title: 2018HC346 [08-2-B]

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.6.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample


title: 2018HC173 [6115-I]

status: Public on Jan 18 2019

type: SRA

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

library_source: transcriptomic

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal carcinoma samples

extract_protocol:
Total RNA was extracted from each samples using Macherey-Nagel RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: genotype

value: p16INK4A positive expression

tag: tissue

value: Colorectal carcinoma


title: PLM1

city: London

first: Francesca

last: Capon

address: Great Maze Pond

department: Genetics and Molecular Medicine

country: United Kingdom

institute: King's College London

description: affected status

data_processing:
Quality of fastq files was assessed using fastQC.
Reads were trimmed using fatx-toolkit
Genome was alligned using TopHat and Bowtie
Reads were counted using htseq-count
Genome_build: HG38
Supplementary_files_format_and_content: tab delimeted file containing normalised counts

molecule: polyA RNA

source_name: Neutrophils

extract_protocol:
mRNA was extracted from isolated neutrophils using GeneJet  kit by ThermoFisher.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: patient diagnosis

value: Generalised Pustular Psoriasis

tag: cell type

value: Neutrophils


title: M19

description: affected status


title: M35

description: affected status


title: M36

description: affected status


title: M43

description: affected status


title: M14

description: affected status


title: 2018HC100 [C]

value: p16INK4A negative expression


title: 2017HC070 [C-2]


title: 2018HC173 [6115-C]


title: M6

description: affected status


title: 2018HC346 [08-2-A]


title: M4

description: affected status


title: PLM11

description: healthy

value: Healthy


title: PLM9

description: healthy


title: M28

description: healthy


title: M26

description: healthy


title: M37

description: healthy


title: M25

description: healthy


title: M41

description: healthy


title: M44

description: healthy


title: M40

description: healthy


title: M29

description: healthy


title: M18

description: healthy


title: inflamed sigmoid colon DMSO: Intact Tissue 468914

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

data_processing:
STAR used for mapping and alignment 2.4.0k
Featurecounts used for gene quantification 1.4.6
Limma-voom package used for differential analysis
Genome_build: Hg38
Supplementary_files_format_and_content: data matrix with raw counts. Column header IDs are available above in the 'description' field.

source_name: IBD UC Colon Biopsy

extract_protocol:
Qiazol extraction of total RNA was performed according to the manufacturer's instructions.
Libraries were constructed manually using Illumina's stranded total RNAseq kit according to the manufacturers instructions

treatment_protocol: Colon biopsies were placed in RNALater  or DMSO freezing media and stored frozen until processed

tag: collection media

value: DMSO

tag: status

value: inflamed

value: sigmoid colon

tag: age

tag: Sex

tag: sample id


title: inflamed sigmoid colon RNA Later 468914

value: RNA Later


title: uninflamed transverse colon RNA Later 162573

value: uninflamed

value: transverse colon

value: female


title: inflamed sigmoid colon DMSO: Intact Tissue 162573


title: inflamed descending colon DMSO: Intact Tissue 533145

value: descending colon

value: male


title: uninflamed ascending colon RNA Later 533145

value: ascending colon


title: inflamed descending colon RNA Later 533145


title: inflamed sigmoid colon RNA Later 162573


title: uninflamed transverse colon DMSO: Intact Tissue 162573


title: uninflamed ascending colon RNA Later 150329


title: inflamed sigmoid DMSO: Intact Tissue 150329

value: sigmoid


title: uninflamed right colon DMSO: Intact Tissue 468914

value: right colon


title: uninflamed right colon RNA Later 468914


title: uninflamed ascending colon DMSO: Intact Tissue 533145


title: inflamed sigmoid RNA Later 150329


title: uninflamed right colon DMSO: Intact Tissue 424848


title: PSO_005_non-lesional

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the human reference genome (b37) using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: b37
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: skin biopsy

extract_protocol:
5mm skin punch biopsies were stored in PaxGene tissue containers (PreAnalytiX) at -80°C until isolation of total RNA with the Qiagen AllPrep DNA/RNA Mini Kit preceded by an additional disruption/homogenization step with innuSPEED Lysis Tubes W (Analytik Jena) and Qiagen QIAshredder spin-columns.
RNA samples were prepared for sequencing using the Illumina Truseq® Stranded total RNA Protocol in combination with the RiboZero rRNA removal Kit and sequenced on the HiSeq2500 with 2x125bp.

tag: patient's condition

value: PSO

tag: skin type

value: non-lesional


title: uninflamed right colon RNA Later 133724


title: inflamed left colon DMSO: Intact Tissue 133724

value: left colon


title: inflamed left colon RNA Later 133724


title: uninflamed ascending colon RNA Later 174784


title: inflamed sigmoid colon RNA Later 174784

description:
PF04637
This sample failed quality control. Therefore processed data are not provided for this sample.


title: uninflamed right colon DMSO: Intact Tissue 361179


title: uninflamed ascending colon DMSO: Intact Tissue 174784


title: inflamed sigmoid colon DMSO: Intact Tissue 174784


title: inflamed sigmoid colon DMSO: Intact Tissue 361179


title: Uninflamed Sigmoid Colon DMSO: Intact Tissue 120143

value: Sigmoid Colon


title: uninflamed right colon RNA Later 361179


title: inflamed rectum DMSO: Intact Tissue 120143

value: rectum


title: uninflamed right colon RNA Later 255220


title: Uninflamed Sigmoid Colon RNA Later 120143


title: inflamed sigmoid colon RNA Later 361179


title: inflamed transverse colon RNA Later 255220


title: inflamed rectum RNA Later 120143


title: uninflamed right colon DMSO: Intact Tissue 490730

value: DMSO


title: inflamed transverse colon DMSO: Intact Tissue 255220

value: inflamed


title: uninflamed right colon DMSO: Intact Tissue 255220


title: inflamed transverse colon DMSO: Intact Tissue 490730


title: inflamed transverse colon RNA Later 490730


title: uninflamed right colon RNA Later 490730


title: uninflamed right colon DMSO: Intact Tissue 133724


title: WT Fat body Rep2 miRNA-seq

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

description:
miRNA
Fat body sample K
miRNA-seq.Readcount_output.txt

data_processing:
RNA-seq: Raw sequence reads were quality-trimmed using Trim Galore! (v0.3.7). Trimmed sequences were aligned using Tophat2 (Kim et al., 2013, v2.0.14) against the the Dm6 reference genome (dos Santos et al., 2015). Multi-mapped reads were filtered using samtools (Li et al., 2009). Data visualization and analysis was performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), custom RStudio (https://www.rstudio.com/) scripts and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO, ReactomePA and org.Dm.eg.db. For visualization of functional enrichment analysis results, we further used the CellPlot package (https://github.com/dieterich-lab/CellPlot).
miRNA-seq: miRNA reads were identified using miRDeep (Friedlander et al. 2008) and miRNAs with a minimum read number of 10 were included for further analysis. The tissue-specificity score was calculated as described previously  (Landgraf et al. 2007) and miRNAs with a tissue-specificity score > 1 were defined as tissue-specific.
Genome_build: Dm6
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each sample; results for differential gene expression analysis.miRNA-seq: tab-delimited text file include raw counts for each sample

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: Fly stocks were kept at 25¡C on a 12 h light and 12 h dark cycle and fed a standard sugar/yeast/agar diet (Bass et al. 2007). In all experiments, flies were reared at controlled larval densities and once-mated female flies were used. Flies were snap frozen with liquid nitrogen. Dissections were carried out in phosphate_buffered saline (PBS) and tissues either directly analysed or frozen on dry ice. Transgenic flies were backcrossed into a white Dahomey (wDah) or red Dahomey (rDah) wild_type strain with the endosymbiont Wolbachia for at least six generations.

extract_protocol:
miRNA-seq: Total RNA including miRNAs was extracted using the Qiagen miRNeasy Mini kit following the manufacturers protocol. Small RNA was enriched from 2 µg total RNA by gel electrophoresis using a Bio-Rad PROTEAN® II xi Cell with a 15 % polyacrylamide/urea gel in 0.5 x TBE buffer. Samples were mixed with loading dye (2x; 89.75 % Formaldehyde, 10 % TBE (5x), 0.05 % sodium dodecyl sulfate, 0.05 % bromophenol blue) and run at 300 V for 300 min. Small RNA between 19 and 26 bp was cut out and used for library preparation.
miRNA-seq: Small RNA sequencing libraries were generated using the Small RNA v1.5 Kit (Illumina), following the manufacturers protocol. miRNA sequencing was performed with an Illumina HighSeq2500, single-end reads and 100 bp read length at the Max Planck Genome Centre Cologne (Germany).

treatment_protocol: We used  the CRISPR/Cas9 system  according to previous publications (Port et al. 2014) to generate miR-210KO flies. First, transgenic flies expressing two guideRNAs up-stream and down-stream of the miR-210 gene were generated (pCFD4-miR-210). Finally, pCFD4-miR-210 flies were crossed with flies expressing Cas9 and progeny screened by PCR.

tag: strain

value: wDah

value: Fat body

value: wildtype

value: 10 days after eclosion

tag: developmental stage

value: Adult


title: WT Fat body Rep1 miRNA-seq

description:
miRNA
Fat body sample J
miRNA-seq.Readcount_output.txt


title: WT Gut Rep2 miRNA-seq

description:
miRNA
Gut sample H
miRNA-seq.Readcount_output.txt

source_name: Gut

value: Gut


title: WT Gut Rep1 miRNA-seq

description:
miRNA
Gut sample G
miRNA-seq.Readcount_output.txt


title: WT Thorax Rep3 miRNA-seq

description:
miRNA
Thorax sample  F
miRNA-seq.Readcount_output.txt

source_name: Thorax

value: Thorax


title: uninflamed ascending colon DMSO: Intact Tissue 150329

value: uninflamed

value: ascending colon

value: male


title: WT Thorax Rep2 miRNA-seq

description:
miRNA
Thorax sample  E
miRNA-seq.Readcount_output.txt


title: uninflamed right colon RNA Later 424848

value: RNA Later

value: right colon


title: inflamed rectum RNA Later 424848


title: inflamed rectum DMSO: Intact Tissue 424848


title: WT Thorax Rep1 miRNA-seq

description:
miRNA
Thorax sample  D
miRNA-seq.Readcount_output.txt


title: WT Brain Rep2 miRNA-seq

description:
miRNA
Brain sample  B
miRNA-seq.Readcount_output.txt

source_name: Brain

value: Brain


title: WT Gut Rep3 miRNA-seq

description:
miRNA
Gut sample I
miRNA-seq.Readcount_output.txt


title: WT Brain Rep3 miRNA-seq

description:
miRNA
Brain sample  C
miRNA-seq.Readcount_output.txt


title: WT Fat body Rep3 miRNA-seq

description:
miRNA
Fat body sample L
miRNA-seq.Readcount_output.txt


title: mir210KO Rep3 RNA-seq

description:
mRNA
Differential_Gene_expression_Analysis_results_mir210KO_vs_WT.txt
RNA-seq.Readcount_output.txt

source_name: Head

extract_protocol:
RNA-seq: Total RNA was extracted by Trizol (ThermoFisher) following standard protocols.
RNA-seq: . Poly (A) capture libraries were generated at the Max Planck-Genome-Centre Cologne (Germany). According to the facility’s procedure, stranded TruSeq RNA-seq libraries were prepared as described in (Sultan et al., 2012), using 3 μg of rRNA-depleted RNA as input. RNA sequencing was performed with an Illumina HighSeq2500 and 25 million single-end reads/sample and 150 bp read length at the Max Planck Genome Centre Cologne (Germany).

value: Head

value: 1 hr after eclosion


title: inflamed transverse colon DMSO: Intact Tissue 43821

value: DMSO

value: transverse colon


title: inflamed transverse colon RNA Later 43821

value: inflamed


title: mir210KO Rep2 RNA-seq

extract_protocol:
RNA-seq: Total RNA was extracted by Trizol (ThermoFisher) following standard protocols. miRNA-seq: Total RNA including miRNAs was extracted using the Qiagen miRNeasy Mini kit following the manufacturers protocol.
RNA-seq: . Poly (A) capture libraries were generated at the Max Planck-Genome-Centre Cologne (Germany). According to the facility’s procedure, stranded TruSeq RNA-seq libraries were prepared as described in (Sultan et al., 2012), using 3 μg of rRNA-depleted RNA as input. RNA sequencing was performed with an Illumina HighSeq2500 and 25 million single-end reads/sample and 150 bp read length at the Max Planck Genome Centre Cologne (Germany).

value: wDah


title: uninflamed right colon DMSO: Intact Tissue 964151


title: WT Rep3 RNA-seq

value: wildtype


title: uninflamed right colon DMSO: Intact Tissue 43821


title: WT Brain Rep1 miRNA-seq

description:
miRNA
Brain sample  A
miRNA-seq.Readcount_output.txt

value: 10 days after eclosion


title: mir210KO Rep1 RNA-seq

value: Adult


title: inflamed rectum DMSO: Intact Tissue 964151

value: rectum


title: WT Rep2 RNA-seq


title: Uninflamed Sigmoid Colon DMSO: Intact Tissue 190398

value: Sigmoid Colon

value: female


title: Uninflamed Sigmoid Colon RNA Later 190398

value: uninflamed


title: inflamed rectum RNA Later 964151

value: male


title: inflamed transverse colon DMSO: Intact Tissue 190398


title: elav_3_RNAseq

city: Ramat Gan

first: Galit

last: Shohat-Ophir

address: The Nanotechnology Building 206, Room C-663

country: Israel

institute: Bar Ilan University

data_processing:
Low quality bases were trimmed from RNA-seq reads using Trim Galore and mapped to the dm6 using STAR (v2.4.2) --twopassMode.
For gene expression analysis: featureCounts from the Subread package (v1.4.5) was used to determine read counts overlapping exons in the BDGP6.88 transcriptome from ensembl. DESeq2 was used to calculate normalized counts and gene expression differences from these counts.
For RNA editing analysis: Picard tools were used to mark duplicates and samtools mpileup function was used to determine base calls at known editing sites from non-duplicate, uniquely mapped reads. Editing levels were calculated as (G reads)/(A+G reads) at each site.
Genome_build: dm6
Supplementary_files_format_and_content: For gene expression analysis: read counts for transcripts from featureCounts. Tab-delimited files are formatted as: gene id, chr, start, end, strand, length, counts.
Supplementary_files_format_and_content: For RNA editing analysis: A and G counts and editing levels at known editing sites. Tab-delimited files are formatted as: chr, position, a counts, g counts, editing level.

molecule: nuclear RNA

source_name: all brain neurons nuclei

growth_protocol: Flies were raised at 25°C in a 12-h light/12-h dark cycle in 60% relative humidity and maintaned on cornmeal, yeast, molasses, and agar medium. Approximately 300 heads were collected from 2-3 day old flies.

extract_protocol:
Heads were separated by vigorous vertexing followed by separation over dry-ice cooled sieves.  9ml of homogenization buffer (20mM β-Glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40 supplemented with RNAase inhibitor,10mg/ml t-RNA, 50mg/ml ultrapure BSA, 0.5mM Spermidine, 0.15mM Spermine and 140ul of carboxyl Dynabeads -270 Invitrogene: 14305D) was added to each sample. The heads were minced on ice by a series of mechanical grinding steps followed by filtering the homogenate using a 10um Partek filter assembly (Partek: 0400422314). After removing the carboxyl-coated Dynabeads using a magnet, the homogenate was filtered using a 1um pluriSelect filter (pluriSelect: 435000103). The liquid phase was carefully placed on a 40% optiprep cushion layer and centrifuged in a 4oC centrifuge for 30min at ~2300Xg. The homogenate/Optiprep interface was incubated with anti-GFP antibody (Invitrogen: G10362) and protein G Dynabeads (Invitrogen: 100-03D) for 40 minutes at 4oC . Beads were then washed once in NUN buffer (20mM β-Glycerophosphate pH7, 300mM NaCl, 1M Urea, 0.5% NP40, 2mM EDTA, 0.5mM Spermidine, 0.15mM Spermine, 1mM DTT, 1X Complete protease inhibitor, 0.075mg/ml Yeast torula RNA, 0.05Units/ul Superasin). Bead-bound nuclei were separated using a magnet stand, and RNA was extracted using the Picopure Kit (Invitrogen KIT0204).
The NuGEN RNAseq v2 (7102-32) kit was used to prepare cDNA from the INTACT purified RNA, followed by library preparation using the SPIA - NuGEN Encore Rapid DR prep kit. Samples were sequenced on an Illumina HiSeq using single-end 60 base pair reads.

value: UAS-unc84-2XGFP; elav-GAL4

tag: neuronal population

value: all brain neurons

tag: replicate


title: elav_1_RNAseq

source_name: all brain neuron nuclei


title: inflamed transverse colon RNA Later 190398

value: RNA Later


title: elav_2_RNAseq


title: uninflamed right colon RNA Later 43821

value: right colon


title: uninflamed right colon DMSO: Intact Tissue 614819


title: OK107_3_RNAseq

source_name: mushroom body neuron nuclei

value: UAS-unc84-2XGFP; OK107-GAL4

value: mushroom body


title: uninflamed right colon RNA Later 614819


title: Fru_3_RNAseq

source_name: fruitless neuron nuclei

value: UAS-unc84-2XGFP; Fru-GAL4

value: fruitless


title: inflamed transverse colon DMSO: Intact Tissue 614819

value: DMSO

value: inflamed

value: transverse colon


title: OK107_2_RNAseq


title: OK107_1_RNAseq


title: uninflamed right colon RNA Later 964151


title: uninflamed right colon RNA Later 951932


title: WT Rep1 RNA-seq

value: wDah

value: Head

value: wildtype

value: 1 hr after eclosion

value: Adult


title: inflamed rectum RNA Later 951932

value: rectum

value: female


title: Fru_2_RNAseq


title: Fru_1_RNAseq


title: Trh_3_RNAseq

source_name: serotonergic neuron nuclei

value: UAS-unc84-2XGFP; Trh-GAL4

value: serotonergic


title: uninflamed right colon DMSO: Intact Tissue 108776

value: uninflamed

value: right colon


title: Trh_2_RNAseq


title: TH_3_RNAseq

source_name: dopaminergic neuron nuclei

value: UAS-unc84-2XGFP; TH-GAL4

value: dopaminergic


title: Trh_1_RNAseq


title: inflamed transverse colon RNA Later 614819

value: RNA Later


title: TH_1_RNAseq


title: uninflamed right colon RNA Later 108776


title: inflamed rectum DMSO: Intact Tissue 951932

value: DMSO


title: uninflamed right colon DMSO: Intact Tissue 951932


title: TH_2_RNAseq


title: inflamed rectum DMSO: Intact Tissue 108776

value: inflamed


title: uninflamed ascending colon RNA Later 186931

value: ascending colon


title: inflamed rectum DMSO: Intact Tissue 186931


title: uninflamed ascending colon DMSO: Intact Tissue 186931


title: Tdc2_3_RNAseq

source_name: octopaminergic neuron nuclei

value: UAS-unc84-2XGFP; Tdc2-GAL4

value: octopaminergic


title: inflamed rectum RNA Later 186931


title: Crz_2_RNAseq

source_name: corzonin neuron nuclei

value: UAS-unc84-2XGFP; Crz-GAL4

value: corzonin


title: Crz_1_RNAseq


title: Crz_3_RNAseq


title: Tdc2_1_RNAseq


title: Tdc2_2_RNAseq


title: NPFR_2_RNAseq

source_name: neuropeptide F receptor neuron nuclei

value: UAS-unc84-2XGFP; NPFR-GAL4

value: neuropeptide F receptor


title: NPFR_3_RNAseq


title: NPF_2_RNAseq

source_name: neuropeptide F neuron nuclei

value: UAS-unc84-2XGFP; NPF-GAL4

value: neuropeptide F


title: NPF_1_RNAseq


title: Dh44_3_RNAseq

source_name: diuretic hormone 44 neuron nuclei

value: UAS-unc84-2XGFP; Dh44-GAL4

value: diuretic hormone 44


title: NPFR_1_RNAseq


title: Dh44_2_RNAseq


title: NPF_3_RNAseq


title: Dh44_1_RNAseq


title: kinase dead Cdk8 r3

city: St. Louis

first: Yiming

last: Kang

state: MO

address: 1 Brookings Dr

department: Computer Science and Engineering

institute: Washington University in St. Louis

data_processing:
Reads aligned to reference genome using NovoAlign version 3.07.00 with default parameters
Raw read counts performed using HTSeq version 0.9.1
Genome_build: C. neoformans H99 reference sequence v2
Supplementary_files_format_and_content: tsv files were generated using HTSeq-count; Values associated to the genes represent raw read count

organism: Cryptococcus neoformans

source_name: Fungal cells

extract_protocol:
Ice-cold stop solution was added directly to cultures before resuspension in TRIzol reagent and lysis with mechanical bead beating using 0.5-mm silica-zirconia beads (4 rounds of 3 min, 2 min rest on ice between each round). Poly (A) RNA was selected with the mRNA Catcher Plus Kit with an epMotion 5075 liquid handling robot.
First strand cDNA synthesis was performed with random hexameric primers and SuperScript III Reverse Trnascriptase. Samples were treated with E. coli DNA ligase, DNA polymerase I, and Rnase H for second-strand synthesis. The cDNA libraries were then end-repaired with a Quick Blunting kit, A-tailed with Klenow exo- with dATP, and Illumina adapters with four base barcodes were ligated to the cDNA. 150-250 bp fragments were selected using gel electrophoresis and enriched with PCR (10 cycles) using Phusion Hot Start II HF DNA Polymerase, purified, and pooled equimolarly for sequencing.

tag: genotype/variation

value: kinase dead Cdk8


title: WT control Cdk8 r1

value: WT control Cdk8


title: kinase dead Cdk8 r2


title: inflamed rectum RNA Later 108776

source_name: IBD UC Colon Biopsy

value: rectum

tag: subject id

value: female


title: kinase dead Cdk8 r1


title: WT control Cdk8 r3


title: cdk8 deletion r1

value: cdk8 deletion


title: cdk8 deletion r3


title: med12 deletion r2

value: med12 deletion


title: med12 deletion r3


title: med12 deletion r1


title: med13 deletion r3

value: med13 deletion


title: WT control Cdk8 r2


title: med13 deletion r1


title: ssn801 deletion r2

value: ssn801 deletion


title: ssn801 deletion r3


title: KN99alpha r1


title: med13 deletion r2


title: KN99alpha r2


title: ssn801 deletion r1


title: KN99alpha r3


title: 425_1 Affymetrix OncoScan AT GC

type: genomic

city: Atlanta

first: Zachary

last: Buchwald

state: GA

address: 1365 Clifton Rd # 1-A

institute: Emory University

description: Affymetrix OncoScan

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:
For the Emory Institutional dataset, Affymetrix OncoScan FFPE single nucleotide polymorphism (SNP) array was used for raw genomic data acquisition. Two data tracks are produced from SNP arrays: total signal intensity and allelic contrast. Log ratio (R) represents the total signal intensity, which reflects the total copy number on a logarithmic scale. The B allele frequency (BAF) represents the allelic contrast and demonstrates the relative presence at each SNP locus evaluated of the two alternative nucleotides. For the TCGA dataset, Affymetrix Genome-Wide Human SNP Array 6.0 was utilized for the raw genomic data. Following acquisition of the raw genomic data from biopsy or resected tumor samples, we opened each microarray case in Affymetrix Chromosome Analysis Suite v3.0 and used the "Export Probe Level Data" function to create a text file with the microarray probe set name, log 2 ratio (log R) signal, and B-allele frequency (BAF) BAF signal suitable for processing with the ASCAT v2.4.4 library in R v3.4.1. For the TCGA data set, raw data was previously acquired with the Affymetrix Genome-Wide Human SNP Array 6.0, which was processed using an R-package “Rawcopy” to create the probe level BAF and log R data. These data were input into the ASCAT algorithm. As a function of the SNP data, ASCAT models the allele-specific copy number and arrives at the solution that is closest to integer copies at all assessed loci. To do this accurately, the ASCAT algorithm accounts for important factors including polyploidy and aberrant cell fraction when calculating the CNV profile.8 Aneuploidy, a deviation from the normal chromosomal number, can confound copy number analysis. Non-aberrant cell admixture or aberrant cell fraction reflects the non-tumor component of the sample and can differ significantly between samples again confounding copy number studies. As an intermediate output of the ASCAT algorithm, we quantified the number of segments with changes in the log R and BAF. A segment is defined as a region of the genome with a fixed copy number. For a representative log R data sample, there were an average of 4,866,610 base pairs and 332 probes per segment with a range of 109,439 – 8,276,5227 base pairs and 7 – 5,997 probes. The total number of segments reflects the number of CNV inflection points or changes in copy number in the genome.
primary data description: Total genome segment counts - a segment is defined as a region of the genome with a fixed copy number.

label: Biotin

molecule: genomic DNA

source_name: FFPE tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Affymetrix’s DNA extraction protocol was utilized with a few modifications: FFPE slides instead of block cuts, Citrosolv instead of xylene for deparaffinization, and one thermomixer instead of two. Because some of the samples we obtained during the initial microarray validation, we received the DNA already isolated.

treatment_protocol: Patient's tumors were treated with temozolomide and 60 Gy of ionizing radiation

tag: disease state

value: glioblastoma


title: 434_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 435_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 433_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 428_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: cdk8 deletion r2


title: 424_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 432_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 418_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 421_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 422_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 419_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 420_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 416_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 414_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 412_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 410_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 407_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 431_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 405_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 400_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 398_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 399_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 392_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 397_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 396_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 389_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 372_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 388_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 373_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 370_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 360_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 351_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 359_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 357_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 354_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 348_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 350_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 411_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 347_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 345_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 409_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 403_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 352_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 343_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 394_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 377_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 341_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 342_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 340_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 339_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 116_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 338_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 335_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 334_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: 106_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: TMZ_U251 replicate 2

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

country: China

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to hg19 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Hi-C were mapped to hg19 with HIC-Pro (2.11.1). Then we obtained the matrix
Clean reads of Capture Hi-C were cut into two pieces in the DpnII sites
All the reads were mapped to hg19 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: Text files include genes counts values, Hi-C matrixes and Capture Hi-C signal peaks for each Sample

source_name: U251_Cell line

growth_protocol: U251 cell line was cultured in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA-seq:Total RNA was extracted using the Eastep® Super Total RNA Extraction Kit following the manufacturer’s instruction. Then, ribosomal RNA was deleted from 5 μg of total extracted RNA using the Ribo-Zero Gold Kit. Hi-C and Capture Hi-C: Cells were fixed in formalin for 10min and DNA was isolated and digested with Dpn II then sheared to 200-300bp fragments by sonication. Libraries were prepared using the NEBNext DNA library kit according to the manufacturer's instructions (New England BioLabs).
RNA, Hi-C and Capture Hi-C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TMZ_U251 groups were 1mM TMZ treated for 72h,and DMSO_U251 groups were control groups for the same conditions

tag: cell line

value: glioblastoma cells

tag: agent

value: TMZ


title: DMSO_U251 replicate 2

tag: cell type

value: DMSO


title: 346_1 Affymetrix OncoScan AT GC

description: Affymetrix OncoScan


title: TMZ_U251 replicate 1


title: H3.3-HA_Input-DNA_Hira-null_Day15_CM

first: Rasha

middle: Noureldin

last: Saleh

address: 30 Guilford street

institute: University College London

library_source: genomic

data_processing:
Data were aligned using Bowtiev2
only 3 mismatches were allowed, duplicates were removed
Peak calling was performed using MACS 1.4.2 using the default parameters (p-value ≤10-5)
Relevant peaks were validated by qChIP
Genome_build: mm9
Supplementary_files_format_and_content:  Bed file of peaks under mm9

organism: Mus musculus

source_name: Clone104 Hira-null mESCs cell line

extract_protocol:
Native ChIP was performed on 1x10^7 cells.  Cell pellets were lysed and chromatin was digested using MNase (Sigma N5386) at 37°C with an ideal fragmentation between 200 and 1000bp. The reaction was stopped using 5mM EDTA. HA antibody was collected with dynabeads (Invitrogen, 112.03D, 112.01D) from 12AC5 hybridoma supernatants and then incubated with the lysates overnight at 4oC. After several washes, the samples were treated with proteinase K and RNAse. DNA was purified using the PCR-purification Qiagen kit (28104).
Libraries were prepped using the NEB DNA Ultra kit, with bead bases size selection for an insert ~200bp and sequenced on the Illumina NextSeq 500, v2 chemistry

value: ESC

tag: day of differentiation

tag: genotype

value: Hira-null

tag: chip antibody


title: DMSO_U251 replicate 1


title: H3.3-HA_Input-DNA_WT_Day15_CM

source_name: W9.5 mESCs cell line

value: Wild type


title: H3.3-HA_Input-DNA_Hira-null_undifferentiated_mESCs

description: H3.3-HA_Hira-null-undifferentiated-mESCs_peaks.bed

value: Day 0


title: H3.3-HA_Input-DNA_WT_undifferentiated_mESCs

description: H3.3-HA_WT_undifferentiated_mESCs_peaks.bed


title: H3.3-HA_ChIPseq_WT_Day15_CM

value: anti-HA (collected from Hybridoma cell line 12AC5 which we cultured in the lab)


title: H3.3-HA_ChIPseq_Hira-null_undifferentiated_mESCs


title: H3.3-HA_ChIPseq_WT_undifferentiated_mESCs


title: RNAseq_zfSp5_r2

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads from our sequenced samples were mapped onto the Human GRCh37 (hg19) genome assembly using the STAR RNA-seq aligner workflow impolemented in Galaxy. The fastq files from the three biological replicates of each condition where merged and remapped in order to obtain the average coverage profile. Coverage files were normalized by the millions of mapped reads in each sample using a manually created R script.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

growth_protocol: HEK293T cells, a kind gift from the laboratory of Ariel Ruiz i Altaba (University of Geneva Medical School), were maintained in DMEM High Glucose + 1mM Na pyruvate + 6mM L-glutamine + 10% fetal bovine serum.

extract_protocol:
Cells were washed with ice cold PBS, scraped, transferred to 15ml tubes and centrifugated at 1000 rpm for 5 min. Total RNA was extracted using the kit E.Z.N.A. Total RNA Kit I. ____________
A total of 100ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. RNA sequencing (RNA-seq) libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on a HiSeq 4000 machine, as single-end, 100 base pairs (bp) reads. The preparation of libraries and sequencing were performed by the genomic platform of the University of Geneva.

treatment_protocol: HEK293T cells were seeded into a 6well plate (156 500 cells) and transfected  18-19 hours later with X-tremeGENETM HP DNA transfection reagent (Roche).  Plasmids used were: HySp5-420, ZfSp5-377, HySp5-ΔDBD-337, ZfSp5-ΔDBD-289, 626 ng and huΔβ-cat 313 ng.

tag: time

value: 24h post- transfection

tag: transfected with

value: plasmid coding for zfSp5 and pCS2


title: RNAseq_bcar_r3

value: plasmid coding for contitutively active human b-catenin


title: RNAseq_zfSp5_r3


title: RNAseq_bcar_r2


title: RNAseq_zfSp5_dDBD_bcat_r3

value: plasmids coding for zfSp5-dDBD and contitutively active human b-catenin


title: RNAseq_bcar_r1


title: RNAseq_zfSp5_r1


title: RNAseq_zfSp5_dDBD_r3

value: plasmid coding for zfSp5-dDBD  and pCS2


title: RNAseq_zfSp5_dDBD_r1


title: RNAseq_zfSp5_dDBD_bcat_r1


title: RNAseq_zfSp5_dDBD_r2


title: RNAseq_zfSp5_bcat_r3

value: plasmids coding for zfSp5 and contitutively active human b-catenin


title: RNAseq_zfSp5_dDBD_bcat_r2


title: H3.3-HA_ChIPseq_Hira-null_Day15_CM


title: RNAseq_zfSp5_bcat_r1


title: C9

description: healthy

source_name: Whole blood

extract_protocol:
mRNA was extracted from whole blood using a Tempus™ Spin RNA Isolation Kit. Globin was deplet using GLOBINclear™ Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: whole blood

tag: patient diagnosis

value: healthy


title: C8

description: healthy


title: C7

description: healthy


title: RNAseq_hySp5_r2

value: plasmid coding for hySp5 and pCS2


title: RNAseq_hySp5_r3


title: RNAseq_zfSp5_bcat_r2


title: C5

description: healthy


title: RNAseq_hySp5_r1


title: C3

description: healthy


title: Cardiac muscle_28 days tail-suspension_rep1

type: RNA

city: suzhou

first: wenyi

last: yuan

address: renai road No.199

institute: IBMS

description: Gene expression in 28 days tail-suspension mouse cardiac muscle

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was  fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE(8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray  Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area  61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set  to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

source_name: Cardiac muscle,28 days tail-suspension, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color  Low RNA Input Linear Amplification PLUS kit (Agilent) according to the  manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,  Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop  ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: 10-week-old mice were tail-suspended for 28 days, and the sham group mice were fed under the same feeding conditions in the same space.

tag: strain

value: Cardiac muscle

tag: gender

value: male

tag: age

value: 11 weeks


title: Cardiac muscle_28 days tail-suspension_rep2

source_name: Cardiac muscle,28 days tail-suspension, replicate 2


title: Cardiac muscle_28 days tail-suspension_rep3

source_name: Cardiac muscle,28 days tail-suspension, replicate 3


title: Cardiac muscle_Sham_rep3

description: Gene expression in sham mouse cardiac muscle

source_name: Cardiac muscle, Sham, replicate 3


title: Cardiac muscle_Sham_rep2

source_name: Cardiac muscle, Sham, replicate 2


title: Cardiac muscle_Sham_rep1

source_name: Cardiac muscle, Sham, replicate 1


title: GPP8

description: affected

value: Generalised Pustular Psoriasis


title: GPP9

description: affected


title: C2

description: healthy


title: C1

description: healthy


title: GPP7

description: affected


title: RNAseq_hySp5_dDBD_r2

value: plasmid coding for hySp5-dDBD  and pCS2


title: RNAseq_hySp5_dDBD_r3


title: GPP5

description: affected


title: RNAseq_hySp5_dDBD_r1


title: RNAseq_hySp5_dDBD_bcat_r2

value: plasmids coding for hySp5-dDBD and contitutively active human b-catenin


title: RNAseq_hySp5_dDBD_bcat_r1


title: RNAseq_hySp5_dDBD_bcat_r3


title: GPP1

description: affected


title: RNAseq_hySp5_bcat_r1

value: plasmids coding for hySp5 and contitutively active human b-catenin


title: RNAseq_ctrl_r2

value: pCS2 plasmid


title: RNAseq_ctrl_r1

value: 24h post- transfection


title: GPP6

description: affected


title: RNAseq_hySp5_bcat_r3


title: RNA-seq in activated Foxp1- Treg cells, rep3

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
RNA-seq
rna_fl_atr3
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt

data_processing:
RNA-seq: Reads were aligned to the mouse genome using HISAT2 v2.0.1-beta with default parameters including splice sites obtained from gene annotations. Uniquely aligned reads were extracted using grep with parameters "-v 'NH:i:[2- 9]'" and SAMtools v1.2 with parameters "view -h -F 4 -q 20 -b" and sorted and indexed using SAMtools. For analysis of RNA-seq in naïve or activated Foxp1+ or Foxp1- Treg samples, reads aligned to genes were counted using Rsubread v1.22.3 in R v3.3.0 (2016-05-03). Read counting for RNA-seq in naive and activated Tconv and Treg cells was done using R version 3.4.0, Rsubread v1.26.0. Differential gene expression between any pair of cell states was assessed using DESeq2 v1.16.1, using default FDR adjustment of p-values for multiple hypothesis testing.
ChIP-seq: Transcription factor ChIP-seq datasets for Foxp3 and Foxp1 were generated for Foxp1+ and Foxp1- Treg and Foxp1+ naive Tconv cells. Reads were aligned to the mouse genome using Bowtie2 v2.2.5 with parameters "--no-unal -X 500 --no-mixed --no-discordant". Uniquely aligned reads were extracted using SAMtools v1.1 with parameters "view -h -bS -F 4 -q 20" and sorted and indexed using SAMtools. For peak calling, MACS2 v2.1.1.20160309 was used with parameters "-f BAM -B --SPMR -g mm -p 0.1 --keep-dup 'auto' --call-summits". For Foxp1, pooled Foxp1+ Treg and Foxp1+ Tconv ChIP-seq samples were used, with Foxp1- Treg samples as control, to obtain a list of 55265 putative peaks on standard chromosomes (chr1-chr19, chrX, chrY, chrM), with multiple summits per peak. ChIP-seq fragment length was estimated by MACS2 as 198bp. To obtain peaks with significant coverage in Treg, ChIP-seq reads from each Foxp1+ Treg sample and from pooled control samples were counted in putative peaks using Rsubread v1.26.0, and DESeq2 v1.16.1 was applied to these counts, with FDR adjustment of p-values for multiple hypothesis testing. To estimate sample size factors, DESeq2 was applied to read counts from the same samples in flanking regions of putative peaks, defined by shifting the putative peaks by 2Kb upstream and by 2Kb downstream and taking only those flanking regions that do not overlap with the original putative peaks. This analysis resulted in 3071 Foxp1 peaks in Treg at MACS2 q-value < 0.05 and DESeq2 FDR < 0.01 that contained 4619 summits. The same procedure was applied to each Foxp1+ Tconv sample and pooled control samples and resulted in 1088 Foxp1 peaks in Tconv. Out of 3071 Foxp1 peaks in Treg, 881 peaks were also detected among 1088 Foxp1 peaks in Tconv. However, out of these 3071 Foxp1 peaks in Treg, 2521 peaks were detected as Foxp1 peaks in Tconv at a relaxed threshold (MACS2 q-value < 0.05 and DESeq2 FDR < 0.1), while 550 were not. Out of 1088 Foxp1 peaks in Tconv, 1049 peaks were detected as Foxp1 peaks in Treg at a relaxed threshold (MACS2 q-value < 0.05 and DESeq2 FDR < 0.1), while 39 were not.
The same procedure for peak calling was applied to pooled Foxp3 ChIP-seq samples from Foxp1+ and Foxp1- Treg, using Foxp3 ChIP-seq in Foxp1+ and Foxp1- naive Tconv cells as controls. This resulted in 141556 putative Foxp3 peaks on standard chromosomes, with estimated ChIP-seq fragment length also 198bp. The same procedure for significant ChIP-seq coverage assessment was applied to each Foxp3 ChIP-seq sample in Foxp1+ Treg cells and pooled control samples. This procedure resulted in 7174 Foxp3 peaks in Foxp1+ Treg at MACS2 q-value < 0.05 and DESeq2 FDR < 0.01 that contained 13997 summits. The same procedure applied to each Foxp3 ChIP- seq sample in Foxp1- Treg cells and pooled control samples resulted in 3935 Foxp3 peaks in Foxp1- Treg.
Each peak was associated with the closest gene according to distance in genomic coordinates, if this distance was not more than 20Kb. Peaks within 2Kb from a transcription start site of any annotated transcript were classified as promoter peaks; the remaining peaks were classified as exonic if overlapping with any exon of any annotated transcript; the remaining peaks were classified as intronic if within a gene body of any annotated gene; the remaining peaks within 20Kb of a gene were classified as intergenic; all the remaining peaks were left unclassified in this classification.
Genome_build: mm10.GRCm38
Supplementary_files_format_and_content: rnaseq-foxp1fl-over-wt-results.txt: Results of differential expression analysis between naive Foxp1+ and Foxp1- Treg cells, and between activated Foxp1+ and Foxp1- Treg; peaks-foxp1.txt: Significant Foxp1 peaks; peaks-foxp3.txt: Significant Foxp3 peaks.

source_name: Foxp1-deficient Treg cells from pooled spleen and lymph nodes

growth_protocol: Mice were bred and housed in the pathogen-free animal facility at Memorial Sloan-Kettering Cancer Center and were used in accordance with institutional guidelines. Mouse experiments were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center. Unless otherwise noted, 8- to 10-week-old male and female sex-matched mice were used for all experiments. The Foxp1 conditional targeting construct was designed to use 2 site-specific recombinations in vivo: (1) Flp recombinase to delete the neo marker from the mouse germline, and (2) Cre recombinase to conditionally delete Foxp1 exon 11 flanked by 2 loxP sites. Foxp1f/+ mice (C57Bl/6/129 mixed background) were backcrossed with C57BL/6 mice for at least 5 generations. Genotypes of Foxp1fl/+, Foxp1fl/fl mice were determined by polymerase chain reaction (PCR) amplification. The wild-type allele was identified by the production of a 376–base pair PCR product and mutated Foxp1 allele was identified by the production of a 257–base pair PCR product (Supplementary Table 6). Foxp1fl/fl mice were crossed with Foxp3YFP-Cre transgenic mice to generate Foxp3YFP-Cre/+Foxp1fl/+ female mice. These mice were bred to Foxp3+Foxp1fl/+ male mice. Foxp3YFP-Cre/+Foxp1fl/fl and Foxp3YFP- Cre/+Foxp1+/+ female offspring and Foxp3YFP-CreFoxp1fl/fl and Foxp3YFP-CreFoxp1+/+ male offspring were used in experiments. In mammary tumor experiments, Foxp3YFP-Cre/YFP-CreFoxp1fl/fl mice were used as experimental mice and Foxp3YFP-Cre/+Foxp1fl/fl mice were used as control mice. Foxp1fl/fl mice were crossed with CD4Cre transgenic mice to generate CD4CreFoxp1fl/+ mice. These mice were crossed to generate CD4CreFoxp1fl/fl experimental and CD4CreFoxp1+/+ control mice. Tcrb/Tcrd−/− mice and C57Bl/6 Ly5.1 mice were purchased from Jackson Laboratories and bred in-house. No blinding was performed during the mouse experiments.

extract_protocol:
Single cell suspensions of cells were prepared from spleen and lymph nodes. For exclusion of dead cells, samples were first stained with Ghost Dye (Tonbo) cell viability reagent for 10 min in PBS on ice. Cells were then stained for 30 min on ice in FACS buffer (PBS, 2% FBS, 2 mM EDTA) with antibodies against cell surface proteins. For downstream in vitro assays, cells were sorted into fetal bovine serum (FBS). For intracellular staining, cells were washed and fixed with Fix/Perm buffer (BD Biosciences) for 20 min on ice or with Foxp3 staining buffer (eBioscience) for 45 min on ice, washed and stained with antibodies against intracellular proteins. Stained cells were either analyzed on a LSRII flow cytometer (BD) or sorted using a FACSAria II (BD). Flow cytometry data were analyzed with FlowJo software (TreeStar).
RNA-seq: CD44hi or CD62Lhi YFP+ Foxp1+ or Foxp1- Treg cell populations were FACS- sorted from Foxp3YFP-Cre/+Foxp1+/+ and Foxp3YFP-Cre/+Foxp1fl/fl mice directly into Trizol-LS (ThermoFisher) and volume was adjusted post-sort. Samples were stored at −80°C prior to RNA extraction. Total RNA was extracted and assessed for nucleic acid quantity and quality on the Agilent BioAnalyzer. SMARTer amplification with 12-16 cycles of PCR was followed by Illumina TruSeq paired- end library preparation following manufacturer’s protocols. Samples were sequenced on the Illumina HiSeq 2500 to an average depth of 30 million 50-bp read pairs per sample.  ChIP-seq: FACS-sorted cell populations (2x106 cells for Foxp3-ChIP-seq; 6x106 cells for Foxp1-ChIP-seq) were crosslinked in 1% paraformaldehyde I PBS for 10 minutes at RT. The reaction was quenched by addition of 125mM glycine. Crosslinked cells were lysed and digested nuclei were resuspended in nuclear lysis buffer containing 1% SDS. Cells were sonicated for three rounds of 10x30s with a Bioruptor (Diagenode) on high setting. Following sonication, chromatin was diluted with nuclear lysis buffer to final SDS concentration of 0.1% and pre- cleared for 1h at 4°C with rotation with protein A/G magnetic beads (Pierce). 5% of pre-cleared DNA was saved as input. Chromatin was incubated overnight at 4°C with rotation with polyclonal antibodies against Foxp3 (Rudensky lab) or Foxp1 (EMD Millipore ABE68). Immunocomplexes were incubated with protein A/G magnetic beads for 1h at 4°C with rotation. Immunocomplexes were precipitated and washed. After washing, precipitated chromatin and input DNA was decrosslinked overnight at 65°C in the presence of proteinase K and DNA fragments were isolated using Qiagen PCR-purification kit. Purified DNA was processed for sequencing on Illumina Hiseq 2500 to an average depth of 30 million 50-bp read pairs per sample.

value: Treg

value: Foxp3YFP-Cre Foxp1f/f

tag: activation status


title: RNAseq_hySp5_bcat_r2


title: GPP2

description: affected


title: RNAseq_ctrl_r3


title: GPP4

description: affected


title: RNA-seq in activated Foxp1- Treg cells, rep2

description:
RNA-seq
rna_fl_atr2
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: TIC_ZfSp5 replicate 2

data_processing:
Adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Demultiplexed ChIP-seq reads from our sequenced samples were mapped onto the Human GRCh37 (hg19) genome assembly using bowtie2, version 2.2.6.2, implemented in Galaxy. Significantly enriched regions were identified using MACS2 (version 2.1.0.20151222.0 command line: macs2 callpeak -t input.bam --call-summits -B). Coverage files were normalized by the millions of mapped reads in each sample using a manually created R script. Normalized bedgraph files were converted to bigwig using the Wig/BedGraph-to-bigWig converter tool (version 1.1.1) implemented in the pubblic Galaxy server (https://usegalaxy.org/). The fastq files from the two biological replicates of each condition where merged and remapped in order to obtain the average coverage profile.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of theChIPseq read coverage files, divided by the number of millions of mapped reads in each sample.

source_name: HEK293 cells transfect with the zfSp5 construct

extract_protocol:
24 hours after transfection, cells were collected by scraping, washed twice in pre-warmed culture medium and fixed in 1% FA solution (Sigma) for 15 minutes. The fixative was quenched by adding Glycine (125 mM) and incubation for 3 minutes. The cells were washed once in ice-cold PBS and re-suspended in 5 mL chromatin prep buffer (Active Motif), containing 0.1mM PMSF and 0.1% protease inhibitor cocktail (PIC). To release the nuclei the sample was transferred into a pre-cooled 15 mL glas Douncer and dounced with 30 strokes. After 10 minutes incubation on ice and centrifugation at 1250 g for 5 minutes at 4°C, the nuclei were re-suspended in 500 uL sonication buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1 mM PMSF, 1% PIC). Following another 10 minutes incubation on ice, the chromatin was sonicated with a Bioblock Scientific VibraCell 75042 sonicator (Amplitude: 25%, Time: 12 minutes, 30 seconds on, 30 seconds off, 24 cycles). Note: The sonication conditions were optimized to have a fragmentation size of around 250 bp. Then 100 uL of the sonicated chromatin was added to 900 uL ChIP dilution buffer (0.1% NP-40, 0.02 M HEPES pH 7.3, 1 mM EDTA pH 8.0, 0.15 M NaCl, 1 mM PMSF, 1% PIC) and incubated with 4 ug anti-HA antibody (NB600-363, Novus Biologicals) over night at 4°C on a rotator. Next, the sample was loaded on a ChIP-IT ProteinG Agarose Column (Active Motif) and incubated for 3 hours at 4°C on a rotator. The column was washed 6 times with 1 mL buffer AM1 (Active Motif) and the DNA eluted with 180 uL of pre-warmed buffer AM4 (Active Motif). The sample was decrosslinked by adding 30 uL 10x TE buffer, 18 uL 5 M NaCl, 57 uL H2O and incubated for 5 hours at 65°C. 5 uL of RNAse A (10 ug/uL) was added and the sample incubated at 37°C for 30 minutes before adding 10 uL of Proteinase K (10 ug/uL), and further incubation for 2 hours at 55°C. The DNA was purified with the MiniElute PCR purification kit (Qiagen). For preparing the Input DNA, 5 uL sonicated chromatin was added to 5 uL 5M NaCL in 40 uL H2O, and incubated for 15 minutes at 95°C. Next the sample was incubated at 37°C for 5 minutes with 2.5 uL of RNAse A (10 ug/ul), 2.5 uL PK (10 ug/uL) was then added, and the incubation continued at 55°C for 30 minutes. 10 uL were taken for purification (MiniElute PCR purification kit from Qiagen).
5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

treatment_protocol: HEK293T cells were seeded into a 10 cm dish (920 000 cells) and transfected  18-19 hours later with X-tremeGENETM HP DNA transfection reagent (Roche).  Plasmids used were: HySp5-420, ZfSp5-377, HySp5-ΔDBD-337, ZfSp5-ΔDBD-289, 3666 ng

value: zfSp5 construct

tag: antibody


title: TIC_ZfSp5 replicate 1


title: GPP3

description: affected


title: RNA-seq in activated Foxp1+ Treg cells, rep3

description:
RNA-seq
rna_wt_atr3
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt

source_name: Treg cells from pooled spleen and lymph nodes

value: Foxp3YFP-Cre Foxp1+/+


title: RNA-seq in activated Foxp1- Treg cells, rep1

description:
RNA-seq
rna_fl_atr1
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: TIC_ZfSp5_dDBD replicate 2

source_name: HEK293 cells transfect with the zfSp5_dDBD construct

value: zfSp5_dDBD construct


title: TIC_HySp5 replicate 2

source_name: HEK293 cells transfect with the hySp5 construct

value: hySp5 construct


title: RNA-seq in naïve Foxp1- Treg cells, rep2

description:
RNA-seq
rna_fl_ntr2
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: RNA-seq in activated Foxp1+ Treg cells, rep1

description:
RNA-seq
rna_wt_atr1
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: TIC_HySp5_dDBD replicate 1

source_name: HEK293 cells transfect with the hySp5_dDBD construct

value: hySp5_dDBD construct


title: ChIP_ZfSp5 replicate 2

value: anti-HA (Novus biologicals NB600-363)


title: ChIP_ZfSp5 replicate 1


title: RNA-seq in naïve Foxp1- Treg cells, rep1

description:
RNA-seq
rna_fl_ntr1
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: RNA-seq in naïve Foxp1+ Treg cells, rep3

description:
RNA-seq
rna_wt_ntr3
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: TIC_HySp5_dDBD replicate 2


title: ChIP_ZfSp5_dDBD replicate 2


title: RNA-seq in naïve Foxp1+ Treg cells, rep2

description:
RNA-seq
rna_wt_ntr2
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: RNA-seq in naïve Foxp1+ Treg cells, rep1

description:
RNA-seq
rna_wt_ntr1
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: Foxp3 ChIP-seq in Foxp1- conventional T cells, rep3 (genetic control)

description:
Foxp3 ChIP-seq
chip_fltc3_foxp3
peaks-foxp3.txt

source_name: Foxp1-deficient conventional T cells from pooled spleen and lymph nodes

value: Tconv


title: ChiP_HySp5 replicate 2


title: Foxp3 ChIP-seq in Foxp1- conventional T cells, rep2 (genetic control)

description:
Foxp3 ChIP-seq
chip_fltc2_foxp3
peaks-foxp3.txt


title: ChIP_HySp5 replicate 1


title: TIC_ZfSp5_dDBD replicate 1


title: RNA-seq in activated Foxp1+ Treg cells, rep2

description:
RNA-seq
rna_wt_atr2
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: Foxp3 ChIP-seq in Foxp1- conventional T cells, rep1 (genetic control)

description:
Foxp3 ChIP-seq
chip_fltc1_foxp3
peaks-foxp3.txt


title: RNA-seq in naïve Foxp1- Treg cells, rep3

description:
RNA-seq
rna_fl_ntr3
rnaseq-foxp1fl-over-wt-results.txt; rnaseq-counts-raw.txt


title: ChIP_HySp5_dDBD replicate 2


title: ChIP_HySp5_dDBD replicate 1


title: Foxp3 ChIP-seq in Foxp1+ conventional T cells, rep3 (genetic control)

description:
Foxp3 ChIP-seq
chip_wttc3_foxp3
peaks-foxp3.txt

source_name: conventional T cells from pooled spleen and lymph nodes


title: GS689_rep3 (HiSeq 4000)

city: Los Angeles

first: Zijun

last: Zhang

address: 650 Charles E. Young Drive South

institute: UCLA

data_processing:
mapping with STAR (2.5.2a_modified)
gene expression estimation with Kallisto (v0.43.0)
splicing analysis with rMATS (v4.0.1)
splicing analysis with Darts (v0.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: kallisto.tar.gz: processed files for HiSeq 4000 experiments
Supplementary_files_format_and_content: RASL_count.txt (MiSeq): the two comma-separated values correspond to the number of reads supporting Inclusion Isoform (first number) vs. Skipping Isoform (second number)
Supplementary_files_format_and_content: darts_read_counts.txt: "I1", "S1" represent the number of RNA-seq reads supporting Inclusion/Skipping isoforms in PC3E cell line, where the read counts in replicate 1,2,3 are separated by comma. Similarly, "I2", "S2" are read counts from GS689 replicate 1,2,3.

source_name: GS689.Li prostate cancer cell line

growth_protocol: Cell lines were maintained in DMEM/F12 with 10% FBS, 1%NEAA and 400 μg/ml G418.

extract_protocol:
Cells were washed with PBS 3x and then extracted with Trizol and flash frozen at -80C
Libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA kit according to the manufacturer's instructions.

treatment_protocol: Plated 3M cells of each type in 10 cm diameter dishes and harvested after overnight incubation

value: prostate cancer

value: wild type

tag: media


title: Foxp3 ChIP-seq in Foxp1+ conventional T cells, rep2 (genetic control)

description:
Foxp3 ChIP-seq
chip_wttc2_foxp3
peaks-foxp3.txt


title: shATRX, P15, replicate 2

city: New York

first: Yuxiang

last: Wang

state: NY

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

description:
JH1883-B8_NHA shATRX P15_2.CEL
Hybridized to Affymetrix SNP 6.0 array.

hyb_protocol: As described by the manufacturer.

scan_protocol: As described by the manufacturer.

data_processing: The CNA_NHA_YW-JTH.seg file is the copy number variations of normal human astrocytes (NHA) that have been passaged for 5 or 15 passages (shATRX P5 and P15), along with their corresponding controls (control shRNA, P5 and P15), in reference to the start point (P0). The aim was to reveal the genomic consequences of ATRX deficiency along time. The .seg file was generated by Partek Genomic Suites 6.6 through its built-in copy number analysis tool, with the data being log2 transformed through the process.

label: biotin

source_name: normal human astrocytes

label_protocol: As described by the manufacturer.

growth_protocol: Cells grow in attachment to 15-cm culture dishes, in DMEM+10%FBS.

extract_protocol: Qiagen DNeasy Blood & Tissue Kit.

treatment_protocol: Continuous passaging.

value: immortalized astrocytes

tag: shRNA

value: shATRX

tag: time point


title: ChIP_ZfSp5_dDBD replicate 1

tag: cell line


title: GS689_rep1 (HiSeq 4000)

value: DMEM/F12 with 10% FBS, 1%NEAA and 400 μg/ml G418


title: shATRX, P5, replicate 1

description:
JH1883-B1_NHA shATRX P5_1.CEL
Hybridized to Affymetrix SNP 6.0 array.

tag: cell type


title: control shRNA, P15, replicate 2

description:
JH1883-A11_NHA CTRL P15_2.CEL
Hybridized to Affymetrix SNP 6.0 array.

value: control


title: shATRX, P5, replicate 3

description:
JH1883-B3_NHA shATRX P5_3.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: shATRX, P15, replicate 3

description:
JH1883-B9_NHA shATRX P15_3.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: control shRNA, P15, replicate 3

description:
JH1883-A12_NHA CTRL P15_3.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: control shRNA, P5, replicate 3

description:
JH1883-A6_NHA CTRL P5_3.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: PC3E_rep3 (HiSeq 4000)

source_name: PC3E prostate cancer cell line


title: Foxp3 ChIP-seq in Foxp1+ conventional T cells, rep1 (genetic control)

description:
Foxp3 ChIP-seq
chip_wttc1_foxp3
peaks-foxp3.txt


title: Foxp3 ChIP-seq in Foxp1- Treg, rep2

description:
Foxp3 ChIP-seq
chip_fltr2_foxp3
peaks-foxp3.txt

value: pooled


title: Foxp3 ChIP-seq in Foxp1- Treg, rep1

description:
Foxp3 ChIP-seq
chip_fltr1_foxp3
peaks-foxp3.txt


title: control shRNA, P5, replicate 2

description:
JH1883-A5_NHA CTRL P5_2.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: GS689_rep2 (HiSeq 4000)


title: PC3E_rep2 (HiSeq 4000)


title: shATRX, P15, replicate 1

description:
JH1883-B7_NHA shATRX P15_1.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: control shRNA, P15, replicate 1

description:
JH1883-A10_NHA CTRL P15_1.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: control shRNA, P5, replicate 1

description:
JH1883-A4_NHA CTRL P5_1.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: Foxp3 ChIP-seq in Foxp1+ Treg, rep2

description:
Foxp3 ChIP-seq
chip_wttr2_foxp3
peaks-foxp3.txt


title: start point (P0), replicate 3

description:
JH1883-A3_NHA P0_3.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: start point (P0), replicate 2

description:
JH1883-A2_NHA P0_2.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: shATRX, P5, replicate 2

description:
JH1883-B2_NHA shATRX P5_2.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: start point (P0), replicate 1

description:
JH1883-A1_NHA P0_1.CEL
Hybridized to Affymetrix SNP 6.0 array.


title: Foxp3 ChIP-seq in Foxp1+ Treg, rep1

description:
Foxp3 ChIP-seq
chip_wttr1_foxp3
peaks-foxp3.txt


title: Foxp1 ChIP-seq in conventional T cells, rep2

description:
Foxp1 ChIP-seq
chip_ntc2_foxp1
peaks-foxp1.txt


title: WT6

city: Hamburg

first: Matthias

last: Rath

address: Am Kaiserkai 1

department: Institute of Molecular Medicine

country: Germany

institute: MSH Medical School Hamburg

description:
NOISeq_normalized_counts.xlsx
WT6_S8.trim2

data_processing:
Base calls were processed with the MiSeq Reporter software (MSR v2.5.1)
Adapter sequences were trimmed with cutadapt v1.14
NOISeq package of the iSmaRT toolkit was used for read alignment and differential expression analysis (Panero R, Rinaldi A, Memoli D, et al. iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinformatics. 2017; 33: 938-40.)
Genome_build: miRBase 21
Supplementary_files_format_and_content: Excel file with normalized counts

source_name: CI-huVEC (InSCREENeX)

extract_protocol:
RNA was harvested using PeqGold TriFast reagent (Peqlab-VWR, Radnor, USA) and extracted with the Absolutely RNA miRNA Kit (Agilent Technologies, Santa Clara, USA)
The NEXTflex Small RNA-Seq kit v3 (Bioo Scientific, Austin, USA) was used for library preparation. Following barcodes/indices were used: K5 GTAGAG; K7 GTGAAA; K9 GTCCGC; K15 GTGGCC; WT1 GTTTCG; WT2 CGTACG; WT5 GAGTGG; WT6 GGTAGC

value: CI-huVEC HKO

tag: passage

value: wild-type


title: Kc167 rep2

first: Nicolae Radu

last: Zabet

address: 4 Newark Street

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

data_processing:
HiSeq Control Software HD 3.4.0.38 was used for basecalling (for Kc167 smaples) and RTAVersion 2.7.7  was used for basecalling (for BG3 smaples) .
Each pair of the PE reads were aligned separately to Drosophila melanogaster (dm6) genome using BWA-mem (version 0.7.15-r1140) with options -t 20 -A1 -B4 -E50 -L0. HiCExplorer (version 2.1.1) was used to build and correct the contact matrices and detect TADs. The contact matrices were built at the DpnII restriction sites. Using a minimum allowed distance between restriction sites of 150 bp and a maximum distance of 1 Kb. We merged the two BG3 biological replicates and the two Kc167 replicates. The matrices were corrected using the thresholds (-1.4 and 5). Using the corrected contact matrices, we detected TADs of at least 5 Kb width using a p-value threshold of 0.01, a minimum threshold of the difference between the TAD-separation score of 0.04 and FDR correction for multiple testing (--step 2000, --minBoundaryDistance 5000 --pvalue 0.01 --delta 0.04 --correctForMultipleTesting fdr). Finally, we called strong TAD borders using a stringent value of the threshold of the difference between the TAD-separation score of 0.08. Since, the Kc167 cell line is a female derived cell line and BG3 is a male derived cell line, we excluded sex chromosomes from our analysis.
Chromatin loops were called with the HICCUPS tool from the Juicer software suite (version 1.7.6). Loops were called using a 2 Kb resolution, 0.05 FDR, Knight-Ruiz normalisation, a window of 10, peak width of 5, thresholds for merging loops of 0.02,1.5,1.75,2 and distance to merge peaks of 20 Kb (-k KR -r 2000 -f 0.05 -p 5 -i 10 -t 0.02,1.5,1.75,2 -d 20000).
Genome_build: dm6
Supplementary_files_format_and_content: BED files contain the coordinates of TADs; bepe files contain the coordinates of chromatin loops

source_name: Kc167 cells

growth_protocol: Kc167 and BG3 cells were grown to 80-90% confluence in Schneider’s Drosophila medium with 5%FBS or 10% FBS respectively and antibiotics (Pen-Strep) in 100 mm cell culture plates.

extract_protocol:
Hi-C libraries were generated from 10 million cells by following the Insitu Hi-C protocol as mentioned in (Rao et al. 2014) with minor modifications. Crosslinked cells were lysed and genome was digested using DpnII (NEB) overnight. The overhangs were filled with Bioton-16-dATP (Jena Bioscience) followed by ligation and de-crosslinking with proteinase K digestion. The sample was further sonicated using Bioruptor.
Biotinylated DNA was pulled down using Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602). Selected biotinylated DNA fragments ranging from 200-500bp were then ligated with illumina adaptors (NEB).

value: Kc167 cells


title: Foxp1 ChIP-seq in conventional T cells, rep1

description:
Foxp1 ChIP-seq
chip_ntc1_foxp1
peaks-foxp1.txt

tag: genotype


title: WT5

description:
NOISeq_normalized_counts.xlsx
WT5_S7.trim2


title: WT2

description:
NOISeq_normalized_counts.xlsx
WT2_S6.trim2


title: WT1

description:
NOISeq_normalized_counts.xlsx
WT1_S5.trim2


title: Foxp3 ChIP-seq in Foxp1- Treg, rep3

description:
Foxp3 ChIP-seq
chip_fltr3_foxp3
peaks-foxp3.txt

value: Treg

value: Foxp3YFP-Cre Foxp1f/f


title: BG3 rep1

source_name: BG3 cells

value: BG3 cells


title: Foxp1 ChIP-seq in Foxp1- Treg (genetic control)

description:
Foxp1 ChIP-seq
chip_trfl_foxp1
peaks-foxp1.txt


title: BG3 rep2


title: K15

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing
NOISeq_normalized_counts.xlsx
K15_S4.trim2


title: Kc167 rep1


title: elav_2_mmPCR

description: Heads were collected from a mixed population of males and females.

data_processing:
Low quality bases were trimmed from RNA-seq reads using Trim Galore and mapped to the dm6 using STAR (v2.4.2) --twopassMode.
The samtools mpileup function was used to determine base calls at known editing sites from uniquely mapped reads. Editing levels were calculated as (G reads)/(A+G reads) at each site.
Genome_build: dm6
Supplementary_files_format_and_content: A and G counts and editing levels at known editing sites. Tab-delimited files are formatted as: chr, position, a counts, g counts, editing level.

source_name: all brain neuron nuclei

extract_protocol:
Heads were separated by vigorous vertexing followed by separation over dry-ice cooled sieves.  9ml of homogenization buffer (20mM β-Glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40 supplemented with RNAase inhibitor,10mg/ml t-RNA, 50mg/ml ultrapure BSA, 0.5mM Spermidine, 0.15mM Spermine and 140ul of carboxyl Dynabeads -270 Invitrogene: 14305D) was added to each sample. The heads were minced on ice by a series of mechanical grinding steps followed by filtering the homogenate using a 10um Partek filter assembly (Partek: 0400422314). After removing the carboxyl-coated Dynabeads using a magnet, the homogenate was filtered using a 1um pluriSelect filter (pluriSelect: 435000103). The liquid phase was carefully placed on a 40% optiprep cushion layer and centrifuged in a 4oC centrifuge for 30min at ~2300Xg. The homogenate/Optiprep interface was incubated with anti-GFP antibody (Invitrogen: G10362) and protein G Dynabeads (Invitrogen: 100-03D) for 40 minutes at 4oC . Beads were then washed once in NUN buffer (20mM β-Glycerophosphate pH7, 300mM NaCl, 1M Urea, 0.5% NP40, 2mM EDTA, 0.5mM Spermidine, 0.15mM Spermine, 1mM DTT, 1X Complete protease inhibitor, 0.075mg/ml Yeast torula RNA, 0.05Units/ul Superasin). Bead-bound nuclei were separated using a magnet stand, and RNA was extracted using the Picopure Kit (Invitrogen KIT0204).
We performed mmPCR-seq to quantify editing levels at 605 loci harboring know editing sites. We prepared samples for microfluidic PCR at 605 loci with a 15-cycle pre-amplification PCR reaction using 10 ul of cDNA made from INTACT RNA extractions, using the High capacity cDNA Reverse Transcriptase Kit, 6 ul of a pool of all primers used in the multiplex microfluidic PCR, and 4 ul of 5X KAPA2G Fast Multiplex. The pre-amplification reactions were purified using AMPure XP PCR purification beads. We loaded the pre-amplified samples and 48 pools of PCR primers into a 48.48 Access Array IFC (Fluidigm) and performed target amplification. Multiplex PCR products were barcoded using a 13-cycle PCR reaction.
microfluidic multiplex PCR and sequencing (mmPCR-seq)

value: UAS-unc84-2XGFP; elav-GAL4

tag: neuronal population

value: all brain neurons

tag: replicate


title: Foxp1 ChIP-seq in Foxp1+ Treg, rep3

description:
Foxp1 ChIP-seq
chip_tr3_foxp1
peaks-foxp1.txt

value: Foxp3YFP-Cre Foxp1+/+


title: Foxp1 ChIP-seq in Foxp1+ Treg, rep2

description:
Foxp1 ChIP-seq
chip_tr2_foxp1
peaks-foxp1.txt


title: K5

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing
NOISeq_normalized_counts.xlsx
K5_S1.trim2


title: K9

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing
NOISeq_normalized_counts.xlsx
K9_S2.trim2


title: K7

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing
NOISeq_normalized_counts.xlsx
K7_S3.trim2


title: OK107_2_mmPCR

source_name: mushroom body neuron nuclei

value: UAS-unc84-2XGFP; OK107-GAL4

value: mushroom body


title: OK107_3_mmPCR


title: GS689_rep2 (MiSeq)

description: RASL-seq was performed solely on MiSeq

value: prostate cancer

value: wild type


title: Fru_3_mmPCR

description: Heads were collected from female and male populations separately, and fastq files were combined after sequencing for data processing.

source_name: fruitless neuron nuclei

value: UAS-unc84-2XGFP; Fru-GAL4

value: fruitless


title: OK107_1_mmPCR


title: elav_3_mmPCR


title: GS689_rep1 (MiSeq)

description: RASL-seq was performed solely on MiSeq

value: DMEM/F12 with 10% FBS, 1%NEAA and 400 μg/ml G418


title: GS689_rep3 (MiSeq)

description: RASL-seq was performed solely on MiSeq


title: Foxp1 ChIP-seq in Foxp1+ Treg, rep1

description:
Foxp1 ChIP-seq
chip_tr1_foxp1
peaks-foxp1.txt

value: pooled


title: elav_1_mmPCR


title: Fru_2_mmPCR


title: PC3E_rep2 (MiSeq)

description: RASL-seq was performed solely on MiSeq


title: Trh_3_mmPCR

source_name: serotonergic neuron nuclei

value: UAS-unc84-2XGFP; Trh-GAL4

value: serotonergic


title: Fru_1_mmPCR


title: PC3E_rep1 (MiSeq)

description: RASL-seq was performed solely on MiSeq


title: Trh_2_mmPCR


title: PC3E_rep3 (MiSeq)

description: RASL-seq was performed solely on MiSeq


title: Trh_1_mmPCR


title: TH_3_mmPCR

source_name: dopaminergic neuron nuclei

value: UAS-unc84-2XGFP; TH-GAL4

value: dopaminergic


title: exp.4_no_tag

city: Edinburgh

first: Marie-Luise

last: Winz

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

description: CRAC sample

data_processing:
Library strategy: CRAC
Base calling was done using Illumina standard software.
Data were split according to i7 indices using Illumina software.
Reads from different lanes belonging to the same sample were concatenated.
Reads were split according to in-line barcodes.
For submission to GEO, reads from the same sample, but carrying different i7 indices were combined and only identical parts of adapters were removed, while random nucleotides and parts of the 5'linkers that differed between samples were retained. For further data processing, these parts were removed.
Further processing: 3'-adapters were removed using flexbar. pyFastqDuplicateRemover.py from the pyCRAC package (Webb et al., 2014) was used to collapse data (files belonging to the same sample but with different indices & 5'linkers with 3'-terminal N were treated separately, as reads definitely result from separate RNA molecules, to retain greater sequencing depth and collapsed files were combined thereafter - available upon request).
Collapsed and uncollapsed data were aligned using novoalign. Reads were mapped using pyReadCounters from the pyCRAC package. Bedgraphs were generated from pyReadCounters output and converted to bigwig format using bedGraphToBigWig.
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: bedgraph files containing hit densities for aligned, collapsed data.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in SD media lacking Trp and containing 2% glucose to OD600 0.5.

extract_protocol:
Cells were lysed, UV-crosslinked protein-RNA complexes were purified by tandem purification on IgG, TEV cleavage and immobilisation on Ni-NTA.
Libraries were constructed using the published CRAC protocol with minor modifications (Granneman et al., 2009).

treatment_protocol: Cells were crosslinked for 100s and harvested by centrifugation.

tag: 5'-linker identifier

value: NNNACTCAGC

tag: molecule

value: protein-crosslinked RNA


title: TH_2_mmPCR


title: Sample_Chap_DMSO_control_1

city: Haifa

first: Benny

last: Horwitz

address: Faculty of Biology

institute: Technion

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.14.1
Genome_build: GCF_000354255.1_CocheC4_1
Supplementary_files_format_and_content: Normalized counts were created using DESeq2 software.

organism: Bipolaris maydis

growth_protocol: The wild-type C4 (MAT1-2 Tox1+) and the chap1 deletion mutant (∆chap1) strains of C. heterostrophus were grown at 22ºC on complete xylose medium (CMX)  in 16 h white light, 8 h dark cycles

extract_protocol:
Mycelia were harvested, ground in liquid nitrogen and extracted with TriReagent following the manufacturer's instructions.
Illumina TruSeq RNA Library Preparation Kit v2

treatment_protocol: Spores were transferred to liquid CMX medium and incubated with shaking (200 rpm) at 22ºC for 3 days; the cultures were then treated with 0 (DMSO controls) and 0.5, 1, 2 mM ferulic acid acid were incubated for 30 min at 22ºC with shaking (200 rpm).

value: chap1 deletion

tag: treatment

value: DMSO control

tag: tissue

value: mycelia


title: TH_1_mmPCR


title: exp.4_Hel2-HTP-6

description: CRAC sample

value: NNNCGTGATN


title: Sample_Chap_DMSO_control_2

tag: strain


title: exp.3_Hel2-HTP-4

description: CRAC sample

value: NNNCACTAGC


title: exp.4_Hel2-HTP-5

description: CRAC sample

value: NNNGACTTAGC


title: Sample_Chap_2mM_3

value: 2 mM FA


title: Crz_3_mmPCR

source_name: corzonin neuron nuclei

value: UAS-unc84-2XGFP; Crz-GAL4

value: corzonin


title: Sample_Chap_DMSO_control_3


title: exp.3_Hel2-HTP-3

description: CRAC sample

value: NNNGTGAGC


title: Crz_2_mmPCR


title: Sample_Chap_2mM_1


title: exp.2_Hel2-HTP-2

description: CRAC sample

value: NNNACAGTGN


title: exp.2_no_tag

description: CRAC sample

value: NNNGTGACAN


title: Sample_Chap_1mM_3

value: 1 mM FA


title: Crz_1_mmPCR


title: exp.1_no_tag

description: CRAC sample

value: NNNCGCTTAGC


title: Tdc2_3_mmPCR

source_name: octopaminergic neuron nuclei

value: UAS-unc84-2XGFP; Tdc2-GAL4

value: octopaminergic


title: PC3E_rep1 (HiSeq 4000)

value: prostate cancer

value: wild type

value: DMEM/F12 with 10% FBS, 1%NEAA and 400 μg/ml G418


title: exp.1_Hel2-HTP-1

description: CRAC sample

value: NNNCTAGC

value: protein-crosslinked RNA


title: Tdc2_2_mmPCR


title: exp.3_no_tag

description: CRAC sample

value: NNNAGAGC


title: exp.4_wt-Hel2-HTP

description: CRAC sample

data_processing:
Library strategy: CRAC
Base calling was done using Illumina standard software.
Data were split according to i7 indices using Illumina software.
Reads from different lanes belonging to the same sample were concatenated.
Reads were split according to in-line barcodes.
For submission to GEO, reads from the same sample, but carrying different i7 indices, and for exp.1 and exp.2 from two different size fractions, were combined and only identical parts of a5'-linkers were removed, while random nucleotides and parts of the 5'linkers that differed between samples were retained. For further data processing, these parts were removed.
Further processing: 3'-adapters were removed using flexbar. pyFastqDuplicateRemover.py from the pyCRAC package (Webb et al., 2014) was used to collapse data (files belonging to the same sample but with different indices & 5'linkers with 3'-terminal N were treated separately, as reads definitely result from separate RNA molecules, to retain greater sequencing depth and collapsed files were combined thereafter - available upon request).
Collapsed and uncollapsed data were aligned using novoalign. Reads were mapped using pyReadCounters from the pyCRAC package. Bedgraphs were generated from pyReadCounters output and converted to bigwig format using bedGraphToBigWig.
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: bedgraph files showing hit density (actual counts) for aligned, collapsed data.

value: NNNCACTAGC

tag: additional notes

value: single size fraction


title: Sample_Chap_1mM_1

value: chap1 deletion

value: mycelia


title: Sample_Chap_0_5mM_3

value: 0.5 mM FA


title: Sample_Chap_0_5_mM_2


title: Tdc2_1_mmPCR


title: NPFR_3_mmPCR

source_name: neuropeptide F receptor neuron nuclei

value: UAS-unc84-2XGFP; NPFR-GAL4

value: neuropeptide F receptor


title: NPFR_2_mmPCR


title: Sample_WT_DMSO_control_4

value: wild type C4

value: DMSO control


title: exp.3_wt-Hel2-HTP

description: CRAC sample

value: NNNTAAGC


title: exp.4_asc1D-Hel2-HTP

description: CRAC sample

value: NNNTCTCTAGC


title: NPFR_1_mmPCR


title: exp.3 no tag

description: CRAC sample

value: NNNACAGTGN


title: TvAt_96h_rep2

city: Hermosillo

first: Miguel

middle: Angel

last: Hernandez

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas No. 46

department: Coordinación de Tecnología de Alimentos de Origen Vegetal

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo

description:
Biological replicate 2 of T. virens co-cultivated with A. thaliana seedlings collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR012

data_processing:
Sequenced reads (fastq files) were quality checked using FastQC v0.11.2. Reads were mapped against the predicted genes of the T. virens genome version 2 using the Burrows-Wheeler Aligner (BWA) software with default parameters.Visualization and quantification of reads per gene was carried out using the Tablet tool, and only reads with unique hits were maintained and used for the quantification of read number per gene. Correlation and biological coefficient of variation between samples and biological replicates were determined with a Pearson´s correlation and multidimensional scaling analyzes (MDS) using the normalized expression data by trimmed mean of M values (TMM). Only the biological replicates with a Pearson´s correlation factor ≥ 0.9 between them were considered for subsequent analyzes. To assess the transcriptional response of T. virens to the presence of A. thaliana, we determined the differentially expressed genes by comparison of T. virens growing in MS medium versus T. virens in co-culture with A. thaliana at 48, 72 and 96 hpi, using the edgeR package (R version 3.0.1, edgeR version 3.2.4), applying a statistical methods based on pairwise comparisons and a common dispersion calculated as suggested by edgeR manual. Genes that exhibited a false discovery rate (FDR) £ 0.05 and a log2 Fold Change ³ 1 (log2FC) were considered as differentially expressed genes (DEG).
Genome_build: NCBI GenBank the project accession number ABDF00000000.2, Trichoderma virens (Kubicek et al. 2011. Genome Biology)
Supplementary_files_format_and_content: tab-delimited text TvAt_interaction_reads_per_gene.txt file includes the counts of reads for each predicted gene in the T. virens genome

organism: Trichoderma virens

growth_protocol: All fungal strains were routinely grown at 28 °C on potato dextrose agar (PDA; DIFCO)

extract_protocol:
Total RNA was extract by the TRIzol method (Invitrogen) following the protocol recommended by manufacturer. DNA contamination was eliminated with TURBO DNase (Life Technologies). RNA samples were quantified by measuring the absorbance ratio at A260/280 and A260/230 using an Epoch Spectrophotometer (Biotek).
RNA-seq libraries were prepared from 3 biological RNA replicates for each treatment, and sequenced in the SOLiD platform (Sequencing by Oligonucleotide Ligation and Detection; Applied Biosystems) following the manufacturer’s instructions.

treatment_protocol: Twenty ten-day-old Arabidopsis seedlings grown on MS 1× plates were root inoculated with T. virens WT (wild-type), and mycelia were collected at 48, 72 and 96 hpi (hours post inoculation). T. virens growing in MS 1× plates were used as control

tag: protocol

value: TvAt

tag: time

value: 96 hpi (hours post inoculation).

value: Mycelium


title: TvAt_72h_rep3

description:
Biological replicate 3 of T. virens co-cultivated with A. thaliana seedlings collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR017

value: 72 hpi (hours post inoculation).


title: TvAt_96h_rep3

description:
Biological replicate 3 of T. virens co-cultivated with A. thaliana seedlings collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR018


title: Sample_WT_DMSO_control_3


title: TvAt_96h_rep1

description:
Biological replicate 1 of T. virens co-cultivated with A. thaliana seedlings collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR006


title: TvAt_72h_rep2

description:
Biological replicate 2 of T. virens co-cultivated with A. thaliana seedlings collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR011


title: exp.3_Hel2-543-HTP

description: CRAC sample

value: NNNGCGCAGC

value: protein-crosslinked RNA


title: Sample_Chap_1mM_2

value: 1 mM FA


title: NPF_2_mmPCR

source_name: neuropeptide F neuron nuclei

value: UAS-unc84-2XGFP; NPF-GAL4

value: neuropeptide F


title: TvAt_72h_rep1

description:
Biological replicate 1 of T. virens co-cultivated with A. thaliana seedlings collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR005


title: Sample_WT_DMSO_control_2

value: mycelia


title: Sample_WT_DMSO_control_1


title: exp.3_Hel2-1-492-HTP

description: CRAC sample

value: NNNATTAGC

value: single size fraction


title: Sample_WT_2mM_4

value: wild type C4

value: 2 mM FA


title: TvAt_48h_rep3

description:
Biological replicate 3 of T. virens co-cultivated with A. thaliana seedlings collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR016

value: 48 hpi (hours post inoculation).


title: exp.4 no tag

description: CRAC sample

value: NNNGTGAGC


title: NPF_1_mmPCR


title: exp.3_asc1D-Hel2-HTP

description: CRAC sample

value: NNNCGCTTAGC


title: Sample_Chap_0_5mM_1

value: chap1 deletion

value: 0.5 mM FA


title: Dh44_3_mmPCR

source_name: diuretic hormone 44 neuron nuclei

value: UAS-unc84-2XGFP; Dh44-GAL4

value: diuretic hormone 44


title: TvAt_48h_rep2

description:
Biological replicate 2 of T. virens co-cultivated with A. thaliana seedlings collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR010

value: TvAt

value: Mycelium


title: Dh44_2_mmPCR


title: exp.2_wt-Hel2-HTP

description: CRAC sample

value: NNNACTCAGC

value: 2 size fractions

value: protein-crosslinked RNA


title: NPF_3_mmPCR

value: UAS-unc84-2XGFP; NPF-GAL4

value: neuropeptide F


title: TvAt_48h_rep1

description:
Biological replicate 1 of T. virens co-cultivated with A. thaliana seedlings collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR004


title: exp.2_Hel2-LKDD

description: CRAC sample

value: NNNATCACGN


title: Sample_WT_2mM_2

value: wild type C4

value: mycelia


title: Tv_96h_rep3

description:
Biological replicate 3 of T. virens growing in MS 1× plates collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR015

value: Tv

value: 96 hpi (hours post inoculation).


title: Sample_WT_2mM_1

value: 2 mM FA


title: Tv_96h_rep2

description:
Biological replicate 2 of T. virens growing in MS 1× plates collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR009


title: Sample_WT_2mM_3


title: Sample_WT_1mM_4

value: 1 mM FA


title: exp.2_Hel2-1-543-HTP-2

description: CRAC sample

value: NNNGCACTAN


title: MDA-MB-436 shEZH2

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

data_processing:
All RNAseq fastq files were aligned to human genome (GRCh38) using STAR with parameter --outFilterMismatchNmax 2.
Gene read numbers were counted using HTSeq-count.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all samples

source_name: human MDA-MB-436 cell line

growth_protocol: Cells were cultured in DMEM medium with 10% FBS and penicillin/streptomycin in 37°C incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
Libraries were prepared by BGI (Hongkong).

treatment_protocol: Cells were transduced with GSK343 inhibitor, shEZH2 or no treatment as control.

value: shEZH2 treatment


title: exp.2_Hel2-1-543-HTP-1

description: CRAC sample

value: NNNCGTGATN


title: Sample_WT_1mM_3


title: Tv_72h_rep3

description:
Biological replicate 3 of T. virens growing in MS 1× plates collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR014

value: 72 hpi (hours post inoculation).


title: MDA-MB-453 shEZH2

source_name: human MDA-MB-453 cell line


title: exp.2_Hel2-LKAA

description: CRAC sample

value: NNNTAGTGCN


title: Tv_96h_rep1

description:
Biological replicate 1 of T. virens growing in MS 1× plates collected at 96 hpi (hours post inoculation).
Tvirens_02AHTVTR003

value: Mycelium


title: MDA-MB-231 shEZH2

source_name: human MDA-MB-231 cell line


title: Tv_72h_rep2

description:
Biological replicate 2 of T. virens growing in MS 1× plates collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR008


title: Sample_WT_1mM_2


title: MDA-MB-453 GSK343

treatment_protocol: Cells were transduced with GSK343 inhibitor, shEZh2 or no treatment as control.

value: GSK343 treatment


title: exp.2_Hel2-1-492-HTP

description: CRAC sample

value: NNNGACTTAGC

value: 2 size fractions

value: protein-crosslinked RNA


title: exp.1_wt-Hel2-HTP

description: CRAC sample

value: NNNGTGAGC


title: MDA-MB-436 GSK343


title: Dh44_1_mmPCR

description: Heads were collected from a mixed population of males and females.

value: UAS-unc84-2XGFP; Dh44-GAL4

value: diuretic hormone 44


title: MDA-MB-231 GSK343


title: Tv_48h_rep3

description:
Biological replicate 3 of T. virens growing in MS 1× plates collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR013

value: Tv

value: 48 hpi (hours post inoculation).


title: exp.1_Hel2-LKDD-HTP

description: CRAC sample

value: NNNCTAGC


title: Sample_WT_0_5mM_3

value: wild type C4

value: 0.5 mM FA

value: mycelia


title: Tv_72h_rep1

description:
Biological replicate 1 of T. virens growing in MS 1× plates collected at 72 hpi (hours post inoculation).
Tvirens_02AHTVTR002


title: MDA-MB-453 Control

value: no treatment


title: Sample_WT_1mM_1

value: 1 mM FA


title: Sample_WT_0_5mM_4


title: Sample_WT_0_5mM_2


title: MDA-MB-436 Control


title: Tv_48h_rep1

description:
Biological replicate 1 of T. virens growing in MS 1× plates collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR001


title: Tv_48h_rep2

description:
Biological replicate 2 of T. virens growing in MS 1× plates collected at 48 hpi (hours post inoculation).
Tvirens_02AHTVTR007


title: Sample_WT_0_5mM_1


title: exp.1_Hel2-LKAA-HTP

description: CRAC sample

value: NNNTCTCTAGC


title: MDA-MB-231 Control


title: exp.1 no tag

description: CRAC sample

value: NNNAGAGC


title: exp.1_Hel2-1-492-HTP

description: CRAC sample

value: NNNCACTAGC


title: Lung_Exposed_Day90_rep4

status: Public on Jan 17 2019

city: Vadoeuvre-lès-Nancy

first: Laëtitia

last: CHEZEAU

address: 1 rue du Morvan

country: France

institute: INRS

description:
2288
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 90 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were quantile normalized using the software Solo (http://www-microarrays.u-strasbg.fr/Solo/index.html)

organism: Rattus norvegicus

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 90, replicate 4

label_protocol: For each of the 50 samples (5 control and 5 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 12 week old male F344 rats were exposed by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to an aerosol of TiO2 P25 nanoparticles (Evonik, 10 mg/m3).

value: accessory lobe of lung

tag: gender

value: male

tag: age

value: 12 weeks-old


title: Lung_Control_Day180_rep3

description:
2244
Gene expression in lung of control rat 180 days post exposure

source_name: Rat, Lung, Control, Day 180, replicate 3


title: Lung_Control_Day90_rep4

description:
2239
Gene expression in lung of control rat 90 days post exposure

source_name: Rat, Lung, Control, Day 90, replicate 4


title: Lung_Exposed_Day180_rep2

description:
2245
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 180 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 180, replicate 2


title: Lung_Control_Day180_rep5

description:
2226
Gene expression in lung of control rat 180 days post exposure

source_name: Rat, Lung, Control, Day 180, replicate 5


title: Lung_Exposed_Day180_rep1

description:
2291
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 180 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 180, replicate 1


title: Lung_Exposed_Day180_rep5

description:
2296
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 180 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 180, replicate 5


title: Lung_Control_Day180_rep2

description:
2243
Gene expression in lung of control rat 180 days post exposure

source_name: Rat, Lung, Control, Day 180, replicate 2


title: Lung_Exposed_Day90_rep1

description:
2280
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 90 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 90, replicate 1


title: Lung_Exposed_Day28_rep2

description:
2273
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 28 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 28, replicate 2


title: Lung_Exposed_Day28_rep1

description:
2272
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 28 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 28, replicate 1


title: Lung_Control_Day90_rep5

description:
2240
Gene expression in lung of control rat 90 days post exposure

source_name: Rat, Lung, Control, Day 90, replicate 5


title: Lung_Exposed_Day180_rep4

description:
2295
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 180 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 180, replicate 4


title: Lung_Exposed_Day90_rep3

description:
2287
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 90 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 90, replicate 3


title: Lung_Control_Day90_rep3

description:
2238
Gene expression in lung of control rat 90 days post exposure

source_name: Rat, Lung, Control, Day 90, replicate 3


title: Lung_Control_Day180_rep1

description:
2242
Gene expression in lung of control rat 180 days post exposure

source_name: Rat, Lung, Control, Day 180, replicate 1


title: Lung_Exposed_Day28_rep3

description:
2277
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 28 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 28, replicate 3


title: Lung_Control_Day180_rep4

description:
2225
Gene expression in lung of control rat 180 days post exposure

source_name: Rat, Lung, Control, Day 180, replicate 4


title: Lung_Exposed_Day28_rep5

description:
2279
Gene expression in lung of rat exposed to a nanoaerosol of TiO2 (10 mg/m3) 28 days post exposure

source_name: Rat, Lung, Exposed to TiO2 (10 mg/m3), Day 28, replicate 5