title: Test_isotype_IP_mouse_IgG1

city: Glasgow

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

description: seCLIP library of mouse IgG1 control interacting RNA.

data_processing:
Libraries from the first experiment comparing antibodies were sequenced on a MiSeq with a v3 150 cycle kit in paired-end mode. Libraries from the Rnmt cKO vs. control CD4 T cell libraries were sequenced on a NextSeq 500 with a mid output v2.5 kit (150 cycles) in single end mode.
First the 10nt randomer barcode was extracted using umi_tools, then adapter sequences were trimmed from the reads using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA). For paired end libraries only read one was used since reads were too short for the second read to be advantageous.
Reads were aligned to mm10 with gencode vM12 basic annotation using STAR 2.5.2b, then demultiplexed using umi_tools to remove PCR duplicates.
Secondary alignments and alignments with a MAPQ <20 were removed using samtools.
Bedgraph files were generated using deeptools, options -bs 10 --Offset 1 1 -of bedgraph.
Genome_build: Peaks were called using pureCLIP (Krakau et al., 2017) (options -iv 'chr1;chr2;chr3;chr4;chr5;' --mtc 10000 --ctr --dm 30) using the size matched input control for the input.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bedgraph files have the counts of reads starting within the 10bp windows. Read start sites should be 1 nt downstream of crosslinked nucleotides so these footprints indicate areas of protein/RNA interaction in the LARP1 IP samples.
Supplementary_files_format_and_content: Bed files contain the coordinates of LARP1 binding peaks determined using PureCLIP.

source_name: naive CD4 T cells

growth_protocol: CD4 T cells were sorted from control and Rnmt cKO mouse lymph nodes using an EasySep mouse CD4 T cell isolation kit.

extract_protocol:
eCLIP was carried out essentially as described in the seCLIP protocol (Van Nostrand et al., 2017). Cells were thawed into lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40 (Igepal CA630), 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail III (Sigma), 1:200 murine RNAse inhibitor (NEB)) and lysed on ice for 15 minutes. Lysates were incubated with 1µl/ml turbo DNase (Thermo Fisher Scientific) and 1µl/ml of a 1:2000 (1:1000 in test experiment) dilution of RNase1 (Thermo Fisher Scientific) in PBS for 5 mins at 37°C then returned to ice then centrifuged to remove insoluble material.
Lysates were precleared with protein G dynabeads (Thermo Fisher Scientific) at 4°C for 1hour. Lysates underwent immunoprecipitation with 50µl of protein G dynabeads preincubated with 4 µg of either LARP1, or isotype control antibody overnight at 4°C, 10% of the LARP1 samples were taken for the size matched input control. Beads were washed three times for 5 minutes with high salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) with 2M urea. For the ProteinTech and Santa Cruz antibodies (and their isotype controls) used in the preliminary experiment a medium salt buffer (50 mM Tris-HCl pH 7.4, 600mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) was used for these washes. RNA linker ligation was performed on bead using High concentration T4 RNA Ligase (NEB) for LARP1 and isotype libraries. RNA-protein complexes were denatured in NuPage loading buffer (Thermo Fisher Scientific) + 50mM DTT, resolved 3-8% Tris Acetate gel (Thermo Fisher Scientific) in Tris Acetate SDS buffer (Thermo Fisher Scientific), and transferred to a nitrocellulose membrane in NuPage transfer buffer (Thermo Fisher Scientific). RNA protein complexes and size matched input samples were cut from the membrane. RNA was released by incubating with Proteinase K for 20 minutes at 37°C, then with 420mg/ml urea in Proteinase K buffer for 20 minutes at 37°C and purified by phenol chloroform extraction. The RNA lnker was then ligated to the size matched input samples. All samples were reverse transcribed and ligated to a DNA linker ready for PCR amplification of libraries. Further details of the library preparation method are available in the seCLIP protocol (Van Nostrand et al., 2017).

value: Rnmt +/+ CD4cre+ and Rnmt fl/+ CD4cre-

tag: Sex

value: Female

value: Naive CD4 T cells

tag: antibody

value: Mouse IgG1 (eBioscience 14-4714-85)


title: Naïve-BS-rep1

status: Public on May 13 2021

type: SRA

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
The BS and PB reads were mapped to mouse genome mm9 using the BSMAP mapping tool. The mapping was done using the paired end datasets with the following parameter values: -p 4 -w 2 -v 5 -q 30 for BS-seq, and -p 4 -w 2 -v 0 -q 30 for PB-seq.
For each of the samples, the number of reads in which each cytosine within the amplicons was converted into thymine was counted.
For BS-seq, these counts were used to calculate the proportions for each cytosine to be nonmethylated/formylmethylated/carboxylmethylated (T), or methylated/hydroxymethylated (C).
For PB-seq, to compensate redundant reads derived from the opposite strand, number of reads standing for nonmethylated/methylated/hydroxymethylated (C) was multiplied by 0.5, and the proportions for each cytosine to be formylmethylated/carboxylmethylated (T) was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: methylation_ratio .txt file

molecule: genomic DNA

organism: Mus musculus

source_name: Naïve CD4 T-cells

growth_protocol: Total CD4+ T cells were isolated with the EasySep Mouse CD4+ T cell isolation kit (STEMCELL Technologies, Canada) from the spleen and lymph nodes. Then, CD4+CD25−CD62LhiCD44lo naive CD4+ T cells were FACS sorted.

extract_protocol:
Genomic DNA (gDNA) was isolated by PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific). 0.5 μg of gDNA samples were treated with sodium BS (MethylCode Bisulfite Conversion kit; Invitrogen).
The PCR amplicons were generated using the PyroMark PCR kit (QIAGEN) and quantified using Qubit assays (Invitrogen). PCR amplicons were pooled and then used for library preparation using NEB Next DNA Library Modules for Illumina platform (New England Biolabs, Inc.).
bisulfite or pyridine borane sequencing

tag: strain

tag: genotype

value: wild type

tag: treatment

tag: cell type

value: T-cells from the spleen and lymphnodes


title: Q001S0002B0012R1N

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

country: USA

institute: USDA/ARS

description:
processed data file: Q001S0002B0012_salmon_counts.matrix_norm.csv
Sample 44
44_S44

library_source: transcriptomic

data_processing:
library strategy: Amplicon-seq
Adapter Trimming - Each sample was processed using Trimmomatic to trim off adapters. Fastqc analysis revealed that most of the reads are of high quality. Hence, no quality trimming was performed.
Alignment - Reads from each sample was aligned to the genome of barley, Blumeria and vector sequences using STAR (dobin et. Al 2013).
Fusion read recognition - Custom python scripts was used to recognize fusion reads based on the partial alignment to the genomes and vector sequences. Vector portions were trimmed off from fusion reads.
Differential expression analysis - Salmon (Patro 2017) was used to obtain gene counts. Samples were size normalized and differential expression analysis was carried out using DESeq2 (Love 2014)
In-frame fusion reads  - Fusion reads expressed in-frame with the protein was recognized by using translating the entire sequence and comparing with the protein
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew

molecule: total RNA

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: Yeast were grown at 28C shaking at 225rpm. Cells were subcultured once they reached saturation (OD600 >2.5).

extract_protocol:
Yeast cells were treated with lyticase to digest cell walls and Y2H plasmids were extracted using alkaline lysis and precipitation.
Libraries were constructed using the Nugen Ultralow System V2 with Custom AnyDeplete to reduce the abundance of an amplicon common to all libraries using the manufacturer's instructions.

treatment_protocol: Yeast were incubated in SC-Leu-Trp (no selection) or SC-Leu-Trp-His (reporter selection) liquid media. Two rounds of growth selection were performed.

tag: plant genotype

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

tag: fungal isolate

value: Bgh isolate 5874 (AVRa6)

value: Non-selected

tag: tissue

value: Barley infected first leaf (PO:0007094)


title: Test_size_matched_input

first: Alison

country: United Kingdom

description: seCLIP library of size matched input RNA.

treatment_protocol: CD4 T cells were suspended in PBS and exposed to 400mJ of 254nm UV then snap frozen on dry ice.


title: DNMT3B-delPWWP_ChIP-seq_parental

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr Penfield Ave

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
For ChIP-seq DNA input: Following alignment with BWA, bigwigs were generated with read coverage for 200-bp bins smoothed across 1-kb, computed with deepTools bamCoverage. Excludes mm10 ENCODE blacklist regions.
For ChIP-seq signal: Following alignment with BWA, bigwigs were generated with enrichment scores represented as input-normalized (log2-ratio), read-depth normalized signal per 200-bp bins, smoothed across 1-kb bins using deepTools. Excludes mm10 ENCODE blacklist regions.  See publication Methods for details.
For ChIP-seq signal peaks: Following alignment with BWA, SICER2 was used to call broad H2AK119Ub peaks. Processed output is a BED file in the format "chrom, start, end, read-count".
For RRBS: Following alignment with Bismark, bedGraph files were generated representing methylation scores at CpGs of at least 10X read coverage, computed using MethylDackel. See publication Methods for details.
Genome_build: mm10 for Mus musculus, dm6 for Drosophila melanogaster
Supplementary_files_format_and_content: Filetype suffix explanation: bw = bigWig

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
Cross-linking ChIP in MSCs was performed as described previously (Weinberg et al. 2019) using ~2x107 cells per immunoprecipitation. Prior to fixation, media was aspirated and cells washed once with PBS. Cells were cross-linked directly on the plate using 1% paraformaldehyde for 5 min at room temperature with gentle shaking. Glycine was added to quench (final concentration 125 mM, incubated for 5 min at room temperature), then cells were washed once with cold PBS, scraped off the plates, and pelleted. To obtain a soluble chromatin extract, cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or 75 μl protein A Dynabeads (Invitrogen) bound to anti-H2AK119Ub (Cell Signaling, 8240) or anti-H3K27me3 (Cell Signaling Tech, 9733) antibodies and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were sequentially washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). Beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep kit

tag: chip antibody

value: HA (ThermoFisher, #88836)

tag: cell line

value: C3H embryo-derived mesenchymal progenitor cells

value: Parental line expressing FLAG-HA tagged DNMT3B delPWWP


title: SAMD1_WT_repl2

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 or mm10 using Bowtie 1.0, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM.
RNA-Seq data were aligned to mouse transcriptome GenCode.M23 using RNA Star. Counts per gene were determined using FeatureCounts . Differentially expressed genes and normalized reads were determined using DeSeq2.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: bw

growth_protocol: E14 mouse ES cells (E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine, 1 x Non-essential amino acids, 1 x Sodium pyruvate, 1 x Penicillin/Streptomycin , 0.15% β-mercaptoethanol and 100 Units/ml of LIF  on gelatin-coated plates.

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode). Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

value: SAMD1 (self-made)

value: WT


title: MM134_siMDC1_E2_3

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description:
si_treatment: siMDC1_E2
Compiled_counts.txt

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded.
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (hg38.p12, release 96).
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset.
Differential gene expression was calculated using the voom function in limma.
Genome_build: GRCh38
Supplementary_files_format_and_content: Compiled_counts.txt: Tab-delimited text file containing STAR gene count values.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were hormone-deprived via maintenance in medium supplemented with charcoal-stripped serum for 3 days prior to further treatment.

extract_protocol:
RNA extractions were performed using the RNeasy Mini kit (Qiagen).
Illumina Stranded mRNA Prep, for sequencing on NovaSEQ6000 with 2x150 paired-end reads.

treatment_protocol: After 3d hormone-deprivation, cells were transfected with the indicated siRNA (siNT = non-targeting control). 24hrs post-siRNA transfection, cells were treated with vehicle (0.01% EtOH) or 100pM estradiol. 24hrs after vehicle or E2 treatment, cells were collected for RNA extraction, processing, and sequencing.

tag: sirna


title: DNMT3A2-delPWWP_ChIP-seq_parental

value: Parental line expressing FLAG-HA tagged DNMT3A2 delPWWP


title: Q001S0002B0012R2S

description:
processed data file: Q001S0002B0012_salmon_counts.matrix_norm.csv
Sample 62
62_S62

value: Selected


title: MM134_siMDC1_E2_2


title: DNMT3A2-WT_ChIP-seq_parental_input

value: Parental line expressing FLAG-HA tagged DNMT3A2


title: Test_LARP1_IP_SantaCruz_mouse_ab

description: seCLIP library of LARP1 interacting RNA.

value: Rnmt +/+ CD4cre+ and Rnmt fl/+ CD4cre-

value: Female

value: LARP1 (Santa Cruz sc-515873)


title: MM134_siMDC1_E2_1


title: Test_LARP1_IP_ProteinTech_rabbit_ab

value: Naive CD4 T cells

value: LARP1 (Protein Tech 13708-1-AP)


title: Test_LARP1_IP_abcam_rabbit_ab

value: LARP1 (abcam ab86359)


title: Q001S0002B0012R1S

description:
processed data file: Q001S0002B0012_salmon_counts.matrix_norm.csv
Sample 50
50_S50

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)


title: DNMT3A1-D333N_ChIP-seq_sgRing1a-b_input

value: sgRing1a/b line expressing FLAG-HA tagged DNMT3A1 D333N


title: MM134_siFOXA1_E2_3

description:
si_treatment: siFOXA1_E2
Compiled_counts.txt


title: Test_isotype_IP_rabbit_IgG

description: seCLIP library of rabbit IgG control interacting RNA.

value: Rabbit IgG (Fisher 31235)


title: Q001S0002B0011R2N

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 43
43_S43

value: Non-selected

value: Barley infected first leaf (PO:0007094)


title: Q001S0002B0011R3N

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 55
55_S55


title: DNMT3A1-W330R_ChIP-seq_sgRing1a-b_input

value: C3H embryo-derived mesenchymal progenitor cells

value: sgRing1a/b line expressing FLAG-HA tagged DNMT3A1 W330R


title: DNMT3A1-D333N_ChIP-seq_sgRing1a-b

value: HA (ThermoFisher, #88836)


title: sgTAOK1_G1

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
U5-NPCs, CRISPR KO of TAOK1 using sgTAOK1-1, G0/G1 subpopulation (sorted)
Single cell RNA-seq

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode in the i7 index read (14 nt), sample index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
Raw bcl files were processed using cellranger mkfastq and cellranger count.
Bam files from output of cell ranger count are submitted as raw files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv and matrix.mtx (3 files per sample, output from cellranger count) are submitted as processed files.

source_name: cell line

growth_protocol: U5-NPCs were grown on laminin-coated substrate in N2B27 media supplemented by EGF and FGF in subconfluent conditions.

extract_protocol:
5000 cells from subconfluent NPCs (matched for density and media changes) were loaded on a GemCode Single Cell Instrument (10x Genomics) to generate single-cell GEMs for library preparation using Single Cell Gel Bead Kit (P/N 120217) according to manufacturer's guidelines. G0/G1 cells were first sorted on an FACSAria II (BD Biosciences) for the cells positive only for mCherry-hCDT1(aa30/120).
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.

treatment_protocol: CRISPR KO was performed through lentiviral transduction (lentiCRISPR v2 (Zhang lab)) and KO samples were collected at least 14 days post-selection.

tag: subpopulation

value: G0/G1 sorted

tag: crispr status


title: MM134_siER_E2_3

description:
si_treatment: siER_E2
Compiled_counts.txt

value: ER


title: U5_G1

description:
U5-NPCs, no CRISPR, G0/G1 sorted
Single cell RNA-seq


title: Q001S0002B0011R1N

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 33
33_S33


title: sgTAOK1_all

description:
U5-NPCs, CRISPR KO of TAOK1 using sgTAOK1-1, all cells (unsorted)
Single cell RNA-seq

value: all


title: Q001S0002B0011R3S

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 61
61_S61

value: Selected


title: MM134_siER_E2_2


title: DNMT3A1-W330R_ChIP-seq_sgRing1a-b


title: MM134_siFOXA1_E2_1


title: U5_ALL

description:
U5-NPCs, no CRISPR, unsorted
Single cell RNA-seq


title: DNMT3A1-R318W_ChIP-seq_sgRing1a-b_input

value: sgRing1a/b line expressing FLAG-HA tagged DNMT3A1 R318W


title: Q001S0002B0011R2S

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 49
49_S49


title: DNMT3A1-K299I_ChIP-seq_sgRing1a-b_input

value: sgRing1a/b line expressing FLAG-HA tagged DNMT3A1 K299I


title: DNMT3A2-WT_ChIP-seq_parental

value: Parental line expressing FLAG-HA tagged DNMT3A2


title: U5_NPC_Retest_Day21_R4

description:
Post-selection Day 21 for U5-NPCs transduced with a custom retest library; replicate 4
sgDNA

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a single-end, 50 base read length (SE50) sequencing strategy.
Reads were aligned to the guide library using Bowtie and counted for gene associations against the guide library used.
Raw counts for each guide are supplied for every sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw read counts for each Sample.

extract_protocol:
Cells were harvested at Day 0 post-selection and at the final timepoint and DNA was extracted using DNA Blood Mini Kit (Qiagen).
Guides were PCR-amplified and sequencing adapters for standard Illumina sequencing and sample indices for multiplexing were attached through two rounds of PCR.

treatment_protocol: Cells were transduced with lentiCRISPR v2 plasmids (Zhang lab) for each of the libraries at a MOI <1 (.2-.6) at a representation >250x. Two days after transduction, infected cells were selected using treatment with 1 ug/mL puromycin for 3 days.

tag: library

value: Custom Retest

tag: timepoint

value: Day 21


title: MM134_siER_E2_1


title: MM134_siFOXA1_E2_2


title: U5_NPC_Retest_Day21_R2

description:
Post-selection Day 21 for U5-NPCs transduced with a custom retest library; replicate 2
sgDNA


title: DNMT3A1-R318W_ChIP-seq_sgRing1a-b


title: HCC1428_siNT_E2_3

description:
si_treatment: siNT_E2
Compiled_counts.txt

value: NT


title: DNMT3A1-K299I_ChIP-seq_sgRing1a-b


title: U5_NPC_Retest_Day21_R3

description:
Post-selection Day 21 for U5-NPCs transduced with a custom retest library; replicate 3
sgDNA


title: DNMT3A1-delPWWP_ChIP-seq_sgRing1a-b_input

value: sgRIng1a/b line expressing FLAG-HA tagged DNMT3A1 delPWWP


title: Q001S0002B0010R3S

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 60
60_S60

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)


title: U5_NPC_Retest_Day0_R3

description:
Post-selection Day 0 for U5-NPCs transduced with a custom retest library; replicate 3
sgDNA

value: Day 0


title: DNMT3A1-delPWWP_ChIP-seq_sgRing1a-b

value: C3H embryo-derived mesenchymal progenitor cells


title: HCC1428_siNT_2

description:
si_treatment: siNT
Compiled_counts.txt

value: Untreated


title: Q001S0002B0010R1N

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 32
32_S32

value: Non-selected

value: Barley infected first leaf (PO:0007094)


title: HCC1428_siNT_3

description:
si_treatment: siNT
Compiled_counts.txt


title: HCC1428_siNT_E2_4


title: Q001S0002B0010R2S

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 48
48_S48


title: Q001S0002B0010R2N

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 42
42_S42


title: Q001S0002B0011R1S

description:
processed data file: Q001S0002B0011_salmon_counts.matrix_norm.csv
Sample 38
38_S38


title: U5_NPC_Retest_Day21_R1

description:
Post-selection Day 21 for U5-NPCs transduced with a custom retest library; replicate 1
sgDNA


title: U5_NPC_Retest_Day0_R1

description:
Post-selection Day 0 for U5-NPCs transduced with a custom retest library; replicate 1
sgDNA


title: HCC1428_siNT_E2_2


title: U5_NPC_Tiling_Day22_R2

description:
Post-selection Day 22 for U5-NPCs transduced with custom tiling library; replicate 2
sgDNA

value: Tiling

value: Day 22


title: DNMT3A1-D333N_ChIP-seq_parental_input

value: Parental line expressing FLAG-HA tagged DNMT3A1 D333N


title: U5_NPC_Tiling_Day22_R3

description:
Post-selection Day 22 for U5-NPCs transduced with custom tiling library; replicate 3
sgDNA


title: HCC1428_siMDC1_E2_3

description:
si_treatment: siMDC1_E2
Compiled_counts.txt


title: U5_NPC_Retest_Day0_R2

description:
Post-selection Day 0 for U5-NPCs transduced with a custom retest library; replicate 2
sgDNA


title: Q001S0002B0010R3N

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 54
54_S54


title: HCC1428_siNT_1

description:
si_treatment: siNT
Compiled_counts.txt


title: Q001S0002B0010R1S

description:
processed data file: Q001S0002B0010_salmon_counts.matrix_norm.csv
Sample 37
37_S37

value: Selected


title: HCC1428_siMDC1_E2_2


title: DNMT3A1-WT_ChIP-seq_sgRing1a-b

value: HA (ThermoFisher, #88836)


title: Q001S0002B0009R3N

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 53
53_S53


title: Q001S0002B0009R1N

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 31
31_S31


title: DNMT3A1-W330R_ChIP-seq_parental_input

value: Parental line expressing FLAG-HA tagged DNMT3A1 W330R


title: Q001S0002B0009R2N

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 41
41_S41


title: HCC1428_siFOXA1_E2_3

description:
si_treatment: siFOXA1_E2
Compiled_counts.txt


title: DNMT3A1-D333N_ChIP-seq_parental


title: DNMT3A1-W330R_ChIP-seq_parental


title: DNMT3A1-R318W_ChIP-seq_parental_input

value: Parental line expressing FLAG-HA tagged DNMT3A1 R318W


title: U5_NPC_Tiling_Day0_R2

description:
Post-selection Day 0 for U5-NPCs transduced with custom tiling library; replicate 2
sgDNA


title: U5_NPC_Tiling_Day22_R1

description:
Post-selection Day 22 for U5-NPCs transduced with custom tiling library; replicate 1
sgDNA


title: U5_NPC_Tiling_Day0_R3

description:
Post-selection Day 0 for U5-NPCs transduced with custom tiling library; replicate 3
sgDNA


title: DNMT3A1-R318W_ChIP-seq_parental


title: HCC1428_siFOXA1_E2_1


title: Q001S0002B0009R2S

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 47
47_S47


title: DNMT3A1-WT_ChIP-seq_sgRing1a-b_input


title: U5_NPC_Tiling_Day0_R1

description:
Post-selection Day 0 for U5-NPCs transduced with custom tiling library; replicate 1
sgDNA


title: HCC1428_siFOXA1_E2_2


title: Q001S0001B0012R3N

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 25
25_S25


title: HCC1428_siER_E2_2

description:
si_treatment: siER_E2
Compiled_counts.txt

value: ER


title: U5_NPC_Brunello_Day10_R2

description:
Post-selection Day 10 for U5-NPCs transduced with Brunello library (Doench et al. 2016); replicate 1
sgDNA

value: Brunello

value: Day 10


title: Q001S0001B0012R2N

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 15
15_S15

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)


title: U5_NPC_Brunello_Day10_R3


title: DNMT3A1-K299I_ChIP-seq_parental_input

value: Parental line expressing FLAG-HA tagged DNMT3A1 K299I


title: HCC1428_siER_E2_1


title: DNMT3A1-K299I_ChIP-seq_parental


title: Q001S0002B0009R3S

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 59
59_S59

value: Bgh isolate 5874 (AVRa6)


title: DNMT3A1-delPWWP_ChIP-seq_parental_input

value: C3H embryo-derived mesenchymal progenitor cells

value: Parental line expressing FLAG-HA tagged DNMT3A1 delPWWP


title: HCC1428_siMDC1_E2_1

description:
si_treatment: siMDC1_E2
Compiled_counts.txt


title: Q001S0001B0012R1N

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 05
5_S5

value: Non-selected


title: DNMT3A1-delPWWP_ChIP-seq_parental


title: Q001S0002B0009R1S

description:
processed data file: Q001S0002B0009_salmon_counts.matrix_norm.csv
Sample 36
36_S36

value: Barley infected first leaf (PO:0007094)


title: U5_NPC_Brunello_Day0_R3

description:
Post-selection Day 0 for U5-NPCs transduced with Brunello library (Doench et al. 2016); replicate 3
sgDNA

value: Day 0


title: TetWT-BMDMstim-rep2 (RNA28)

data_processing:
RNAseq data were aligned to the mouse reference genome (mm9) by Hisat2. Gene expression was summarized by HTSeq-counts.
The DESeq2 package v1.30.0 was used to normalize the raw counts and identify differentially expressed genes (adjusted p-value < 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: BMDMs

growth_protocol: 10 million bone marrow cells were seeded per 10 cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS, 30% L929-cell conditioned laboratory-made media (as source of M-CSF), and 100 U/ml penicillin/streptomycin+L-glutamine (GIBCO). After 4 days of differentiation, 20 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated Petri dishes overnight in DMEM containing 20% FBS, 30% L929-cell conditioned laboratory-made media, and 100 U/ml penicillin/streptomycin+L-glutamine.

extract_protocol:
Total RNA was isolated with a combination of RNeasy Plus Kit (Qiagen, Germany) and Trizol (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturers’ instructions.
Libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB). The starting RNA material was 200 ng.

value: wild type

value: bone marrow derived macrophages


title: Q001S0001B0012R3S

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 30
30_S30

value: Selected


title: Q001S0001B0012R1S

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 10
10_S10


title: TetTKO-BMDMstim-rep2 (RNA26)

value: TET-iTKO


title: Perifovea_donor_8

city: Iowa City

last: Voigt

state: Iowa

address: 375 Newton Road

institute: University of Iowa

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build GRCh38 with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 400 (to remove cells with poor read quality) or greater than 6500 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-")
For each of the eight libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: my _object <- NormalizeData(my_object, normalization.method = "LogNormalize", scale.factor = 10000), my_object <- FindVariableFeatures(my_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 25 dimensions of the canonical correlation analysis were used to integrate data with the following commands: retina.anchors <- FindIntegrationAnchors(object.list = my_object_list, dims=1:25), RETINA.combined <- IntegrateData(anchorset = retina.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: RETINA.combined <- ScaleData(RETINA.combined, verbose = FALSE), RETINA.combined <- RunPCA(retina.combined, npcs = 30, verbose = FALSE), RETINA.combined <- RunUMAP(RETINA.combined, reduction = "pca", dims = 1:23), RETINA.combined <- FindNeighbors(RETINA.combined, reduction = "pca", dims = 1:23), RETINA.combined <- FindClusters(RETINA.combined, resolution = 0.35)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: retina

extract_protocol:
A 1 mm foveal and 4 mm parafoveal punch of neural retina was acquired from human donors 5-8. After dissection away from the rpe and choroid, the retinal tissue was dissociated in 20 units/mL of papain with 0.005% DNase I (Worthington Biochemical Corporation, Lakewood NJ) on a shaker at 37 °C for 1 - 1.25 hours. Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors 5-8 were rapidly thawed before barcoding with the 10X Genomics chromium system. Libraries were pooled and sequenced using the Illumina NovaSeq platform (San Diego, CA).

tag: donor

value: retina

tag: region

value: parafovea


title: Perifovea_donor_6


title: U5_NPC_Brunello_Day0_R2

description:
Post-selection Day 0 for U5-NPCs transduced with Brunello library (Doench et al. 2016); replicate 2
sgDNA


title: TetTKO-BMDM-rep2 (RNA25)


title: Perifovea_donor_5


title: U5_allcells_C

description: U5-NPCs, no CRISPR, unsorted, undifferentiated replicate 3

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq.
All data were combined and normalized using a CPM method from the R/Bioconductor package, edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.HTSeqCts.txt: Tab-delimited text files include cpm values for each Sample.

growth_protocol: U5-NPCs and GSCs were grown on laminin-coated substrate in N2B27 media supplemented by EGF and FGF. Differentiation was induced by removal of FGF and EGF (growth factor withdrawal).

extract_protocol:
RNA was isolated from 0.5-1.0×10^6 cells either from subconfluent NPCs and GSCs (matched for density and media changes) or after 1 week removal of growth factors using TRIzol reagent (Thermo Fisher). G0/G1 cells were sorted on an FACSAria II (BD Biosciences) for the cells positive only for mCherry-hCDT1(aa30/120). Total RNA was prepared using Direct-zol™ RNA MiniPrep Plus Kit (ZymoResearch). RNA concentration and quality (RIN) were measured using an Agilent 4200 Tapestation.
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-Seq Kit (KAPA biosystems) according to manufacturer's guidelines.

tag: growth conditions

value: Undifferentiated

tag: cell isolate

value: all cells


title: Q001S0001B0012R2S

description:
processed data file: Q001S0001B0012_salmon_counts.matrix_norm.csv
Sample 20
20_S20


title: Perifovea_donor_7


title: TetTKO-BMDMstim-rep1 (RNA24)

tag: strain

tag: genotype


title: U5_allcells_B

description: U5-NPCs, no CRISPR, unsorted, undifferentiated replicate 2


title: Fovea_donor_6

value: fovea


title: Q001S0001B0004R2N

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 14
14_S14

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

tag: treatment


title: Fovea_donor_8


title: HCC1428_siER_E2_3

value: ER


title: U5_allcells_A

description: U5-NPCs, no CRISPR, unsorted, undifferentiated replicate 1


title: U5_NPC_Brunello_Day10_R1

tag: cell type

value: Brunello

value: Day 10


title: G1_WT_B

description: U5-NPCs, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2

value: G0/G1 sorted


title: Q001S0001B0004R1N

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 04
4_S4

tag: plant genotype

tag: fungal isolate

value: Bgh isolate 5874 (AVRa6)

value: Non-selected


title: TetWT-BMDM-rep2 (RNA27)


title: G1_TP53_B

description: U5-NPCs, CRISPR KO with sgTP53-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2


title: TetWT-BMDMstim-rep1 (RNA22)


title: Q001S0001B0004R1S

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 09
9_S9

tag: tissue

value: Barley infected first leaf (PO:0007094)


title: U5_NPC_Brunello_Day0_R1

description:
Post-selection Day 0 for U5-NPCs transduced with Brunello library (Doench et al. 2016); replicate 1
sgDNA

value: Day 0


title: TetWT-BMDM-rep1 (RNA21)

value: wild type

value: bone marrow derived macrophages


title: Input on A673 STAG2 WT [BA_A673_STAG2WT_Input]

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All of the ChIP-Seq data sets were aligned to the GRCh37/hg19 human genes and Drosophila Melanogaster dm6 genes using bowtie2-2.3.5 with the standard options. PCR duplicates were removed with the Picard v2.18.2 MarkDuplicates tool (Li and Durbin, 2010). The Active Motif Spike-in Normalization protocol was then applied to each hg19 sample by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample. For each mark the reads mapped on the STAG2 wild-type clones A673.sgNT-1c4 and A673.sgNT-2c3 were merged and labeled as "STAG2 WT" and similarly, the reads mapped on the STAG2 knockout clones A673.sgSTAG2-1c6, A673.sgSTAG2-4c5 were merged and labeled as "STAG2 KO".  The mapped reads for individual and merged clones were normalized in units of Reads Per Kilobase per Million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools v2.5.3. (Ramirez et al., 2016).
Peak calling was performed against input control using the model-based MACS2 v2.1.1.20160309 software (Zhang et al., 2008), with the cut-off FDR ≤ 0.01. Narrow peaks were identified for all marks except H3K27Me3 for which macs2 was called with the broad peak option.  Area under Curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software (Pohl and Beato, 2014). Peaks with low area under curve coverage (< 300 RPKM)  were disregarded and the ENCODE black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/) were removed from each set of peak regions. Quality control tests for the mapped reads were performed by using the ChIPQC library available from Bioconductor v3.6 (Carroll et al., 2014). The distances between replicates for STAG2 WT and STAG2 KO clones were estimated based on the multiBamSummary function available from the deepTools v2.5.3. (Ramirez et al., 2016) and visualized on correlation heatmaps and PCA plots. The peaks were annotated with the closest hg19 genes by using the annotatePeaks function available in the Homer v4.11 package (Heinz et al., 2010) and the GREAT annotation platform (McLean et al., 2010).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp).  Coverage was computed for  bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.  The Active Motif Spike-in Normalization protocol was then applied to each hg19 sample -except Input- by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.

source_name: A673 clones with STAG2 wild type

extract_protocol:
Cells (20 million per ChIP reaction for all but EWS/FLI1, which required 40 million cells) were crosslinked with warm 1% methanol-free formaldehyde (ThermoFisher) for 10 minutes at room temperature rotating at 12 RPM. The reaction was quenched by adding glycine to a final concentration of 0.125M and incubating for an additional 5 minutes at room temperature rotating at 12 RPM. Cell pellets were washed three times with ice cold PBS and resuspended in 1 ml of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH8) supplemented with protease inhibitor cocktail including phenylmethylsulfonyl fluoride (PMSF) and incubated at RT for 2 minutes with gentle rotation. Lysates were centrifuges at 15,000 G for 10 minutes at 4°C and the pellet was re-suspended in 900 µl of ChIP IP buffer (2:1 SDS lysis buffer : triton dilution buffer), transferred to milliTUBE (covaris). Sonication was performed on a E220 Focus Ultra Sonicator (Covaris) using the setting (duty cycle 5%, peak power 140W, cycles per burst 200, Temperature 4°C, time 30 minutes/millitube). ChIP inputs from sheared chromatin were de-crosslinked by adding de-crosslinking buffer (NaHCO3, NaCl, RNase A, Proteinase K) and incubating for two hours at 65°C in a thermal cycler. The remaining sheared chromatin was incubated with primary antibody coupled to Protein A DynaBead (Beckman Coulter, antibody bead conjugation was performed for 16 hours) overnight, rotating at 4°C. As a calibration control, antibody against a drosophila specific histone variant H2Av and drosophila chromatin (active motif) were used as per the recommendation of the manufacturer.  The next day, ChIP product was eluted from the Dynabeads in 100 µl of elusion buffer and de-crosslinked for 12 hours at 65°C. For both Input and chipped material, AMPure XP beads (Beckman coulter) were used to purify DNA.
Chromatin immunoprecipitation sequencing for EWS/FLI1, SMC1A, STAG1, STAG2, H3K27me3:  ChIP-seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1 ng of DNA according to the manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by a Qubit fluorometer and samples were QC’D using a Bioanalyzer Tapestation (Agilent Technologies 2200) to determine  fragment size. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on a NovaSeq targeting 40 million 100bp read pairs by the Molecular Biology Core facilities at Dana-Farber Cancer Institute.  Chromatin immunoprecipitation sequencing for H3K27ac: Chromatin was sheared to about 200 bp fragments using the Covaris ultra-sonication. The lysate was diluted with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 16.7 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS) and cleared by centrifugation. 5% of the supernatant volume set aside as an input control. The remaining lysate was incubated over night at 4°C with 5 ug of antibody (3 ug for histone antibodies).

tag: cell line

value: Ewing sarcoma cell line

tag: genotype/variation

value: STAG2 wild-type

tag: chip antibody

value: Input


title: Q001S0001B0004R3N

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 24
24_S24


title: TetTKO-BMDM-rep1 (RNA23)

value: TET-iTKO


title: H3K27me3 on A673 STAG2 WT [BA_A673_STAG2WT_H3K27me3]

value: Rabbit anti-H3K27me3 Cell Signaling Cat# 4395, RRID AB_11220433


title: G1_WT_A

description: U5-NPCs, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1

value: Undifferentiated

tag: subpopulation

tag: crispr status


title: G1_TAOK1_A

description: U5-NPCs, CRISPR KO with sgTAOK1-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1


title: Fovea_donor_5

value: retina

value: fovea


title: Q001S0001B0004R2S

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 19
19_S19

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Selected


title: SMC1A on A673 STAG2 KO [BA_A673_STAG2KO_SMC1A]

source_name: A673 clones with STAG2 knocked-out

value: STAG2 knocked-out

value: Rabbit anti-SMC1A Bethyl Cat# A300-055A RRID  AB_2192467


title: Input on A673 STAG2 KO [BA_A673_STAG2KO_Input]


title: Fovea_donor_7


title: Q001S0001B0003R3N

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 23
23_S23

value: Bgh isolate 5874 (AVRa6)

value: Non-selected


title: Q001S0001B0003R3S

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 28
28_S28

value: Barley infected first leaf (PO:0007094)


title: SMC1A on A673 STAG2 WT [BA_A673_STAG2WT_SMC1A]


title: TdgKO-Th2-rep4 (RNA20)

source_name: Th2 cells

growth_protocol: For Th2 polarization naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (clone 2C11) and anti-CD28 (clone 37.51) antibodies at 1 μg/ml in the presence of 1000 U/ ml IL-4, 1 μg/ml anti-IFN-γ, for 2 days. On day 3 of culture, cells were removed from TCR/CD28 costimulation conditions and expanded in the presence of 20 U/mL IL-2 for 3 days.

value: Tdg-iKO

value: T-cells from the spleen and lymphnodes


title: G1_TAOK1_B

description: U5-NPCs, CRISPR KO with sgTAOK1-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2

value: G0/G1 sorted


title: SA2 on A673 STAG2 KO [BA_A673_STAG2KO_SA2]

value: Ewing sarcoma cell line

value: Rabbit anti-STAG2 (ChIP-seq) Cell Signaling Cat#5882 RRID  AB_10834529


title: Q001S0001B0003R2N

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 13
13_S13


title: Q001S0001B0004R3S

description:
processed data file: Q001S0001B0004_salmon_counts.matrix_norm.csv
Sample 29
29_S29


title: TdgWT-Th2-rep4 (RNA19)

value: wild type


title: G1_NTC_B

description: U5-NPCs, sgNTC, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2

value: sgNTC


title: Q001S0001B0003R1S

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 08
8_S8


title: TdgKO-Th2-rep3 (RNA18)


title: Q001S0001B0003R1N

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 03
3_S3


title: Q001S0001B0002R3N

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 22
22_S22


title: G1_PTPN14_B

description: U5-NPCs, CRISPR KO with sgPTPN14-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2

value: Undifferentiated


title: G1_NF2_A

description: U5-NPCs, CRISPR KO with sgNF2-3, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1


title: Q001S0001B0002R1N

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 02
2_S2


title: Q001S0001B0003R2S

description:
processed data file: Q001S0001B0003_salmon_counts.matrix_norm.csv
Sample 18
18_S18


title: EWS/FLI1 on A673 STAG2 WT [BA_A673_STAG2WT_FLI1]

value: STAG2 wild-type

value: Rabbit anti-EWS/FLI1 Abcam Cat# ab15289 RRID AB_301825


title: G1_PTPN14_A

description: U5-NPCs, CRISPR KO with sgPTPN14-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1


title: TdgWT-Th2-rep3 (RNA17)


title: TdgWT-BMDMstim-rep1 (RNA7)

value: bone marrow derived macrophages


title: Input on A673 [BA_A673_Input]

source_name: A673 clones untreated

value: Input


title: G1_TP53_A

description: U5-NPCs, CRISPR KO with sgTP53-1, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1


title: TdgWT-BMDMstim-rep2 (RNA12)


title: SA2 on A673 STAG2 WT [BA_A673_STAG2WT_SA2]


title: TdgKO-BMDM-rep1 (RNA6)


title: EWS/FLI1 on A673 [BA_A673_FLI1]


title: TdgWT-BMDM-rep1 (RNA5)


title: TdgWT-BMDM-rep2 (RNA11)


title: G1_NTC_A

description: U5-NPCs, sgNTC, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1


title: SA1 on A673 STAG2 KO [BA_A673_STAG2KO_SA1]

value: STAG2 knocked-out

value: Rabbit anti-STAG1(ChIP-seq) Bethyl Cat# A302-578A RRID AB_2034858


title: SA1 on A673 STAG2 WT [BA_A673_STAG2WT_SA1]


title: G1_NF2_B

description: U5-NPCs, CRISPR KO with sgNF2-3, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2


title: TdgKO-BMDMstim-rep2 (RNA10)


title: Q001S0001B0002R3S

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 27
27_S27

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)

value: Selected


title: Q001S0001B0001R3N

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 21
21_S21

value: Non-selected

value: Barley infected first leaf (PO:0007094)


title: TdgKO-BMDM-rep2 (RNA9)

value: Tdg-iKO


title: H2AK119Ub_ChIP-Rx_parental-DNMT3A1-W330R_input

organism:
Drosophila melanogaster
Mus musculus

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma). Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

value: C3H embryo-derived mesenchymal progenitor cells

value: Parental line expressing FLAG-HA tagged DNMT3A1 W330R


title: H2AK119Ub_ChIP-Rx_TKO

value: H2AK119Ub (Cell Signaling Tech, #8240)


title: G1_CREBBP_A

description: U5-NPCs, CRISPR KO with sgCREBBP-2, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 1

value: G0/G1 sorted


title: EWS/FLI1 on A673 STAG2 KO [BA_A673_STAG2KO_FLI1]

value: Ewing sarcoma cell line


title: TdgWT-Th2-rep1 (RNA2)

value: wild type

value: T-cells from the spleen and lymphnodes


title: TdgKO-BMDMstim-rep1 (RNA8)

value: bone marrow derived macrophages


title: G1_GSC_827_B

description: GSC-0827, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated, replicate 2

value: Undifferentiated


title: G1_GSC_827_A

description: GSC-0827, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated, replicate 1


title: Q001S0001B0001R2N

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 11
11_S11


title: Q001S0001B0002R2S

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 17
17_S17


title: Q001S0001B0001R3S

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 26
26_S26


title: G1_GSC_131_B

description: GSC-0131, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated, replicate 2


title: Q001S0001B0002R2N

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 12
12_S12


title: H2AK119Ub_ChIP-Rx_parental-DNMT3A1-W330R


title: diff_TP53_A

description: U5-NPCs, CRISPR KO with sgTP53-3, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1

value: 1 week growth factor withdrawal differentiation

value: all cells


title: Q001S0001B0002R1S

description:
processed data file: Q001S0001B0002_salmon_counts.matrix_norm.csv
Sample 07
7_S7

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)


title: diff_TAOK1_B

description: U5-NPCs, CRISPR KO with sgTAOK1-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2


title: Q001S0001B0001R2S

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 16
16_S16

value: Bgh isolate 5874 (AVRa6)


title: G1_GSC_131_A

description: GSC-0131, no CRISPR, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated, replicate 1


title: H2AK119Ub_ChIP-Rx_parental-rep-2

value: Parental


title: TdgWT-Th2-rep2 (RNA4)


title: TdgKO-Th2-rep2 (RNA3)


title: G1_CREBBP_B

description: U5-NPCs, CRISPR KO with sgCREBBP-2, G0/G1 sorted (mCherry-hCDT1(30/120)-positive), undifferentiated replicate 2


title: diff_TP53_B

description: U5-NPCs, CRISPR KO with sgTP53-3, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2


title: Mbre_control2

city: Dallas

first: Arielle

last: Woznica

state: Texas

address: 6000 Harry Hines Blvd., NL4.110M

institute: UT Southwestern

description: + vehicle control rep 2

data_processing:
Single-end/paired-end 76 bp read length fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.05).
Trimmed fastq files were mapped to M. brevicollis genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v2.10.10)
Read counts were generated using featureCounts (subread) for coding genes using gtf (Monosiga_brevicollis_mx1.V1.0)
Normalized read counts generated using edgeR
Genome_build: Monosiga brevicollis mx1.V1.0
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

organism: Monosiga brevicollis

source_name: choanoflagellate cells

growth_protocol: M. brevicollis were grown in High Nutrient Medium (10% Cereal Grass Media, 2.5% Sea Water Complete Media in artificial sea water) at room temperature

extract_protocol: RNA libraries were generated with the Illumina TruSeq® Stranded mRNA Library prep kit (cat # 20020594), using a starting total RNA input of 2-3 µg. To remove contaminating bacterial RNA, samples were first poly-A selected using oligo-dT attached magnetic beads. Following purification, the mRNA was fragmented at 94ºC for 4 minutes, and cleaved RNA fragments were synthesized into cDNA. After an end repair step, UMI adapters (synthesized by IDT) were ligated to the cDNA, and the products were twice purified using AMPure XP beads before amplification.     Library quantity was measured using the Quant-iT™ PicoGreen dsDNA Assay kit by Invitrogen (cat # P7589) and a PerkinElmer Victor X3, 2030 Multilabel Reader. Library quality was verified on an Agilent 2100 Bioanalyzer instrument using Agilent High sensitivity DNA kit (cat # 5067-4626) or DNA 1000 kit (cat # 5067-1504). Libraries were pooled, and sequenced on either the Illumina NovaSeq 6000 system with S4 flowcell and XP PE-100 workflow, or on the Illumina NextSeq 550 system with SE-75 workflow.

treatment_protocol: To grow large numbers of cells for RNA-seq, cells were seeded one to two days prior to the experiment in either 3-layer flasks (Falcon; Corning, Oneonta, NY, USA; Cat. No. 14-826-95) or 75 cm2 flasks (Falcon; Corning, Oneonta, NY, USA; Cat. No. 13-680-65), and grown at room temperature. Bacteria were washed away from choanoflagellate cells through two rounds of centrifugation and resuspension in artificial seawater (ASW). To count the cell density, cells were diluted 100-fold in 200 µl of ASW, and fixed with 1 µL of 16% paraformaldehyde. Cells were counted on a hemocytometer, and the remaining cells were diluted to a final concentration of 4×106 choanoflagellate cells/mL. The resuspended cells were divided into 2.5 mL aliquots and plated in 6-well plates prior to treatment. After treatment, cells were transferred to a 15 mL conical and pelleted by centrifugation at 2400 x g for 5 min, flash frozen with liquid nitrogen, and stored at -80°C.

value: M. brevicollis MX1 ATCC PRA-258

value: water control for 3 hours

value: choanoflagellate cells


title: H3K36me2_ChIP-Rx_sgEzh2

value: C3H embryo-derived mesenchymal progenitor cells


title: H2AK119Ub_ChIP-Rx_TKO_input


title: Mbre_control1

description: + vehicle control rep 1


title: TdgKO-Th2-rep1 (RNA1)

value: Tdg-iKO


title: H2AK119Ub_ChIP-Rx_parental-rep-2_input


title: Q001S0001B0001R1S

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 06
6_S6

value: Selected

value: Barley infected first leaf (PO:0007094)


title: TdgKO-CD4cre-Th2-1st-PB-rep1

data_processing:
Library strategy: PB-seq
The BS and PB reads were mapped to mouse genome mm9 using the BSMAP mapping tool. The mapping was done using the paired end datasets with the following parameter values: -p 4 -w 2 -v 5 -q 30 for BS-seq, and -p 4 -w 2 -v 0 -q 30 for PB-seq.
For each of the samples, the number of reads in which each cytosine within the amplicons was converted into thymine was counted.
For BS-seq, these counts were used to calculate the proportions for each cytosine to be nonmethylated/formylmethylated/carboxylmethylated (T), or methylated/hydroxymethylated (C).
For PB-seq, to compensate redundant reads derived from the opposite strand, number of reads standing for nonmethylated/methylated/hydroxymethylated (C) was multiplied by 0.5, and the proportions for each cytosine to be formylmethylated/carboxylmethylated (T) was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: methylation_ratio .txt file

source_name: Th2-1st cells

value: Tdg-KO


title: TetWT-Th2-2nd-BS-rep2

source_name: Th2-2nd cells

growth_protocol: For the 2nd cycle of the cultivation, Th2-1st cells differentiated for 6 days were washed and cultured under resting conditions (medium without any cytokine) for 1 day. Cells were harvested, counted, and plated at 1M cells/ml for 2nd stimulation with plate-bound anti-CD3 (clone 2C11) and anti-CD28 (clone 37.51) antibodies at 1 μg/ml in the presence of 1000 U/ ml IL-4, 1 μg/ml anti-IFN-γ, for 1 day. On day 2 of the 2nd cycle, cells were removed from TCR/CD28 costimulation conditions and expanded in the presence of 20 U/mL IL-2 for 4 days.

value: wild type


title: TdgWT-CD4cre-Th2-1st-PB-rep1

value: T-cells from the spleen and lymphnodes


title: Q001S0001B0001R1N

description:
processed data file: Q001S0001B0001_salmon_counts.matrix_norm.csv
Sample 01
1_S1

value: Non-selected


title: diff_TAOK1_A

description: U5-NPCs, CRISPR KO with sgTAOK1-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1


title: diff_NTC_B

description: U5-NPCs, CRISPR KO with sgNTC, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2

value: sgNTC


title: H3K36me2_ChIP_Rx_sgEzh2_input


title: H3K27me3_ChIP-Rx_sgEzh2

value: H3K27me3 (Cell Signaling Tech, #9733)


title: Th2-TAPS-rep1

data_processing:
Library strategy: TAPS (TET assisted PB-seq)
The BS and PB reads were mapped to mouse genome mm9 using the BSMAP mapping tool. The mapping was done using the paired end datasets with the following parameter values: -p 4 -w 2 -v 5 -q 30 for BS-seq, and -p 4 -w 2 -v 0 -q 30 for PB-seq.
For each of the samples, the number of reads in which each cytosine within the amplicons was converted into thymine was counted.
For BS-seq, these counts were used to calculate the proportions for each cytosine to be nonmethylated/formylmethylated/carboxylmethylated (T), or methylated/hydroxymethylated (C).
For PB-seq, to compensate redundant reads derived from the opposite strand, number of reads standing for nonmethylated/methylated/hydroxymethylated (C) was multiplied by 0.5, and the proportions for each cytosine to be formylmethylated/carboxylmethylated (T) was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: methylation_ratio .txt file


title: H2AK119Ub_ChIP-Rx_sgEzh2

value: H2AK119Ub (Cell Signaling Tech, #8240)


title: diff_PTPN14_B

description: U5-NPCs, CRISPR KO with sgPTPN14-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2

value: 1 week growth factor withdrawal differentiation

value: all cells


title: Mbre_cGamp2

description: + 2'3' cGAMP rep 2

value: 100 uM 2'3' cGAMP for 3 hours


title: H2AK119Ub-H3K27me3_ChIP-Rx_sgRing1a-b_input

description: Used as input DNA for H2AK119Ub and H3K27me3 ChIP-Rx in the sgRing1a/b background.


title: Naïve-TAPS-rep1


title: H2AK119Ub-H3K27me3_ChIP-Rx_sgEzh2_input

description: Used as input DNA for H2AK119Ub and H3K27me3 ChIP-Rx in the sgEzh2 background.


title: diff_PTPN14_A

description: U5-NPCs, CRISPR KO with sgPTPN14-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1


title: 3prime3prime-cGAMP-A

description: + 3'3' cGAMP rep 1

value: M. brevicollis MX1 ATCC PRA-258

value: 200 uM 3'3' cGAMP for 3 hours


title: 3prime3prime-cGAMP-B

description: + 3'3' cGAMP rep 2

value: choanoflagellate cells


title: MB_h20_3

description: + vehicle control rep 3

value: water control for 3 hours


title: TetTKO-Th2-2nd-BS-rep2

value: TET-iTKO


title: TdgKO-Th2-2nd-BS-rep2

value: Tdg-iKO


title: diff_NTC_A

description: U5-NPCs, CRISPR KO with sgNTC, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1


title: TetWT-Th2-1st-BS-rep2


title: H2AK119Ub_ChIP-Rx_sgRing1a-b

value: C3H embryo-derived mesenchymal progenitor cells


title: TdgWT-Th2-2nd-BS-rep2


title: diff_NF2_B

description: U5-NPCs, CRISPR KO with sgNF2-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2


title: Mbre_cGamp1

description: + 2'3' cGAMP rep 1


title: TetTKO-Th2-1st-BS-rep2


title: H3K27Ac on A673 STAG2 null

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
ChIP-seq reads were aligned to the hg19 genome assembly using bwa v0.7.17  with the mem -M configuration. Quality control tests for the mapped reads were performed by using the ChIPQC library available from Bioconductor v3.5.
Data were filtered for duplicate reads with Picard tools.
Peak calling was performed using the model-based MACS v1.4.3 software, with  the cut-offs P ≤ 1e-09 for H3K27Ac and P ≤ 1e-05 for all other marks.  The ENCODE  black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/)  were removed from each set of peak regions.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp).  Coverage was computed for  bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.

source_name: A673 clones with STAG2 null

growth_protocol: Chromatin immunoprecipitation sequencing for EWS/FLI, H3K27Ac, and CTCF: Adherent A673 cells with and without STAG2 knockout (sgNT-1c4, sgNT-2c3, sgSTAG2-1c6, and sgSTAG2-4c5) were grown to 70-80% confluence, crosslinked with 1% formaldehyde for 5 min and then quenched with 0.125 M glycine. The fixed cells were harvested with trypsin and washed twice in ice cold PBS before resuspension in lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS) supplemented with protease inhibitors (Roche).  Chromatin immunoprecipitation sequencing for SMC1a: SMC1a ChIP was performed as previously described with a few adaptations. Adherent A673 cells with and without STAG2 knockout (sgNT-1c4, sgNT-2c3, sgSTAG2-1c6, and sgSTAG2-4c5) were crosslinked for 15 minutes at room temperature by the addition of one-tenth volume of fresh 11% formaldehyde solution (11% formaldehyde, 50 mM HEPES pH 7.3, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) to the growth media followed by 5 min quenching with 125 mM glycine. Cells were rinsed twice with 1X PBS and harvested using a silicon scraper and flash frozen in liquid nitrogen. Frozen crosslinked cells were stored at -80°C. 100µl of Protein G Dynabeads (Life Technologies #10009D) were washed 3X for 5 minutes with 0.5% BSA (w/v) in PBS at 4oC. Magnetic beads were bound with 10 µg of anti-SMC1 antibody (Bethyl A300-055A) overnight at 4°C, and then washed 3X with 0.5% BSA (w/v) in PBS.

extract_protocol:
Chromatin immunoprecipitation sequencing for EWS/FLI, H3K27Ac, and CTCF: Chromatin was sheared to about 200 bp fragments using the Covaris ultra-sonication. The lysate was diluted with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 16.7 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS) and cleared by centrifugation. 5% of the supernatant volume set aside as an input control. The remaining lysate was incubated over night at 4°C with 5 ug of antibody (3 ug for histone antibodies). The following antibodies were used for ChIP: Fli (sc-356X, Santa Cruz Biotechnology), H3K27Ac (ab4729, Abcam), and CTCF (07-729, EMD Millipore).   Chromatin immunoprecipitation sequencing for SMC1a: Cells were prepared for ChIP as follows. All buffers contained freshly prepared 1× cOmplete protease inhibitors (Roche, 11873580001). Frozen crosslinked cells were thawed on ice and then resuspended in lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× protease inhibitors) and rotated for 10 minutes at 4°C, then spun at 1350 rcf for 5 minutes at 4°C. The pellet was resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitors) and rotated for 10 minutes at 4°C and spun at 1350 rcf for 5 minutes at 4°C. The pellet was resuspended in sonication buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, and 1% Triton X-100, 1× protease inhibitors) and then sonicated on a Misonix 3000 sonicator for 10 cycles at 30 seconds each on ice (18-21 W) with 60 seconds on ice between cycles. Sonicated lysates were cleared once by centrifugation at 16,000 rcf for 5 minutes at 4°C. 50 µL was reserved for input, and then the remainder was incubated overnight at 4°C with magnetic beads bound with antibody to enrich for DNA fragments bound by the indicated factor.
Chromatin immunoprecipitation sequencing for EWS/FLI, H3K27Ac, and CTCF: The precipitated complexes were bound to protein A/G high-capacity agarose beads (Pierce) for 2 h before washing sequentially with ice cold low salt wash (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS), high salt wash (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl wash (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholic acid, 1% IGEPAL CA-630) and TE wash (10 mM Tris-HCl pH 8.1, 1 mM EDTA) and eluted in elution buffer (0.1 M NaHCO3, 1% SDS). Library preparation for eluted DNA fragments were performed using the NEBNext ChIP-Seq Library Prep for Illumina (New England Biolabs). The Pippin Prep (Sage Science) was used to size select the adaptor ligated DNA in the 175-450 bp range prior to PCR enrichment. Libraries were sequenced on the Illumina HiSeq 2000 instrument.  Chromatin immunoprecipitation sequencing for SMC1a: For ChIP-seq experiments, purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries.

value: A673 Ewing sarcoma

value: STAG2 null


title: Control2

description: No bacteria rep 2

value: wild type

value: No conditioned media for 3 hours


title: diff_NF2_A

description: U5-NPCs, CRISPR KO with sgNF2-1, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1


title: H3K27me3_ChIP-Rx_sgRing1a-b


title: diff_CREBBP_B

description: U5-NPCs, CRISPR KO with sgCREBBP-2, unsorted, 1 week differentiation (growth factor withdrawal), replicate 2


title: MB_cGAMP_3

description: + 2'3' cGAMP rep 3


title: WT control-replicate 1

city: Wageningen

first: Christian

last: Südfeld

state: Gelderland

address: Droevendaalsesteeg 1

department: Bioprocess Engineering

country: Netherlands

institute: Wageningen University & Research

data_processing:
FASTQ raw reads were preprocessed using fastp
Cleaned paired-end reads were mapped to the reference genome using HISAT2
Mapped reads were quantified using the featureCounts package of R statistical software
FPKM values were calculated for gene count comparisons within a sample. For differential expression analysis, gene counts were normalized and compared for log2 fold change and statistical significant difference between sample groups using the DESeq2 package
The false discovery rate was controlled by adjusting the p-values using the Benjamini and Hochberg correction.
Genome_build: N. oceanica IMET1v2 (ftp://nandesyn.single-cell.cn/pub/)
Supplementary_files_format_and_content: Normalized gene counts, FPKM values, log2-fold changes and corresponding p-values, as well as the FDR-adjusted p-values (padjust) are given in an .xlsx data table.  Additional columns indicate the gene's chromsome number (gene_chr) and position (gene_start, gene_end), chromosome strand (gene_strand) and length of the gene (gene_length).

organism: Nannochloropsis oceanica strain IMET1

source_name: WT control

growth_protocol: NO06G03670 knockout mutant strain HLM23 and wild type control samples were inoculated at an optical density at 750 nm of 0.1 into 25 ml of artificial sea water (419.23 mM NaCl, 22.53 mM Na2SO4, 5.42 mM CaCl2, 4.88 mM K2SO4, 48.21 mM MgCl2 and 20 mM HEPES, pH 8), supplemented with 2 ml l-1 of nutribloom plus (Necton, Portugal) growth media. Cultures were kept in 50 ml shake flasks at 600 μmol m-2 s-1 with a 16:8 h diurnal light cycle, in an Algem HT24 photobioreactor (Algenuity, UK) that was placed in a shaking plate incubator operated with 120 rpm, 25 ℃ and 0.2% CO2-enriched air. Samples were harvested 1 h before onset of the dark phase after 3 days of cultivation.

extract_protocol:
22 ml of culture was harvested (4,255 x g, 10 min, 4 ℃) and cell pellets were snap-frozen. RNA extraction, mRNA library preparation and sequencing, transcript mapping and quantification were performed by Novogene (UK) Company Limited. RNA was extracted from cell pellets using the RNeasy Plus Universal Mini Kit (Qiagen #73404) according to manufacturer instructions
A total of 1 μg RNA was used for RNA-seq library preparation with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s instructions.
Linear double-stranded cDNA fragments were subjected to PCR using Phusion High-Fidelity DNA polymerase with Index primers or Universal PCR primers provided for the NEBNext Ultra RNA Library Prep system. Barcoded PCR products were purified using the AMPure XP system, and the library quality was checked using a Agilent Bioanalyzer 2100. Index-coded samples were clustered using a cBot Cluster Generation System with the PE Cluster Kit cBot-HS (Illumina) according to manufacturer recommendations. After this, libraries were sequenced on an Illumina Novaseq 6000 platform and paired-end reads were generated.


title: HLM23-replicate 3


title: Input on A673 STAG2 WT matched for H3K27Ac

value: STAG2 wild-type

value: Input matched for H3K27Ac


title: H3K27Ac on A673 STAG2 WT


title: TdgKO-Th2-1st-PB-rep2

value: T-cells from the spleen and lymphnodes


title: Flavo4

description: +Flavobacterium rep 4

value: Flavobacterium sp. conditioned media for 3 hours


title: diff_CREBBP_A

description: U5-NPCs, CRISPR KO with sgCREBBP-2, unsorted, 1 week differentiation (growth factor withdrawal), replicate 1

value: 1 week growth factor withdrawal differentiation

value: all cells


title: WT control-replicate 3


title: Th2-sgGATA3-2-BS-rep1


title: Control4

description: No bacteria rep 4

value: M. brevicollis MX1 ATCC PRA-258


title: Flavo3

description: +Flavobacterium rep 3


title: Input on A673 STAG2 null matched for H3K27Ac


title: Control3

description: No bacteria rep 3


title: Th2-sgGATA3-1-BS-rep1


title: STING2d12-2prime3primecgamp-2

description: STING KO + 2'3'cGAMP rep 2

value: Sting-

value: 100 uM 2'3' cGAMP for 3 hours


title: Flavo2

description: +Flavobacterium rep 2

value: choanoflagellate cells


title: A673 STAG2 KO sg4 rep2

data_processing:
The CRISPR plasmids pSpCas9(BB)-2A-GFP (PX458) and lentiCRISPR v2 were acquired from Addgene. STAG2 wild-type clones and and STAG2 null clones by CRISPR Cas9 editing were created on  A673 cells (STAG2 wild-type: A673.sgNT-1c4, A673.sgNT-2c3, A673.sgLacZ-2c1; STAG2 null: A673.sgSTAG2-1c4, A673.sgSTAG2-1c6, A673.sgSTAG2-4c3, A673.sgSTAG2-4c5)  and on TC71 cells (STAG2 wild-type:  TC71.sgNT-1c6, TC71.sgNT-2c5; STAG2 null: TC71.sgSTAG2-1c6, TC71.sgSTAG2-4c15, TC71.sgSTAG2-4c18, TC71.sgSTAG2-1c3). Total RNA was extracted with an RNeasy Kit (Qiagen) from STAG2 wild-type and STAG2 null clones (A673.sgNT-1c4, A673.sgNT-2c3, A673.sgLacZ-2c1, A673.sgSTAG2-1c4, A673.sgSTAG2-1c6, A673.sgSTAG2-4c3, A673.sgSTAG2-4c5, TC71.sgNT-1c6, TC71.sgNT-2c5, TC71.sgSTAG2-1c6, TC71.sgSTAG2-4c15, TC71.sgSTAG2-4c18, TC71.sgSTAG2-1c3). For the A673 clones, Poly(A) RNA was isolated using the NEBNext mRNA magnetic isolated module (New England Biolabs) and paired-end libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New Englad Biolabs) according to the manufacturer’s protocols with the following modifications: the PCR library enrichment conditions were adjusted to 12 cycles and the PCR library reaction was purified twice by size selection with Agencourt AMPure XP beads (Beckman Coulter). Libraries were subjected to 50 base paired-end sequencing (Illumina HiSeq 2000).    Total RNA was extracted from triplicate samples of TC71 STAG2 clones with the RNeasy Kit and on-column DNA digestion (Qiagen). Poly(A) mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol.  Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-40M reads/sample.
Quality control tests for the sequenced reads  were performed using the FASTQC v0.11.5 software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2.1.1. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2.1 and the SARTools  pipelines.
Gene level reads and gene level expression estimated as log2(1+FPKM) (Fragments Per Kilobase of transcript per Million mapped reads) scores were computed using the Feature Counts method implemented in the Bioconductor v3.5  RSubread v1.5.3 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: A673 Ewing sarcoma cell line

extract_protocol:
RNAseq library construction protocol - A673 cells:  For the A673 clones, Poly(A) RNA was isolated using the NEBNext mRNA magnetic isolated module (New England Biolabs) and paired-end libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New Englad Biolabs) according to the manufacturer’s protocols with the following modifications: the PCR library enrichment conditions were adjusted to 12 cycles and the PCR library reaction was purified twice by size selection with Agencourt AMPure XP beads (Beckman Coulter). Libraries were subjected to 50 base paired-end sequencing (Illumina HiSeq 2000).
RNAseq library construction protocol - TC71 cells:  Poly(A) mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol.  Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-40M reads/sample.

tag: genotype/variaton

tag: crispr-cas9 guides


title: Control1

description: No bacteria rep 1


title: HLM23-replicate 2


title: Th2-Mock-BS-rep1

data_processing:
The BS and PB reads were mapped to mouse genome mm9 using the BSMAP mapping tool. The mapping was done using the paired end datasets with the following parameter values: -p 4 -w 2 -v 5 -q 30 for BS-seq, and -p 4 -w 2 -v 0 -q 30 for PB-seq.
For each of the samples, the number of reads in which each cytosine within the amplicons was converted into thymine was counted.
For BS-seq, these counts were used to calculate the proportions for each cytosine to be nonmethylated/formylmethylated/carboxylmethylated (T), or methylated/hydroxymethylated (C).
For PB-seq, to compensate redundant reads derived from the opposite strand, number of reads standing for nonmethylated/methylated/hydroxymethylated (C) was multiplied by 0.5, and the proportions for each cytosine to be formylmethylated/carboxylmethylated (T) was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: methylation_ratio .txt file


title: BMDM-24h-BS-rep2

value: bone marrow derived macrophages


title: Flavo1

description: +Flavobacterium rep 1


title: PAO4

description: +P. aeruginosa rep 4

value: P. aeruginosa conditioned media for 3 hours


title: TdgWT-Th2-1st-PB-rep2


title: TdgKO-Th2-1st-BS-rep3

value: Tdg-iKO


title: HLM23-replicate 1


title: WT control-replicate 2


title: PAO3

description: +P. aeruginosa rep 3


title: A673 STAG2 KO sg4 rep1


title: A673 STAG2 WT rep3


title: A673 STAG2 WT rep2


title: PAO2

description: +P. aeruginosa rep 2


title: A673 STAG2 KO sg1 rep2


title: TdgWT-Th2-1st-BS-rep3


title: STING2d12-2prime3primecgamp-1

description: STING KO + 2'3'cGAMP rep 1


title: A673 STAG2 KO sg1 rep1


title: STING2d12_control_2

description: STING KO + vehicle control rep 2

value: water control for 3 hours


title: PAO1

description: +P. aeruginosa rep 1


title: BMDM-6h-BS-rep2


title: ATAC-seq on A673  STAG2 WT

data_processing:
Basecalls performed using HiSeq 3000 Illumina. Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequencing reads were aligned to the hg19 genome assembly using bwa v0.7.17  with the mem -M configuration.
Mapped chrM reads and  duplicate reads were removed.
Peak calling was performed using the model-based MACS v1.4.3 software with  the cut-off P ≤ 1e-05. The ENCODE  black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/)  were removed from each set of peak regions.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp).  Coverage was computed for  bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.

growth_protocol: Cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks.

extract_protocol:
Cells were harvested at a concentration of 500,000 cells/ml.
Illumina Nextera DNA Sample prep kit

value: A673 Ewing sarcoma


title: BMDM-0h-BS-rep2

value: wild type


title: Exo3-26_90

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

data_processing:
Standard Illumina base-calling (HiSeq 2500)
Adapter trimming, allignment and annotation on rnaworld (PMID: 22836126)
Genome_build: hg19
Supplementary_files_format_and_content: Excel files showing miRNA read counts and sample metadata

organism:
Homo sapiens
Mus musculus

source_name: exosomes from the medium of RAW 264.7 murine macrophages spiked into human plasma and immunopurified with anti-mouse C63 (exo-CATCHER protocol)

extract_protocol:
Total RNA extraction from serum, plasma or pulled exosomes using miRNeasy Serum/Plasma kit (Qiagen, # 217184)
In-house small RNA library preparation (as described in PMID 28335433)

tag: disease severity

tag: library preparation

value: In-house

tag: 3' adapter sequence

value: TAATATCGTATGCCGTCTTCTGCTTG


title: WT BMDC supernatants, sample 1

status: Public on May 12 2021

type: protein

city: Piscataway

first: Fumio

last: Matsumura

address: 604 Allison Rd

department: MBB

institute: Rutgers

hyb_protocol: As directed by RayBioTech protocol.

scan_protocol: As directed by RayBioTech protocol.

data_processing:
As directed by RayBioTech protocol.
normalized signal intensity using stadard curves.

label: biotin

molecule: protein

source_name: WT, experiment 1

label_protocol: As directed by RayBioTech protocol.

growth_protocol: BMDC were activated by 1ng/ml of LPS and cultured overnight in ISCOv's media containing10% FCS

extract_protocol: Supernatantw were used as they were.

treatment_protocol: Supernatants were prepared from overnight culture.

value: WT


title: WT BMDC supernatants, sample 2

source_name: WT, experiment 2


title: A673 STAG2 WT rep1

value: STAG2 wild-type


title: ATAC-seq on A673  STAG2 null

value: STAG2 null


title: KO BMDC supernatant, sample 1

source_name: KO, experiment 1

value: fascin1 KO


title: Exo3-26_78

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: STING2d12_control_1

description: STING KO + vehicle control rep 1

tag: strain

value: M. brevicollis MX1 ATCC PRA-258


title: KO BMDC supernatant, sample 2

source_name: KO, experiment 2

tag: genotype


title: E15.5 WT eyes, biological replicate 3

type: RNA

city: LOS ANGELES

first: SONIA

last: GUHA

state: CA

address: 650 Charles E Young Dr, S

department: Ophthalmology, SEI

institute: UCLA

description: Gene expression from E15.5 WT mouse Eyes

hyb_protocol: Hybridization was performed at 45°C for 16 hours in an Affymetrix Hybridization oven.The arrays were then washed and stained with Streptavidin Phycoerythrin in the Affymetrix Fluidics station (model 450)

scan_protocol: Scanning done with the Affymetrix 7G scanner.The Affymetrix GeneChip Command Console 4.0 (AGCC) was used for controlling the system and for acquisition of array images.

data_processing: Data was processed with Affymetrix MAS5 software, which includes scaling all probes to a target intensity (TGT) of 500.

label: Biotin

source_name: E15.5 WT Mouse Eyes

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 12.5μg of total RNA (Expression Analysis Technical Manual, Affymrtrix)

growth_protocol: Six pregnant females, three Oa1-/- and three WT, were sacrificed at day 15.5 days post coitum

extract_protocol: RNA was extracted using the Ambion RNA extraction kit

treatment_protocol: Eyes from six embryos from each pregnant mouse were isolated and treated as one biological sample. After enucleation, the anterior segments were dissected out and the posterior segments used for RNA extraction

tag: sample type

value: E15.5 mouse eyes


title: E15.5 Oa1-/- eyes, biological replicate 1

description: Gene expression from E15.5 Oa1-/- mouse Eyes

source_name: E15.5 Oa1-/- Mouse Eyes


title: E15.5 Oa1-/- eyes, Biological replicate 3


title: E15.5 WT eyes, biological replicate 2


title: E15.5 WT eyes, biological replicate 1


title: E15.5 Oa1-/- eyes, biological replicate 2


title: 2006664626

city: London

first: Michael

middle: R

last: Barnes

address: William Harvey Research Institute, Charterhouse Square

institute: QMUL

description: replicate 1114

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background substracted and normalised using quantile normalisation with limma's neqc function

source_name: SIX-MONTHS

label_protocol: 140ng total RNA was converted to double-stranded cDNA, followed by an amplification step (in vitro transcription) to generate labeled cRNA,using the Ambion Illumina TotalPrep-96 RNA Amplification Kit.This produces an amplified pool of biotin-labeled cRNA corresponding to the polyadenylated (mRNA) fraction.

extract_protocol: Cell subset RNA was extracted using miRNeasy minikits (Qiagen) following the manufacturer’s protocol. Whole blood RNA was extracted from Tempus Blood tubes using MagMAX RNA isolation kits (Ambion) and then was subjected to removal of globin mRNA using GLOBINclear human 20 reaction kits (Ambion) following the manufacturer’s protocol.

value: PBMCs for RNA

value: Yes

value: U/mL

value: iU/mL

value: u/mL

value: iu/mL

value: No

value: DAS28CRP Class 1

value: SDAI Class 3

value: 6 days/week

value: Oral

value: Once daily

value: Weekly

value: Intramuscular

value: White - Irish

value: Female

value: 1-2 days a month

value: Cigarrette

value: Previous Smoker

value: Completed


title: T-10215-1

description: replicate 1122

value: RNA-Tempus

value: Yes

value: EU/ml

value: IU/ml

value: Asian or Asian British - Any other Asian background


title: T-10796-1

description: replicate 1119

value: u/ml

value: iu/ml

value: No

value: DAS28CRP Class 1

value: SDAI Class 2

value: TSA normalized

value: Knee (right)

value: White- British

value: Male

value: 1-2 days a week


title: 2008483111

description: replicate 1117

value: PBMC CD8

value: 6 days/week

value: Oral

value: Weekly

value: Once daily

value: Intramuscular

value: Cigarrette

value: Previous Smoker


title: T-10577-1

description: replicate 1116

value: RNA-Tempus

value: Yes

value: U/mL

value: iU/mL

value: u/mL

value: iu/mL

value: SDAI Class 3

value: White - Irish

value: Female

value: 1-2 days a month

value: Completed


title: 2008041003

description: replicate 1123

value: PBMC CD4

value: EU/ml

value: IU/ml

value: No

value: DAS28CRP Class 1

value: Oral

value: Asian or Asian British - Any other Asian background


title: 2008040778

description: replicate 1126

value: PBMC CD8

value: Yes

value: Weekly

value: Once daily


title: 2008483194

description: replicate 1109

value: U/ml

value: IU

value: iu/ml

value: DAS28CRP Class 2

value: SDAI Class 1

value: 5 days/week

value: Knee (right)

value: Intraarticular

value: White- British

value: 3 - 4 days a week

value: Cigarrette

value: Previous Smoker


title: 2008480890

description: replicate 1118

value: PBMCs for RNA

value: u/ml

value: No

value: DAS28CRP Class 1

value: SDAI Class 2

value: 6 days/week

value: Oral

value: TSA normalized

value: Intramuscular

value: Male

value: 1-2 days a week

value: Completed


title: 2008480474

description: replicate 1121

value: PBMC CD14

value: Yes

value: iu/ml

value: Weekly

value: Once daily

value: Knee (right)


title: 2008040828

description: replicate 1125

value: PBMCs for RNA

value: EU/ml

value: IU/ml

value: SDAI Class 3

value: Asian or Asian British - Any other Asian background


title: 2008504776

description: replicate 1105

value: U/ml

value: iu/mL

value: No

value: DAS28CRP Class 2

value: SDAI Class 1

value: Oral

value: 5 days/week


title: 2006665150

description: replicate 1113

value: PBMC CD8

value: Yes

value: U/mL

value: iU/mL

value: u/mL

value: DAS28CRP Class 1

value: 6 days/week

value: Intramuscular

value: White - Irish

value: Female

value: 1-2 days a month

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2008041109

description: replicate 1124

value: PBMC CD14

value: EU/ml

value: IU/ml

value: No

value: SDAI Class 3

value: Weekly

value: Once daily

value: Asian or Asian British - Any other Asian background


title: 2008480842

description: replicate 1120

value: PBMC CD4

value: Yes

value: u/ml

value: iu/ml

value: DAS28CRP Class 1

value: SDAI Class 2

value: Oral

value: TSA normalized

value: Knee (right)

value: White- British

value: Male

value: 1-2 days a week


title: 2008482984

description: replicate 1110

value: U/ml

value: IU

value: No

value: DAS28CRP Class 2

value: SDAI Class 1

value: 5 days/week

value: Intraarticular

value: Female

value: 3 - 4 days a week

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2006664340

description: replicate 1115

value: PBMC CD4

value: Yes

value: U/mL

value: iU/mL

value: u/mL

value: iu/mL

value: DAS28CRP Class 1

value: SDAI Class 3

value: 6 days/week

value: Oral

value: Once daily

value: Weekly

value: Intramuscular

value: White - Irish

value: 1-2 days a month


title: 2006664924

description: replicate 1112

value: PBMC CD14

value: No

value: Female

value: Cigarrette

value: Previous Smoker


title: 2008507133

description: replicate 1103

value: PBMC CD4

value: Yes

value: U/ml

value: DAS28CRP Class 2

value: SDAI Class 1

value: 5 days/week


title: 2008483064

description: replicate 1107

value: IU

value: iu/ml

value: Oral

value: Knee (right)

value: Intraarticular

value: White- British

value: 3 - 4 days a week

value: Completed


title: 2008507259

description: replicate 1106

value: PBMC CD14

value: iu/mL

value: No

value: Weekly

value: Once daily


title: 2008504880

description: replicate 1102

value: PBMC CD8

value: Yes

value: U/ml


title: T-10391-1

description: replicate 1104

value: RNA-Tempus

value: DAS28CRP Class 2

value: SDAI Class 1

value: 5 days/week


title: 2008483200

description: replicate 1111

value: PBMCs for RNA

value: IU

value: iu/ml

value: Oral

value: Knee (right)

value: Female

value: Cigarrette

value: Previous Smoker


title: 2006670518

description: replicate 1101

value: PBMC CD4

value: IU/ml

value: No

value: DAS28CRP Class 3

value: SDAI Class 2

value: Twice daily

value: Weekly

value: Asian or Asian British - Any other Asian background


title: 2006670623

description: replicate 1100

value: PBMC CD8

value: Yes

value: U/ml


title: T-10807-1

description: replicate 1108

value: RNA-Tempus

value: IU

value: iu/ml

value: DAS28CRP Class 2

value: SDAI Class 1

value: 5 days/week

value: Intraarticular

value: White- British

value: 3 - 4 days a week

value: Completed


title: 2006670798

description: replicate 1098

value: PBMCs for RNA

value: IU/ml

value: No

value: DAS28CRP Class 3

value: SDAI Class 2

value: Oral


title: 2006670443

description: replicate 1099

value: PBMC CD14

value: Yes

value: U/ml

value: Twice daily

value: Weekly

value: Asian or Asian British - Any other Asian background


title: 2008045210

description: replicate 1090

value: DAS28CRP Class 1

value: 6 days/week

value: TSA normalized

value: Soft tissue

value: Female

value: Cigarrette

value: Previous Smoker


title: T-10739-1

description: replicate 1091

value: RNA-Tempus

value: No

value: White- British

value: Completed


title: 2008040680

description: replicate 1094

value: PBMC CD8

value: U/ML

value: IU/ML

value: DAS28CRP Class 2

value: SDAI Class 1

value: Oral

value: 5 days/week


title: T-10330-1

description: replicate 1092

value: Yes

value: Weekly


title: 2008045271

description: replicate 1089

value: PBMC CD4

value: U/ml

value: DAS28CRP Class 1

value: SDAI Class 2

value: 6 days/week

value: TSA normalized

value: Soft tissue


title: 2008047580

description: replicate 1088

value: PBMC CD14

value: No

value: White- British

value: Female

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2008043481

description: replicate 1096

value: PBMCs for RNA

value: U/ML

value: IU/ML

value: DAS28CRP Class 2

value: SDAI Class 1

value: Oral

value: 5 days/week


title: T-10136-1

description: replicate 1085

value: RNA-Tempus

value: Yes

value: u/ml

value: DAS28CRP Class 3

value: SDAI Class 2

value: Weekly

value: Twice daily

value: Once daily


title: 2008045269

description: replicate 1087

value: PBMC CD8

value: U/ml

value: No

value: DAS28CRP Class 1

value: 6 days/week

value: TSA normalized

value: Soft tissue

value: White- British

value: Female

value: Cigarrette

value: Previous Smoker


title: 2007018815

description: replicate 1086

value: PBMC CD4

value: Yes

value: u/ml

value: Oral


title: 2007096286

description: replicate 1082

value: PBMCs for RNA

value: IU/ml

value: DAS28CRP Class 2

value: SDAI Class 3

value: Twice daily

value: Alternate days


title: 2008040864

description: replicate 1093

value: PBMC CD14

value: U/ML

value: IU/ML

value: No

value: SDAI Class 1

value: Weekly

value: 5 days/week


title: 2007018315

description: replicate 1084

value: DAS28CRP Class 3

value: SDAI Class 2

value: Once daily


title: T-10175-1

description: replicate 1079

value: RNA-Tempus

value: Yes

value: U/ml

value: Oral


title: 2007096356

description: replicate 1080

value: IU/ml

value: DAS28CRP Class 2

value: SDAI Class 3


title: 2007098676

description: replicate 1081

value: PBMC CD8

value: Twice daily

value: Alternate days


title: 2007098943

description: replicate 1078

value: PBMC CD4

value: No


title: T-10800-1

description: replicate 1077

value: U/ML

value: IU/ML

value: Weekly

value: TSA normalized

value: Intramuscular

value: White- British

value: Male

value: 3 - 4 days a week

value: more than 20

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2008483135

description: replicate 1076

value: PBMC CD8

value: Yes

value: U/ml

value: DAS28CRP Class 3

value: SDAI Class 2

value: Oral

value: 5 days/week


title: 2008043199

description: replicate 1095

value: PBMC CD4

value: U/ML

value: IU/ML

value: No

value: DAS28CRP Class 2

value: SDAI Class 1

value: Weekly


title: 2007075913

description: replicate 1071

value: PBMCs for RNA

value: IU/ml

value: DAS28CRP Class 1

value: Twice daily

value: Once daily

value: TSA normalized

value: Intramuscular

value: Ankle (left)

value: Intraarticular

value: Ankle (right)

value: White - any other White background

value: Male

value: Cigarrette

value: Current Smoker

value: Withdrawn -lost to follow up


title: 2007075001

description: replicate 1070

value: PBMC CD14

value: Yes

value: U/ml

value: No

value: SDAI Class 2

value: Oral


title: T-10128-2

description: replicate 1073

value: RNA-Tempus

value: IU/ml

value: DAS28CRP Class 1

value: Weekly

value: Twice daily

value: Once daily


title: T-10265-1

description: replicate 1097

value: DAS28CRP Class 3

value: Asian or Asian British - Any other Asian background


title: 2008480629

description: replicate 1074

value: PBMC CD4

value: U/ML

value: IU/ML

value: 5 days/week

value: TSA normalized

value: Intramuscular

value: White- British

value: Male

value: 3 - 4 days a week

value: more than 20

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2008483238

description: replicate 1075

value: PBMC CD14

value: Yes

value: U/ml

value: No

value: SDAI Class 2

value: Weekly

value: Oral


title: 2007076908

description: replicate 1072

value: PBMC CD8

value: IU/ml

value: DAS28CRP Class 1

value: Twice daily

value: Once daily

value: Ankle (left)

value: Intraarticular

value: Ankle (right)

value: White - any other White background

value: Current Smoker

value: Withdrawn -lost to follow up


title: 2007018801

description: replicate 1083

value: Yes

value: u/ml

value: DAS28CRP Class 3


title: T-10575-1

description: replicate 1067

value: RNA-Tempus

value: No

value: U/mL

value: iu/mL

value: iu/ml

value: SDAI Class 2

value: 6 days/week

value: TSA normalized

value: Intramuscular

value: White- British

value: Male

value: 3 - 4 days a week


title: 2006664268

description: replicate 1065

value: PBMCs for RNA

value: Oral

value: Weekly

value: Twice daily


title: 2006664828

description: replicate 1066

value: PBMC CD4

value: Yes

value: DAS28CRP Class 3


title: 2007075039

description: replicate 1069

value: U/ml

value: IU/ml

value: No

value: DAS28CRP Class 1

value: Once daily

value: Ankle (left)

value: Intraarticular

value: Ankle (right)

value: White - any other White background

value: Cigarrette

value: Current Smoker

value: Withdrawn -lost to follow up


title: 2006663594

description: replicate 1052

value: U/mL

value: iu/mL

value: SDAI Class 2

value: 6 days/week

value: Oral

value: Weekly

value: Wrist (right)

value: White- British

value: Female

value: 1-2 days a week

value: Never Smoked

value: Completed


title: 2007096488

description: replicate 1061

value: PBMC CD14

value: No

value: iu/ml

value: Yes

value: DAS28CRP Class 3


title: 2008040923

description: replicate 1058

value: PBMCs for RNA

value: U/ML

value: IU/ML

value: DAS28CRP Class 1

value: SDAI Class 3

value: 5 days/week


title: 2008041066

description: replicate 1057

value: PBMC CD8

value: Weekly

value: Oral


title: 2006665071

description: replicate 1068

value: U/mL

value: iu/mL

value: SDAI Class 2

value: 6 days/week

value: Twice daily

value: TSA normalized

value: Intramuscular

value: White- British

value: Male

value: 3 - 4 days a week


title: 2008043099

description: replicate 1055

value: PBMC CD4

value: Yes

value: U/ML

value: IU/ML

value: No


title: T-10243-1

description: replicate 1059

value: RNA-Tempus

value: iu/ml

value: DAS28CRP Class 3

value: Weekly


title: 2008470222

description: replicate 1048

value: PBMCs for RNA

value: u/ml

value: DAS28CRP Class 2

value: SDAI Class 1

value: Oral

value: Female

value: Cigarrette

value: Previous Smoker

value: Completed


title: 2008472609

description: replicate 1047

value: PBMC CD4

value: Yes

value: TSA normalized

value: White- British

value: 3 - 4 days a week


title: 2007096486

description: replicate 1060

value: No

value: iu/ml

value: iu/mL

value: SDAI Class 2


title: T-10681-1

description: replicate 1053

value: RNA-Tempus

value: U/mL

value: DAS28CRP Class 3

value: 6 days/week

value: Weekly

value: Wrist (right)

value: Intraarticular

value: 1-2 days a week

value: Never Smoked


title: 2006665205

description: replicate 1064

value: PBMC CD8

value: Yes

value: Oral

value: Twice daily

value: Intramuscular

value: Male


title: 2007096546

description: replicate 1062

value: No

value: iu/ml

value: iu/mL