title: OW16_1% EtOH_HFHC_13dpf_1

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW16

value: HFHC diet

value: AB


title: 2236F17-1: nrde3_H3K9me3_2

status: Public on Dec 01 2020

type: SRA

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

library_source: genomic

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2).
The qCount function in the QuasR package was used to count reads overlapping the ce6 genome assembly split into fragments of 500bp.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains seqnames, followed by start and end position and columns contain raw counts of reads overlapping each fragment for each sample.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: early embryo

growth_protocol: chromatin was isolated from early embryos (before bean stage) grown after L1 synchronization (60–65 h depending on each strain) in two independent biological replicates.

extract_protocol:
ChIP experiments were performed as previously described (Zeller et al., 2016). In brief: Embryos were harvested from synchronized animals in three replicates. 40 μg of chromatin was incubated overnight with 3 μg of anti-LEM-2 antibody (Novus Biologicals) coupled to Dynabeads Sheep Anti-Rabbit IgG (Invitrogen), in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl)) containing 1% SDS. Antibody bound chromatin was washed 3 × 5 min FA buffer; 5 min FA buffer with 1 M NaCl; 10 min FA buffer with 500 mM NaCl; 5 min with TEL buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) and 2 × 5 min with TE. Complexes were eluted in 1% SDS in TE with 250 mM NaCl at 65°C for 15 min. Samples and inputs were treated with 20 μg of RNAse A for 30 min at 37°C and 20 μg of proteinase K for 1 hr at 55°C. Crosslinks were reversed by overnight incubation at 65°C. DNA was subsequently purified using Zymo DNA purification columns (Zymo Research).
Libraries were prepared from chromatin IP and input samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturers recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 12 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).

tag: strain

tag: tissue

value: early embryo


title: 4TGFB_2dwithdrawn_Rep1

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

country: USA

institute: Baylor University

description: 4d +TGFB, 2d -TGFB MCF10A mRNA

library_source: transcriptomic

data_processing:
Adapter sequences and bases with lower quality than three removed using Trimmomatic (Galaxy Version 0.38.0).
Bases of reads less than window size 4, mean quality 15 were trimmed using Trimmomatic (Galaxy Version 0.38.0).
Reads trimmed to 36 bp using Trimmomatic (Galaxy Version 0.38.0).
Aligned to reference genome UCSC hg19 with HISAT2 (Galaxy Version 2.1.0+galaxy5)
Known genes assembled via StringTie (Galaxy Version 1.3.6)
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: MCF10A cells

growth_protocol: Cells were plated at 10,000 cells/mm^2 and treated with TGFB.  Cell density was maintained every other day and media was removed and replenished with TGFB

extract_protocol:
Cells lysed in TriZol reagent and phenol/chloroform extracted
Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: 5 ng/mL TGFB in 4 mM HCL with 0.01% BSA

tag: treatment

value: 4d +TGFB, 2d -TGFB MCF10A mRNA


title: p1035812-7

city: Oklahoma City

first: Courtney

middle: G

last: Montgomery

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Single-cell libraries were processed with 10x Genomics cellranger informatics pipeline (v 3.0.2) with the count and aggr commands
Resulting count matrices output by cellranger aggr were generated with the Read10x function in Seurat v3.0.
genome build: GRCh38
processed data files format and content: RDS file, containing an R data object of the class "Seurat" following integration of control and sarcoid data: see https://satijalab.org/seurat/. The meta.data slot of the object contains 6 columns: donor (order sample is processed by cellranger aggr), library.id (sample subject name) , Barcode (10x Cell barcode identifier), celltype (the assigned cell type), classification (disease status for either Sarcoidosis or Control) and coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_counts.mtx (Matrix market coordinate text file) containing raw scRNA-seq counts for genes for all cells (columns).
processed data files format and content: matrix_colData.txt (tab-delimited text file, the rows of which report information about cells in the order they are presented along columns in matrix_counts.mtx). The columns of this file contain 1) the column of the sparse matrix in matrix_counts.txt identifying the cell; 2) donor (order sample is processed by cellranger aggr);   3) library.id (sample subject name); 4) classification (whether the cell is classified as control or sarcoidosis), 5) celltype (the assigned cell type); 6) Barcode (10x Cell barcode identifier); 7 & 8) coordinates for the UMAP projection (UMAP_1, UMAP_2).
processed data files format and content: matrix_rowData.txt (tab-delimited text file, the rows of which report the genes in the order they are presented along rows in matrix_counts.mtx)

source_name: PBMC mixture

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) and neutrophils (PMNs) were collected using LSM (Gibco) and Polymorphprep™ (Alere Technologies, Oslo, Norway). Fresh PBMCs (target 4,000/patient) and PMNs (target 1,000/patient) were combined and loaded at a concentration of 1000 cells/µL into a 10x Genomics Single Cell A v2 chip into the Chromium controller.
Following single cell emulsion generation, uniquely identifiable first strand template cDNA was generated by emulsion PCR and after emulsion was broken, the second cDNA strand was generated and Illumina compatible adapters were ligated.

tag: study classification

value: Sarcoidosis

tag: subject age

tag: subject sex

value: Male

tag: subject race

value: White

tag: active disease as defined by omrf sru

value: Active

tag: currently on any immunosuppressant

tag: currently on >20mg prednisone

tag: currently on biologics


title: OW11_1% EtOH_ND_13dpf_2

city: Boston

first: Olivia

last: Weeks

state: MA

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW11

data_processing:
For larval RNAseq (13 dpf), reads were aligned to the GRCz10 reference assembly with the STAR aligner (v2.4, default parameters) and differential gene expression was performed with DESeq2 software (default parameters). Heatmap visualization and hierarchical clustering was performed using the R package pheatmap with the default parameters.
For the adult liver RNAseq, FASTQ files were analyzed using FASTQC to ensure uniform read quality (phred>30). Single end reads were aligned using Star v2.3 (default parameters) to the zebrafish genome (GRCz10). The mapped reads were counted using htseq-count (v0.6.0, parameters –t exon) and gene models from Ensembl transcriptome v89. Analysis of differential gene expression was performed using DESeq2 (default parameters).
Genome_build: GRCz10
Supplementary_files_format_and_content: .csv files containing gene names, raw read counts, and normalized read counts. For adult RNAseq, the differential gene expression analysis for manuscript-relevant pairwise comparisons are included.

organism: Danio rerio

source_name: whole zebrafish larvae

growth_protocol: Larval zebrafish were housed on the nursery in 0.8L tanks with mesh baffles at a density of 32 fish per tank beginning at 5 dpf. At 5 dpf, fish received a paramecia starter culture and were kept overnight without flow. At 6 dpf, flow was initiated, and larvae were administered a specified diet. For larval RNA-seq studies, 6 dpf larvae were started on a normal or HFHC diet. Normal larval diet included hatched artemia two times per day at a density of ~8.8mg dry weight/fish. HFHC larval diet included the artemia plus a dietary supplement of 0.5g/tank of Hoosier Hill Farm Whole Egg Powder re-suspended in system water. All larvae were maintained on their diet until the point of collection (13 dpf) or grown until 30 dpf, during which time they were transferred from the nursery to the adult system. For adult studies, larvae were maintained on a normal larval diet until graduation from the nursery. Upon graduation from the nursery at ~30 days, juvenile fish were maintained at equal tank densities in 2.8L tanks and fed a standard artemia diet two times per day at a density of ~14.7mg dry weight/fish. Beginning at 65 dpf, fish were housed at a density of 12 fish/tank and fed a normal or HFHC diet. Adult normal diet consisted of 0.013 g/fish of Skretting Gemma Micro 300 feed per day (59% protein, 14% lipids, 14% ash, 8% moisture, 0.2% crude fiber, and 1.9% starch by mass). HFHC diet tanks received 0.063 g/fish of Skretting Gemma Micro 300 per day plus 0.02g/fish of Hoosier Hill Farm Whole Egg Powder (~49% lipids, ~49% protein, ~1.7% cholesterol).

extract_protocol:
RNA was extracted in TRIzol (Life Technologies) from whole pooled (15 individuals/sample) 13 dpf larvae or single livers isolated from WT (AB) fish and purified using the Qiagen RNeasy Mini Kit. RNA quality was verified on the Aligent Bioanalyzer and DNA contamination was removed with the TURBO DNA-free (Invitrogen) kit.
Single-end NextSeq Series High-Output RNA sequencing was performed on poly-A selected coding mRNAs at the Dana Farber Center for Cancer Computational Biology.

treatment_protocol: Zebrafish larvae were exposed to 0%, 0.5%, and 1.0% EtOH dissolved in fish water from 12 hpf – 5 dpf and administered the relevant diet as described under "growth parameters."

value: 1% EtOH

tag: diet

value: normal

tag: developmental stage

value: 13 dpf

value: homogenized whole animals


title: 2236F16-2: nrde3_H3K9me3_1


title: 2236F16-1: nrde3_H3K9me3_1


title: OW10_1% EtOH_ND_13dpf_1

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW10


title: 2236F15-2: N2_H3K9me3_3

value: N2 (Bristol)


title: 10dTGFB_6dwithdrawn_Rep1

description: 10d +TGFB, 6d -TGFB MCF10A mRNA

value: 10d +TGFB, 6d -TGFB MCF10A mRNA


title: 10dTGFB_10dwithdrawn_Rep1

description: 10d +TGFB, 10d -TGFB MCF10A mRNA

value: 10d +TGFB, 10d -TGFB MCF10A mRNA


title: ZR75-1 Tamoxifen Resistant

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

data_processing:
Raw fastq is mapped to human genome, filtered and then generated SIFs with HiSIF package.
Genome_build: HG19
Supplementary_files_format_and_content: HiSIF_T47D.peak.txt, HiSIF_T47D-TamR.peak.txt, HiSIF_ZR75-1.peak.txt, HiSIF_ZR75-1-TamR.peak.txt are files of SIFs generated by HiSIF

growth_protocol: Routine cell media for all cell lines, respectively.

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Rao et al. 2014).
In situ Hi-C was performed as described (Rao et al. 2014).

treatment_protocol: Untreated

tag: cell line background

tag: cell type

value: immortalized breast epithelial cell line

tag: phenotype

value: Tamoxifen Resistant

tag: analysis

value: in situ Hi-C


title: 2236F15-1: N2_H3K9me3_3

tag: strain


title: OW9_CT_ND_13dpf_3

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW9

value: 0% EtOH

value: AB

tag: tissue


title: p1035811-5

value: Female

value: Non-active


title: ZR75-1 parental

value: control; parental


title: OW7_CT_ND_13dpf_1

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW7

tag: treatment


title: OW8_CT_ND_13dpf_2

description:
whole larvae (siblings) of mixed sizes were combined into three independent tubes/group and homogenized. Embryos were treated with EtOH from 12 hpf - 5 dpf.
20180702_OGWFAE_raw.data.csv
20180702_OGWFAE_TPM.csv
OW8


title: 2236F14-2: N2_H3K9me3_2

value: early embryo


title: 10dTGFB_4dwithdrawn_Rep1

description: 10d +TGFB, 4d -TGFB MCF10A mRNA

value: 10d +TGFB, 4d -TGFB MCF10A mRNA


title: T47D Tamoxifen Resistant


title: 10dTGFB_2dwithdrawn_Rep1

description: 10d +TGFB, 2d -TGFB MCF10A mRNA

value: 10d +TGFB, 2d -TGFB MCF10A mRNA


title: 2236F14-1: N2_H3K9me3_2


title: 10dTGFB_Rep1

description: 10d +TGFB MCF10A mRNA

value: 10d +TGFB MCF10A mRNA


title: T47D parental


title: 8dTGFB_Rep1

description: 8d +TGFB MCF10A mRNA

value: 8d +TGFB MCF10A mRNA


title: 2236F13-2: N2_H3K9me3_1


title: 2236F13-1: N2_H3K9me3_1


title: 6dTGFB_Rep1

description: 6d +TGFB MCF10A mRNA

value: 6d +TGFB MCF10A mRNA


title: 4dTGFB_Rep1

description: 4d +TGFB MCF10A mRNA

value: 4d +TGFB MCF10A mRNA


title: 2dTGFB_Rep1

description: 2d +TGFB MCF10A mRNA

value: 2d +TGFB MCF10A mRNA


title: Untreated_D20_Rep1

description: Untreated MCF10A mRNA

value: Untreated MCF10A mRNA


title: 2236F8-2: nrde3_input_2


title: 2236F9-1: nrde3_input_3


title: Untreated_D2_Rep1

description: Untreated MCF10A mRNA


title: 2236F8-1: nrde3_input_2


title: K562_CRISPR_IGF1KO_IGF2_rep2_4Cseq

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
4C experiment using a bait designed at IGF2 promoter in K562 MRR2-A1 knockout cells. This region (MRR2-A1) is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
ZY_IGF1G10_K562KO_R2

data_processing:
library strategy : 4C-seq
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  paired-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content:
*.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.

source_name: K562 cells with CRISPR/Cas9 vector targeting MRR2-A1 region

growth_protocol: Cell cultures were maintained at 37 °C, 5% CO2 humidified incubator.

extract_protocol:
Briefly, 4 × 107 cells were cross-linked with 1% formaldehyde. The nuclei pellets were isolated by cell lysis with cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 5mM EDTA, 0.5% NP 40) supplemented with protease inhibitors (Roche). First step digestion was performed overnight at 37°C with HindIII enzyme (NEB). Digestion efficiency was measured by RT-qPCR with HindIII site–specific primers. After confirmation of good digestion efficiency, DNA was ligated overnight at 16°C by T4 DNA ligase (Thermo Scientific) and de-crosslinked. Following de-crosslinking, DNA was extracted by phenol-chloroform. The DNA was then processed for second digestion with DpnII enzyme (NEB) overnight at 37°C. After final ligation, 4C template DNA was obtained and the concentration was determined using Qubit assays (Thermo Scientific).
The 4C template DNA was then amplified using specific primers with illumina Nextera adapters and sent for sequencing on the MiSeq system.


title: 2236F7-1: nrde3_input_1


title: Test 2

type: RNA

city: Kobe

first: Sentaro

last: Kusuhara

state: Hyogo

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Department of Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

organism: Mus musculus

source_name: retina

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kiting Kit (Affymetrix, Santa Clara, CA).

extract_protocol: mRNA was isolated using TRIzol according to manufacturer's protocol.

value: retina

tag: genotype/variation

value: homozygous Mrp4 knockout mice

tag: age

value: 46-55 weeks old


title: K562_CRISPR_IGF1KO_IGF2_rep1_4Cseq

description:
4C experiment using a bait designed at IGF2 promoter in K562 MRR2-A1 knockout cells. This region (MRR2-A1) is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
ZY_IGF1G10_K562KO_R1

value: CRISPR/Cas9 vector targeting MRR2-A1 region


title: hTERT-MSC, cultured with Gln, sample 3

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Gln, sample 3

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure.

label: biotin

source_name: hTERT-MSC

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of total RNA, according to the Affymetrix WT Plus Expression Protocol.

extract_protocol: Extraction of total RNA was performed using AllPrep DNA/RNA/miRNA isolation kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol.

treatment_protocol: hTERT-MSCs were cultured for 2 weeks in osteogenic differentiating Dulbecco’s Modified Medium (DMEM) low glucose (1g/l) containing ascorbic acid (50 μg/ml), dexamethasone (Dex,10E−8 M) and 5% FBS, in the presence or absence of 2 mM Gln, and in absence of Gln with 380 µM Asparagine (Asn).

value: Mesenchymal stromal cell line


title: Control 2

value: wild-type


title: K562_CRISPR_EV_IGF2_rep2_4Cseq

description:
4C experiment using a bait designed at IGF2 promoter in K562 empty vector transfected cells.
ZY_IGF2_K562_R2

source_name: K562 cells with empty vector

value: empty vector


title: hTERT-MSC, sample 3

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, sample 3


title: Control 3


title: Control 1


title: K562_CRISPR_EV_IGF2_rep1_4Cseq

description:
4C experiment using a bait designed at IGF2 promoter in K562 empty vector transfected cells.
ZY_IGF2_K562_R1


title: Control 4


title: Test 4


title: hTERT-MSC, cultured with Gln, sample 1

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Gln, sample 1


title: Test 3


title: 2236F9-2: nrde3_input_3


title: hTERT-MSC, sample 2

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, sample 2


title: 2236F6-2: met2nrde3_input_3


title: P.g.4

city: Tokyo

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

hyb_protocol: cRNAs were analyzed by hybridization onto an Agilent SurePrint G3 Unrestricted Gene Expression 8 × 60 K Microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Fluorescence signals from the hybridized microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies) according to the manufacturer’s instructions.

data_processing: Raw microarray data were extracted using Feature Extraction Software (ver. 11.0.1.1; Agilent Technologies).

source_name: brown adipose tissue

label_protocol: The Agilent Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, California, USA) was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray

growth_protocol: C57BL/6J mice, 12 weeks old

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, California, USA) with NucleoSpin RNA (TaKaRa Bio, Shiga, Japan). cDNA was synthesized using a PrimeScript RT Master Mix (TaKaRa Bio) according to the manufacturer’s instructions.

treatment_protocol: A total of 108 colony-forming units (CFU) of sonicated P. gingivalis suspended in 100 μL of saline was injected. In controls, saline was injected.

value: brown adipose tissue

value: 12 weeks old

value: 18hr after intravenous injection of P. gingivalisin


title: hTERT-MSC, cultured with Gln, sample 2

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Gln, sample 2


title: Test 1


title: hTERT-MSC, cultured with Asn (no Gln), sample 3

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Asn (no Gln), sample 3


title: hTERT-MSC, cultured with Asn (no Gln), sample 1

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Asn (no Gln), sample 1


title: 2236F6-1: met2nrde3_input_3

value: early embryo


title: 2236F5-2: met2nrde3_input_2


title: KO mice received anti-PD-1 treament rep4

city: Beijing

first: Liqing

last: Cheng

state: Beijing

address: Tsinghua University,Hai Dian, Beijing

department: school of medicine

country: China

institute: Tsinghua university

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using HISAT2 version 2.1.0 with parameters -p 16 -5 9 --qc-filter --mm --dta
raw counts were calculated by htseq-count version 0.11.2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

source_name: Mixed macrophages and MDSCs cells

extract_protocol:
Total RNA was extracted by using Trizol according to the manufactural protocol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Clec4d KO

tag: treament

value: anti-PD-1 treatment

value: Mixed macrophages and MDSCs cells


title: hTERT-MSC, sample 1

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, sample 1


title: K562_CRISPR_EV_MRR1A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region in K562 empty vector transfected cells. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
ZY_FGF18S1_K562_R2


title: Control4

value: 18hr after intravenous injection of saline


title: hTERT-MSC, cultured with Asn (no Gln), sample 2

description: human Telomerase Reverse Transcriptase transduced Mesenchymal Stromal Cell line, cultured with Asn (no Gln), sample 2


title: 2236F7-2: nrde3_input_1


title: K562_CRISPR_EV_MRR1A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region in K562 empty vector transfected cells. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
ZY_FGF18S1_K562_R1


title: KO mice received anti-PD-1 treament rep3


title: K562_CRISPR_EV_MRR2A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region in K562 empty vector transfected cells. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
ZY_IGF2S1_K562_R3


title: 2236F3-2: N2_input_3

value: N2 (Bristol)


title: 2236F5-1: met2nrde3_input_2


title: KO mice received IgG treament rep2

value: IgG treatment


title: KO mice received anti-PD-1 treament rep2


title: Control2


title: K562_CRISPR_EV_MRR2A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region in K562 empty vector transfected cells. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
ZY_IGF2S1_K562_R4


title: KO mice received IgG treament rep3


title: KO mice received anti-PD-1 treament rep1


title: 2236F4-1: met2nrde3_input_1


title: P.g.3


title: WT mice received anti-PD-1 treament rep6

value: wild type


title: P.g.1


title: Control1


title: Control3


title: 2236F3-1: N2_input_3


title: 1μMGSK343treatment_K562_GSK343_MRR2A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
GSK343_R1_IGF2S1

source_name: K562 cells treated with 1μM GSK343

treatment_protocol: Small molecular inhibitor GSK343 (Sigma-Aldrich) targeting EZH2 were solubilized in DMSO (Sigma-Aldrich) according to manufacturer’s instructions and used at a final concentration of 1μM. K562 cells with GSK343 were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: 1uM GSK343


title: P.g.2


title: 1μMGSK343treatment_K562_GSK343_MRR1A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
GSK343_R2_FGF18S1


title: 2236F2-1: N2_input_2


title: 2236F4-2: met2nrde3_input_1


title: KO mice received IgG treament rep1


title: 1μMGSK343treatment_K562_GSK343_MRR2A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
GSK343_R2_IGF2S1


title: WT mice received anti-PD-1 treament rep5


title: 1μMGSK343treatment_K562_GSK343_ZDHHC11_rep2_4Cseq


title: 2236F1-1: N2_input_1


title: 2236F1-2: N2_input_1


title: WT mice received anti-PD-1 treament rep3


title: 1μMGSK343treatment_K562_GSK343_ZDHHC11_rep1_4Cseq


title: 2236F2-2: N2_input_2


title: 1μMGSK343treatment_K562_GSK343_MRR1A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
GSK343_R1_FGF18S1


title: 1μMGSK343treatment_K562_GSK343_LINC00910_rep2_4Cseq


title: WT mice received anti-PD-1 treament rep2


title: UCI_11: Inflamed UC scRNA-seq

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
The Cellranger software suite (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) from 10X was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens/Info/Index) and perform UMI counting
From filtered counts Seurat1 version 3.1.3 was used to process the single cell data including normalization, integration, dimension reduction, UMAP representation
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited count files, rows are genes and columns are cells

molecule: polyA RNA

source_name: CD45+, Colonic lamina propria

growth_protocol: Approximately four to ten mucosal pinch biopsies were obtained from each patient. For UC patients, all biopsies were obtained from the rectum. For J-pouch patients, all biopsies were obtained from the pouch body or inlet.  If active endoscopic inflammation was present, this area was targeted. For each location sampled, one biopsy was collected for standard histopathology assessment and read by two expert pathologists for the PDAI histology subscore and histologic pouch activity score (PAS). In most instances 6 pinch biopsies were performed for each patient, however, at the time of endoscopy fewer pinches were taken in severely inflamed patients to prevent the risk of risk of excess bleeding and perforation. We observe a slight decrease in cell viability reflected in the number of cells recovered per sample.

extract_protocol:
From pinch biopsies all samples were sorted and CD45+ cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10,000 cells were loaded per channel. scRNA-Seq libraries were prepared using the following Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, Single Cell 3’ Chip Kit v2, and i7 Multiplex Kit (catalog# PN-120237, PN-120236, # PN-120262, 10x Genomics)19 and following the Single Cell 3’ Reagent Kits v2 User Guide (Manual Part # CG00052)
RNA libraries were prepared using standard 10X genomics protocols were sequenced on Illumina HiSeq 4000 as 2×150 paired-end reads, one full lane per sample, for approximately >90% sequencing saturation.

treatment_protocol: All biopsies were collected in ice cold complete RPMI 1640 (10% FBS, 100x penicillin/streptomycin/glutamine, 50uM 2-mercaptoethanol, Sigma) and subsequently cryopreserved in freezing media (90% FBS + 10% DMSO) for long-term storage. We found that there was considerable variation in the recovery of cells from the freezing medium based on the “batch/lot” of FBS that was used to generate the freezing medium. Hence, it was extremely important to “batch/lot” test different FBS from different vendors to optimize the yield of immune cells. Cryopreserved biopsies were gently thawed at 37°C and enzymatically digested in collagenase VIII (Sigma) and DNase (Sigma) for 1h to obtain single cell suspensions. After live/dead cell staining with near-IR stain (Invitrogen), cell surface markers were labeled with the following antibodies: CD45 PE-Cy7, CD3 PerCP-Cy5.5, CD19 PE, CD14 FITC, and CD16 Pacific Blue (BioLegend). Sorted CD45+ cellular suspensions were isolated using the Sony SY3200 cell sorter and prepared for scRNA-seq.

tag: disease state

value: Inflamed UC

value: CD45+, Colonic lamina propria


title: UCI_9: Inflamed UC scRNA-seq


title: UCI_10: Inflamed UC scRNA-seq


title: 1μMGSK343treatment_K562_GSK343_LINC00910_rep1_4Cseq


title: WT mice received IgG treament rep6


title: 1μMGSK343treatment_K562_GSK343_MYC_rep2_4Cseq


title: skeletal muscle-HFD_Cont-Rep8

city: clermont ferrand

first: frederic

last: capel

address: 28 place henri dunant

department: alimentation humaine

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 32766 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30124 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: skeletal muscle

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water

value: HFD

tag: lineage

value: Cont


title: UCI_8: Inflamed UC scRNA-seq


title: 1μMGSK343treatment_K562_GSK343_MYC_rep1_4Cseq


title: skeletal muscle-HFD_Cont-Rep7


title: skeletal muscle-HFD_O3-Rep8


title: WT mice received IgG treament rep5


title: skeletal muscle-HFD_O3-Rep7


title: skeletal muscle-HFD_Cont-Rep6


title: WT mice received anti-PD-1 treament rep4


title: skeletal muscle-STD_Cont-Rep8

value: STD


title: skeletal muscle-STD_Cont-Rep7


title: UCI_7: Inflamed UC scRNA-seq


title: 1μMGSK343treatment_K562_GSK343_PSMD5_rep2_4Cseq


title: WT mice received IgG treament rep4


title: UCI_6: Inflamed UC scRNA-seq


title: 1μMGSK343treatment_K562_GSK343_PSMD5_rep1_4Cseq


title: WT mice received IgG treament rep3


title: 1μMGSK343treatment_K562_GSK343_HOXD13_rep2_4Cseq


title: UCI_5: Inflamed UC scRNA-seq


title: skeletal muscle-HFD_O3-Rep6


title: WT mice received anti-PD-1 treament rep1


title: WT mice received IgG treament rep2


title: 1μMGSK343treatment_K562_GSK343_HOXD13_rep1_4Cseq


title: skeletal muscle-STD_Cont-Rep5


title: UCI_4: Inflamed UC scRNA-seq


title: UCI_3: Inflamed UC scRNA-seq


title: mESC-AP-PD_rep2

first: Howard

last: MENG

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: AP-seq PD rep2 in mES cell

data_processing:
Library strategy: AP-seq
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software with the following command: "cutadapt --times 1  -e 0.1  -O 3  --quality-cutoff 25  -m 50 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -A  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o {read1.out}  -p {read2.out}  {read1.in}  {read2.in}"
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome, hg38 for HEK293T and MCF7, mm10 for mESC, with bowtie2 aligner. And only record the best hit of alignment for each read.
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Remove duplication step: The sorted BAM files are removed the PCR amplification bias with the PICARD MarkDuplicates command.
Peak calling step: The final AP site peak are generated by the macs2 software
Genome_build: mm10, hg38
Supplementary_files_format_and_content: The bigwig files are generated by the deeptools bamCoverage software with parameters as follows: "bamCoverage --bam {input} -o {output} -of bigwig --scaleFactor 1 --binSize 10  --normalizeUsing RPKM"

source_name: mESC cells

growth_protocol: The HEK293T and MCF7 is separately cultivated in DMEM and MEM  with 10% FBS and 1% PS at 37°C cultivator with 5% CO2., while ESCs were cultured in the absence of feeder cells in DMEM supplemented with 15% mouse ESC (mESC)-screened fetal bovine serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, and 1,000 U/mL murine LIF on 0.1% gelatin-coated tissue culture plastics at 37°C in humidified air with 5% CO2.

extract_protocol:
The human and mouse genome is extracted by Universal Genomic DNA Kit (CWbiotech, CW2298)from cultivated cells and was then digested to 200–500 bp with NEBNext dsDNA Fragmentase.
The fragmented genomic DNA was end repaired with NEBNext End Repair Module (NEB, E6050) and E. coli ligase was added to repair nicks in fragmented genomic DNA following NEBNext dA-Tailing Module (NEB, E6053) kit to add dA to the 3′ end of double-stranded DNA. Next is the AP labeling steps the following pull-down and Y adaptor ligation. Then the template is PCR amplified and sequenced on the Illumina HiSeq X Ten.

tag: cell line

value: mESC cells

value: mouse embryo-derived stem cells

value: Wild Type

value: PD


title: 1μMGSK343treatment_K562_GSK343_IGF2_rep2_4Cseq


title: UCI_2: Inflamed UC scRNA-seq


title: UCI_1: Inflamed UC scRNA-seq


title: mESC-AP-PD_rep1

description: AP-seq PD rep1 in mES cell


title: 1μMGSK343treatment_K562_GSK343_IGF2_rep1_4Cseq


title: 1μMGSK343treatment_K562_GSK343_FGF18_rep2_4Cseq


title: mESC-AP-Input_rep2

description: AP-seq Input rep2 in mES cell

value: Input


title: 1μMGSK343treatment_K562_GSK343_FGF18_rep1_4Cseq


title: mESC-AP-Input_rep1

description: AP-seq Input rep1 in mES cell


title: 1μMGSK343treatment_K562_DMSO_MRR2A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
DMSO_R2_IGF2S1

source_name: K562 cells treated with DMSO

treatment_protocol: K562 cells with DMSO vehicle control were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: DMSO


title: PI_9: Pouchitis scRNA-seq

source_name: CD45+, pouch lamina propria

value: Pouchitis

value: CD45+, pouch lamina propria


title: PI_10: Pouchitis scRNA-seq


title: skeletal muscle-HFD_O3-Rep5


title: skeletal muscle-HFD_O3-Rep4


title: skeletal muscle-HFD_Cont-Rep4


title: WT mice received IgG treament rep1

value: Mixed macrophages and MDSCs cells


title: skeletal muscle-HFD_Cont-Rep5


title: skeletal muscle-STD_Cont-Rep4


title: 1μMGSK343treatment_K562_DMSO_MRR2A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR2-A1 region. This region is inside a H3K27me3-rich region (MRR2) and interacts with IGF2 gene promoter through HiC interactions.
DMSO_R1_IGF2S1


title: Input SolycDNA

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Sample 25
Input-SolycDNA for samples 22-24

data_processing:
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

organism: Solanum lycopersicum

source_name: 21 days-old plantlets

growth_protocol: 10 days-old seedlings grown in MS medium

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

tag: protein

value: Input-SolycDNA for samples 22-24

tag: gene id

tag: protein expression

value: Input DNA


title: skeletal muscle-STD_Cont-Rep6

tag: diet


title: PI_8: Pouchitis scRNA-seq

tag: cell type


title: PI_7: Pouchitis scRNA-seq


title: DAP-SlMYC2r.2

description:
Sample 24
Protein-DNA interaction

value: E.coli expressed


title: skeletal muscle-HFD_O3-Rep3


title: 1μMGSK343treatment_K562_DMSO_MRR1A1_rep2_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
DMSO_R2_FGF18S1

tag: cell line background


title: DAP-SlMYC2r

description:
Sample 23
Protein-DNA interaction


title: skeletal muscle-HFD_Cont-Rep3


title: skeletal muscle-HFD_Cont-Rep2


title: PI_6: Pouchitis scRNA-seq


title: DAP-SlMYC2

description:
Sample 22
Protein-DNA interaction


title: 1μMGSK343treatment_K562_DMSO_ZDHHC11_rep2_4Cseq


title: PI_5: Pouchitis scRNA-seq


title: PI_4: Pouchitis scRNA-seq


title: 1μMGSK343treatment_K562_DMSO_LINC00910_rep2_4Cseq


title: 1μMGSK343treatment_K562_DMSO_ZDHHC11_rep1_4Cseq


title: PI_3: Pouchitis scRNA-seq


title: skeletal muscle-HFD_O3-Rep2


title: water-sprayed 16C leaf 5dps_bioReplicate_1

city: Neustadt-Mußbach

first: Veli Vural

last: Uslu

state: DEUTSCHLAND

address: Epigenetics, Breitenweg 71

department: Epigenetics

institute: AgroScience GmbH AlPlanta-Institute for Plant Research

description: sRNA

data_processing:
Bowtie2 & samtools algorithms are used to convert fastq file into bam files.
TABLET is used for quantitative data and graphical representation of sRNAs mapping to region of interest.
Genome_build: matching GFP sequence (the regiion of interest) is obtained according to the Philips JG et al 2017 provided in roi1_gfp.txt fasta file
Supplementary_files_format_and_content: the fasta file of the region of interest (roi1_gfp.txt)
normalized.xlsx contains information on raw read counts and reads mapping to the region of interest (roi1_gfp.txt). Different normalization approaches are clarified in Uslu VV et al 2020.

organism: Nicotiana benthamiana

source_name: two mature sprayed leaves

growth_protocol: 16C and WT N.benthamiana plants grown on soil in the greenhouse (22C) with 60h watering intervals

extract_protocol:
miRVANA Kit is used for sRNA enriched RNA extraction
250ng of RNA per sample was used in library preparation and small RNA libraries were prepared by GenXPro GmbH using the TrueQuant SmallRNA Seq Kit according to the manual of the manufacturers (GeneXPro GmbH, Germany). The libraries were sequenced on an Illumina NextSeq500 instrument using 75 cycles of sequencing.

treatment_protocol: Three replicates treated with High-Pressure-Spraying protocol with 6 bars for the experiment and the control and a single 16C plant is sprayed with water for normalization purposes.

tag: size

value: 10cm tall plants

value: leaves

value: water-sprayed


title: PI_2: Pouchitis scRNA-seq


title: 1μMGSK343treatment_K562_DMSO_LINC00910_rep1_4Cseq


title: dsRNA-midGFP-sprayed WT-Nb leaf 5dps_bioReplicate_3

description: sRNA

value: WT-Nb

value: dsRNA-sprayed


title: skeletal muscle-HFD_O3-Rep1

value: HFD


title: Patient 32

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

institute: National Cancer Centre Singapore

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter Digital Analyser at 555 FOV

data_processing: Normalization was performed using the nSolver 4.0 Advanced Analysis software using default parameters

source_name: Angiosarcoma tissue

label_protocol: 100 ng total RNA was used as input into the hybridisation step and carried out according to the manufacturer's protocol

extract_protocol: Total RNA was extracted using FFPE RNA/DNA Purification Plus Kit (Norgen) from five 10 μm tissue sections with adequate tumor available and analyzed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). After excluding samples with suboptimal RNA integrity and content, the remaining samples were included in the nCounter analysis.

tag: Sex

value: Male

tag: Stage

value: Metastatic


title: skeletal muscle-HFD_Cont-Rep1

value: Cont


title: Patient 34

value: Non-metastatic


title: Patient 33


title: P_5: uninflamed pouch scRNA-seq

value: uninflamed pouch


title: 1μMGSK343treatment_K562_DMSO_MRR1A1_rep1_4Cseq

description:
4C experiment using a bait designed at MRR1-A1 region. This region is inside a H3K27me3-rich region (MRR1) and interacts with FGF18 gene promoter through HiC interactions.
DMSO_R1_FGF18S1

tag: treatment

value: DMSO


title: dsRNA-midGFP-sprayed WT-Nb leaf 5dps_bioReplicate_2

description: sRNA

tag: tissue


title: skeletal muscle-STD_Cont-Rep2

value: STD


title: dsRNA-midGFP-sprayed WT-Nb leaf 5dps_bioReplicate_1

description: sRNA


title: PI_1: Pouchitis scRNA-seq

value: Pouchitis

value: CD45+, pouch lamina propria


title: Patient 31

tag: age


title: 1μMGSK343treatment_K562_DMSO_MYC_rep2_4Cseq


title: P_4: uninflamed pouch scRNA-seq


title: Patient 35

value: Female


title: 1μMGSK343treatment_K562_DMSO_PSMD5_rep2_4Cseq


title: dsRNA-midGFP-sprayed 16C leaf 5dps_bioReplicate_3

description: sRNA

tag: genotype


title: 1μMGSK343treatment_K562_DMSO_MYC_rep1_4Cseq


title: Patient 29


title: Patient 30


title: P_3: uninflamed pouch scRNA-seq


title: skeletal muscle-STD_Cont-Rep1


title: Patient 28


title: 1μMGSK343treatment_K562_DMSO_HOXD13_rep2_4Cseq


title: P_1: uninflamed pouch scRNA-seq


title: Patient 27


title: ES-2 _100nM_AZ MKG9

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: ES-2 _100nM_AZ

data_processing:
Salmon index was created uinsg salmon (v0.10.2) index options  -k 31
Read quantitiation was performed using salmon (v0.10.2) quant using options  -l ISR --gcBias
Genome_build: hg38
Supplementary_files_format_and_content: tab delmited files contain read counts and TPM values per transcripts

growth_protocol: All experiments were performed on cultures within 10 passages of supply. Cell lines were cultured in DMEM (ES-2; 41965, Thermo Fisher Scientific, Paisley, UK),  supplemented with 10% FCS, Non-Essential Amino Acids (11140-035, Thermo Fisher Scientific), 10% FCS, Non-Essential Amino Acids (11140-035, Thermo Fisher Scientific), 1 mM Sodium Pyruvate, 2 mM L-Glutamine and Penicillin (100 U/ml) - Streptomycin (100 mg/ml) at 37?C, 5% CO2 mM Sodium Pyruvate, 2 mM L-Glutamine and Penicillin (100 U/ml) - Streptomycin (100 mg/ml) at 37?C, 5% CO2.

extract_protocol:
Cells were grown in 25cm2 flasks until they reached 70% confluency then total RNA was extracted using the RNeasy mini kit (74104, Qiagen Ltd., Manchester, UK) according to the manufacturers’ instructions.
RNA was quantified and DNA contamination assessed using Qubit RNA HS and dsDNA HS assay kits (Thermo Fisher Scientific) on a Qubit 2.0 Fluorimeter. Samples were checked for RNA integrity with the RNA 6000 Nano Kit (Agilent Technologies UK Ltd., Edinburgh, UK) using an Agilent 2100 Bioanalyser. RIN numbers for all samples were >9.6, well in excess of the 8.0 quality threshold for RNA-Seq, which was performed at the Wellcome Trust Clinical Research Facility, Western General Hospital, Edinburgh. 500ng of each RNA sample was processed for total RNA library preparation using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina, Cambridge, UK) according to the provided protocol

treatment_protocol: To isolate clones resistant to Wee1 inhibitor AZD1775 (S1525, Selleckchem, Houston, TX), cells were plated at 500 and 1000 cells/well in 96-well plates in medium containing the selective AZD1775 concentration. Single colonies arising in individual wells were picked and expanded for analysis under continuous selection. 16 samples (MKG1-16) from ES-2 and ES-2 derived resistant clones:  duplicate cultures of untreated ES-2 parent and ES-2 parent treated for 24 hours with 100nM AZD1775,  triplicate cultures of four resistant clones maintained in AZD1775- two clones resistant to 1000nM AZD1775 and their progenitors resistant to 250nM AZD1775.

tag: concentration  nm

tag: parent

tag: type


title: Patient 25


title: ES-2 AZ_1000:2_250:7 MKG8

description: ES-2 AZ_1000:2_250:7


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgZFP36L1 and Sp_sgNGN3-Rep3

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

description: RNA-seq

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest human reference genome (GRCh38) using the aligner STAR (Langmead et al., 2009)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 running on R.
Genome_build: hg38
Supplementary_files_format_and_content: Comma separated value file with TPM gene counts

source_name: TUBB3-2A-mCherry iPSC

extract_protocol:
Total RNA was isolated using RNeasy Plus (Qiagen, 74136) and QIAshredder kits (Qiagen, 79656).
Libraries were prepped and sequenced by Genewiz on an Illumina Hiseq with 2x150 bp paired-end reads.

value: induced pluripotent stem cell

value: Sa_sgZFP36L1 + Sp_sgNGN3


title: Patient 26


title: Patient 24


title: ES-2 AZ_1000:2_250:3 MKG6

description: ES-2 AZ_1000:2_250:3


title: ES-2 AZ_1000:2_250:3 MKG7

description: ES-2 AZ_1000:2_250:3


title: dsRNA-midGFP-sprayed 16C leaf 5dps_bioReplicate_2

description: sRNA

value: 10cm tall plants

value: leaves


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgZFP36L1 and Sp_sgNGN3-Rep1

description: RNA-seq


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgHES3 and Sp_sgNGN3-Rep3

description: RNA-seq

value: Sa_sgHES3 + Sp_sgNGN3


title: 1μMGSK343treatment_K562_DMSO_PSMD5_rep1_4Cseq


title: Patient 23


title: ES-2 AZ_250:7 MKG5

description: ES-2 AZ_250:7


title: HAP1_EZH2KO_ZDHHC11_rep2_4Cseq

source_name: HAP1 EZH2 KO cells

value: HAP1 EZH2 knock-out cells purchased from Horizon

tag: genotype/variation

value: EZH2 knock-out


title: 1μMGSK343treatment_K562_DMSO_FGF18_rep2_4Cseq


title: 1μMGSK343treatment_K562_DMSO_FGF18_rep1_4Cseq


title: dsRNA-midGFP-sprayed 16C leaf 5dps_bioReplicate_1

description: sRNA

value: dsRNA-sprayed


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgHES3 and Sp_sgNGN3-Rep2

description: RNA-seq


title: P_2: uninflamed pouch scRNA-seq

tag: disease state


title: 1μMGSK343treatment_K562_DMSO_HOXD13_rep1_4Cseq


title: ES-2 AZ_250:3 MKG4

description: ES-2 AZ_250:3


title: 1μMGSK343treatment_K562_DMSO_IGF2_rep1_4Cseq


title: 1μMGSK343treatment_K562_DMSO_IGF2_rep2_4Cseq


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgHES3 and Sp_sgNGN3-Rep1

description: RNA-seq


title: HAP1_EZH2KO_LINC00910_rep2_4Cseq


title: Patient 21

value: Male


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgScrambled and Sp_sgNGN3-Rep3

description: RNA-seq

value: Sa_sgScrambled + Sp_sgNGN3


title: ES-2 AZ_250:3 MKG3

description: ES-2 AZ_250:3


title: ES-2 (untreated) MKG2

description: ES-2 (untreated)

value: untreated


title: Patient 19

value: Non-metastatic


title: HAP1_EZH2KO_LINC00910_rep1_4Cseq


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgScrambled and Sp_sgNGN3-Rep2

description: RNA-seq


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgScrambled and Sp_sgNGN3-Rep1

description: RNA-seq


title: ES-2 AZ_1000:2_250:7 MKG16

description: ES-2 AZ_1000:2_250:7


title: Patient 22


title: HAP1_EZH2KO_MYC_rep1_4Cseq


title: ES-2 AZ_1000:2_250:7 MKG15

description: ES-2 AZ_1000:2_250:7


title: ES-2 AZ_1000:2_250:3 MKG14

description: ES-2 AZ_1000:2_250:3


title: HAP1_EZH2KO_PSMD5_rep2_4Cseq


title: K562_CRISPR_IGF1KO_IgG_rep2_ChIPSeq

data_processing:
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  pair-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content: *.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.

source_name: K562 cells with CRISPR/Cas9 vector targeting MRR2-A1 region

extract_protocol:
5 million cells per ChIP was harvested, washed twice and resuspended in PBS. The cells were crosslinked with 1% methanol-free formaldehyde (Thermo Scientific) at room temperature for 10 minutes, followed by quenching with glycine for 5 minutes at room temperature. The cell pellet was washed with twice with PBS supplemented with 1mM PMSF (Sigma). The fixed cell pellet was lysed in 1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% SDS) supplemented with protease inhibitor cocktail tablet (Roche), and sonicated using Bioruptor (Diagenode) and 200-500bp DNA fragments were achieved. The cell lysate was cleared through centrifugation at 13,200rpm for 35 minutes at 4°C. 9 volumes of dilution buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate) was added to the lysate to achieve 0.1% SDS lysis buffer, and the precleared through incubation with Protein G Dynabeads (Invitrogen) overnight at 4°C, with rotation. Antibody-conjugated beads were prepared by incubating 3.5ug antibody in 15uL Protein G Dynabeads in 50uL wash buffer (PBS, 0.1% Triton X-100) overnight at 4°C, with rotation. The precleared lysate was added into the prepared antibody-conjugated beads, and was incubated overnight at 4°C, with rotation. The beads were washed thrice in 0.1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in high salt wash buffer (50 mM HEPES pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in lithium chloride wash buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Igepal- CA-630, 0.5% Sodium Deoxycholate), and once in TE buffer. The beads were then eluted in elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS), treated with RNase A (Qiagen) with 55°C for 30 minutes, and decrosslinked with Proteinase K (Ambion) at 37°C overnight. ChIP DNA was cleaned up with QIAquick PCR purification kit (Qiagen), and quantitated using Qubit High Sensitivity dsDNA Assay (Invitrogen).
1ng of ChIP DNA was used for the construction of DNA library for Illumina HiSeq 4000 NGS sequencing using ThruPLEX DNA-seq 48D Kit (Rubicon) as per protocol. Final libraries were quantitated and pooled at the same molarity using Agilent High Sensitivity DNA Kit (Agilent).

tag: chip antibody

value: mouse IgG (#sc-2025, Santa Cruz)

tag: cell line

value: K562 cell line


title: Patient 16

value: Metastatic


title: Patient 17


title: Patient 18


title: HAP1_EZH2KO_ZDHHC11_rep1_4Cseq


title: ES-2 AZ_250:7 MKG13

description: ES-2 AZ_250:7


title: K562_CRISPR_IGF1KO_IgG_rep1_ChIPSeq

value: CRISPR/Cas9 vector targeting MRR2-A1 region


title: K562_CRISPR_IGF1KO_H3K27ac_rep2_ChIPSeq

description: processed data file: K562_IGF2KOG10_H3K27ac_peaks.narrowPeak

value: H3K27ac  (#ab4729, Abcam)


title: Patient 15

value: Female


title: HAP1_EZH2KO_PSMD5_rep1_4Cseq


title: Patient 20


title: K562_CRISPR_IGF1KO_H3K27ac_rep1_ChIPSeq


title: ES-2 AZ_250:7 MKG12

description: ES-2 AZ_250:7


title: HAP1_EZH2KO_MYC_rep2_4Cseq


title: Patient 14


title: ES-2 AZ_250:3 MKG11

description: ES-2 AZ_250:3


title: HAP1_EZH2KO_HOXD13_rep1_4Cseq


title: HAP1_EZH2KO_HOXD13_rep2_4Cseq


title: Patient 13


title: TUBB3-2A-mCherry iPS cells transduced with Sa_sgZFP36L1 and Sp_sgNGN3-Rep2

description: RNA-seq

value: induced pluripotent stem cell

value: Sa_sgZFP36L1 + Sp_sgNGN3


title: ES-2 (untreated) MKG10

description: ES-2 (untreated)


title: K562_CRISPR_IGF1KO_H3K27me3_rep1_ChIPSeq

description: processed data file: K562_IGF2KOG10_H3K27me3_peaks.broadPeak

value: H3K27me3  (C36B11, Cell Signaling Technologies)


title: K562_CRISPR_IGF1KO_H3K27me3_rep2_ChIPSeq


title: ES-2_100nM_AZ MKG1


title: K562_CRISPR_EV_IgG_rep2_ChIPSeq

value: empty vector


title: HAP1_EZH2KO_IGF2_rep1_4Cseq

value: HAP1 EZH2 knock-out cells purchased from Horizon


title: Patient 12


title: K562_CRISPR_EV_IgG_rep1_ChIPSeq


title: MKG112_OVCAR8 AZ_300:4

source_name: OVCAR8 AZ_300:4

growth_protocol: All experiments were performed on cultures within 10 passages of supply. Cell lines were cultured in RPMI-1640 medium (OVCAR8; 21875, Thermo Fisher Scientific),  supplemented with 10% FCS, Non-Essential Amino Acids (11140-035, Thermo Fisher Scientific), 10% FCS, Non-Essential Amino Acids (11140-035, Thermo Fisher Scientific), 1 mM Sodium Pyruvate, 2 mM L-Glutamine and Penicillin (100 U/ml) - Streptomycin (100 mg/ml) at 37˚C, 5% CO2 mM Sodium Pyruvate, 2 mM L-Glutamine and Penicillin (100 U/ml) - Streptomycin (100 mg/ml) at 37˚C, 5% CO2.

extract_protocol:
Cells were grown in 25cm2 flasks until they reached 70% confluency then total RNA was extracted using the RNeasy mini kit (74104, Qiagen Ltd., Manchester, UK) according to the manufacturers’ instructions.
Libraries were prepared from each total-RNA sample using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (#RS-122-2302) according to the provided protocol.  500ng of total-RNA was processed to deplete rRNA before being purified, fragmented and primed with random hexamers. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. AMPure XP beads (Beckman Coulter, #A63881) were then used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to another during the subsequent adapter ligation reaction, and a corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. Multiple indexing adapters were then ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 12 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing.

value: high grade serous ovarian cancer cell line

tag: clone phentoype/genotype

value: C4A1; OVCAR8-derived clones resistant to 300nM AZD1775

tag: concentration (nm)


title: HAP1_EZH2KO_FGF18_rep2_4Cseq

tag: cell line background

tag: cell type

value: EZH2 knock-out


title: Patient 11

tag: Sex


title: Patient 9

value: Male

tag: Stage


title: K562_CRISPR_EV_H3K27ac_rep2_ChIPSeq

description: processed data file: K562_empVec_H3K27ac_peaks.narrowPeak

tag: treatment


title: MKG111_OVCAR8 AZ_300:4


title: HAP1_EZH2KO_FGF18_rep1_4Cseq


title: MKG110_OVCAR8 AZ_300:4


title: K562_CRISPR_EV_H3K27ac_rep1_ChIPSeq


title: HAP1_WT_ZDHHC11_rep2_4Cseq

source_name: HAP1 wildtype cells

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)


title: Patient 8

value: Non-metastatic


title: HAP1_EZH2KO_IGF2_rep2_4Cseq


title: MKG109_OVCAR8 AZ_300:3

source_name: OVCAR8 AZ_300:3

value: C3A1; OVCAR8-derived clones resistant to 300nM AZD1775


title: HAP1_WT_ZDHHC11_rep1_4Cseq


title: K562_CRISPR_EV_H3K27me3_rep2_ChIPSeq

description: processed data file: K562_empVec_H3K27me3_peaks.broadPeak

source_name: K562 cells with empty vector

value: K562 cell line


title: HAP1_WT_LINC00910_rep2_4Cseq


title: K562_CRISPR_EV_H3K27me3_rep1_ChIPSeq


title: MKG108_OVCAR8 AZ_300:3


title: Patient 7


title: HAP1_WT_LINC00910_rep1_4Cseq


title: Patient 6


title: 5μMGSK343treatment_K562_5μMGSK343_rep2_RNASeq

source_name: K562 cells treated with 5μM GSK343

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen), with on-column DNase I treatment (Qiagen). The quality of the RNA extracted was checked using Agilent RNA 6000 Nano Kit (Agilent), and quantitated using Nanodrop ND1000 (Thermo Scientific).
850ng of RNA was used for the construction of cDNA library for Illumina HiSeq 2500 High Output v4 NGS sequencing using TruSeq Stranded Total RNA LT (w/ Ribo- Zero Gold) Set A (Illumina) as per protocol.

treatment_protocol: Small molecular inhibitor GSK343 (Sigma-Aldrich) targeting EZH2 were solubilized in DMSO (Sigma-Aldrich) according to manufacturer’s instructions and used at a final concentration of 5μM. K562 cells with GSK343 were incubated at 37 °C, 5% CO2 humidified incubator for 48 hours before harvesting for various experiments.

value: 5μM GSK343


title: MKG106_OVCAR8 AZ_300:2

source_name: OVCAR8 AZ_300:2

value: C2A1; OVCAR8-derived clones resistant to 300nM AZD1775


title: MKG107_OVCAR8 AZ_300:3


title: Patient 5


title: 5μMGSK343treatment_K562_5μMGSK343_rep1_RNASeq


title: HAP1_WT_MYC_rep2_4Cseq


title: Patient 10

value: Metastatic


title: MKG105_OVCAR8 AZ_300:2


title: HAP1_WT_MYC_rep1_4Cseq


title: MKG104_OVCAR8 AZ_300:2


title: 5μMGSK343treatment_K562_DMSO_rep2_RNASeq

value: DMSO


title: HAP1_WT_PSMD5_rep2_4Cseq


title: MKG103_OVCAR8 (treated 100nM AZD1775)

source_name: OVCAR8 (treated 100nM AZD1775)

value: parent


title: HAP1_WT_PSMD5_rep1_4Cseq


title: 5μMGSK343treatment_K562_DMSO_rep1_RNASeq


title: K562_5μMGSK343_IgG_rep2_ChIPSeq

value: mouse IgG (#sc-2025, Santa Cruz)


title: Patient 3


title: Patient 2


title: Patient 1


title: MKG102_OVCAR8 (treated 100nM AZD1775)


title: WT.MMS.2

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

institute: IGH

data_processing:
fastq files were mapped on genome refere,ce using STAR v2.5.3, using these parameter values options : --outFilterType BySJout --outFilterMismatchNmax 3 --outFilterMultimapNmax 2  --alignIntronMin 10 –alignIntronMax 3000
reads in bam files were filtered using samtools 0.1.19 to remove secondary and supplementary alignment, and reads with mapping quality MAPQ < 20
read counts for each annotated feature in the annotation file were obtained using a custom R script were each annotated feaure count is incremented if its genomic position overlaps a read (unless read CIGAR indicates N)
read counts were normalized using DESeq2 size factors (function estimateSizeFactorsForMatrix, using protein coding gene counts)
densities for annotated feature were calculated as read count divided by feature length
Genome_build: S288C_reference_genome_R64-2-1_20150113 (www.yeastgenome.org)
Supplementary_files_format_and_content: tab delimited file, with genomic location of annotated features used in the analysis, read count and densities for each sample, and mean value for replicates

organism: Saccharomyces cerevisiae

growth_protocol: Growth medium : YEP + 2% glucose

extract_protocol:
Total RNA was extracted from G1 synchronized cells using standard hot phenol procedure.
Strand-specific total RNA-seq libraries from rRNA-depleted total RNA with Illumina’s TruSeq kit

treatment_protocol: MATa cells were synchronized in G1 by adding α-factor (5 μg.ml-1) for 170 min at 25°C. For MMS treatment, cells were released from G1 into S phase +  0.033% MMS for 60 min

tag: strain

value: WT

tag: cell-cycle phase

value: S phase


title: K562_5μMGSK343_IgG_rep1_ChIPSeq


title: WT.MMS.1

tag: genotype


title: MKG101_OVCAR8 (treated 100nM AZD1775)


title: HAP1_WT_HOXD13_rep1_4Cseq

extract_protocol:
Briefly, 4 × 107 cells were cross-linked with 1% formaldehyde. The nuclei pellets were isolated by cell lysis with cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 5mM EDTA, 0.5% NP 40) supplemented with protease inhibitors (Roche). First step digestion was performed overnight at 37°C with HindIII enzyme (NEB). Digestion efficiency was measured by RT-qPCR with HindIII site–specific primers. After confirmation of good digestion efficiency, DNA was ligated overnight at 16°C by T4 DNA ligase (Thermo Scientific) and de-crosslinked. Following de-crosslinking, DNA was extracted by phenol-chloroform. The DNA was then processed for second digestion with DpnII enzyme (NEB) overnight at 37°C. After final ligation, 4C template DNA was obtained and the concentration was determined using Qubit assays (Thermo Scientific).
The 4C template DNA was then amplified using specific primers with illumina Nextera adapters and sent for sequencing on the MiSeq system.


title: HAP1_WT_HOXD13_rep2_4Cseq


title: skeletal muscle-STD_Cont-Rep3

source_name: skeletal muscle

tag: diet

value: STD

tag: lineage

value: Cont


title: K562_5μMGSK343_H3K27ac_rep2_ChIPSeq

description: processed data file: K562_GSK5UM_H3K27AC_peaks.narrowPeak

value: H3K27ac  (#ab4729, Abcam)


title: Patient 4

tag: age


title: xrn1.G1.2


title: K562_5μMGSK343_H3K27ac_rep1_ChIPSeq


title: xrn1.G1.1


title: HAP1_WT_IGF2_rep2_4Cseq


title: K562_5μMGSK343_H3K27me3_rep2_ChIPSeq

description: processed data file: K562_GSK5UM_H3K27ME3_peaks.broadPeak

value: H3K27me3  (C36B11, Cell Signaling Technologies)


title: Dialout12

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
Dialout for sample 12
Same underlying biological sample as for Perturb-seq12

data_processing:
10X fastqs were run through CellRanger (v2.1.0) count using the standard mm10 reference
Count matrices were extracted.
Perturb-seq count matrices were combined, and cells with <500 gene were removed, as was sample 17.
Perturb-seq cells were clustered with Seurat (v 2.2), and cell types identified
The same pipeline was run with the single perturbation samples
For samples with multiple dialout fastqs, the fastqs were combined if they had the same tag (TAG or GCA)
Dialout reads were run through our dialout pipeline (https://github.com/klarman-cell-observatory/ivPerturbSeq) using the cell barcodes produced by CellRanger to extract a perturbation by cell count matrix. For samples with both tags, the one with more assigned cells was used.
For downstream analysis, cells were assigned to a pertubation if they had UMI supporting that perturbation and the number of UMI supporting it were >1.3 times the next highest.
Perturbation labels were uploaded to the Seurat object
Uploaded fastq are from the dialout library, uploaded bam files are from the single cell expression data.
Genome_build: mm10
Supplementary_files_format_and_content: csv matrix containing perturbation barcode by cell barcode UMI counts from dialout
Supplementary_files_format_and_content: h5 containing raw count data from CellRanger

molecule: other

source_name: Whole Cortex

extract_protocol:
Each single-cell library was made by combining the BFP+ cells from 1-3 litters (4-20 animals) of P7 animals harvested on the same day. The FACS-purified cells were sorted into cold Hibernate A/B27 medium and subjected to single-cell RNA sequencing library preparation.
Single-cell RNA sequencing libraries were created using the Chromium Single Cell 3' Solution v2 kit (10x Genomics) following the manufacturer’s protocol.
We used the Chromium Single Cell 3' Solution v2 kit (10x Genomics) to construct all the libraries, which are experimental replicates for the pooled Perturb-Seq.

treatment_protocol: In utero lentiviral injection into the lateral ventricles was performed at E12.5 in Cas9 transgenic mice (4-6 month old, Jax #026179).

tag: targeted genes

value: All 35 genes

tag: data type

value: Dialout for perturbation barcode


title: rrp6.G1.2


title: Dialout13

description:
Dialout for sample 13
Same underlying biological sample as for Perturb-seq13


title: Dialout11

description:
Dialout for sample 11
Same underlying biological sample as for Perturb-seq11


title: K562_5μMGSK343_H3K27me3_rep1_ChIPSeq

tag: chip antibody


title: rrp6.G1.1


title: HAP1_WT_FGF18_rep2_4Cseq

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)


title: K562_DMSO_IgG_rep2_ChIPSeq

source_name: K562 cells treated with DMSO

tag: cell line


title: GM12878_TOR1A_rep2_4Cseq

source_name: GM12878 cells


title: Dialout10

description:
Dialout for sample 10
Same underlying biological sample as for Perturb-seq10


title: GM12878_TOR1A_rep1_4Cseq


title: mre11H.G1.2


title: Dialout9

description:
Dialout for sample 9
Same underlying biological sample as for Perturb-seq9


title: K562_DMSO_IgG_rep1_ChIPSeq


title: HAP1_WT_FGF18_rep1_4Cseq


title: mre11.G1.2


title: Dialout7

description:
Dialout for sample 7
Same underlying biological sample as for Perturb-seq7


title: mre11H.G1.1


title: Dialout6

description:
Dialout for sample 6
Same underlying biological sample as for Perturb-seq6

value: GFP, Dyrk1a, Mll1


title: HAP1_WT_IGF2_rep1_4Cseq


title: K562_DMSO_H3K27ac_rep2_ChIPSeq

description: processed data file: K562_DMSO_H3K27AC_peaks.narrowPeak

value: K562 cell line


title: GM12878_PSMD5_rep1_4Cseq


title: mre11.G1.1


title: Dialout8

description:
Dialout for sample 8
Same underlying biological sample as for Perturb-seq8


title: K562_DMSO_H3K27ac_rep1_ChIPSeq


title: rad50.G1.2


title: K562_DMSO_H3K27me3_rep2_ChIPSeq

description: processed data file: K562_DMSO_H3K27ME3_peaks.broadPeak


title: K562_DMSO_H3K27me3_rep1_ChIPSeq


title: Dialout4

description:
Dialout for sample 4
Same underlying biological sample as for Perturb-seq4


title: GM12878_PSMD5_rep2_4Cseq


title: rad50.G1.1


title: K562_TOR1A_rep2_4Cseq

source_name: K562 cells


title: Dialout5

description:
Dialout for sample 5
Same underlying biological sample as for Perturb-seq5


title: K562_PSMD5_rep2_4Cseq


title: Dialout3

description:
Dialout for sample 3
Same underlying biological sample as for Perturb-seq3


title: WT.G1.4


title: K562_PSMD5_rep1_4Cseq


title: Dialout2

description:
Dialout for sample 2
Same underlying biological sample as for Perturb-seq2


title: Dialout1

description:
Dialout for sample 1
Same underlying biological sample as for Perturb-seq1


title: K562_LINC00910_rep2_4Cseq


title: YAP-TFE3_Input_Rep1 (chipseq)

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the SW872 line was aligned against the ensembl reference ‘hg38’
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: SW872 liposarcoma cells ATCC

growth_protocol: SW872 cells were stably transduced and grown to 90% confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Cells were cross-linked and prepared using the SimpleChIP Enzymatic Chromatin IP KIt according to manufacturer's instructions. Flag tagged proteins were immunoprecipated with the anti-DYKDDDDK rabbit monoclonal antibody (Cell Signaling)
The SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina was used to prepare the DNA library according to manufacturer's instructions

value: SW872 liposarcoma cells


title: ku70.G1.1


title: WT.G1.3


title: YAP-TFE3 rep 3 (chipseq)


title: YAP-TFE3_Input_Rep2 (chipseq)


title: K562_LINC00910_rep1_4Cseq

data_processing:
library strategy : 4C-seq
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  paired-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content:
*.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.


title: YAP-TFE3_FLAG_IP_Rep 1 (chipseq)


title: KLF4_FL_ChIP-seq

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

description: SMC eYFP+/+ Klf4Δ/Δ

data_processing:
Each sample was ran twice.ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following configuration
bowtie --sam -q --nomaqround -m 10 --best --strata --chunkmbs 500 --offrate 7 --seedmms 2 -p 12
Bam files were merged using picardtools. Samtools nohup command was used to remove unmapped reads
Data files were then converted to bam and duplicates removed using Samtools
Peaks were called using Macs. KLF4_FL (KO sample) was used as input/control
Genome_build: mm9
Supplementary_files_format_and_content: bed file containing peaks called by Macs

source_name: Mesenteric Arcades

extract_protocol:
Mesenteric arcades were isolated from SMC eYFP+/+ Klf4WT/WT and SMC eYFP+/+ Klf4Δ/Δ mice and snap-frozen in liquid nitrogen. Frozen tissues were ground in a mortar and pestle and the stromal vascular fractions were isolated. Cells were fixed with 1% paraformaldehyde for 10 minutes at room temperature. Cross-linked chromatin was then sheared by sonication into fragments 200-600 base pairs in size. The chromatin fragments were then immunoprecipitated with anti-Klf4 (Sanda Cruz sc20691, 2 µg) antibody complexed with magnetic bead-coupled protein G
Library was performed following TruSeq DNA Sample Guide protocol by Illumina

treatment_protocol: Animals were maintened in chow diet until harvest time

value: Mixture of cell types (Smooth Muscle Cells, Epithelial, Macrophages, other)

tag: genotype/variation

value: eYFP+/+ Klf4delta/delta

tag: antibody

value: anti-Klf4 (Sanda Cruz sc20691)


title: WT.G1.1


title: K562_TOR1A_rep1_4Cseq

first: Melissa

last: Fullwood

institute: Cancer Science Institute

tag: cell line background


title: YAP5SA_Input_Rep2 (chipseq)


title: MicroC-XL_WT_Async

description:
MicroC-XL of Asynchronous WT cells
Pair end
MicroC-XL

data_processing:
MicroC-XL analyses were performed with Deeptools/MicroC-XLexplorer (Wolff et al., 2018)
sacCer3
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)

growth_protocol: S. cerevisiae cells were grown on YPD at 25°C

extract_protocol:
Standard protocol for preparation of yeast genomic DNA for MicroC-XL Hsieh et al., 2016
Standard Library Prep for MicroC-XL Hsieh et al., 2016

treatment_protocol: Samples were either collected from G1 synchronised cultures or from asynchronous cultures

value: Untreated

value: Async

tag: sample type

value: MicroC-XL


title: G3

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

institute: Longyan University

data_processing:
Each library was indexed in order to multiplex four samples per sequencing run on the Illumina HiSeq platform.
A minimum of 17 million 50bp sequencing reads were collected from each sample and data were analyzed using Genesifter software.
Raw data for each sample were aligned to the most recent mirBASE database with remaining reads aligned to the most recent Gallus gallus genome build in order to identify previously unknown regions that may encode for unique miRNAs.
Pairwise comparison of the alignment results was done using Genesifter for identification of miRNAs that are differentially expressed at a significant level, i.e. up- or down-regulated.

organism: Gallus gallus

source_name: abdominal fat tissue

extract_protocol: none provided by submitter

tag: tissue

value: abdominal fat tissue

value: day 35

value: control


title: K562_ZDHHC11_rep2_4Cseq

address: 14 Medical Drive


title: K562_ZDHHC11_rep1_4Cseq


title: K562_CCND3_rep2_4Cseq


title: G2


title: YAP5SA_Input_Rep1 (chipseq)


title: YAP5SA_FLAG_IP_Rep3 (chipseq)


title: G1


title: K562_CCND3_rep1_4Cseq


title: E3

value: 50 IU VE


title: WT.G1.2

value: WT


title: K562_TMCO4_4Cseq


title: YAP-TFE3 rep 2 (chipseq)


title: IP-GFP_WT_Untagged_G1

description:
Ip-GFP of Wild type strain with Mlp1 Untagged. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-GFP antibody

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
sacCer3
Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step  with ratio relative to Input (IP) or relative to G1 (ADNg)

source_name: Untagged

extract_protocol:
Standard protocol for preparation of yeast genomic DNA
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)

value: IP-GFP


title: YAP5SA_FLAG_IP_Rep2 (chipseq)


title: YAP5SA_FLAG_IP_Rep1 (chipseq)


title: KLF4_WT_ChIP-seq

tag: cell type

value: eYFP+/+ Klf4WT/WT


title: IP-GFP_WT_Mlp1GFP_G1

description:
Ip-GFP of Wild type strain with Mlp1 tagged with GFP. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-GFP antibody

tag: treatment


title: MicroC-XL_rad50_Async

description:
MicroC-XL of Asynchronous rad50Δ cells
Pair end
MicroC-XL

tag: strain


title: IP-GFP_rad50_Mlp1GFP_G1

description:
Ip-GFP of rad50Δ strain with Mlp1 tagged with GFP. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-GFP antibody

tag: cell-cycle phase


title: TFE3_Input_Rep2 (chipseq)


title: TFE3_Input_Rep1 (chipseq)


title: IP-HA_WT_Untagged_G1

description:
Ip-HA of Wild type strain with Rad50 Untagged. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-HA antibody

tag: genotype

value: IP-HA


title: TFE3_FLAG_IP_Rep3 (chipseq)


title: IP-HA_WT_Rad50HA_G1

description:
Ip-HA of Wild type strain with Rad50 tagged with HA. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-HA antibody


title: TFE3_FLAG_IP_Rep2 (chipseq)


title: Input_WT_G1_Rpb1ChIP

description:
INPUT of Wild type. Cells are synchronized in G1 phase of the cell cycle
Single end
gDNA-seq

value: Input


title: IP-Rpb1_WT_Untagged_G1

description:
Ip-Rpb1 of Wild type strain. Cells are synchronized in G1 phase of the cell cycle
Single end
ChIP-Seq, a-Rpb1 antibody


title: E2


title: TAZ-CAMTA1_Input_2 (chipseq)


title: TFE3_FLAG_IP_Rep1 (chipseq)


title: E1


title: TAZ-CAMTA1_Input_1 (chipseq)


title: Input-HAChIP_WT_Rad50HA_G1

description:
INPUT of Wild type strain with Rad50 tagged with HA. Cells are synchronized in G1 phase of the cell cycle
Single end
gDNA-seq

value: Input-HAChIP


title: Input-GFPChIP_WT_Mlp1GFP_Async

description:
INPUT of Wild type strain with Mlp1 tagged with GFP. Asynchronous cells
Single end
gDNA-seq

value: Input-GFPChIP


title: Input-GFPChIP_rad50_Mlp1GFP_Async

description:
INPUT of rad50Δ strain with Mlp1 tagged with GFP. Asynchronous cells
Single end
gDNA-seq


title: TAZ-CAMTA1_FLAG_IP_Rep 2 (chipseq)

value: SW872 liposarcoma cells


title: TAZ-CAMTA1_FLAG_IP_Rep 3 (chipseq)


title: IgG treated, replicate 4

city: Heidelberg

first: Nicolas

last: Gengenbacher

address: Im Neuenheimer Feld 280

department: Vascular Oncology and Metastasis

institute: German Cancer Research Center

description: Ret #8

hyb_protocol: 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays.

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: All intensity data were quantile normalized with R using the normalize.quantiles function from the Bioconductor package preprocessCore

label: Biotin

source_name: MT-ret tumor tissue

label_protocol: Biotin-labeled ss-cDNA samples were prepared from 250ng total RNA according to Affymetrix's recommended sample labeling procedure as described in the Gene Chip WT Plus Reagent Kit guide

growth_protocol: MT-ret tumor fragments were implanted on the ventral flank of C57BL/6N mice.

extract_protocol: Total tumor RNA was isolated by smashing tissue pieces in TRIzol (Thermo Fisher Scientific) followed by Chloroform extraction. Afterwards, RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Neo-adjuvant antibody treatment was initiated 7 days post fragment implantation and discontinued after primary tumor resection. Total tumor RNA was analyzed

value: IgG

value: MT-ret tumor


title: OIN3_liver_106000_OT-I_cell

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 130ng of each fluorescently labelled cRNA population was used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20). Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.
Text files resulting from the first data processing step were first imported into R (version 3.4.0) using the read.maimages() function from the R package Limma (version 3.32.10). Preprocessing steps included background correction and quantile normalization and were performed with the Limma functions backgroundCorrect() and normalizeBetweenArrays(), respectively. Afterwards, control probes and lowly variable genes were filtered out using the rowSds() function from the genefilter package (version 1.58.1). The microarray data then was condensed using the avereps() function from Limma so that values for within-array replicate probes are replaced with their average.

label: Alexa Fluor 555 Reactive Dye

source_name: OIN3 liver, 106000  OT-I cell

label_protocol: 3.5ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to each processed sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

extract_protocol: Isolation of total RNA from samples obtained by flow cytometry sorting using >99% purified specific CD8 T cells (OT-I) was performed according to the manufacturer´s protocol (RNeasy Plus Micro Kit, Qiagen, Hilden, Germany) at the Research Core Unit Genomics (RCUG) of the Hannover Medical School (MHH).

treatment_protocol: C57BL/6 wild-type (CD90.2+) mice either received HDI for the generation of OVA+ liver tumors or were left untreated. Tumors were allowed to grow for 2 weeks and 5×10^3 naive, CD90.1+ OT-I cells were adoptively transferred into both mice groups. One day after T cell transfer all mice received PLGA-SIINFEKL+ PolyI:C priming, followed by LM-OVA infection 7 days later. OT-I cells were isolated on day 12 after LM-OVA from each group. Naive OT-I cells were isolated from uninfected mice as reference. Technical procedure for the isolation of OT-I cells for subsequent RNA-Isolation: livers of OVA+ tumor-bearing mice or livers from control mice, respectively, were cardially perfused, prior to harvesting using 37°C pre-warmed PBS, in order to remove in blood circulating lymphocytes. Livers/liver tumors were sliced to small pieces, treated with digestion medium (collagenase IV (0,2mg/ml), DNaseI (0,01mg/ml), penicillin (50 U/ml), streptomycin (50 μg/ml) in RPMI-1640 + GlutaMAX-I medium) for 30 minutes at 220 rpm at 37°C. Tissue digestion was stopped by adding RPMI-1640 medium with 10% fetal calve serum. Cells were pelleted by centrifugation (300 g for 10 minutes at 4°C) and subsequently resuspended in MACS buffer (PBS with added 1% FCS, penicillin (50 U/ml), streptomycin (50 μg/ml)). Fc receptors were blocked by treatment with anti-mouse CD16/32 antibody (TruStain FcX, Biolegend, San Diego, CA, USA). The specific CD8 T cells (the adoptively transferred CD90.1+ OT-I cells) were enriched by MACS technology (Miltenyi Biotec, Germany) using CD90.1 MicroBeads and LS Columns according to the manufacturer´s instructions. Afterwards, flow cytometry sorting using FACSAria IIu (Becton Dickinson, San Jose, CA, USA) was performed to receive specific CD8 T cells (OT-I) of >99% purity. The OT-I cells were isolated from OVA+ tumor-bearing livers (exhausted T cells) or livers of tumor-free control mice  (effector T cells), respectively. As additional reference data, naive OT-I cells (naive T cells) were isolated from spleens of naive mice, that have previously received adoptive transfer of naive OT-I cells.

value: OVA+ tumor-bearing livers

value: CD8 T cells

tag: phenotype

value: exhausted


title: OIN2_liver_200000_OT-I_cell

source_name: OIN2 liver, 200000  OT-I cell


title: OIN9_liver_69000_OT-I_cell

source_name: OIN9 liver, 69000  OT-I cell


title: IgG treated, replicate 3

description: Ret #7


title: IgG treated, replicate 2

description: Ret #20


title: NC21_liver_186000_OT-I_cell

source_name: NC21 liver, 186000  OT-I cell

value: tumor-free liver

value: effector


title: myogenic progenitor cell extracellular vesicles

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

description: Extracellular vesicles from myogenic progenitor cell conditioned media

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. A prolonged hybridization of >40 hours was employed to maximize yield

scan_protocol: Affymetrix Gene ChIP Scanner 7G

data_processing: Data were processed using Command Console Software and analyzed using Expression Console Software.

source_name: C57BL6/J primary myogenic progenitor cells

label_protocol: Samples were biotinylated using the Flashtag Biotin HSR kit

growth_protocol: Myogenic progenitor cells conditioned media for 24 hours

extract_protocol: Extracellular vesicles were isolate using ExoQuick TC, and total RNA was extracted using a Qiagen RNA kit

treatment_protocol: not applicable

value: >4 month old

value: forelimb and hindlimb

value: wild-type


title: NC18_liver_452000_OT-I_cell

source_name: NC18 liver, 452000 OT-I cell


title: OIN5_liver_575000_OT-I_cell

source_name: OIN5 liver, 575000  OT-I cell


title: TAZ-CAMTA1_FLAG_IP_Rep 1 (chipseq)


title: anti-Ang2 treated replicate 4

description: Ret #2


title: anti-Ang2 treated replicate 3

description: Ret #16


title: NC20_liver_652000_OT-I_cell

source_name: NC20 liver, 652000 OT-I cell


title: IgG treated, replicate 1

description: Ret #21


title: anti-Ang2 treated replicate 2

description: Ret #14


title: 21b, brain, male

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: microRNA

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV3.2
filtering: UEA sRNA WorkbenchV4.6; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Sscrofa10.2 genome and miRBase 22.1, using miRCat tool embeded in UEA sRNA WorkbenchV4.6. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V4.6. They include the number of reads of detected sequences.
miRNA mapping.xlsx

organism: Sus scrofa

source_name: 990 synthetic line brain tissue

extract_protocol:
The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were frozen in liquid nitrogen and stored at -80°C

tag: breed

value: Polish 990 synthetic line

value: brain

tag: gender

value: male


title: TAZ4SA_Input_Rep2 (chipseq)


title: TAZ4SA_Input_Rep1 (chipseq)


title: 20b, brain, female

description: microRNA

value: female


title: NC22_liver_115000_OT-I_cell

source_name: NC22 liver, 115000  OT-I cell


title: TAZ4SA_FLAG_IP_Rep3 (chipseq)