newly-diagnosed, pediatric, not IBD patient
01-040-R


title: 100_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
04-096-R


title: 98_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
03-115-R


title: 83_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
22-036-R


title: 89_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
27-041-R


title: 94_RISK_Rectal_NotIBD

description:
Rectal biopsy from a newly-diagnosed, pediatric, not IBD patient
03-060-R


title: 86_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
24-023-R


title: 79_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
19-015-R


title: 77_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
16-005-R


title: 82_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
21-005-R


title: 78_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
18-010-R


title: 81_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
20-013-R


title: 97_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
03-083-R


title: 87_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
27-012-R


title: 80_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
20-002-R


title: 85_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
23-016-R


title: 76_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
15-021-R


title: 74_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
14-035-R


title: 73_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
14-013-R


title: 75_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
15-003-R


title: 91_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
29-018-R


title: 96_RISK_Rectal_NotIBD

description:
Rectal biopsy from a pediatric, not IBD control
03-076-R


title: 88_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
27-024-R


title: 90_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
29-017-R


title: 84_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
22-039-R


title: 71_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
14-006-R


title: 68_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
13-168-R


title: 63_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
11-009-R


title: 65_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
12-028-R


title: 67_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
13-141-R


title: 69_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
13-170-R


title: 66_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
13-055-R


title: 62_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
11-002-R


title: 59_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
09-020-R


title: 61_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
09-042-R


title: 60_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
09-025-R


title: 51_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-069-R


title: 52_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-072-R


title: 56_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
08-015-R


title: 58_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
09-001-R


title: 70_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
14-003-R


title: 53_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-075-R


title: 49_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-062-R


title: 48_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-047-R


title: 46_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
05-116-R


title: 45_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
05-082-R


title: 44_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
05-077-R


title: 55_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
07-032-R


title: 47_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-016-R


title: 72_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
14-012-R


title: 54_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-099-R


title: 43_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
05-072-R


title: 42_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
04-132-R


title: 64_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
11-019-R


title: 38_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-181-R


title: 39_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
04-063-R


title: 40_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
04-103-R


title: 36_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-120-R


title: 31_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
27-008-R

value: colonic CD


title: 32_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
29-010-R


title: 33_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-062-R


title: 30_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
22-008-R


title: 34_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-106-R


title: 27_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
18-029-R


title: 26_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
18-012-R


title: 25_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
16-006-R


title: 28_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
19-029-R


title: 37_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-163-R


title: 23_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
15-011-R


title: 24_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
16-001-R


title: 35_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
03-114-R


title: 22_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
14-042-R


title: 20_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
14-037-R


title: 18_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
14-009-R


title: 19_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
14-010-R


title: 21_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
14-038-R


title: 17_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
13-064-R


title: 14_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
09-014-R


title: 16_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
11-014-R


title: 15_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
09-035-R


title: 12_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
08-031-R


title: MeCP2_ChIPRx_GSK343_rep2

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

description: processed data file: GSK343_MeCP2.ext200_RPM.bw

library_source: genomic

data_processing:
The sequences were separately aligned to either human genome(hg19) or the D. melanogaster melanogaster genome(dm3) using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3. PCR duplicate are removed for further analysis.
PCR duplicate are removed using samtools rmdup for further analysis.
For quantitative comparisons of H3K27me3 ChIPed reads between the samples, the exogenous genome derived normalization factor (α-x) for each experiment was derived according to the protocol of Orlando et al. As follows: 1 over the number of reads mapping to drosophila (dm3) per million. Then, the uniquely aligned readings for homo sapiens (hg19) were standardized using the normalization factor, α-x, for quantitative comparisons between samples.
For quantitative comparisons of MeCP2 ChIPed reads between the samples, the normalization factor (α) for each experiment was derived as follow: 1 over the number of reads mapping to homo sapiens (hg19) per million. Then, the uniquely aligned readings for homo sapiens (hg19) were standardized using the normalization factor, α, for quantitative comparisons between samples.
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated from exogenous reference normalized alignment read using the deepTools package

source_name: Neuroblastoma

growth_protocol: SH-SY5Y (Korean Cell Line Bank, 22266) were maintained in DMEM/F12 (Gibco, 11320033) supplemented with 10% fetal bovine serum (Welgene, S001-01) and Penicillin/Streptomycin (Lonza, 17-602E) at 5% CO2 in 37°C. Drosophila S2 cells (ATCC, CRL-1963) were cultured in Schneider’s Drosophila Medium (Gibco, 21720024) supplemented with 10% fetal bovine serum (Welgene, S001-01) in 25°C.

extract_protocol:
The SH-SY5Y cells were washed with 10ml of PBS and cross-linked with 1% formaldehyde for 5minutes.   The crosslinking reactions were quenched with 10x Glycine stop solution. The cross-linked SH-SY5Y cells were lysed in lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% IGEPAL CA-630, pH 8.0) using a dounce homogenizer (Kimble-Kontes. 885300-0002) to aid in nuclei release. The released nuclei was pelleted by centrifugation (10min, 5000rpm at 4°C). As a reference exogenous genome, Drosophila S2 cells were cross linked with 1% formaldehyde for 5 minutes and were quenched with 10x Glycine stop solution. The Drosophila S2 cells were then washed 3 times with ice cold PBS. For each ChIP-Rx experiment, SH-SY5Y cells and drosophila S2 cells ratio of 3:1, 12 million crosslinked SH-SY5Y nuclei and 4 million crosslinked S2 cells were combined and sonicated for 15 minutes with 30 second intervals to shear genomic DNA using Bioruptor XL (Diagenode). Each sheared genomic DNA preparation was split into two equal portions and incubated with either H3K27me3 (Diagenode, pAb-069-050), or MeCP2 (Diagenode, pAb-052-050). A magnetic bar was used to pull down antibody corresponding protein-genomic DNA complex. Genomic DNA in the complex was reverse cross-linked by DNase-free Proteinase K and purified.
H3K27me3 ChIPed or input DNA were used to prepare the ChIP-Seq library as described (NEXTflex ChIP-Seq kit, Bio Scientific, NOVA 5143-01 and NEXTflex ChIP-Seq Barcodes-6, NOVA 514120) followed by high throughput sequencing.

treatment_protocol: SH-SY5Y cells (density of 0.5~0.6 x 10^6 cells/ml) were treated with either DMSO or 5 uM GSK343 (an inhibitor of H3K27me3-specific HMTase) for 72hours.

value: Neuroblastoma

tag: spike-in reference

value: Drosophila melanogaster

value: 3 to1

tag: treatment

tag: chip antibody


title: 13_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
08-045-R


title: 29_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
20-006-R


title: 11_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
07-031-R


title: MeCP2_ChIPRx_GSK343_rep1

tag: cell type


title: 9_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
06-040-R


title: 10_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
06-053-R


title: 8_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
05-133-R


title: MeCP2_ChIPRx_DMSO_rep1

description: processed data file: DMSO_MeCP2.ext200_RPM.bw

value: DMSO


title: MeCP2_ChIPRx_DMSO_rep2


title: 7_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
05-120-R


title: 6_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
04-123-R


title: 5_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
04-045-R


title: 3_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
03-143-R


title: E12_DHL_WT_Hoxd13vp

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: mouse E12.5 WT distal hindlimb Hoxd13 viewpoint

data_processing:
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to either the mm10 or galGal5 chicken genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “--end-to-end --sensitive -k 20”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads.
Fragments scores are normalized to the mean score of fragments falling into a region defined as the bait coordinated either ± 1Mb or ± 2Mb and the data was smoothed by using a running mean with window size of 11 fragments. During the procedure, information of excluded fragments at specific regions from the analysis were described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph)

source_name: Hindlimb

extract_protocol:
The dissected limb bud tissues were dissociated with collagenase (Sigma Aldrich) and filtered through cell strainer to obtain single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of samples were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. All primer and barcode information are described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).

tag: age

tag: tissues

value: Distal hindlimb

tag: genotype

value: wild type


title: E12_PHL_HoxDdel(8-13)_Hoxd11vp

description: mouse E12.5 del(8-13) proximal hindlimb Hoxd11 viewpoint

value: Proximal hindlimb


title: 4_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
03-176-R


title: E12_PFL_HoxDdel(8-13);HoxDdel(attp-SB3)_Hoxd11vp

description: mouse E12.5 del(8-13);del(attp-SB3) proximal forelimb Hoxd11 viewpoint

source_name: Forelimb

value: Proximal forelimb


title: E12_PHL_WT_Hoxd13vp

description: mouse E12.5 WT proximal hindlimb Hoxd13 viewpoint


title: E12_PHL_HoxDdel(8-13);HoxDdel(attp-SB3)_Hoxd11vp

description: mouse E12.5 del(8-13);del(attp-SB3) proximal hindlimb Hoxd11 viewpoint


title: 1_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
01-070-R

value: rectum


title: 2_RISK_Rectal_cCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, colonic CD patient
03-107-R


title: E12_PFL_HoxDdel(8-13)_Hoxd11vp

description: mouse E12.5 del(8-13) proximal forelimb Hoxd11 viewpoint


title: 57_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
08-054-R


title: E12_DHL_WT_Hoxd11vp

description: mouse E12.5 WT distal hindlimb Hoxd11 viewpoint


title: UC male112

description: NIDDK_ID: 14392

data_processing:
Reads were quantified by kalliso using Gencode v25 as the reference genome with transcripts per million as the output.
We included 14085 protein-coding mRNA genes with TPM >1 in 20% of the samples.

source_name: Rectal mucosal biopsy from UC Male age 14 at diagnosis

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DAN Mini Kit.  We employed polyA-RNA selection.
TrueSeq RNAsample prep, with paired-end 75bp reads on the Illumina HiSeq2500.

treatment_protocol: Rectal mucosal biopsies were obtained during diagnostic colonoscopies.

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: Sex

value: Male

tag: age at diagnosis

tag: pucai

tag: total mayo score

tag: eosinophil grade ≥ 32

value: Y

tag: week 4 remission

value: No

tag: histology severity score

tag: initial treatment

value: CS-Oral

tag: baseline calprotectin

value: unknown

tag: week 4 calprotectin


title: UC male109

description: NIDDK_ID: 7204

source_name: Rectal mucosal biopsy from UC Male age 12 at diagnosis

tag: tissue

tag: diagnosis

value: Yes


title: UC male110

description: NIDDK_ID: 1395

source_name: Rectal mucosal biopsy from UC Male age 11 at diagnosis

value: N

value: CS-IV


title: UC male111

description: NIDDK_ID: 15368


title: E12_PHL_WT_RNA-seq

description: mouse E12.5 WT proximal hindlimb RNA-seq

data_processing:
Demultiplexed RNA-seq reads were mapped onto mm10 genome or galGal5, respectively. Regarding chick distal hindlimb at HH30, the two fastq files derived from phalanges and metatarsals were concatenated and used for analysis.
The RNA-seq data were aligned against respective genomes using Tophat2 (Version 2.0.9)(Kim et al. 2013) and the unique mapped reads were extracted. The number of uniquely mapped reads was calculated using FLAGSTAT (Samtools, Version 0.1.18) (Li et al. 2009) and this value was used for the subsequent normalization of each coverage data to be the million reads number.
All analysis was done by our Galaxy server (the Bioteam Appliance Galaxy Edition; https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of the forward or reverse strand unique read coverage, divided by the number of millions of mapped reads in each sample.

extract_protocol:
Micro-dissected limb tissues either from mouse or chick were used for RNA extraction by using the RNeasy Micro Kit (QIAGEN) according to manufacturer instruction.
A total of 100 ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. Libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on either Illumina HiSeq 2500 or NextSeq 500.

tag: strain


title: UC male108

description: NIDDK_ID: 12966

source_name: Rectal mucosal biopsy from UC Male age 6 at diagnosis


title: UC male107

description: NIDDK_ID: 9479

source_name: Rectal mucosal biopsy from UC Male age 16 at diagnosis


title: STAM_treated3

city: Collegeville

first: Sarah

middle: A

last: Middleton

state: PA

address: 1250 S Collegeville Rd

department: Target Sciences - Computational Biology

institute: GSK

data_processing:
Reads were mapped using STAR v.2.5.1b with default parameters
Uniquely mapped reads were used as input to gene quantification using htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing read counts for each gene in each sample

source_name: Liver tissue

extract_protocol:
Trizol with phase separation and a Qiagen miRNeasy kit with DNase digestion
Sample libraries were prepped on the Tecan using an Illumina TruSeq mRNA stranded kit with 1 μg input, 7 min fragmentation, and 10 PCR cycles. Libraries were quantified using a Kapa qPCR kit and QuantStudio and then sequenced on an Illumina HiSeq 2500 with 101bp paired end reads to a depth of over 100 million reads per sample.

tag: mouse model

value: STAM

tag: treatment

value: I-BET151 10mg/kg


title: STAM_treated4


title: UC male106

description: NIDDK_ID: 9924


title: 41_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
04-109-R

value: CD

tag: location

tag: population

value: pediatric

tag: biopsy location

value: rectal

tag: disease subtype

value: ileal CD


title: UC male105

description: NIDDK_ID: 8856

source_name: Rectal mucosal biopsy from UC Male age 17 at diagnosis

tag: Sex

tag: age at diagnosis

tag: pucai


title: E12_PHL_WT_Hoxd11vp

description: mouse E12.5 WT proximal hindlimb Hoxd11 viewpoint

tag: age

tag: tissues

value: Proximal hindlimb

tag: genotype

value: wild type


title: STAM_treated1


title: STAM_vehicle4

value: Vehicle


title: STAM_treated2


title: Naive_vehicle4

value: WT


title: UC male104

description: NIDDK_ID: 5796

value: Rectal mucosal biopsy

value: Ulcerative Colitis

value: Male

tag: total mayo score

tag: eosinophil grade ≥ 32

tag: week 4 remission

tag: histology severity score

tag: initial treatment

tag: baseline calprotectin


title: STAM_vehicle2

tag: strain

tag: mouse model

tag: treatment


title: UC male103

description: NIDDK_ID: 3578

source_name: Rectal mucosal biopsy from UC Male age 15 at diagnosis

tag: tissue

tag: diagnosis

tag: week 4 calprotectin


title: UC male100

description: NIDDK_ID: 5028

tag: Sex

tag: age at diagnosis

value: No


title: STAM_vehicle1


title: UC male101

description: NIDDK_ID: 8298

tag: pucai

value: Yes

value: CS-Oral


title: UC male102

description: NIDDK_ID: 9149

source_name: Rectal mucosal biopsy from UC Male age 13 at diagnosis

value: N

value: CS-IV


title: Naive_vehicle3


title: Naive_vehicle2


title: STAM_vehicle3

value: STAM


title: UC male97

description: NIDDK_ID: 1318

value: unknown


title: UC male99

description: NIDDK_ID: 7506

value: Y


title: UC male96

description: NIDDK_ID: 13099

source_name: Rectal mucosal biopsy from UC Male age 10 at diagnosis


title: UC male98

description: NIDDK_ID: 7505


title: E12_DHL_WT_RNA-seq

description: mouse E12.5 WT distal hindlimb RNA-seq

tag: age

tag: tissues

value: Distal hindlimb


title: UC male95

description: NIDDK_ID: 6184

tag: total mayo score


title: UC male94

description: NIDDK_ID: 2648

tag: eosinophil grade ≥ 32


title: Naive_vehicle1


title: CSC12_Neg_d0

city: Minneapolis

first: Nobuaki

last: Kikyo

state: Minnesota

department: Stem Cell Institute

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using HISAT 2 v2.0.2.
Read assignments were performed by SUBREAD featureCounts v1.4.6.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include SUBREAD assigned raw reads for each sample.

molecule: polyA RNA

source_name: Mouse myoblast C2C12_Control

growth_protocol: C2C12 Cells were maintained in 10% fetal bovine serum (FBS) supplemented Dulbecco’s Modified Eagle’s Medium (DMEM) in an incubator at 37°C with 5% CO2.

extract_protocol:
Cells were collected at day 0, day 3 and day 5. Total RNA were extracted using RNeasy Plus Mini Kit (Qiagen, Catalog: 74136), according to manufacturer’s protocol.
Library construction were performed by University of Minneosta Genomic Center using TruSeq RNA v2 library preparation kits (Illumina; Catalog: RS-122-2001) according to manufacturer’s protocol.

treatment_protocol: Differentiation for C2C12 was induced as follows. On day -2, cells were seeded at 1x105 cells/well in a 12-well plate. On day 0 cells were rinsed twice with phosphate buffered saline (PBS) and cultured with 1% Insulin-Transferrin-Selenium in DMEM. Medium was changed with fresh DMEM with HS every two days.’

tag: cell line

tag: cell type

value: Mouse myoblast

tag: genotype/variation

value: Control

tag: time point


title: CSC12_Fkbp5_d5_kd

source_name: Mouse myoblast C2C12_Fkbp5 knockdown

value: Fkbp5 knockdown


title: CSC12_Fkbp5_d3_kd


title: UC male92

description: NIDDK_ID: 8181

tag: week 4 remission

tag: histology severity score

tag: initial treatment

tag: baseline calprotectin


title: CSC12_Neg_d3


title: UC male93

description: NIDDK_ID: 11668

tag: tissue

tag: diagnosis


title: CSC12_Fkbp5_d0_kd


title: UC male91

description: NIDDK_ID: 11323

tag: Sex

tag: week 4 calprotectin


title: CSC12_Fkbp4_d5_kd

source_name: Mouse myoblast C2C12_Fkbp4 knockdown

value: Fkbp4 knockdown


title: UC male90

description: NIDDK_ID: 9563

tag: age at diagnosis

tag: pucai


title: CSC12_Fkbp4_d0_kd


title: CSC12_Fkbp4_d3_kd


title: UC male88

description: NIDDK_ID: 6991


title: UC male87

description: NIDDK_ID: 14597


title: WT_Infected 3

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted ILC2s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

value: Mesenteric lymph node

tag: treatment

tag: strain


title: CSC12_Neg_d5


title: WT_Infected 2


title: WT_Agonist 2

value: Clenbuterol in drinking water


title: UC male86

description: NIDDK_ID: 11730

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: total mayo score

tag: eosinophil grade ≥ 32


title: UC male85

description: NIDDK_ID: 11833

value: Male

value: No


title: WT_Agonist 1

tag: cell type


title: 50_RISK_Rectal_iCD

description:
Rectal biopsy from a newly-diagnosed, pediatric, ileal CD patient
06-065-R

source_name: Rectal biopsy

value: rectum

value: CD

tag: location

tag: population

value: pediatric

tag: biopsy location

value: rectal

tag: disease subtype

value: ileal CD


title: UC male84

description: NIDDK_ID: 15058

value: N

tag: week 4 remission

tag: histology severity score

tag: initial treatment

value: CS-Oral

value: unknown


title: WT_Infected 1

tag: tissue


title: UC male83

description: NIDDK_ID: 7011

tag: diagnosis

tag: Sex

value: Y

value: CS-IV

tag: baseline calprotectin


title: UC male82

description: NIDDK_ID: 6160

tag: age at diagnosis

tag: pucai

value: Yes

tag: week 4 calprotectin


title: UC male81

description: NIDDK_ID: 11542

source_name: Rectal mucosal biopsy from UC Male age 9 at diagnosis

tag: total mayo score


title: UC male77

description: NIDDK_ID: 4160

tag: eosinophil grade ≥ 32


title: UC male79

description: NIDDK_ID: 11516


title: UC male80

description: NIDDK_ID: 15259


title: UC male78

description: NIDDK_ID: 9131


title: UC male89

description: NIDDK_ID: 3939


title: UC male75

description: NIDDK_ID: 12674


title: UC male73

description: NIDDK_ID: 10647


title: UC male71

description: NIDDK_ID: 11369


title: UC male72

description: NIDDK_ID: 3159


title: UC male70

description: NIDDK_ID: 894


title: UC male69

description: NIDDK_ID: 12052


title: UC male68

description: NIDDK_ID: 15102


title: UC male67

description: NIDDK_ID: 8821


title: Htr2a_KO_40

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

institute: KRIBB

data_processing:
Illumina Casava software used for basecalling.
The FastQC (FastQC v0.11.3) and cut-adapt (v1.1) were used to filter sequencing reads of low quality.
Then reads were mapped to mouse genome build mm10 using TopHat (TopHat v2.0.11) with default parameters. The HTseq (v0.9.1) was used for raw read counts. The DESeq2 (DESeq2 v3.1) was used for selecting differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: Liver

extract_protocol:
Mice liver RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) and used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Liver

tag: age

value: 20 weeks

tag: genotype

value: Albumin-Cre+/-; Htr2aflox/flox


title: UC male66

description: NIDDK_ID: 9270

source_name: Rectal mucosal biopsy from UC Male age 14 at diagnosis

value: Rectal mucosal biopsy

value: Ulcerative Colitis


title: Htr2a_KO_41


title: Htr2a_WT_42


title: Htr2a_WT_37


title: UC male64

description: NIDDK_ID: 2506

value: Male


title: Htr2a_KO_39


title: Htr2a_WT_36


title: UC male63

description: NIDDK_ID: 4050


title: UC male62

description: NIDDK_ID: 11827


title: UC male60

description: NIDDK_ID: 9334


title: UC male61

description: NIDDK_ID: 7551


title: UC male59

description: NIDDK_ID: 9756


title: UC male76

description: NIDDK_ID: 2637


title: UC male74

description: NIDDK_ID: 11250


title: UC male58

description: NIDDK_ID: 2390


title: UC male57

description: NIDDK_ID: 8816

source_name: Rectal mucosal biopsy from UC Male age 7 at diagnosis

value: No


title: UC male56

description: NIDDK_ID: 855

source_name: Rectal mucosal biopsy from UC Male age 11 at diagnosis


title: UC male65

description: NIDDK_ID: 12815


title: UC male55

description: NIDDK_ID: 5463


title: UC male54

description: NIDDK_ID: 2923


title: UC male50

description: NIDDK_ID: 12868

source_name: Rectal mucosal biopsy from UC Male age 5 at diagnosis


title: UC male53

description: NIDDK_ID: 1035

source_name: Rectal mucosal biopsy from UC Male age 16 at diagnosis


title: UC male51

description: NIDDK_ID: 11229


title: UC male49

description: NIDDK_ID: 7218


title: UC male48

description: NIDDK_ID: 5964


title: villus_recurrent spontaneous abortion_rep3

first: Zhenyao

last: Huang

address: Dongshan

institute: Nanjing Medical University

description: villus samples from recurrent spontaneous abortion patients

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using tophat with default parameters
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using a protocol from Cole Trapnell  et al., Nature Protocols volume 7, pages 562–578 (2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: villus

extract_protocol:
RNA was extracted by RNeasy Kits (Qiagen, Hilden, NRW, Germany) and treated with DNase I (Thermo Fisher Scientific, Wilmington, DE, USA) according to standard protocols. RNA-sequencing was done in Genesky using TruSeq Stranded mRNA Library Preparation (Genesky, Shanghai, China). Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: villus

tag: developmental stage

value: Twelve weeks before pregnancy

value: 25 years old


title: villus_recurrent spontaneous abortion_rep1

value: 24 years old


title: C029: Jurkat Hi-C

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

country: Spain

institute: CRG

data_processing:
Paired-end Hi-C reads were mapped to hg19 running bwa 0.7.5a with options -P -k17 -U0 -L0,0 -T25.
The hg19 reference was virtually digested at MboI sites. Contacts mapping to the same MboI-digested fragment or with insert sizes over 2000 nt to the MboI restriction site were discarded.
Hi-C matrices were filled with valid contacts (mapping quality greater than 10 on both ends) using cooler 0.7.6 at a resolution of 5 kb (fixed bins).
Each chromosome matrix was normalized using Iterative Correction (ICE) and Observed over Expected diagonal normalization (OE). The normalized matrix was subsequently smoothed by thresholding the maximum values to the 90th percentile.
The correlation matrix was computed for each chromosome and was further smoothed by thresholding to the 5th and 95th percentiles.
Fifteen intrachromosomal clusters were derived for each matrix with the KMeans algorithm, applied on the first 15 principal components of the smoothed correlation matrices.
Finally, a matrix was filled with the Hi-C contacts between all intrachromosomal clusters, normalized by the cluster lengths. Five global conformation clusters were derived using KMeans on the first 5 principal components of the matrix. The code to compute the clusters is avaiable at https://github.com/gui11aume/genome_structure_and_HIV_integration
Genome_build: hg19
Supplementary_files_format_and_content: jurkat_wt_hg19_5k_q10.cool: Jurkat wild-type Hi-C matrix at 5 kb resolution in cooler/hdf5 format
Supplementary_files_format_and_content: jurkat_wt_clusters.txt: Inferred 3D conformation clusters

source_name: Immortalized human T lymphocyte Jurkat cell line

growth_protocol: Jurkat human T cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 1% Pen Strep (Gibco) and 1% GlutaMAX (100x, Gibco) at 37℃ under a 95% air / 5% CO2 atmosphere. Jurkat T cells were passaged every 2 days with 1 to 5 dilution.

extract_protocol:
Nuclear DNA was extracted after 1 million Jurkat T cells were crosslinked with 1 % formaldehyde for 10 min at room temperature with gentle rotation and permeabilized with freshly prepared ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Igepal CA630 and 1x Roche complete protease inhibitors).
Nuclear DNA was digested by MboI; the ends of the digested fragments were filled in with biotin-14-dATP. The crosslinks were reversed after overnight proximity ligation of the crosslinked DNA fragments. Ligated DNA was purified and sheared to a length of 400 bp; ligation junctions were pulled down with streptavidin C1 beads. Pulled down DNA-on-beads was amplified by PCR with NEBNext Universal primers and index primers. PCR products (library) were cleaned up by 1.0x Agencourt AMPure XP beads. The purified library was run as a smear on 1.5% agarose gel and validated with ClaI digestion.

tag: cell line

value: Jurkat

tag: cell type

value: T lymphocyte

tag: start number of the cells

value: 1 million cells


title: C034: Jurkat Hi-C


title: UC male46

description: NIDDK_ID: 2710

value: Y

tag: week 4 remission

tag: histology severity score

tag: initial treatment

value: CS-Oral

value: unknown


title: UC male47

description: NIDDK_ID: 11985

tag: tissue

tag: diagnosis

tag: Sex

value: N

value: Yes

value: CS-IV


title: AS-065 #99 - Intact + PBS

city: Boulder

first: Aimee

last: Jackson

state: CO

address: 6200 Lookout Rd.

institute: miRagen Therapeutics

description: Biological replicate 2 of 3. Mouse skin: Intact + PBS

hyb_protocol: Hybridization was performed as per Agilent's standard protocols at Mogene (St. Louis, MO)

scan_protocol: Scan was performed as per Agilent's standard protocols at Mogene (St. Louis, MO)

data_processing: ArrayStudio (version 9.0.2.46)

source_name: Skin: Intact + PBS

label_protocol: Samples were labeled with Cy5 using Agilent reagents and manufacturer's standard protocols at Mogene (St. Louis, MO). Mouse universal reference RNA was labeled with Cy3 using Agilent reagents and manufacturer's standard protocols at Mogene (St. Louis, MO).

growth_protocol: ~8 week old C57BL/6 male mice

extract_protocol: Mice were euthanized and skin samples (~20-100 mg) from the treatment areas were taken 24 hours after intradermal injection. Samples were homogenized in 1.5 mL TriReagent (Invitrogen). Total RNA was extracted as per the manufacturer’s standard protocol.

treatment_protocol: 1cm long sutured incisional wounds were treated with intradermal injection of vehicle (PBS) or 100nmol miR-29b mimic 72 hours after wound creation. Uninjured skin was intradermally injected with vehicle (PBS) or 100nmol miR-29 inhibitor.

tag: wound

value: Intact

tag: treatment

value: PBS

source_name: Agilent

tag: sample type

value: Agilent mouse universal reference RNA


title: AS-065 #125 - Intact + 100nmol antimiR-29

description: Biological replicate 2 of 3. Mouse skin: Intact + 100nmol antimiR-29

source_name: Skin: Intact + 100nmol antimiR-29

value: antimiR-29 100nmol


title: AS-065 #97 - Intact + PBS

description: Biological replicate 1 of 3. Mouse skin: Intact + PBS


title: AS-065 #127 - Intact + 100nmol antimiR-29

description: Biological replicate 3 of 3. Mouse skin: Intact + 100nmol antimiR-29


title: UC male52

description: NIDDK_ID: 6333

source_name: Rectal mucosal biopsy from UC Male age 17 at diagnosis

value: Rectal mucosal biopsy

value: Ulcerative Colitis

value: Male

tag: age at diagnosis

tag: pucai

tag: total mayo score

tag: eosinophil grade ≥ 32

value: No

tag: baseline calprotectin

tag: week 4 calprotectin


title: AS-065 #121 - Intact + 100nmol antimiR-29

description: Biological replicate 1 of 3. Mouse skin: Intact + 100nmol antimiR-29

tag: strain


title: AS-065 #32 - Incision + 100nmol promiR-29

description: Biological replicate 3 of 3. Mouse skin: Incision + 100nmol promiR-29

source_name: Skin: Incision + 100nmol promiR-29

value: Incision

value: promiR-29 100nmol


title: AS-065 #4 - Incision + PBS

description: Biological replicate 2 of 3. Mouse skin: Incision + PBS

source_name: Skin: Incision + PBS


title: villus_induced abortion_rep2

description: villus sample from induced abortion patients

value: villus

tag: developmental stage

value: Twelve weeks before pregnancy

tag: age

value: 23years old


title: villus_induced abortion_rep1

value: 25 years old


title: AS-065 #3 - Incision + PBS

description: Biological replicate 1 of 3. Mouse skin: Incision + PBS


title: UC male43

description: NIDDK_ID: 519

value: Y

tag: week 4 remission

tag: histology severity score


title: AS-065 #25 - Incision + 100nmol promiR-29

description: Biological replicate 1 of 3. Mouse skin: Incision + 100nmol promiR-29


title: villus_recurrent spontaneous abortion_rep2

tag: tissue

value: 24 years old


title: UC male42

description: NIDDK_ID: 3115

tag: diagnosis

value: Yes

tag: initial treatment

value: CS-Oral


title: UC male41

description: NIDDK_ID: 750

source_name: Rectal mucosal biopsy from UC Male age 12 at diagnosis

tag: Sex

value: N


title: UC male40

description: NIDDK_ID: 9763

value: unknown


title: AS-065 #5 - Incision + PBS

description: Biological replicate 3 of 3. Mouse skin: Incision + PBS

tag: wound

tag: treatment

value: PBS

value: Agilent mouse universal reference RNA


title: UC male39

description: NIDDK_ID: 14401

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: age at diagnosis

value: CS-IV


title: UC male37

description: NIDDK_ID: 1108

source_name: Rectal mucosal biopsy from UC Male age 13 at diagnosis

value: Male

tag: pucai

value: No


title: villus_induced abortion_rep3

value: villus


title: UC male35

description: NIDDK_ID: 13172

source_name: Rectal mucosal biopsy from UC Male age 15 at diagnosis

tag: total mayo score


title: UC male45

description: NIDDK_ID: 9998

tag: eosinophil grade ≥ 32


title: UC male34

description: NIDDK_ID: 11001

tag: baseline calprotectin


title: UC male36

description: NIDDK_ID: 2667

source_name: Rectal mucosal biopsy from UC Male age 9 at diagnosis

tag: week 4 calprotectin


title: UC male44

description: NIDDK_ID: 2171


title: UC male33

description: NIDDK_ID: 8397


title: UC male32

description: NIDDK_ID: 9975


title: UC male29

description: NIDDK_ID: 3286


title: UC male31

description: NIDDK_ID: 6565


title: UC male30

description: NIDDK_ID: 7802


title: UC male38

description: NIDDK_ID: 14516


title: AS-065 #102 - Intact + PBS

description: Biological replicate 3 of 3. Mouse skin: Intact + PBS

tag: strain

value: Intact

tag: sample type


title: UC male17

description: NIDDK_ID: 8045

source_name: Rectal mucosal biopsy from UC Male age 14 at diagnosis


title: UC male14

description: NIDDK_ID: 12976


title: UC male15

description: NIDDK_ID: 10003


title: UC male16

description: NIDDK_ID: 5366


title: UC male21

description: NIDDK_ID: 4199


title: UC male25

description: NIDDK_ID: 12881


title: UC male27

description: NIDDK_ID: 399


title: UC male28

description: NIDDK_ID: 133


title: UC male20

description: NIDDK_ID: 14224


title: UC male13

description: NIDDK_ID: 9687


title: UC male26

description: NIDDK_ID: 8328

source_name: Rectal mucosal biopsy from UC Male age 10 at diagnosis


title: AS-065 #27 - Incision + 100nmol promiR-29

description: Biological replicate 2 of 3. Mouse skin: Incision + 100nmol promiR-29

value: Incision

value: promiR-29 100nmol


title: UC male11

description: NIDDK_ID: 6261

source_name: Rectal mucosal biopsy from UC Male age 11 at diagnosis

value: Y


title: UC male12

description: NIDDK_ID: 13760


title: UC male10

description: NIDDK_ID: 4289


title: UC male8

description: NIDDK_ID: 1568


title: UC male7

description: NIDDK_ID: 5206


title: UC male9

description: NIDDK_ID: 2458


title: UC male18

description: NIDDK_ID: 2433


title: UC male22

description: NIDDK_ID: 1474


title: UC male24

description: NIDDK_ID: 12617


title: UC male19

description: NIDDK_ID: 13362


title: UC male23

description: NIDDK_ID: 12532

source_name: Rectal mucosal biopsy from UC Male age 4 at diagnosis


title: UC male6

description: NIDDK_ID: 13958


title: UC male5

description: NIDDK_ID: 4390


title: UC male4

description: NIDDK_ID: 10710


title: RNA-Seq_HUVEC_hypoxia_rep1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
Sequencing results were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded. Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best). RNA-Seq reads were aligned to the hg19 genome using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
GRO-Seq: The nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted usign Trizol LS
RNA-Seq: RNA was purified using RNeasy Mini Kit (Qiagen) and depleted from rRNAs using  Ribo-Zero Gold Kit (Illumina).
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol:
GRO-Seq: Confluent cultures of HUVECs were washed with PBS, followed by transduction with adenovirus encoding for empty transgene cassette under CMV promoter (AdCMV) and for constitutively active forms of HIF1a (AdHIF1a) and HIF2a (AdHIF2a) for 48h.
RNA-Seq: HUVECs were treated for 6h under hypoxia in 1%FBS EGM.

tag: cell type

value: Human umbilical vein endothelial cell (HUVEC)

value: 6h under hypoxia

tag: molecule subtype

value: rRNA depleted RNA


title: UC male3

description: NIDDK_ID: 12296

tag: week 4 remission

tag: histology severity score

value: CS-Oral


title: RNA-Seq_HUVEC_hypoxia_rep2


title: RNA-Seq_HUVEC_normoxia_rep2

value: normoxia


title: GRO-Seq_HUVEC_AdHIF2a

tag: genotype/variation

value: constitutively active forms of HIF2a (AdHIF2a)

value: nascent RNA


title: RNA-Seq_HUVEC_normoxia_rep1


title: UC male2

description: NIDDK_ID: 4491

tag: tissue

value: Rectal mucosal biopsy

tag: diagnosis

value: N

value: Yes

tag: initial treatment


title: GRO-Seq_HUVEC_AdHIF1a

value: constitutively active forms of HIF1a (AdHIF1a)


title: GRO-Seq_HUVEC_AdCMV

value: empty transgene cassette under CMV promoter (AdCMV)


title: UC female92

description: NIDDK_ID: 1682

source_name: Rectal mucosal biopsy from UC Female age 11 at diagnosis

value: Ulcerative Colitis

tag: Sex

value: Female

value: No

value: CS-IV

value: unknown


title: 32_MVA-B13R_SHIV_Ms2_MVA1_Day6

city: Atlanta

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
PolyA RNA
processed data file: 493_Amara_DESeq2_NormCounts.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the mouse (GRCm38.p3) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1).
Genome_build: GRCm38.p3 from ENCODE (GRCm38.p3.genome.fa, gencode.vM3.annotation.gtf)
Supplementary_files_format_and_content: 493_Amara_DESeq2_NormCounts.txt: Tab-delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Lymph node

extract_protocol:
Total RNA was purified using RNeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA).
Libraries were prepared on cDNA generated using SMART-Seq v4 Ultra Low Input RNA Kit. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.

treatment_protocol: Mice were intramuscularly immunized at 10^7 pfu/dose with MVA expressing SHIV antigens or MVA-B13R expressing SHIV. At days 1, 2, and 6 post immunization, draining inguinal lymph node cells were harvested for RNA extraction. 5 naive mice as a control group.

tag: strain/background

value: BALB/c

tag: gender

value: Lymph node

tag: virus

value: MVA-B13R SHIV

tag: time

value: Day 6


title: 35_MVA-B13R_SHIV_Ms5_MVA1_Day6


title: UC female93

description: NIDDK_ID: 13332

source_name: Rectal mucosal biopsy from UC Female age 9 at diagnosis

tag: age at diagnosis

tag: pucai

tag: total mayo score

value: CS-Oral

tag: baseline calprotectin


title: 34_MVA-B13R_SHIV_Ms4_MVA1_Day6


title: UC female87

description: NIDDK_ID: 3185

source_name: Rectal mucosal biopsy from UC Female age 16 at diagnosis

tag: eosinophil grade ≥ 32

tag: week 4 calprotectin


title: UC female88

description: NIDDK_ID: 8108

source_name: Rectal mucosal biopsy from UC Female age 7 at diagnosis

value: Y

tag: week 4 remission


title: UC female89

description: NIDDK_ID: 11383

source_name: Rectal mucosal biopsy from UC Female age 14 at diagnosis

tag: histology severity score


title: UC female90

description: NIDDK_ID: 14381

source_name: Rectal mucosal biopsy from UC Female age 17 at diagnosis


title: 31_MVA-B13R_SHIV_Ms1_MVA1_Day6


title: 30_MVA_SHIV_Ms5_MVA1_Day6

value: MVA SHIV


title: UC female85

description: NIDDK_ID: 7805

value: Rectal mucosal biopsy


title: UC female86

description: NIDDK_ID: 2198

source_name: Rectal mucosal biopsy from UC Female age 6 at diagnosis


title: UC female80

description: NIDDK_ID: 4096

source_name: Rectal mucosal biopsy from UC Female age 15 at diagnosis


title: UC female82

description: NIDDK_ID: 137


title: UC female84

description: NIDDK_ID: 8534

value: N


title: UC female79

description: NIDDK_ID: 8553

source_name: Rectal mucosal biopsy from UC Female age 13 at diagnosis

value: Yes


title: 27_MVA_SHIV_Ms2_MVA1_Day6


title: UC female83

description: NIDDK_ID: 1061

source_name: Rectal mucosal biopsy from UC Female age 12 at diagnosis


title: UC female81

description: NIDDK_ID: 1555


title: 29_MVA_SHIV_Ms4_MVA1_Day6


title: UC female78

description: NIDDK_ID: 2087


title: UC female91

description: NIDDK_ID: 13305


title: UC male1

description: NIDDK_ID: 13096

value: Male


title: UC female94

description: NIDDK_ID: 13754


title: 33_MVA-B13R_SHIV_Ms3_MVA1_Day6


title: UC female77

description: NIDDK_ID: 1803


title: 26_MVA_SHIV_Ms1_MVA1_Day6


title: 24_MVA-B13R_SHIV_Ms4_MVA1_Day2

value: Day 2


title: 25_MVA-B13R_SHIV_Ms5_MVA1_Day2


title: 23_MVA-B13R_SHIV_Ms3_MVA1_Day2


title: 28_MVA_SHIV_Ms3_MVA1_Day6


title: UC female74

description: NIDDK_ID: 13308

value: Ulcerative Colitis


title: UC female75

description: NIDDK_ID: 13310

value: Female


title: 22_MVA-B13R_SHIV_Ms2_MVA1_Day2


title: 21_MVA-B13R_SHIV_Ms1_MVA1_Day2


title: 18_MVA_SHIV_Ms3_MVA1_Day2


title: 19_MVA_SHIV_Ms4_MVA1_Day2


title: UC female73

description: NIDDK_ID: 2730


title: UC female71

description: NIDDK_ID: 8009

source_name: Rectal mucosal biopsy from UC Female age 8 at diagnosis

value: No


title: 14_MVA-B13R_SHIV_Ms4_MVA1_Day1

value: Day 1


title: 13_MVA-B13R_SHIV_Ms3_MVA1_Day1


title: 15_MVA-B13R_SHIV_Ms5_MVA1_Day1


title: 16_MVA_SHIV_Ms1_MVA1_Day2


title: 17_MVA_SHIV_Ms2_MVA1_Day2


title: 12_MVA-B13R_SHIV_Ms2_MVA1_Day1


title: UC female70

description: NIDDK_ID: 387

value: CS-IV


title: UC female69

description: NIDDK_ID: 5244

value: unknown


title: 11_MVA-B13R_SHIV_Ms1_MVA1_Day1

value: BALB/c

value: Lymph node


title: 9_MVA_SHIV_Ms4_MVA1_Day1


title: 8_MVA_SHIV_Ms3_MVA1_Day1


title: UC female68

description: NIDDK_ID: 19


title: UC female76

description: NIDDK_ID: 5356


title: UC female67

description: NIDDK_ID: 8836


title: 20_MVA_SHIV_Ms5_MVA1_Day2


title: 5_Naive_5_Day0

value: Naive

value: Day 0


title: UC female66

description: NIDDK_ID: 3711

value: Y

value: CS-Oral


title: 3_Naive_3_Day0


title: 10_MVA_SHIV_Ms5_MVA1_Day1

value: MVA SHIV


title: UC female72

description: NIDDK_ID: 12548

value: Rectal mucosal biopsy

value: N


title: 1_Naive_1_Day0


title: UC female65

description: NIDDK_ID: 11688


title: 2_Naive_2_Day0


title: UC female63

description: NIDDK_ID: 2073


title: UC female61

description: NIDDK_ID: 2548


title: UC female62

description: NIDDK_ID: 2766

value: Yes


title: UC female60

description: NIDDK_ID: 8771


title: 7_MVA_SHIV_Ms2_MVA1_Day1


title: 6_MVA_SHIV_Ms1_MVA1_Day1


title: UC female59

description: NIDDK_ID: 3906


title: 4_Naive_4_Day0


title: UC female64

description: NIDDK_ID: 13459


title: UC female57

description: NIDDK_ID: 10840


title: UC female56

description: NIDDK_ID: 4564

source_name: Rectal mucosal biopsy from UC Female age 10 at diagnosis


title: GmBR16_80_DAG_2

city: Viçosa

first: Otavio Jose

middle: Bernardes

last: Brustolini

state: MG

address: Av. PHRolfs, S/N

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Viçosa

data_processing:
Basecalls performed using CASAVA version 1.7
RNA-seq reads were aligned using bowtie2 to Glycine max genome version Wm82.a2.v1 presented at Phytozme 12 repository
The mapped read were counted by the R/Bioconcuctor package Rsubread to create the count table.
log2 of fold change and statistical significane were calculated by the R/Bioconductor package DESeq2

organism: Glycine max

source_name: plant at 80 days after germination

growth_protocol: the plant was grow in vase 3L with soil in greenhouse

extract_protocol:
User Guide Trizol™Reagent Invitrogen
TruSeq® Stranded Sample Preparation utilizando o Low Sample (LS) Protocol da Illumina

value: leaf

tag: age

value: 80 days after germination


title: GmBR16_20_DAG_2

source_name: plant at 20 days after germination

tag: tissue

value: 20 days after germination


title: GmBR16_20_DAG_1


title: GmBR16_20_DAG_3


title: GmBR16_80_DAG_3


title: UC female55

description: NIDDK_ID: 2359

tag: diagnosis

value: Ulcerative Colitis

value: Female


title: GmBR16_80_DAG_1


title: TIC_normoxic_day6_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description: 6d NSC_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Immortalized tumor-initiating cells were cultured in hypoxic stem cell conditions, including a serum-free mammary stem cell medium (MEBM base, Lonza) with 2% Cultrex® supplement (Trevigen) and an atmosphere of 3% O2, 5% CO2, and 92% N2 at 37°C.

extract_protocol: Total RNA was extracted using the peqGOLD Total RNA kit (Peqlab) following the manufacturer's instructions.

treatment_protocol: To analyze iTICs gene expression profile in normoxic standart conditons (1 to 7 days), cells were transferred from hypoxic stem cell conditions into standard medium (DMEM base, Gibco) and an atmosphere of 21% O2, 5% CO2, and 92% N2 at 37°C.

value: 6 days

tag: cell source

value: Immortalized tumor-initiating cells

tag: replicate

value: rep 1

tag: culture condition

value: normoxic standard conditions


title: TIC_normoxic_day7_rep3

description: 7d NSC_3

value: 7 days

value: rep 3


title: TIC_hypoxic_rep2

value: rep 2

value: hypoxic stem cell conditions


title: TIC_normoxic_day2_rep1

description: 2d NSC_1

value: 2 days


title: TIC_hypoxic_rep3


title: TIC_hypoxic_rep1


title: TIC_normoxic_day4_rep1

description: 4d NSC_1

value: 4 days


title: UC female54

description: NIDDK_ID: 13518

value: Rectal mucosal biopsy

tag: Sex

value: Y

tag: initial treatment

value: CS-Oral


title: TIC_normoxic_day7_rep1

description: 7d NSC_1

tag: time


title: TIC_normoxic_day1_rep1

description: 1d NSC_1

value: 1 day


title: TIC_normoxic_day5_rep1

description: 5d NSC_1

value: 5 days


title: UC female53

description: NIDDK_ID: 10272

value: Ulcerative Colitis

tag: age at diagnosis

value: N

value: No

value: unknown


title: UC female58

description: NIDDK_ID: 9764

value: Female

tag: pucai

value: Yes


title: TIC_normoxic_day7_rep2

description: 7d NSC_2

value: 7 days

value: Immortalized tumor-initiating cells

value: normoxic standard conditions


title: TIC_normoxic_day3_rep1

description: 3d NSC_1

value: 3 days

value: rep 1


title: UC female51

description: NIDDK_ID: 13363

tag: total mayo score

value: CS-IV


title: UC female52

description: NIDDK_ID: 13651

value: Rectal mucosal biopsy

tag: baseline calprotectin


title: UC female50

description: NIDDK_ID: 2703

tag: eosinophil grade ≥ 32

value: Y


title: UC female49

description: NIDDK_ID: 2076

tag: week 4 calprotectin


title: UC female48

description: NIDDK_ID: 582

tag: week 4 remission


title: UC female47

description: NIDDK_ID: 1119

tag: histology severity score


title: B6_8h_2

last: Ma

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Streptococcus Suis Serotype 2 infected mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Eight to ten weeks old A/J and C57BL/6 mice were purchased from Model Animal Research Center of Nanjing University (Nanjing, China)

extract_protocol: Their blood samples were collected aseptically at 2, 4 and 8 h after injection respectively. Mice in the fourth control group had blood samples aseptically taken at the same intervals following injection with 1 mL of THB culture.

treatment_protocol: Twenty-four 8-10 week old A/J and C57BL/6 mice were randomly divided into four groups, each of which contained 3 A/J and 3 C57BL/6 mice. Mice in the three experimental groups were injected with the inoculum (1 mL per mouse) via i.p.

tag: sample type

value: Post infection time


title: B6_8h_3


title: B6_8h_1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: UC female46

description: NIDDK_ID: 9761

tag: tissue


title: UC female45

description: NIDDK_ID: 1023

tag: diagnosis

value: CS-Oral


title: B6_4h_2


title: B6_4h_3


title: B6_4h_1


title: B6_0h_3


title: B6_0h_1


title: B6_2h_1


title: B6_0h_2


title: B6_2h_2


title: B6_2h_3


title: UC female44

description: NIDDK_ID: 11783


title: AJ_8h_1


title: AJ_4h_1


title: AJ_8h_2


title: UC female42

description: NIDDK_ID: 4205


title: AJ_2h_1


title: AJ_8h_3


title: AJ_4h_2


title: AJ_4h_3


title: UC female43

description: NIDDK_ID: 9329


title: AJ_2h_3


title: UC female41

description: NIDDK_ID: 3398


title: 445-P-29-NR4A2

city: Houston

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

data_processing:
Sequenced reads were assessed for quality using the Illumina Basespace Cloud Computing Platform.
FASTQ sequence files were used to align reads to the rat reference genome [Rattus norvegicus/Rn5 (Refseq)] using RNA-Seq Alignment Application (using STAR aligner)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were determined using Cufflinks Assembly & DE workflow (v2.1.0)
Genome_build: UCSC Rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Adult rat ventricular myocytes

growth_protocol: ARVMs were isolated according to a modified version of the method developed by Ackers-Johnson and colleagues (PMC5965670). In brief, rats anesthetized with 2-3% inhaled isoflurane were intravenously injected with 200 USP units heparin and their hearts subsequently removed and immediately transferred into ice-cold EDTA buffer. Following aortic cannulation, the hearts were retrogradely perfused first with 20 ml of ice-cold EDTA buffer to wash them free of blood, then with 40 ml of ice-cold perfusion buffer, and lastly with 40 ml of recirculating collagenase buffer pre-warmed at 38ºC. After proceeding with mechanical dissociation of heart tissue, cell separation by gravity settlement, and calcium re-introduction, ARVMs were plated at a density of 35,000-55,000 cells cm-2 in plating media (Medium 199, 5% (v:v) fetal bovine serum, 10 mmol/l 2,3-Butanedione monoxime (BDM), 100 units/ml penicillin, and 100 µg/ml streptomycin) on laminin-coated tissue culture dishes. One hour after plating, the plating media was replaced with culture media (Medium M199, 0.1% (w:v) bovine serum albumin, 1x insulin-transferrin-selenium, 10 mmol/l BDM, 1x chemically defined lipid concentrate, 100 units/ml penicillin, and 100 µg/ml streptomycin).

extract_protocol:
Cells were washed once with 1X DPBS and total RNA was extracted using Trizol Reagent. Total RNA was further purified and DNase-treated with PureLink RNA Mini kit (Ambion Cat. No. 12183018A).
cDNA libraries were developed using the TruSeq mRNA Stranded Library Prep Kit (Set-A-indexes), evaluated by Qubit fluorometer (Invitrogen), and assessed for quality and size using Bio-Rad Experion System.
Samples were pooled into single library (n=12 pooled samples per library) and sequenced using the NextSeq 500 High Output Kit (300 cycles, paired end 101bp) on the Illumina NextSeq 500 platform. The run generated 136.4 Gb at QC30=87.5% with 670 million or 55 million reads passing filter.

treatment_protocol: ARVMs were incubated at 37°C in 5% CO2 and transduced with recombinant adenoviruses (Ad-h-NR4A2 or ad-GFP) with a m.o.i. of 50 at the time of replacement of plating media with the culture media. Cells were kept for another 48 hours until total RNA extraction without changing media.

tag: strain

value: Sprague Dawley

value: Heart

tag: cell type

value: Adult ventricular myocytes

tag: transduction


title: 445-P-28-NR4A2


title: AJ_0h_3

first: Zhe

institute: nanjing agricultural university


title: AJ_2h_2


title: 445-P-27-NR4A2


title: 445-P-26-NR4A2


title: 445-P-25-NR4A2


title: AJ_0h_2


title: AJ_0h_1


title: 445-P-28-GFP

value: ad-GFP


title: 445-P-29-GFP


title: UC female38

institute: Cincinnati Children's Hospital Medical Center

description: NIDDK_ID: 4904

value: Ulcerative Colitis

tag: Sex

value: N

value: No

value: unknown


title: 445-P-24-NR4A2


title: 445-P-26-GFP


title: UC female39

description: NIDDK_ID: 3101

value: Female

value: Yes

tag: initial treatment


title: UC female40

description: NIDDK_ID: 1321


title: 445-P-27-GFP


title: 445-P-25-GFP


title: 445-P-24-GFP