title: MD11913

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 12

tag: peer 13

tag: peer 14


title: MD18776

status: Public on Apr 29 2021

type: RNA

city: Edinburgh

first: Peter

middle: G

last: Vaughan-Shaw

address: Crewe Road

department: IGMM

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol  Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Perform normexp background correction using negative control probes and quantile normalization using negative and positive control probes. Limma bioconductor package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal mucosa

label_protocol: For HT12 analysis, total RNA was converted to double-stranded cDNA, followed by in vitro transcription amplification to generate labelled cRNA (Illumina TotalPrep™ RNA Amplification Kit).  Gene expression profiling was undertaken using the HumanHT-12 v4.0 Expression BeadChip Arrays (Illumina) and IScan NO660 scanner, providing coverage of 47,231 transcripts and >31,000 annotated genes derived from the National Centre for Biotechnology Information Reference Sequence RefSeq Release 38 (November 7, 2009).

extract_protocol: RNA was extracted from mucosa and blood PBMC using a proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to the manufacturer’s protocol. This process initially involved homogenising the sample in 1 mL TRIzol. The homogenates were then incubated for 5 minutes at room temperature to enable the nucleoprotein complexes to completely dissociate. 200 μl of chloroform was added and the tubes vortexed at 2800 rpm for 15 seconds. After 5 minutes’ incubation at room temperature, the homogenate was centrifuged at 12,000 x g for 10 min at 4°C. This separated the homogenate into a lower, red, organic phase (phenol-BCP phase); an interphase; and a colourless, upper, aqueous phase. 400 μl of the aqueous phase was withdrawn to which 200 μl of ethanol was added. The mixture was vortexed at maximum speed for 5 seconds and added to a filter cartridge-collection tube. This was centrifuged at 12,000 x g for 30 seconds at room temperature and the flow-through discarded. Two wash cycles using 500 μl of provided wash solution were undertaken, with a final spin of 12,000 x g for 30 seconds to ensure all wash solution had left the filter. Finally, 50 μl of provided elution buffer was added to the filter cartridge within a new collection tube and spun at 12,000 x g for 30 seconds to elute the RNA. RNA purity (A260/A280 and A260/A230) and concentration was assessed by the Nanodrop 800 spectrophotometer. The RNA yield and integrity of samples to be submitted for microarray expression analysis was assessed using the 2100 Bioanalyzer®.  cDNA synthesis of RNA samples was performed prior to qRT-PCR. RNA was first treated with DNase. 1µg RNA was treated with 1µl (1 unit) DNase 1 (commercial RQ1 RNase-free DNase in 10mM HEPES (pH 7.5), 50% glycerol (v/v), 10mM CaCl2 and 10mM MgCl2; Promega), with 1µl of 10x RQ1 reaction buffer (400mM Tris-HCl (pH 8.0), 100mM MgSO4 and 10mM CaCl2; Promega) and RNase-free DNase-free water (Gibco) to make a 10µl reaction. Following incubation at 37°C for 30 minutes, 1µl DNase STOP (20mM EGTA, pH 8.0, Promega) was added and incubation at 65°C for 10 minutes performed to inactivate the DNase.  DNase treated RNA samples were then reversed transcribed to cDNA. Samples were added to a solution containing 1µl (200 units) Moloney Murine Leukemia Virus Reverse Transcriptase (in 20mM Tris-HCl (pH 7.5), 200mM NaCl, 0.1mM EDTA, 1mM DTT, 0.01% Nonidet® P-40 and 50% glycerol; Promega), 4µl M-M:VRT buffer (50mM Tris-HCl (pH 8.3 at 25°C; Promega), 75mM KCl, 3mM MgCl2 and 10mM DTT; Promega), 2µl dNTP (10mM, containing dATP, dCTP, dGTP and dTTP; Promega), 1µl (20 units) Recombinant RNasin Ribonuclease Inhibitor (in 20mM HEPES-KOH (pH 7.6), 50mM KCl, 8mM DTT, 50% (v/v) glycerol; Promega), 2µl of 0.25µg/µl random primers (Promega) and 1µl RNase-free DNase-free water. This was incubated at 37°C for 30 minutes and 95°C for 5 minutes.

treatment_protocol: Human subjects were sampled at baseline. No interventions were investigated in this study

value: Normal mucosa

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site

value: LEFT

tag: label - sentrix barcode

tag: label - section

value: A

tag: batchnumber


title: STA-ET-7.3

type: SRA

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

library_source: transcriptomic

data_processing:
Reads were trimmed with Atropos.
Mapping and gene quantification were performed with STAR version 2.5.3 against human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab: Tab-delimited files with raw counts for each genes.

molecule: polyA RNA

source_name: Ewing sarcoma cell line

growth_protocol: Cells were grown as previously described (Kovar et al., 1997, Dauphinot et  al., 2001) and recommended by ATCC, DSMZ, or COG Repository.

extract_protocol:
RNA was extracted using RNeasy plus mini kit (74134, Qiagen).
RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library.

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

tag: genotype

value: STAG2 mut


title: MD11559

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 12

tag: peer 13

tag: peer 14

value: D


title: STA-ET-7.1


title: STA-ET-2.2

value: STAG2 WT


title: MD11038

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 10

tag: peer 11

tag: peer 15

tag: label - sampling site

value: J


title: MIC

tag: cell line

value: MIC

tag: cell type

tag: genotype


title: COH

value: COH


title: CHLA258


title: BOU

value: BOU


title: A673


title: TC-71


title: MD18777

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: label - sentrix barcode

tag: label - section

value: E

tag: batchnumber


title: D2IL2

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
First three bases of sequenced reads were trimmed according to the library protocol and low quality sequences were removed. Rest of the reads were aligned to hg19 by using Bowtie2 (ver.2.2.9) in a default setting.
Uniquely mapped reads were selected and the duplicated reads were discarded by using Picard Tools (ver.2.1.1)
Peaks were called using SICER (ver.1.1.1) with the threshold of FDR less than 0.000000001.
Genome_build: hg19
Supplementary_files_format_and_content: bed (chromosome name, the starting position, the ending position, control read count, normalized control read count, case read count, normalized case read count, fold change case vs control, pvalue case vs control, FDR case vs control, fold change control vs case, pvalue control vs case, FDR case vs control)
case is TGM condition, control is TGF condition

molecule: genomic DNA

source_name: regulatory T cells

growth_protocol: Naïve CD4+ T cells were expanded with L-cells (as described above) for 22 days with either TGF-β, or Hp-TGM

extract_protocol:
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody.
Libraries were prepared by using DNA SMART ChIP-Seq kit (Clontech) according to the protocol. 150-400bp products were selected and subjected to the analysis.

tag: individual

tag: treatment

tag: chip antibody

value: H3K27Ac (ab4729, abcam)

value: CD4 T cell


title: MD18775

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: I


title: MD18769

tag: tissue

tag: age

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: D2TGM

tag: individual

tag: treatment

value: TGM

tag: chip antibody

tag: cell type


title: MD18773

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

value: G


title: MD18771

tag: tissue

value: Normal mucosa

tag: age

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

value: L


title: MD18765

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

value: LEFT

tag: batchnumber


title: MD18768

tag: tissue

tag: age

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: peer 14

value: K


title: MD18774

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 15

tag: label - sampling site

value: A


title: MD18763

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: label - sentrix barcode

tag: label - section


title: MD18760

tag: tissue

tag: age

tag: peer 6

tag: peer 10

tag: peer 11

tag: peer 12

value: B

tag: batchnumber


title: MD18764

tag: gender

tag: peer 2

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 13

tag: peer 14


title: D2TGMinput

description: control

tag: individual

tag: treatment

tag: chip antibody

value: none (input)

tag: cell type


title: D2TGF

value: TGF


title: D2IL2input

description: control


title: D1TGF


title: D1TGM


title: D2TGFinput

description: control


title: D1TGFinput

description: control


title: D1IL2


title: D1TGMinput

description: control


title: D1IL2input

description: control


title: MD18752

tag: tissue

tag: age

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

tag: label - section

value: D


title: MD18762

tag: gender

tag: peer 2

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: batchnumber


title: RNA_human_HD_IL2IL15_9

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

country: USA

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by salmon (v0.10.2) using arguments '-l IU --gcBias' and tximport (v1.8.0 or v1.10.1) using the UCSC mm10 known gene transcript assembly (v9).
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.10.2) and imported by tximport (v1.8.0 or v1.10.1). Also provided are gene IDs (Entrez and Ensembl), gene names, gene descriptions, and chromosome (for human).

source_name: peripheral blood NK cells

extract_protocol:
RNA was isolated from sorted and stimulated cell populations using TRIzol (Invitrogen) or the PicoPure RNA Isolation Kit (Thermo Fisher)
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.705-2ng total RNA with RNA integrity numbers ranging from 6.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or HiSeq 2500 in Rapid mode in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit or HiSeq Rapid SBS Kit v2, respectively (Illumina).  An average of 37 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 42% to 70%.

treatment_protocol: Mouse NK cells were stimulated for 3 hr with combinations of 20 ng/mL recombinant mouse IL-2,  20 ng/ml recombinant mouse IL-15, 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, and/or 100 IU recombinant mouse IFN-α. Human NK cells were stimulated with 100 U/ml recombinant human IL-2, 50 ng/ml recombinant human IL-15, 20 ng/ml recombinant human IL-12, 50 ng/ml recombinant human IL-18 and/or 1000 U/ml recombinant human IFN-α.

tag: genotype

value: HD (healthy donor)

tag: cell type

value: ex-vivo NK cells

tag: condition

tag: replicate


title: MD18759

tag: tissue

tag: age

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: RNA_human_HD_IL2IL15_8


title: RNA_human_HD_IL2IL15_7


title: RNA_human_HD_IL2IL15_5


title: MD18680

tag: gender

tag: peer 2

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12

tag: peer 13

tag: label - section


title: MD18678

tag: tissue

tag: age

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 3

tag: peer 4

tag: batchnumber


title: MD18757

tag: gender

tag: peer 2

tag: peer 5

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode

value: F


title: MD18679

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 12


title: RNA_human_HD_IL2IL15_6

tag: genotype

tag: cell type

tag: condition

tag: replicate


title: MD18756

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 13

tag: label - section

tag: batchnumber


title: RNA_human_HD_IL2IL15_4


title: MD18675

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: MD18751

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 2

tag: peer 12


title: MD18677

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 13

tag: label - section

value: E

tag: batchnumber


title: MD18670

tag: peer 7

tag: peer 8

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 14

tag: peer 15


title: MD18671

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: label - sampling site

tag: label - sentrix barcode

value: C


title: RNA_human_HD_IL12IL18_7

tag: genotype

tag: cell type

tag: condition

tag: replicate


title: RNA_human_HD_IL12IL18_6


title: RNA_human_HD_IL12IL18_9


title: MD18665

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 8

tag: peer 12

tag: peer 13

tag: label - section

value: J

tag: batchnumber


title: RNA_human_HD_IL12IL18_8


title: MD18668

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 14

tag: peer 15

tag: label - sampling site


title: MD18645

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 7

tag: label - sentrix barcode

value: H


title: MD18650

tag: tissue

tag: age

tag: peer 8

tag: peer 12

tag: peer 13

tag: label - section

tag: batchnumber


title: MD18667

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 1

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 14


title: MD18647

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 15

tag: label - sampling site


title: RNA_human_HD_IL12IL18_5

tag: genotype

tag: cell type

tag: condition

tag: replicate


title: RNA_human_HD_IL12IL18_4


title: RNA_human_HD_IFNA_9

value: IFNA


title: RNA_human_HD_IFNA_8


title: RNA_human_HD_IFNA_6


title: RNA_human_HD_IFNA_7


title: RNA_human_HD_IFNA_5


title: MD18638

tag: tissue

value: Normal mucosa

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 7

tag: peer 8

tag: peer 12

tag: peer 13

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: RNA_human_HD_UNSTIM_7

value: UNSTIM


title: MD18636

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11

tag: peer 14

tag: peer 15

value: LEFT

value: L


title: MD18635

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 7

tag: peer 8

tag: label - sampling site


title: MD18644

tag: peer 1

tag: peer 2

tag: peer 12

tag: peer 13

tag: label - sentrix barcode

tag: label - section

tag: batchnumber


title: MD18631

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 9

tag: peer 10

tag: peer 11


title: MD18637

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 7

tag: peer 14

tag: peer 15


title: MD18377

tag: peer 1

tag: peer 2

tag: peer 8

tag: peer 12

tag: peer 13

tag: label - sampling site

tag: label - sentrix barcode

value: K


title: MD18379

tag: peer 3

tag: peer 4

tag: peer 5

tag: peer 6

tag: peer 9

tag: label - section

tag: batchnumber


title: MD18380

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 7

tag: peer 10

tag: peer 11

value: B


title: RNA_human_HD_IFNA_4

tag: genotype

tag: cell type

tag: condition

tag: replicate


title: RNA_human_HD_UNSTIM_8


title: MD18374

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

tag: label - sentrix barcode


title: RNA_human_HD_UNSTIM_9


title: B250C23: TC71_WT_CTCF_rep2

data_processing:
Library strategy: HiChIP
All the processing steps were performed with HiC-Pro 2.10.1 pipeline.
Reads were mapped against human genome (GRCh37/hg19 version) with bowtie2.
Default HiC-Pro settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions and generate raw interaction matrices (5kb bins).
Genome_build: hg19
Supplementary_files_format_and_content: Raw interaction matrix (for each 5kb bin, count of valid pairs)

source_name: Ewing sarcoma cell line (TC71)

growth_protocol: A673 and TC71 isogenic models were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum.

extract_protocol:
Several adaptations were made and are detailed below in an overview of the otherwise original protocol described by Mumbach and colleagues (PMID: 27643841). Cells were plated 2 days before starting the experiment to reach a 90-95% confluence at the time of fixation (1% of methanol-free formaldehyde (28908, Thermo-Scientific) in freshly prepared respective cell culture media, 20ml/T150 flask). Cells were fixed at room temperature for 10 min under gentle shaking platform (50mvt/min). 2 mL of glycine solution (2M) were added and cells were incubated for 5 additional min at room temperature under gentle shaking platform. The supernatant was removed and cells were washed 3 times with PBS at room temperature. Cells were scraped vigorously with ice cold PBS supplemented with protease inhibitor cocktail tablets (11836145001, Roche), and flushed five time through a syringe with a 21 gauge needle (301155, BD Microlance). In situ contact libraries were performed starting from 15 million nuclei digested overnight at 37°C with Mbo1 (R0147M, New England Biolabs). After proximity ligation (4 h at room temperature), the nuclear pellet was sonicated and the chromatin immunoprecipitation step was performed using the iDeal ChIP-seq kit for transcription factors (Diagenode) according to the supplier's recommendation with some modification. Nuclei were resuspended in IL1b and IL2 buffer following Diagenode protocol and all centrifugations were performed at 4°C for 5 min at 1,950 RCF for these steps. The chromatin was sonicated (5 million nuclei per tube) with Bioruptor pico (Diagenode) for 10 cycles (30-sec on, 30-sec off) set at position “high”. The tubes were pooled and the chromatin was clarified by centrifugation at 4°C for 10 min at 16,000 RCF. Sonicated chromatin from 11 and 3 million nuclei were used respectively for CTCF and H3K27ac immunoprecipitation step using the equivalent of 3 ChIP reactions pooled in one tube for each HiChIP reaction (final volume was 1050 µl/tube). Immunoprecipitation was then carried out following Diagenode kit instructions by multiplying all reagents by a factor 3 until end of elution step (50µl). Biotin capture was performed following Mumbach et al. protocol (PMID: 27643841).
Library for Illumina sequencing were prepared using 10 ng of chromatin and 0.5 µL of TN5 (15028211, Illumina). A first PCR in a final volume of 50µl with 5 cycles was performed (72 °C for 5 min, 98 °C for 1 min, then 5 cycles at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min). To determine how many additional PCR cycles were required for optimal library preparation, a QPCR with: 5µL of the first PCR product, 1 μL of Nextera Ad1_noMX and Nextera Ad2.X (each at 1.25 μM), 5 µl of phusion HF 2X (M0531S, New England Biolabs), 0,75 µL Evagreen® 20X (31000, Biotium) and 2,25 µL of water was runned (same program as first PCR but with 30 cycles). The optimal number of additional cycle was determined for each library by setting a threshold just before reaching the end of exponential amplification step. The 45µl left from the first PCR were further amplified using additional PCR cycles as determined above. Size selection was performed using Ampure XP beads (A63881, Beckman Coulter) to capture fragments greater than 300 bp. Libraries were quantified and analyzed using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and LabChIP (Perkin Elmer). A first validation of HiChIP experiments was performed using 150 bp paired-end sequencing on MiSeq-microV2-300-PE150 (Illumina). Deep 75 bp paired-end sequencing was then performed on HiSeq 2500 or NovaSeq 6000 systems (Illumina).

tag: tissue

value: Ewing sarcoma cell line (TC71)

value: WT

tag: antibody

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: RNA_human_HD_UNSTIM_6

tag: genotype

value: HD (healthy donor)


title: RNA_human_HD_UNSTIM_5

tag: cell type

value: ex-vivo NK cells


title: MD18643

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 5

tag: peer 6

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: B250C12: TC71_WT_H3K27ac_rep1

value: H3K27ac (ab4729, Abcam)


title: MD18376

tag: peer 1

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14

tag: peer 15

tag: label - sampling site

value: I


title: MD18267

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 5

tag: peer 6

tag: label - sentrix barcode

value: C


title: MD18276

tag: peer 1

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - section

tag: batchnumber


title: MD18373

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 8

tag: peer 12

tag: peer 13

tag: peer 14

value: J


title: MD18360

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 5

tag: peer 15

tag: label - sampling site


title: MD18372

tag: peer 1

tag: peer 6

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 11

tag: label - sentrix barcode


title: MD18277

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 8

tag: peer 12

tag: label - section

value: E

tag: batchnumber


title: MD18278

tag: tissue

tag: age

tag: gender

tag: colorectal cancer status (1=crc, 0=no crc)

tag: peer 5

tag: peer 13

tag: peer 14

value: G


title: MD12043

value: Normal mucosa

tag: peer 1

tag: peer 6

tag: peer 7

tag: peer 9

tag: peer 10

tag: peer 15

tag: label - sampling site

value: RIGHT

value: H


title: B250C26: TC71_SA2m#2_H3K27ac_rep2

tag: genotype

value: SA2 KO

tag: antibody


title: B250C11: TC71_WT_CTCF_rep1


title: B250C14: TC71_SA2m#2_H3K27ac_rep1


title: B250C19: A673_WT_CTCF_rep4

source_name: Ewing sarcoma cell line (A673)

value: Ewing sarcoma cell line (A673)


title: B250C13: TC71_SA2m#2_CTCF_rep1


title: B250C25: TC71_SA2m#2_CTCF_rep2


title: B250C16: A673_WT_H3K27ac_rep2


title: B250C20: A673_WT_H3K27ac_rep3


title: 36_PNL

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Hybridization of the microarray was performed by Service XS (Leiden, The Netherlands). Myometrial samples were randomized over 3 arrays.

scan_protocol: Arrays were scanned.

data_processing: Data analysis was performed using Bioconductor packages (version 3.4) using the statistical software package R (version 3.3.2). The quality control was performed using arrayQualityMetrics Bioconductor package. Normalization was performed on samples starting from the Illumina sample and control probe profiles by a normexp-by-control background correction, quantile normalization, and log2 transformation (limma package). Differential expression between the experimental conditions Preterm labor vs. no labor, was assessed with a moderated t test using the linear model framework (limma package). Resulting P values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Corrected P values ≤0.05 were considered statistically significant. Probes were reannotated using the Bioconductor IlluminaHumanv4.db package.

source_name: Myometrium

label_protocol: cDNA synthesis was performed using the Roche First Strand cDNA Synthesis Kit for RT-PCR (AMV) with 200ng as total RNA input, primed using random primers according to manufacturer's instructions. Labelling of total RNA was performed using the Illumina total prep RNA amplification kit (AMIL1791) with an input of 200ng/μl. The integrity of the RNA was checked using the Agilent Bioanalyser. Samples with a RIN score of 7 or above were used for the microarray experiments. 1ug of labelled total RNA of the samples was used for array hybridization.

extract_protocol: Myometrial tissue from women delivering by cesarean section who gave informed consent to donate a 4 mm by 6 cm stroke of myometrium tissue from the incision site were used for the study. The myometrial tissue was harvested in RNA later at the time of cesarean section and processed according to the manufacturer's instructions. Pregnancies with any kind of infection were excluded. Some of the preterm samples were from pregnancies complicated by preeclampsia and/or HELLP syndrome. Myometrial tissue samples were initially homogenized in a Magna lyser containing 1ml of Trizol reagent. Total RNA from human myometrial tissue was isolated using Trizol reagent (Thermo Fischer Scientific) according to the manufacturer's instructions. Isolated total RNA was cleaned up using RNeasy mini kit (Qiagen).

value: Myometrium

tag: gestational age

tag: group

value: PNL


title: 88_PNL

tag: tissue


title: MD18375

tag: age

tag: gender

tag: peer 2

tag: peer 3

tag: peer 4

tag: peer 8

tag: peer 11

tag: peer 12

value: LEFT

tag: label - sentrix barcode

tag: label - section

value: L

tag: batchnumber


title: 119_PSL

value: PSL


title: A626-A627-A628C2: A673_WT_CTCF_rep1

value: WT

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: 50_PNL


title: B250C15: A673_WT_CTCF_rep3


title: 62_PSL


title: 156_PSL


title: 46_PSL


title: A690C2: A673_WT_CTCF_rep2


title: A626-A627-A628C4: A673_WT_H3K27ac_rep1

value: H3K27ac (ab4729, Abcam)


title: B250C18: A673_SA2m#1_H3K27ac_rep2


title: A626-A627-A628C7: A673_SA2m#1_H3K27ac_rep1


title: B250C21: A673_SA2m#1_CTCF_rep4


title: TC71_WT_STAG2

data_processing:
Reads were mapped with bowtie2 against human genome (hg19)
Peaks were called with MACS2 2.1.1 with the option narrow for FLI1, CTCF and cohesin members ChIP-seq and broad for histone marks. For each cell line, ChIP-seq were normalized according to their respective input DNA sample.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before performing the ChIP experiments, cells were seeded in T150 flask at a concentration allowing to reach a cellular confluence of approximately 90% at the time of fixation of the cells with formaldehyde.

extract_protocol:
ChiP were performed following manufacturer instructions using iDeal ChIP-seq kit for transcription factors and for histones (Diagenode). For this, Ewing cell lines were fixed for 10 minutes with 1% of methanol-free formaldehyde (28908, Thermo-Scientific). Chromatin was sonicated (Bioruptor, Diagenode) for 20 cycles (30-sec on, 30-sec off) set at position “high” to generate DNA fragments with an average size around 150-300pb.
The library were constructed using TruSeq ChIP library preparation kit (Illumina) according to manufacturer recommendations

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

value: STAG2 (ab4463, Abcam)


title: A626-A627-A628C5: A673_SA2m#1_CTCF_rep1

tag: genotype

tag: antibody


title: B250C17: A673_SA2m#1_CTCF_rep3


title: A690C5: A673_SA2m#1_CTCF_rep2


title: 42_PNL

tag: gestational age

tag: group


title: TC71_WT_RAD21

value: RAD21 (ab992, Abcam)


title: 136_PNL

tag: tissue


title: 170_PSL


title: 34_PSL


title: 55_PNL


title: B250C22: A673_SA2m#1_H3K27ac_rep3


title: RR634_mett10-KO_NA22 plates_m6A IP

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Comparison of mouse and worm m6A distribution:  The reads were sorted into individual libraries based on the barcodes and clipped using cutadapt (parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards). The clipped reads were aligned to the mouse (GRCm38 – Ensembl release 95) or worm (WBcel235 – Ensembl release 95) genome using STAR (parameters: --outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). The m6A peak calling was done separately for reads mapped to mouse or worm genome using MACS2 (macs2 callpeak -f BAM  -q 0.01  --nomodel --extsize 50 --call-summits). Consensus peaks from the biological replicates were identified using MSPC (parameters: -r bio -w 1e-4 -s 1e-8).
Comparison of m6A distribution between mett-10 KO and mett-10 WT worms:   The reads were sorted into individual libraries based on the barcodes and clipped using cutadapt (parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards). The clipped reads were aligned to worm transcripts (WBcel235 – Ensembl release 95) using bowtie (parameters: -v 0 -a -k 10 --allow-contain). The read counts were divided by number of transcripts they mapped to and the counts were summarized to gene levels. To find the genes whose transcripts lose m6A methylation in the absence of Mett-10 we looked for genes with significant (padj <=0.1) decrease of m6A-IP/input ratio in Mett-10 KO using DESeq2 likelihood ratio test (LRT) where we compared the full model (~input_or_m6A_IP + genotype + input_or_m6A_IP:genotype) to the reduced model (~input_or_m6A_IP + genotype).  To analyze the effect on m6A distribution, we aligned the reads to the genome (WBcel235 – Ensembl release 95) using STAR (parametres: --outFilterType BySJout –limitBAMsortRAM = 40000000000 --outSAMattributes All) and obtained the coverages along the genomic loci.
Genome_build: mouse (GRCm38 – Ensembl release 95) or worm (WBcel235 – Ensembl release 95)
Supplementary_files_format_and_content: The bigWig files contain the genomic coverages for individual samples separately for + and - DNA strand.  The DESeq2 csv files contain the gene statistics for m6A-IP/input comparisons between the mett-10 KO and WT.  The xlsx file contains the list of identified m6A peaks together with their annotation.

organism: Caenorhabditis elegans

source_name: adult worm

growth_protocol: To be able to compare the m6A levels between the species, the total or poly(A)+ RNA was isolated from the adult worm, mouse testis (P30) and bombyx cell line (BmN4-SID1), mixed in equal amounts and used for m6A IP-Seq.  To identify the transcripts whose m6A methylation is performed by METT-10, we compared the m6A levels in the Mett-10 WT and Mett-10 KO worms by m6A-IP followed by RNA-Seq. The mett-10 knockout strain, VC1743 was obtained from the CGC. All of the C. elegans experiments and worm maintenance was carried at 20°C.    To identify the effect of the diet, the worms were fed on one of the two E. coli bacteria strains, OP50 or NA22, grown on standard (OP50) or peptone-rich (NA22) plates.

extract_protocol:
Comparison of mouse and worm m6A distribution: PolyA+ transcripts were purified from 75 µg of total RNA using the Dynabeads mRNA purification kit (Life Technologies; cat. no 61006). An equal amount (in µg) of total or polyA+ RNA from adult mouse testes and Bombyx mori BmN4-SID1 insect cell line were mixed together with worm polyA+ or total RNA prior to subsequent processing. In this mixed sample, the mouse RNA serves as an internal control for efficient m6A immunoprecipitation via the unambiguous detection of m6A peaks that are already reported. Fragmentation for total or Poly(A)+ RNA mixture from mouse, worm and BmN4-SID1 was performed as described (Wojtas, M. N. et al.,Mol. Cell 68, 374–387 (2017). For total RNA fragmentation; 5µg of total RNA from mouse testis, adult worms and BmN4-SID1 cells each were used. For polyA+ RNA fragmentation, 2µg of poly(A)+ selected RNA from mouse testis, adult worms and BmN4-SID1 cells each was fragmented. Denaturing urea-PAGE confirmed that the majority of the RNA fragments were in size range of 20-80 nucleotides. A small portion (10%) of fragmented RNA was kept aside to be used as the input sample, while the remainder was subjected to immunoprecipitation. The m6A immunoprecipitation was performed as described (Wojtas, M. N. et al.,Mol. Cell 68, 374–387 (2017).
Comparison of m6A distribution between mett-10 KO and mett-10 WT worms: Total RNA was isolated from adult wildtype or Mettl16 (Mett-10) mutant worms (C. elegans), grown on different media, using the Trizol reagent (ThermoFisher Scientific; 15596026). Poly(A)+ transcripts were Comparison of m6A distribution between mett-10 KO and mett-10 WT worms: purified from 75 µg of total RNA using the Dynabeads mRNA purification kit (Life Technologies; cat. no 61006). Poly(A)+ RNAs (2.50 µg) fragmentation and m6A-IP were carried out as described before (Wojtas, M. N. et al.,Mol. Cell 68, 374–387 (2017).
Strand specific RNA libraries from the input and the m6A IP RNA were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB; catalogue No. E7560L) following the manufacturer’s instructions. The libraries were resolved on 3% high-resolution MethaPhor agarose (Lonza; catalog. No. 50180) gels in 1X TAE buffer at 70 V. Fragments in the size-range of ~150-250 bp were gel-extracted with the use of MinElute Gel Extraction Kit (Qiagen; cat No. 28604). Multiple libraries with different barcodes (at 3′ end) were mixed in equimolar ratios and sequenced in EMBL Gene Core facility, Heidelberg or by iGE3 Genomics Platform, University of Geneva.

tag: purification

value: m6A IP

value: adult worm

value: METT-10 KO

tag: growth plate

value: NA22 plates


title: TC71_WT_SMC1

value: SMC1 (A300-055A, Bethyl laboratories)


title: 120_PSL


title: 92_PSL


title: EGFP_1st_round

description:
102803-001-025
Control

data_processing: Data analysis was performed using Bioconductor packages (version 3.4) using the statistical software package R (version 3.3.2). The quality control was performed using arrayQualityMetrics Bioconductor package. Normalization was performed on samples starting from the Illumina sample and control probe profiles by a normexp-by-control background correction, quantile normalization, and log2 transformation (limma package). Differential expression between the experimental conditions was assessed with a moderated t test using the linear model framework (limma package). Resulting P values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Corrected P values ≤0.05 were considered statistically significant. Probes were reannotated using the Bioconductor IlluminaHumanv4.db package.

source_name: Human myometrial cells

growth_protocol: The TERT immortalized human myometrial cell line (hTERT-HM)35 was kindly provided by J. Condon. Cells were maintained in DMEM/F-12, GlutaMAX™ Supplement (Gibco 31331) medium with 10% Fetal calf serum (FCS) (Gibco 10270), and 1% Penicillin and Streptomycin (Gibco 15140) added as additional supplements. The cells were trypsinised using 0.25% trypsin and centrifuged at 1500 rpm to harvest cells before passaging them 1 in 10 twice a week.

extract_protocol: Total RNA from cell pellets was isolated using Trizol reagent (Thermo Fischer Scientific) according to the manufacturer's instructions. Isolated total RNA was cleaned up using RNeasy mini kit (Qiagen).

treatment_protocol: The cDNA encoding the human TBX2 coding sequence (CDS) was cloned into a pLenti-CMV-BLAST-DEST (addgene: 706-1) for lentiviral transduction experiments. The lentiviral expression construct pEGFPCMV-BLAST-DEST was used as mock control. Lentiviral particles were produced by seeding 1×10^6 HEK293T cells per well in a 6-wells plate pre-coated with 0.1 mg/ml Poly-L-Lysine (Sigma-Aldrich). After 24 hours, cells were transiently transfected using X-treme GENE HP DNA Transfection Reagent (Roche) according to the manufacturer’s recommendations. On day 3 post-transfection, the lentivirus-containing culture medium was harvested and concentrated by addition of 1 volume Lenti-X Concentrator (Clontech) to 3 volumes of the cleared supernatant. The efficiency of transfection (% of transfected cells) was estimated using FACS on EGFPpLVX-puro transfected cells and supernatants from experiments which resulted in minimum of 90% of transfection efficiency were used for transduction experiments. 200.000 hTERT-HM cells were seeded on a 9,5 cm2 culture surface and transduced with 50ul of lentiviral particles diffused in medium 24 hours after seeding at 70-80% confluency. The medium was refreshed the next day and cells pellets and supernatant were harvested 3 days post transduction. Transduction efficiency was estimated by FACS on the hTERT-HM cells transduced by EGFPpLVX-puro. TBX2 overexpression was confirmed by qPCR and Western blotting.

value: hTERT-HM

value: TERT immortalised myometrial cells

tag: overexpression

value: Control


title: TBX2_3rd_round

description:
102803-001-013
TBX2


title: 104_PNL

value: Myometrium

value: PNL


title: 54_PNL


title: TC71_WT_input

value: input


title: RR635_mett10-KO_NA22 plates_m6A IP


title: TC71_WT_FLI1

value: WT

value: FLI1 (ab15289, Abcam)


title: TBX2_1st_round

description:
102803-001-022
TBX2


title: EGFP_3rd_round

description:
102803-001-010
Control


title: EGFP_4th_round

description:
102803-001-003
Control


title: RR631_mett10-WT_NA22 plates_m6A IP


title: TC71_SA2m#2_STAG1

value: SA2 KO

value: STAG1 (ab4457, Abcam)


title: TC71_WT_H3K4me3

value: Ewing sarcoma cell line

value: H3K4me3 (C15410003, Diagenode)


title: TC71_WT_H3K27ac

value: H3K27ac (ab4729, Abcam)


title: RR632_mett10-WT_NA22 plates_m6A IP

value: m6A IP

value: adult worm


title: RR633_mett10-KO_NA22 plates_m6A IP

value: METT-10 KO

value: NA22 plates


title: TC71_SA2m#2_RAD21

value: RAD21 (ab992, Abcam)


title: TC71_WT_STAG1


title: RR627_mett10-KO_NA22 plates_input


title: TC71_WT_CTCF

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: TC71_SA2m#2_H3K27ac


title: TBX2_4th_round

description:
102803-001-011
TBX2

value: hTERT-HM

value: TERT immortalised myometrial cells


title: RR625_mett10-WT_NA22 plates_input


title: RR623_mett10-WT_NA22 plates_m6A IP


title: RR630_mett10-WT_NA22 plates_m6A IP


title: TC71_SA2m#2_CTCF


title: TC71_SA2m#2_STAG2

value: STAG2 (ab4463, Abcam)


title: RR624_mett10-WT_NA22 plates_input

value: input


title: TC71_SA2m#1_SMC1

value: SMC1 (A300-055A, Bethyl laboratories)


title: RR628_mett10-KO_NA22 plates_input


title: TC71_SA2m#2_H3K4me3


title: RR629_mett10-KO_NA22 plates_input


title: TC71_SA2m#2_SMC1


title: B250C24: TC71_WT_H3K27ac_rep2

value: Ewing sarcoma cell line (TC71)

value: WT


title: TC71_SA2m#2_FLI1

value: SA2 KO

value: FLI1 (ab15289, Abcam)


title: RR626_mett10-WT_NA22 plates_input


title: TC71_SA2m#1_CTCF

value: Ewing sarcoma cell line


title: RR621_mett10-WT_NA22 plates_m6A IP


title: RR622_mett10-WT_NA22 plates_m6A IP


title: RR620_mett10-WT_NA22 plates_input


title: clf_K9ac_rep2_S2

city: Orsay

first: Sanchari

last: Sircar

address: Batiment 630 Rue Noetzlin

data_processing:
Trimmomatic-0.38: Minimum length of 36 bp; Mean Phred quality > 30; Leading and trailing bases removal with base quality <5. The reads were mapped onto the TAIR10 assembly using Bowtie2 with mismatch permission of 1 bp. MACS2 for peaks detection were set as follows: Number of duplicate reads at a location:1; mfold of 5:50; q-value cutoff: 0.05; extsize 200; broad peak
Genome_build: TAIR10
Supplementary_files_format_and_content: BIGWIG

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: ChIPseq assays were performed on shoot or root of 14‐day‐old seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were then generated using 10ng of DNA and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: clf mutant


title: clf_Input_rep2_S4


title: TC71_SA2m#1_H3K4me3

value: H3K4me3 (C15410003, Diagenode)


title: RR618_mett10-WT_NA22 plates_input

value: adult worm


title: TC71_SA2m#1_FLI1


title: Col_Input_rep2_S3


title: TC71_SA2m#1_H3K27ac

value: H3K27ac (ab4729, Abcam)


title: A673_WT_STAG2


title: A673_WT_STAG1

value: STAG1 (ab4457, Abcam)


title: clf_Input_S4


title: clf_K9ac_S2


title: Col_K9ac_rep2_S1


title: A673_WT_SMC1


title: A673_WT_RAD21

value: RAD21 (ab992, Abcam)


title: RR619_mett10-WT_NA22 plates_input

value: NA22 plates


title: TC71_SA2m#1_RAD21


title: Col_Input_S3


title: A673_WT_input


title: A673_WT_H3K27ac


title: RNA_seq_ref6_shoot_rep2

data_processing:
Trimmomatic-0.38 : Minimum length of 30 bp; Mean Phred quality score > 30; Leading and trailing bases removal with base quality <5. STAR aligner  was used to mapped the reads to TAIR10 genome assembly. Raw read counts were then extracted using featureCounts based on the gene annotations in Araport11_GFF3_genes_transposons.201606.gtf. DESeq2 to identify differentially expressed genes. Genes having read counts ≥ 50 in atleast 2 samples were considered for differential expression analysis.
Genome_build: TAIR10

growth_protocol: RNAseq assays were performed on shoot or root of 14‐day‐old seedlings

extract_protocol:
RNA extraction using Nucleospin RNA kit from Macherey Nagel
Libraries were produced using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
RNA-seq

value: ref6 mutant


title: Col_K9ac_S1


title: A673_WT_H3K4me3


title: RNA_seq_ref6_shoot_rep3


title: A673_WT_FLI1


title: A673_WT_CTCF

value: CTCF (provided in iDeal ChIP-seq kit Diagenode)


title: RNA_seq_ref6_shoot_rep1


title: A673_SA2r_STAG2

value: Rescue of SA2 in SA2 KO cell

value: STAG2 (ab4463, Abcam)


title: RNA_seq_Col0_shoot_rep3


title: RNA_seq_Col0_shoot_rep2


title: RNA_seq_Col0_shoot_rep1


title: A673_SA2r_STAG1


title: A673_SA2r_SMC1

value: SMC1 (A300-055A, Bethyl laboratories)


title: RNA_seq_Col0_clf_shoot_rep2


title: RNA_seq_Col0_clf_shoot_rep1


title: A673_SA2r_RAD21


title: RNA_seq_clf_shoot_rep1


title: RNA_seq_clf_shoot_rep2


title: A673_SA2r_H3K4me3


title: A673_SA2r_H3K27ac


title: A673_SA2r_CTCF


title: A673_SA2m#1_STAG2


title: Chip-seq_ref6

data_processing:
Trimmomatic-0.38: Minimum length of 36 bp; Mean Phred quality > 30; Leading and trailing bases removal with base quality <5. The reads were mapped onto the TAIR10 assembly using Bowtie2 with mismatch permission of 1 bp. MACS2 for peaks detection were set as follows: Number of duplicate reads at a location:1; mfold of 5:50; q-value cutoff: 0.05; extsize 200; broad peak
Genome_build: TAIR10

source_name: Chip seq_ref6

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were then generated using 10ng of DNA and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).
ChIP-seq


title: A673_SA2r_FLI1


title: CHiC_ref6_Shoot_rep2

growth_protocol: Capture Hi-C libraries were performed on shoot and root of Col-0, ref6, and clf

extract_protocol:
For capture Hi-C, in situ HiC libraries were first generated as in Concia et al., 2020.  Capture was then performed using SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library (Agilent) according to manufacturer’s recommendation.
Libraries were performed according to SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library (Agilent) according to manufacturer’s recommendation.
Capture Hi-C libraries


title: Chip-seq_Shoot_K27me3_rep1

source_name: Chip seq_Shoot_K27me3_rep1


title: Chip-seq_Root_K27me3_rep2

source_name: Chip seq_Root_K27me3_rep2


title: A673_SA2m#1_SMC1


title: CHiC_ref6_Shoot_rep1

data_processing:
Trimmomatic-0.38 to remove Illumina sequencing adapters. The 5′ and 3′ ends with a quality score below 5 (Phred+33) were trimmed and reads shorter than 30 bp after trimming were dropped. The trimmed files were then processed with HiC-Pro v2.11.1 (Servant et al., 2015). The reads were aligned using Bowtie2 onto the TAIR10 assembly with default settings, except for the parameter “--score-min L, -0.6, -0.8”.
Genome_build: TAIR10


title: Chip-seq_Root_K27me3_rep1

source_name: Chip seq_Root_K27me3_rep1


title: A673_SA2m#1_RAD21


title: A673_SA2r_input

value: input


title: A673_SA2m#1_Input


title: A673_SA2m#1_H3K4me3


title: CHiC_clf_Shoot_rep1


title: Capture_HiC_Col0_Shoot_rep2


title: A673_SA2m#1_FLI1


title: A673_SA2m#1_H3K27ac


title: Chip-seq_Shoot_K27me3_rep2

source_name: Chip seq_Shoot_K27me3_rep2


title: CHiC_clf_Shoot_rep2


title: A673_SA1m#1_STAG2

value: SA1 KO


title: A673_SA1m#1_STAG1


title: Capture_HiC_Col0_Shoot_rep1


title: Capture_HiC_Col0_Root_rep1


title: HiChIP-K9AC

source_name: HiChIP K9AC

growth_protocol: Hi-ChIP experiments were performed on shoots and roots of 14 day-old-seedlings

extract_protocol:
Hi-ChIP experiments were performed using the same procedure as in Concia et al., 2020 with either anti-H3K9ac (Millipore 07–352) or anti-H3K27me3 (Millipore 07–449).
Libraries were performed using Tn5 transposase using the same procedure as in Concia et al., 2020.
Hi-ChIP libraries


title: Capture_HiC_Col0_Root_rep2


title: A673_SA1m#1_SMC1


title: HiChIP-K27-Shoot-rep2

source_name: HiChIP K27 Shoot rep2


title: A673_SA1m#1_RAD21


title: A673_SA1m#1_input


title: HiChIP-K27-Root-rep1

source_name: HiChIP K27 Root rep1


title: A673_SA1m#1_H3K27ac


title: A673_SA1m#1_H3K4me3


title: HiChIP-K27-Shoot-rep1

source_name: HiChIP K27 Shoot rep1


title: A673_SA1m#1_FLI1


title: A673_SA2m#1_CTCF

value: SA2 KO


title: A673_SA2m#1_STAG1


title: A673_SA1m#1_CTCF


title: TC71_WT rep3

data_processing:
Reads were trimmed with Atropos
Mapping and gene quantification were performed with STAR version 2.5.3 againt human genome (hg19, gencode V19). Option "--quantMode GeneCounts" was used to get abundance measurements.
DESEQ2 1.20.0 was used to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited files with raw counts for each genes.

growth_protocol: A673 and TC71 were cultured respectively in DMEM or RPMI supplemented with 10% fetal bovine serum. Two days before RNA extraction, cells were seeded in 6 well plate dishes at a concentration allowing to reach a cellular confluence of approximately 90% at the time of RNA extraction.

extract_protocol:
RNA was extracted using RNeasy plus mini kit (Qiagen, ref 74134)
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations.

value: WT

value: Ewing sarcoma cell line (TC71)


title: TC71_WT rep1


title: TC71_siEWS-FLI1 rep2


title: TC71_siEWS-FLI1 rep1


title: TC71_siCT rep2

value: siCT


title: HiChIP-K27-Root-rep2

source_name: HiChIP K27 Root rep2


title: TC71_SA2m#2 rep3


title: Healthy 9

city: Gainesville

first: Rob

last: Maile

state: FL

department: Surgery

institute: University of Florida

hyb_protocol: Standard nanostring miRNA hybridisation protocols.

scan_protocol: Long

data_processing: nsolver v3

label: not provided

source_name: Healthy_peripheral blood microvesicles

label_protocol: Standard nanostring miRNA protocols.

extract_protocol: Collected peripheral blood was centrifuged at 2,000g for 30 minutes for plasma separation. Plasma was removed and diluted two times with saline. Diluted plasma was then centrifuged at 20,000g for 30 minutes to remove large EVs prior to ultracentrifugation. Ultracentrifugation (Beckman Coulter) was performed at 100,000g for 120 minutes using a Ti70 rotor to pellet the remaining EVs.

tag: chronic pancreatitis

value: no

tag: tissue/sample type

value: peripheral blood microvesicles

tag: molecule subtype

value: miRNA


title: Healthy 5


title: Healthy 6


title: Healthy 8


title: Healthy 7


title: Healthy 4


title: Healthy 10


title: Healthy 2


title: Healthy 3


title: Healthy 1


title: TC71_SA2m#2 rep2

source_name: Ewing sarcoma cell line (TC71)


title: Patient EXO11

source_name: patient_peripheral blood microvesicles

value: yes


title: Patient EXO10


title: TC71_SA2m#2 rep1


title: TC71_SA2m#1 rep3


title: Patient EXO9


title: TC71_WT rep2


title: TC71_SA2m#1 rep1


title: Patient EXO8


title: TC71_SA2m#1 rep2


title: A673_WT rep1

source_name: Ewing sarcoma cell line (A673)

value: Ewing sarcoma cell line (A673)


title: TC71_siCT rep1


title: Patient EXO7


title: A673_siEWS-FLI1 rep2


title: RR734_mix_m6A IP_poly A

organism:
Caenorhabditis elegans
Bombyx mori
Mus musculus

value: m6A IP

value: adult worm, adult mouse testes and Bombyx mori BmN4-SID1 insect cell line


title: Patient EXO5


title: RR903_mett10-KO_OP50 plates_m6A IP

source_name: adult worm

value: adult worm

value: METT-10 KO

value: OP50 plates


title: A673_siCT rep1


title: Patient EXO3


title: RR732_mix_m6A IP_poly A


title: A673_siCT rep2


title: RR733_mix_m6A IP_poly A


title: Patient EXO4


title: RR731_mix_m6A IP_total RNA


title: RR902_mett10-KO_OP50 plates_m6A IP


title: RR900_mett10-WT_OP50 plates_m6A IP


title: Patient EXO2


title: RR899_mett10-WT_OP50 plates_m6A IP


title: Patient EXO1


title: RR901_mett10-KO_OP50 plates_m6A IP


title: A673_SA2m#1 rep2


title: A673_SA2m#1 rep3


title: RR898_mett10-WT_OP50 plates_m6A IP


title: Patient EXO6


title: RR897_mett10-KO_OP50 plates_input


title: RR896_mett10-KO_OP50 plates_input


title: RR730_mix_m6A IP_total RNA


title: RR895_mett10-KO_OP50 plates_input


title: A673_siEWS-FLI1 rep1


title: RR729_mix_m6A IP_total RNA


title: RR728_mix_input_poly A


title: RR893_mett10-WT_OP50 plates_input


title: RR894_mett10-WT_OP50 plates_input


title: RR727_mix_input_poly A


title: RR892_mett10-WT_OP50 plates_input


title: RR726_mix_input_poly A


title: RR725_mix_input_total RNA


title: A673_SA2m#1 rep1


title: 510 Skull 2

city: HOUSTON

first: Igor

middle: L.

last: Bado

state: Texas

address: One Baylor Plaza, Alkek Building N1130

department: Breast Center

institute: Baylor College of Medicine

description:
510 Skull 2
mutation_count_matrix_510.txt

data_processing:
Library strategy: evolving barcode
Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace. Only the R1 files were used in the following analysis and only the R1  files were submitted.
To identify the barcoding region, we globally aligned each distinct sequence to the A26 reference barcode using TraceQC package in R. The parameters used for alignment are: 2 for match score, -2 for mismatch score, -6 for gap opening penalty and -0.1 for gap extension penalty.
The adapter sequences were trimmed off and sequences with less than 200 alignment score or less than 10 counts were filtered out from the subsequent analysis. The barcode sequence  is 117 bp starting from 58 bp before predicted TSS.
The mutation events were categorized by the TraceQC package on each barcode into 4 attributes: 1) the mutation type (insertion, deletion or point mutation), 2) the starting position of mutation, 3) the length of mutation, and 4) the altered sequence.
The mutation events were normalized by the read count per million (RPM) approach and used to generate the feature count matrix for all the samples.
Supplementary_files_format_and_content: Processed data files are txt files including the count (RPM) of each mutation event.The mutation events are named in the form of A_B_C_D using below criteria: A, type of mutation, including insertion, deletion, or single nucleotide mutation (‘mutation’ in short); B, the starting position of mutation; C, the length of mutation; D, the altered sequence. For deletion, the value is -; for mutation, the value is the replaced nucleotide; for insertion, the value is the inserted sequence.

source_name: breast cancer cells implanted in mouse

growth_protocol: MDA-MB-231 FR and AT-3 FR cells were transduced with TLCV2-hgRNA A26 and selected by puromycin for 2 weeks. 1E5 barcoded cells were then implanted to the fourth pair of mammary fat pad of nude mice or C57BL/6 mice. 5 weeks later for MDA-MB-231 tumors or 18 days  later for AT-3 tumors, the mammary tumors were resected and mice were give with a single dose of 5mg/kg doxycycline weekly for 5 cycles or 4 cycles through I.P. injection. 2 weeks after Dox treatment, the tissues with metastases were collected, and total DNA were exacted. For IIA injection model, 1E5 barcoded MDA-MB-231 cells were then delivered to bone via IIA. 2 weeks later, a single dose of 5mg/kg doxycycline weekly for 5 cycles was applied to the mice carrying bone metastases through I.P. injection. 3 weeks after Dox treatment, lung, right and left hindlimbhind limbs were collected, and total DNA were exacted. For in vitro treatment samples, cells were treated with 100μg/ml doxycycline for 2 hours and then rinsed by pre-warmed PBS twice to completely remove doxycycline and then allow to grow in vitro for 4 days. Then 1 million cells were collected for barcode sequencing and 0.5 million cells were seeded back to the petri dish and received another round of doxycycline treatment 24 hours later.

extract_protocol:
The metastatic lesions were dissected with ex vivo BLI imaging, and the uninvolved tissues were removed. The surgery tools were sterilized with a bead-sterilizer following by 70% isopropanol between different lesions. The collected tissues was snap-frozen in the liquid nitrogen until DNA extraction. The tissues were then rinsed by the gDNA lysis buffer from Quick-DNA Miniprep Plus Kit (Zymo Research, D4068) and homogenized with Precellys Lysing Kit (Bertin Instruments, MK28-R). After the homogenization, samples were lysed at 55℃ for 3 h, followed by 0.33 mg/mL RNaseA treatment at 37℃ for 15 min. Nucleic acid was further extracted following the manufacturer’s instruction. The final DNA was assessed by NanoDrop 2000 (Thermo Scientific) and human/mouse DNA ratio was examined by q-PCR with primers targeting human and mouse GAPDH gene, respectively.
Barcodes were amplified by two rounds of PCR. The first round of PCR was performed with 100 ng genomic DNA using Platinum Taq DNA Polymerase (Invitrogen) with Barcode-For and Barcode-Rev primers in 15 cycles. The second round of PCR were performed in a real-time setting and stopped in mid-exponential phase using PowerUp SYBR Green Master Mix (Thermo Fisher) with Barcode-P5-For and Barcode-P7-Rev primers. PCR products were then column-purified with QIAquick PCR purification Kit (QIAGEN) and assessed with Qubit. The NEBNext Multiplex oligos for Illumina (Dual index primer set 1,NEB, E7600S) and the NEB library preparation kit for Illumina (NEB, #E7645S) were used for library preparation as previously described (Kalhor et al., 2017).

tag: injected cell line

tag: metastic sites

value: Skull

tag: host

value: Athymic Nude

tag: mouse id


title: 510 Skull 3

description:
510 Skull 3
mutation_count_matrix_510.txt


title: 510 Skull 1

description:
510 Skull 1
mutation_count_matrix_510.txt


title: RR724_mix_input_total RNA

value: input


title: RR723_mix_input_total RNA


title: 510 Ribs L3

description:
510 Ribs Left, 3
mutation_count_matrix_510.txt

value: Rib cage


title: 510 Ribs L1

description:
510 Ribs Left, 1
mutation_count_matrix_510.txt


title: 510 Ribs R3

description:
510 Ribs Right, 3
mutation_count_matrix_510.txt


title: sh_NC_3

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

country: China

institute: Jiangsu Jiangyin People's Hospital

data_processing:
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained.  Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly.
All the transcripts were merged using Cuffmerge software. LncRNAs were then identified from the assembled transcripts
Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained. Cuffdiff or edgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 0 & padj < 0.05 were assigned as differentially expressed.
Target gene prediction of lncRNAs was carried out in two ways: the cis-acting target gene prediction, and trans-acting target gene prediction. Based on the theory of cis-acting regulatory element, the protein-coding genes located within 10/100kb from lncRNA were selected as potential cis-acting target. While for trans-acting target prediction, the Pearson’ correlations coefficients between the coding genes and lncRNAs were calculated and analyzed for the identification of trans-acting regulatory elements, which required the sample size was more than five.
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: TE-1_IFI6 gene Interference control

extract_protocol: LncRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Overexpression vectors and interference vectors were constructed and transfected into TE1 cells respectively. After 48h culture, second-generation lncRNA sequencing was arranged

tag: cell line

value: human esophageal cancer cell

tag: genotype/variation

value: IFI6 gene Interference control


title: sh_IFI_3

source_name: TE-1_IFI6 gene Interference

tag: cell type

value: IFI6 gene Interference


title: sh_NC_2


title: OE_NC_3

source_name: TE-1_IFI6 gene Overexpression control

value: IFI6 gene Overexpression control


title: sh_IFI_2


title: OE_IFI_3

source_name: TE-1_IFI6 gene Overexpression

value: IFI6 gene Overexpression


title: Placental mRNA extracted fresh, stored at -80 [20B6]

city: Cambridge

first: Norman

last: Shreeve

address: Rosie Hospital, Dept. of Obstetrics & Gynaecology, Robinson Way

department: O&G

institute: Univerisity of Cambridge

data_processing:
The fastq samples were run through quality control checks, trimmed to remove low quality bases and adapters and mapped to the mouse genome
Mapped reads were counted to determine the amount of expression in each gene using HTSeqCount, counted reads were loaded into the edgeR package in R software, counts were filtered (using 5CPM).
GC corrected using the CQN package and normalised on a per comparison basis
Differential expression was determined using an edgeR generalised linear model, which took into account the batch effect of the samples being compared, by using SVA.
Genome_build: Ensembl Mus_musculus GRCm38 (release 95) reference genome was used to do the mapping of reads, using the annotated transcripts from the ensembl Mus_musculus.GRCm38.95.gtf file.
Supplementary_files_format_and_content: Excel file with all 20 processed samples included. For each sample, each gene is given an expression value and accompanying statistical analysis through various parameters.

organism: Mus musculus

source_name: Bulk mRNA from homogenised placental tissue

extract_protocol:
RNA was extracted using RNeasy Plus Universal Mini Kit (Qiagen) from fresh tissue.
The coding transcriptome was captured and cDNA libraries prepared using TrueSeq Stranded mRNA (Ilumina), and pooled samples were sequenced on a NextSeq 500 system (Ilumina).

tag: maternal strain

tag: paternal strain

value: homogenised placental tissue

tag: batch


title: Placental mRNA extracted fresh, stored at -80 [17B6]

tag: tissue


title: OE_IFI_2


title: sh_IFI_1


title: sh_NC_1


title: OE_IFI_1


title: 510 Ribs R2

description:
510 Ribs Right, 2
mutation_count_matrix_510.txt


title: TC71_SA2m#1_STAG1

value: Ewing sarcoma cell line

tag: genotype

value: SA2 KO

tag: antibody

value: STAG1 (ab4457, Abcam)


title: Placental mRNA extracted fresh, stored at -80 [15B6]


title: L21cov snRNA-seq

city: New York

first: Jana

last: Biermann

state: NY

address: 622 West 168th St

institute: Columbia University

description:
Single-nuclei RNA sequencing
Raw read files to be uploaded to DUOS (https://duos.broadinstitute.org/) due to patient privacy concerns.

data_processing:
Library strategy: single-nuclei RNAseq
Raw 3′ snRNA-seq data were analyzed using Cell Ranger (v.5.0).
Transcripts were aligned to the human GRCh38 reference genome which was appended with the entire SARS-CoV-2 genome (severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome, GenBank MN908947.3) as an additional chromosome to the human reference genome.
Ambient RNA was removed using CellBender (v.0.2.0).
Gene expression matrices were processed individually in R (v.4.0.2) using Seurat (v.3.2.3).
Filters were applied to keep cells with 200–7,500 genes, 400–40,000 UMIs, and less than 10% of mitochondrial reads. Scrublet was applied to identify and remove doublets with an expected doublet rate ranging from 4–9.6% based on the loading rate.
Genome_build: GRCh38_SARSCoV2
Supplementary_files_format_and_content: Gene expression matrix

source_name: Lung tissue

extract_protocol:
Single-nuclei suspension from frozen lung tissue specimens was generated using methods published in Slyper et al. (Nature Medicine, 2020). Salt-tris buffer with Tween-20 (TST) was used for dissociation followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000-20,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics Next GEM 3' v3.1 reagents and a Chromium controler.
Single-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium Next GEM 3' v3.1 reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

tag: disease

tag: age

tag: Sex

value: F

tag: race

tag: ethnicity

value: Lung


title: L22cov snRNA-seq

value: M


title: L18cov snRNA-seq

value: Hispanic


title: Placental mRNA extracted fresh, stored at -80 [14B6]


title: L19cov snRNA-seq


title: Placental mRNA extracted fresh, stored at -80 [11B6]


title: 510 Spine-2

description:
510 Spine-2
mutation_count_matrix_510.txt

tag: injected cell line

tag: metastic sites

value: Spine


title: L17cov snRNA-seq


title: L16cov snRNA-seq


title: 510 Spine-1

description:
510 Spine-1
mutation_count_matrix_510.txt

tag: host

value: Athymic Nude

tag: mouse id


title: OE_NC_1

tag: cell line

tag: genotype/variation


title: L10cov snRNA-seq


title: Placental mRNA extracted fresh, stored at -80 [3KO]

tag: maternal strain


title: Placental mRNA extracted fresh, stored at -80 [5KO]

tag: paternal strain


title: Placental mRNA extracted fresh, stored at -80 [7KO]

tag: batch


title: 510 Ribs L2

description:
510 Ribs Left, 2
mutation_count_matrix_510.txt


title: L13cov snRNA-seq

tag: tissue


title: Placental mRNA extracted fresh, stored at -80 [10KO]


title: OE_NC_2

tag: cell type


title: L12cov snRNA-seq


title: 510 Sternum 1

description:
510 Sternum 1
mutation_count_matrix_510.txt

value: Sternum


title: 510 Forelimb L2

description:
510 Forelimb Left, 2
mutation_count_matrix_510.txt

value: Left Forelimb


title: L09cov snRNA-seq


title: 510 Sternum 2

description:
510 Sternum 2
mutation_count_matrix_510.txt


title: 510 Forelimb L1

description:
510 Forelimb Left, 1
mutation_count_matrix_510.txt


title: L11cov snRNA-seq


title: L08cov snRNA-seq


title: L07cov snRNA-seq


title: 510 Ribs R1

description:
510 Ribs Right, 1
mutation_count_matrix_510.txt

value: Rib cage


title: L06cov snRNA-seq


title: Placental mRNA extracted fresh, stored at -80 [2KO]


title: L05cov snRNA-seq


title: L04covaddon snRNA-seq


title: 510 Forelimb R2

description:
510 Forelimb Right, 2
mutation_count_matrix_510.txt

value: Right Forelimb


title: L15cov snRNA-seq


title: L04cov snRNA-seq


title: Re-run for batch effect [1KO batch]


title: 510 Forelimb R1

description:
510 Forelimb Right, 1
mutation_count_matrix_510.txt


title: L03cov snRNA-seq

value: White


title: Placental mRNA fresh [19B6]


title: L01cov snRNA-seq


title: Placental mRNA fresh [18B6]


title: C55ctr snRNA-seq

value: Control


title: 510 Hindlimb L2

description:
510 Hindlimb Left, 2
mutation_count_matrix_510.txt

value: Left Hindlimb


title: Placental mRNA fresh [13B6]

value: homogenised placental tissue


title: C56ctr snRNA-seq


title: Placental mRNA fresh [16B6]


title: C52ctr snRNA-seq


title: 510 Hindlimb L3

description:
510 Hindlimb Left, 3
mutation_count_matrix_510.txt


title: C54ctr snRNA-seq

value: Asian


title: 510 Hindlimb R

description:
510 Hindlimb Right
mutation_count_matrix_510.txt

value: Right Hindlimb


title: C51ctr snRNA-seq


title: C53ctr snRNA-seq


title: Placental mRNA fresh [12B6]


title: Placental mRNA fresh [9KO]


title: 510 Kidney L

description:
510 Kidney Left
mutation_count_matrix_510.txt

value: Kidney


title: BM_4EPZ

data_processing:
Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
1)Remove reads with adaptor contamination. 2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).3)Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Reference genome and gene model annotation files were downloaded from genome website browser(NCBI/UCSC/Ensembl)directly.Indexes of the reference genome was built using STAR and paired-end clean reads were aligned tothe reference genome using STAR(v2.5). STAR used the method of Maximal Mappable Prefix (MMP) which can generatea precise mapping result for junction reads.
Supplementary_files_format_and_content: text file lists the count of genes in each sample .

source_name: MDA231 SCP21 FRR Bone Tumor 323 Passage 3, plus 1uM EPZ

growth_protocol: SCP21 cells were transplanted into mammary fat pad, lung or bone via different injection routes, and inoculated in vivo for four weeks. Then the mammary fat pad tumors, lung metastases, and bone metastases were collected and subjected to tumor dissociation kit to generate single cell suspension. mRFP positive tumor cells were sorted by flow cytometry, and cultured in vitro on the petri dishes. if not specified, the total RNA subjected to sequencing was collected using TRIZOL with direct-zol RNA column purification kit from Zymo. the total RNAs were immediately shipped to Novogene, and the quality check, library preparation, and deep sequencing was performed by Novogene.

extract_protocol:
The metastatic lesions were dissected with ex vivo BLI imaging, and the uninvolved tissues were removed in the hood. The surgery tools were sterilized with a bead-sterilizer following by 70% isopropanol between different animals. The collected tissues were immediately subjected to the tumor dissociation kit and RFP positive cells were sorted and re-cultured in vitro. The total RNA were extracted using TRIZOL with directzol RNA isolation kit following the manufacturer's protocol.
the library construction was performed by Novogene.

treatment_protocol: cells were passaged every five days. For epz treatment, cells at passage 3 received a five-day treatment of 1uM ezh2 inhibitor, EPZ011989, under regular culture condition.

value: breast cancer

value: bone


title: BM_1EPZ

source_name: MDA231 SCP21 FRR Bone Tumor 320 Passage 3, plus 1uM EPZ


title: BM_3EPZ

source_name: MDA231 SCP21 FRR Bone Tumor 322 Passage 3, plus 1uM EPZ


title: BM_4P_6

source_name: MDA231 SCP21 FRR Bone Tumor 323 Passage 9


title: Placental mRNA fresh [8KO]


title: C57ctr snRNA-seq

value: M

value: Lung


title: Placental mRNA fresh [6KO]


title: 510 Spleen

description:
510 Spleen
mutation_count_matrix_510.txt

value: Spleen


title: BM_2P_6

source_name: MDA231 SCP21 FRR Bone Tumor 321 Passage 9

value: Athymic Nude


title: BM_1P_6

source_name: MDA231 SCP21 FRR Bone Tumor 320 Passage 9


title: 510 Liver-6

description:
510 Liver-6
mutation_count_matrix_510.txt

value: Liver


title: BM_4P_3

source_name: MDA231 SCP21 FRR Bone Tumor 323 Passage 6


title: 510 Brain

description:
510 Brain
mutation_count_matrix_510.txt

value: Brain


title: Placental mRNA fresh [4KO]


title: BM_3P_3

source_name: MDA231 SCP21 FRR Bone Tumor 322 Passage 6


title: Placental mRNA fresh [1KO]


title: 510 Liver-5

description:
510 Liver-5
mutation_count_matrix_510.txt


title: BM_4

source_name: MDA231 SCP21 FRR Bone Tumor 323 Passage 3


title: BM_3

source_name: MDA231 SCP21 FRR Bone Tumor 322 Passage 3


title: BM_1P_3

source_name: MDA231 SCP21 FRR Bone Tumor 320 Passage 6


title: 520 Sternum-2

description:
520 Sternum-2
mutation_count_matrix_520.txt

source_name: mouse mammary carcinoma cells implanted in mouse

value: Sternum


title: 520 Skull

description:
520 Skull
mutation_count_matrix_520.txt

value: Skull


title: BM_2EPZ

source_name: MDA231 SCP21 FRR Bone Tumor 321 Passage 3, plus 1uM EPZ


title: 510 Kidney R

description:
510 Kidney Right
mutation_count_matrix_510.txt

source_name: breast cancer cells implanted in mouse


title: BM_3P_6

source_name: MDA231 SCP21 FRR Bone Tumor 322 Passage 9


title: 520 Sternum-1

description:
520 Sternum-1
mutation_count_matrix_520.txt


title: BM_2

source_name: MDA231 SCP21 FRR Bone Tumor 321 Passage 3


title: BM_1

source_name: MDA231 SCP21 FRR Bone Tumor 320 Passage 3


title: 510 Lung-3

description:
510 Lung-3
mutation_count_matrix_510.txt


title: LM_3

source_name: MDA231 SCP21 FRR Lung Tumor 316 Passage 3

value: lung


title: LM_2

source_name: MDA231 SCP21 FRR Lung Tumor 713 Passage 3


title: 510 Liver-2

description:
510 Liver-2
mutation_count_matrix_510.txt


title: 520 Ribs-R

description:
520 Ribs-Right
mutation_count_matrix_520.txt

value: Rib cage


title: MFP_3

source_name: MDA231 SCP21 FRR MFP Tumor 328 Passage 3

value: mammary fat pad


title: 510 Hindlimb L1

description:
510 Hindlimb Left, 1
mutation_count_matrix_510.txt

value: Left Hindlimb


title: 520 Ribs-L

description:
520 Ribs-Left
mutation_count_matrix_520.txt


title: 510 Lung-1

description:
510 Lung-1
mutation_count_matrix_510.txt


title: 510 Lung-2

description:
510 Lung-2
mutation_count_matrix_510.txt


title: 520 FL-L

description:
520 Forelimb-Left
mutation_count_matrix_520.txt

value: Left Forelimb


title: 510 Liver-3

description:
510 Liver-3
mutation_count_matrix_510.txt


title: MFP_2

source_name: MDA231 SCP21 FRR MFP Tumor 327 Passage 3


title: BM_2P_3

source_name: MDA231 SCP21 FRR Bone Tumor 321 Passage 6


title: MFP_1

source_name: MDA231 SCP21 FRR MFP Tumor 326 Passage 3


title: 510 Tumor

description:
510 Tumor
mutation_count_matrix_510.txt

value: Mammary fat pad


title: Par

source_name: MDA231 SCP21 FRR Parental

value: In vitro, navie parental cells


title: 520 FL-R

description:
520 Forelimb-Right
mutation_count_matrix_520.txt

value: Right Forelimb


title: TC71_siSA2-Dh8_48h_R2

source_name: Ewing sarcoma cell line (TC71)

growth_protocol: Cells were cultured in DMEM (A673) or RPMI (TC71 and EW1) supplemented with 10% fetal bovine serum. CHLA-10 and CHLA-258 were cultured in IMDM supplemented with 20% fetal bovine serum and 1X Insuline-Transferrin-selenium.

extract_protocol:
RNA was extracted using RNeasy plus mini kit and further processed for RNA-seq
The library construction was performed using TruSeq Stranded mRNA (Illumina, ref #20020594) according to manufacturer recommendations

treatment_protocol: Five different Ewing sarcoma cell lines were transfected with siCT or 2 different siRNAs targeting STAG2 (siSA2#6 or siSA2#8). RNA in A673 & TC71 (siSTAG2) was extracted 24, 48 and 72 hours post-transfection. RNA in EW1, CHLA-10 and CHLA-258 (siSTAG2 and siEWSR1-FLI1) was extracted 72 hours post-transfection.

tag: sirna

tag: timepoint


title: TC71_siSA2-Dh8_48h_R1


title: 520 HL-L

description:
520 Hindlimb-Left
mutation_count_matrix_520.txt


title: 509 Skull-2

description:
509 Skull-2
mutation_count_matrix_509.txt


title: 520 HL-R2

description:
520 Hindlimb-Right, 2
mutation_count_matrix_520.txt

value: Right Hindlimb


title: TC71_siSA2-Dh8_24h_R2


title: TC71_siSA2-Dh6_72h_R2


title: LM_1

source_name: MDA231 SCP21 FRR Lung Tumor 712 Passage 3

value: breast cancer


title: 520 HL-R1

description:
520 Hindlimb-Right, 1
mutation_count_matrix_520.txt


title: 509 Skull-1

description:
509 Skull-1
mutation_count_matrix_509.txt


title: 509 Ribs-L2

description:
509 Ribs-Left, 2
mutation_count_matrix_509.txt


title: TC71_siSA2-Dh6_72h_R1


title: 520 Spleen-2

description:
520 Spleen-2
mutation_count_matrix_520.txt


title: 509 Ribs-L1

description:
509 Ribs-Left, 1
mutation_count_matrix_509.txt


title: TC71_siSA2-Dh8_72h_R2


title: Efa-RqcH 50s IP/total tRNA 2-1

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: Biological replicate 2 of 2 Cy3 vs 1 of 1 Atto

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on median fluorescence signal (background fluorescence subtraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards human tRNAGln1, human tRNAHis1, human tRNASer3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios; detailed protocol for  narmalization using the dye control slide is published in: https://www.protocols.io/view/microarray-based-quantification-of-cellular-trnas-hfcb3iw or in : Dittmar KA, Mobley EM, Radek AJ, Pan T. (2004) Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol 12, 31-47

organism: Enterococcus faecalis

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; human tRNAGln1, yeast tRNAPhe, human tRNAHis1, human tRNASer3) were added to 2 µg extracted total RNA.
2. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 1h at RT in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
E. faecalis TX5332 transformed with pCIE plasmids were grown overnight from single colony in BHI supplemented with kanamycin and chloramphenicol.
Next day overnight cultures were diluted to starting OD600 of 0.05 in BHI supplemented with kanamycin and chloramphenicol.

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich)  according to manufacturer's protocol

treatment_protocol: Cells were grown with intensive shaking till OD600 of 0.6 and were induced with cCF10 peptide for 30 minutes prior to harvesting by centrifugation

tag: strain

tag: sample type

value: Enterococcus faecalis  total lysate

value: IP


title: 520 Spleen-1

description:
520 Spleen-1
mutation_count_matrix_520.txt

value: Spleen


title: 520 Kidney-L

description:
520 Kidney-Left
mutation_count_matrix_520.txt

value: Kidney


title: 509 Skull-3

description:
509 Skull-3
mutation_count_matrix_509.txt

value: Athymic Nude


title: 509 Ribs-R4

description:
509 Ribs-Right, 4
mutation_count_matrix_509.txt


title: Efa-RqcH 50s IP/total tRNA 1-1

description: Biological replicate 1 of 2 Cy3 vs 1 of 1 Atto

value: total lysate


title: TC71_siSA2-Dh8_72h_R1


title: TC71_siSA2-Dh6_48h_R1


title: FM_1h_C: Full media 3

city: Stockholm

first: Daniel

middle: Wesley

last: Hagey

address: Nobels vag 3

country: Sweden

institute: Karolinska Institutet

data_processing:
Tophat2.1.1
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data for ENSEMBL genes

source_name: HEK293 cells in Full Media for 1hr 3

extract_protocol:
Trireagent and isopropanol precipitation
Smart-seq2
Illumina Nextera XT

tag: cell media

value: Full media


title: FM_1h_A: Full media 1

source_name: HEK293 cells in Full Media for 1hr 1


title: FM_1h_B: Full media 2

source_name: HEK293 cells in Full Media for 1hr 2


title: TC71_siSA2-Dh6_24h_R1


title: 509 Ribs-R2

description:
509 Ribs-Right, 2
mutation_count_matrix_509.txt

source_name: breast cancer cells implanted in mouse


title: TC71_siSA2-Dh8_24h_R1


title: 520 Liver-3

description:
520 Liver-3
mutation_count_matrix_520.txt

source_name: mouse mammary carcinoma cells implanted in mouse

value: Liver


title: OS_1h_C: Optimem + serum 3

source_name: HEK293 cells in Optimem + serum for 1hr 3

value: Optimem + serum


title: 509 Ribs-R1

description:
509 Ribs-Right, 1
mutation_count_matrix_509.txt

value: Rib cage


title: 520 Liver-2

description:
520 Liver-2
mutation_count_matrix_520.txt


title: TC71_siCT-Dh1_72h_R1


title: 520 Liver-1

description:
520 Liver-1
mutation_count_matrix_520.txt


title: OS_1h_B: Optimem + serum 2

source_name: HEK293 cells in Optimem + serum for 1hr 2


title: OS_1h_A: Optimem + serum 1

source_name: HEK293 cells in Optimem + serum for 1hr 1


title: TC71_siSA2-Dh6_48h_R2


title: 509 Ribs-R3

description:
509 Ribs-Right, 3
mutation_count_matrix_509.txt


title: O_1h_C: Optimem 3

source_name: HEK293 cells in Optimem for 1hr 3

value: Optimem


title: 509 Spine-1

description:
509 Spine-1
mutation_count_matrix_509.txt

value: Spine


title: TC71_siSA2-Dh6_24h_R2


title: 520 Lung-1

description:
520 Lung-1
mutation_count_matrix_520.txt

value: Lung


title: 520 Kidney-R

description:
520 Kidney-Right
mutation_count_matrix_520.txt


title: O_1h_B: Optimem 2

source_name: HEK293 cells in Optimem for 1hr 2


title: TC71_siCT-Dh1_48h_R2


title: 509 Sternum-2

description:
509 Sternum-2
mutation_count_matrix_509.txt

value: Sternum


title: TC71_siCT-Dh1_24h_R2


title: 509 Forelimb-L

description:
509 Forelimb-Left
mutation_count_matrix_509.txt

value: Left Forelimb


title: TC71_siCT-Dh1_48h_R1


title: 509 Sternum-1

description:
509 Sternum-1
mutation_count_matrix_509.txt


title: 520 Tumor

description:
520 Tumor
mutation_count_matrix_520.txt

value: Mammary fat pad


title: TC71_siCT-Dh1_24h_R1


title: 121 Ribs-L

description:
121 Ribs-Left
mutation_count_matrix_121.txt


title: 509 Forelimb-R

description:
509 Forelimb-Right
mutation_count_matrix_509.txt

value: Right Forelimb


title: EW1_siSA2-Dh8_72h_R2

source_name: Ewing sarcoma cell line (EW1)


title: 121 FL-R

description:
121 Forelimb-Right
mutation_count_matrix_121.txt


title: EW1_siSA2-Dh8_72h_R1


title: 509 Hindlimb-L

description:
509 Hindlimb-Left
mutation_count_matrix_509.txt

value: Left Hindlimb


title: 520 Lung-2

description:
520 Lung-2
mutation_count_matrix_520.txt


title: 121 HL-L

description:
121 Hindlimb-Left
mutation_count_matrix_121.txt


title: 509 Hindlimb-R

description:
509 Hindlimb-Right
mutation_count_matrix_509.txt

value: Right Hindlimb


title: EW1_siSA2-Dh6_72h_R2


title: EW1_siSA2-Dh6_72h_R1


title: 509 Brain-1

description:
509 Brain-1
mutation_count_matrix_509.txt

value: Brain


title: 121 Spleen

description:
121 Spleen
mutation_count_matrix_121.txt

value: Spleen


title: O_1h_A: Optimem 1

source_name: HEK293 cells in Optimem for 1hr 1


title: EW1_siEWS-FLI1-type2_72h_R2


title: 509 Brain-2

description:
509 Brain-2
mutation_count_matrix_509.txt

value: Athymic Nude


title: 121 Kidney-L

description:
121 Kidney-L
mutation_count_matrix_121.txt

value: Kidney


title: 509 Kidney L

description:
509 Kidney Left
mutation_count_matrix_509.txt


title: EW1_siEWS-FLI1-type2_72h_R1


title: 509 Kidney R

description:
509 Kidney Right
mutation_count_matrix_509.txt


title: 121 Liver-5

description:
121 Liver-5
mutation_count_matrix_121.txt


title: EW1_siCT-Dh1_72h_R2


title: 121 Liver-1

description:
121 Liver-1
mutation_count_matrix_121.txt


title: 121 Lung

description:
121 Lung
mutation_count_matrix_121.txt


title: 121 HL-R

description:
121 Hindimb-Right
mutation_count_matrix_121.txt


title: 509 Spleen

description:
509 Spleen
mutation_count_matrix_509.txt


title: EW1_siCT-Dh1_72h_R1


title: 509 Liver-5

description:
509 Liver-5
mutation_count_matrix_509.txt


title: Ewing sarcoma sample EW726

first: Didier

last: Surdez

address: 26 rue d'ULM

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.22.0 in R 2.12 environment with quantile normalization and hgu133plus2hsentrezg Brainarray annotation version 14  (http://brainarray.mbni.med.umich.edu/Brainarray/).

source_name: Ewing sarcoma sample EW726

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA usin 3'IVT Express Kit.

growth_protocol: Tumor sample were fozen in liquid nitrogen or on dry ice

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

treatment_protocol: Tumor sample were stored at -80°C until extraction procedure

tag: gender

value: Female

tag: age

tag: tumor type

value: primary tumor


title: Ewing sarcoma sample EW731

source_name: Ewing sarcoma sample EW731

value: Male


title: Ewing sarcoma sample EW724

source_name: Ewing sarcoma sample EW724


title: Ewing sarcoma sample EW730

source_name: Ewing sarcoma sample EW730


title: Ewing sarcoma sample EW717

source_name: Ewing sarcoma sample EW717


title: 509 Liver-4

description:
509 Liver-4
mutation_count_matrix_509.txt

tag: injected cell line

tag: metastic sites

value: Liver

tag: host


title: Ewing sarcoma sample EW716

source_name: Ewing sarcoma sample EW716


title: CHLA258_siSA2-Dh8_72h_R2

source_name: Ewing sarcoma cell line (CHLA-258)


title: Ewing sarcoma sample EW712

source_name: Ewing sarcoma sample EW712


title: 121 Tumor

description:
121 Tumor
mutation_count_matrix_121.txt

tag: mouse id


title: CHLA258_siSA2-Dh8_72h_R1


title: HEK293 YS mutant FUS-HOXA9  (GFP) GFP IP

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
All reads were mapped to the human genome (hg19), drosophila (dm3) or mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools. We filter out reads with a mapping quality score of < 20 for downstream analysis.
Profiles of ChIP-seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: GRCh37/hg19 or GRCm38/mm10

source_name: HEK 293 cells

growth_protocol: HEK 293 cells were grown in DMEM base medium plus 10% FBS and 1% antibiotics. The fusion-transformed mouse HSPCs (leukemia-causing cells) were grown in Opti-MEM base medium plus 10% FBS, 2% of supernatant containing home-made murine stem cell factor (from mSCF-producing CHO cells), 1% of supernatant containing murine FLT3 ligand (from FLT3L-producing cells), 1% antibiotics and 50uM of beta-mercaptoethanol.

extract_protocol:
Fixed cells were sonicated in a Bioruptor sonication device for 45 cycles at a high-energy setting to enrich the sonicated DNA to be ~300bp as described in our method. The sonicated samples were incubated with the indicated antibodies pre-bound to the protein-G/A beads for overnight. Across 293 cell samples with GFP-tagged chimera, the cleared cell lysates from sonicated nuclei were added with the same fraction of the sonicated and cleared chromatin of Drosophila S2 cells (see our Method), and then protein-DNA complexes were isolated with antibodies against GFP and those against Drosophila-specific histone H2Av (Active Motif cat# 39715). Beads were then washed with various washing buffers (please see our method). Bead-bound DNA was eluted and subject to reverse crosslinking and sequential treatments of RNase and protease K. Finally, ChIP DNA was purified with a PCR cleanup kit (Qiagen) and used for library construction.
Multiplexed ChIP-seq sequencing libraries were prepared using the NEBNext Ultra II kit (NEB, #E7645L) following the manufacture’s instruction. ChIP-seq libraries were pooled together and sequenced on a Nextseq 550 system using a Nextseq 550 High Output Kit v2.5 or sent to UNC High-Throughput Sequencing Facility (HTSF) for sequencing by using an Illuminia Hiseq 2500/4000 system.

treatment_protocol: For ChIP-seq experiments, HEK293 cells with stable expression of IDR-WT or IDR-mutated NUP98-HOXA9 and FUS-HOXA9 (GFP-tagged or 3XHA-3XFLAG-tagged) were grown in DMEM medium and fixed with 1% of formaldehyde in PBS for 10 min at room temperature. For 1,6-Hexanediol treatment, growth medium was removed and cells then incubated with 10% of 1,6-hexanediol in PBS for 1 min. Then, formaldehyde was added directly to make up the final concentration formaldehyde to be 1%, followed by incubation at room temperature for 10 min.

tag: antibody used

value: Rabbit anti-GFP antibody(ab290), Rabbit Anti-H2Av (activemotif #39715)

tag: treatment condition

value: GFP-tagged YS mutant FUS-HOXA9


title: HEK293 YS mutant FUS-HOXA9 (GFP) Input

value: n/a (input)


title: 509 Liver-3

description:
509 Liver-3
mutation_count_matrix_509.txt

source_name: breast cancer cells implanted in mouse


title: 509 Liver-2

description:
509 Liver-2
mutation_count_matrix_509.txt


title: CHLA258_siSA2-Dh6_72h_R2


title: CHLA258_siSA2-Dh6_72h_R1


title: HEK293 WT FUS-HOXA9  (GFP) GFP IP

value: GFP-tagged IDR-WT FUS-HOXA9


title: Ewing sarcoma sample EW714

source_name: Ewing sarcoma sample EW714


title: CHLA258_siCT-Dh1_72h_R2


title: 509 Liver-1

description:
509 Liver-1
mutation_count_matrix_509.txt


title: HEK293 WT NUP98-HOXA9  (HA) CTCF IP

value: Rabbit anti-CTCF (Diagenode C1541021)

value: 3XHA-3XFLAG-tagged, IDR-WT NUP98-HOXA9


title: CHLA258_siCT-Dh1_72h_R1


title: 509 Lung R

description:
509 Lung Right
mutation_count_matrix_509.txt

value: Lung


title: CHLA10_siSA2-Dh8_72h_R2

source_name: Ewing sarcoma cell line (CHLA-10)


title: 509 Tumor

description:
509 Tumor
mutation_count_matrix_509.txt

value: Mammary fat pad


title: Ewing sarcoma sample EW702b

source_name: Ewing sarcoma sample EW702b


title: HEK293 FS mutant NUP98-HOXA9 (HA) CTCF IP


title: Ewing sarcoma sample EW709

source_name: Ewing sarcoma sample EW709


title: CHLA10_siSA2-Dh8_72h_R1


title: Ewing sarcoma sample EW704

source_name: Ewing sarcoma sample EW704


title: Ewing sarcoma sample EW249

source_name: Ewing sarcoma sample EW249


title: CTRL-C4_RNA-Seq

city: London

first: Steve

last: West

address: 1 Midland Road

institute: The Francis Crick Institute

description: mRNA-Seq

data_processing:
Sequenced reads were aligned and quantified against human genome version hg19 with Refseq transcript annotations using RSEM v1.2.31 and STAR v2.5.1b.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.

source_name: Lymphoblastoid Cell Line from Control Healthy Individual

growth_protocol: Lymphoblastoid cell lines (LCLs) from control and AOA2 patients were cultured in RPMI 1640 medium (ThermoFisher) containing 20% FBS (Sigma-Aldrich), 1% Penicillin/Streptomycin (P/S; Sigma-Aldrich), 2 mM L-glutamine (ThermoFisher) and 1% Non-Essential Amino Acids (ThermoFisher). All LCLs were grown at 37°C and in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.

treatment_protocol: Cells were harvested by trypsinization followed by two washes with ice-cold PBS.

tag: pair

value: Lymphoblastoid Cell Line transformed by Epstein-Barr Virus

tag: morphology

value: Lymphoblast

tag: genotype

value: Normal


title: CHLA10_siSA2-Dh6_72h_R2

tag: sirna


title: Ewing sarcoma sample EW212

source_name: Ewing sarcoma sample EW212


title: Ewing sarcoma sample EW243

source_name: Ewing sarcoma sample EW243


title: CTRL-C3_RNA-Seq

description: mRNA-Seq

tag: cell type


title: CHLA10_siSA2-Dh6_72h_R1

tag: timepoint


title: HEK293 WT NUP98-HOXA9 (HA) Input (matched for CTCF IP)


title: HEK293 WT FUS-HOXA9 (GFP) Input


title: HEK293 FS mutant NUP98-HOXA9 (GFP; Hexanediol-treated) GFP-IP

value: GFP-tagged FS mutant NUP98-HOXA9; Hexanediol-treated


title: Ewing sarcoma sample EW199

source_name: Ewing sarcoma sample EW199


title: Ewing sarcoma sample EW191

source_name: Ewing sarcoma sample EW191


title: Ewing sarcoma sample EW175

source_name: Ewing sarcoma sample EW175


title: CHLA10_siEWS-FLI1_72h_R2


title: HEK293 FS mutant NUP98-HOXA9 (GFP; Hexanediol-treated) Input


title: Ewing sarcoma sample EW137

source_name: Ewing sarcoma sample EW137


title: CTRL-C1_RNA-Seq

description: mRNA-Seq


title: CHLA10_siEWS-FLI1_72h_R1


title: HEK293 FS mutant NUP98-HOXA9  (GFP; mock-treated) GFP-IP

value: GFP-tagged FS mutant NUP98-HOXA9; mock-treated


title: Ewing sarcoma sample EW142

source_name: Ewing sarcoma sample EW142

value: Female


title: HEK293 FS mutant NUP98-HOXA9  (GFP; mock-treated) Input


title: AOA2-P4_RNA-Seq

description: mRNA-Seq

source_name: Lymphoblastoid Cell Line from AOA2 Patient with SETX Mutation

value: Homozygous mutation in SETX gene, c.1669C>T


title: CHLA10_siCT-Dh1_72h_R2


title: HEK293 WT NUP98-HOXA9 (GFP; Hexanediol-treated) GFP IP

source_name: HEK 293 cells

value: GFP-tagged IDR-WT NUP98-HOXA9; Hexanediol-treated


title: AOA2-P3_RNA-Seq

description: mRNA-Seq

value: Homozygous mutation in SETX gene, c.3466delG


title: HEK293 WT NUP98-HOXA9 (GFP; Hexanediol-treated) Input


title: AOA2-P2_RNA-Seq

description: mRNA-Seq

value: Compound heterozygous mutation in SETX gene, c.7240C>T; c.7626delG


title: AOA2-P1_RNA-Seq

description: mRNA-Seq

value: Homozygous mutation in SETX gene, c.6106+3393_7101-22del20648ins25


title: HEK293 WT NUP98-HOXA9 (GFP; mock-treated) GFP IP

value: Rabbit anti-GFP antibody(ab290), Rabbit Anti-H2Av (activemotif #39715)

value: GFP-tagged IDR-WT NUP98-HOXA9; mock-treated


title: A673_siSA2-Dh8_72h_R1

source_name: Ewing sarcoma cell line (A673)


title: HEK293 WT NUP98-HOXA9 (GFP; mock-treated) Input

value: n/a (input)


title: A673_siSA2-Dh8_48h_R1


title: A673_siSA2-Dh8_48h_R2


title: CHLA10_siCT-Dh1_72h_R1


title: A673_siSA2-Dh8_24h_R2


title: vec_plus_IP2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Differential expression analysis was performed by DESeq2.
Peak calling was performed with exomePeak.
Genome_build: hg19
Supplementary_files_format_and_content: exomePeak output bed file

source_name: HEK cell

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: technology

tag: condition

value: wild type

tag: sample type

value: IP


title: A673_siSA2-Dh8_72h_R2

first: Olivier

last: Delattre


title: vec_plus_IP1


title: A673_siSA2-Dh8_24h_R1


title: vec_plus_Input2

value: input


title: HEK293 FS mutant NUP98-HOXA9 (HA) Input (matched for CTCF IP)


title: Setx-/-_RNA-Seq

description: mRNA-Seq

data_processing:
Sequenced reads were aligned and quantified against mouse genome version mm9 with Refseq transcript annotations using RSEM v1.2.31 and STAR v2.5.1b.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.

source_name: Setx Knockout Mouse Embryonic Fibroblast Cells

growth_protocol: Mouse embryonic fibroblasts were cultured at 37°C with 5% CO2 and 5% O2 in DMEM (ThermoFisher) supplemented with 15% FBS (F2442; Sigma-Aldrich) and 1% Penicillin/Streptomycin (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted from cultured human and mouse cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including an on-column DNase treatment to eliminate any contaminating genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.

value: Mouse Embryonic Fibroblast Cells

value: Fibroblast

value: Setx-/-


title: Ewing sarcoma sample EW125b

source_name: Ewing sarcoma sample EW125b

tag: gender

value: Male

tag: age

value: primary tumor


title: A673_siSA2-Dh6_72h_R2


title: vec_plus_Input1


title: Setx+/+_RNA-Seq

description: mRNA-Seq

source_name: Wild-type Mouse Embryonic Fibroblast Cells

value: Wild-type


title: A673_siSA2-Dh6_72h_R1


title: vec_minus_IP2