title: Run1785

description: R1 contains the cell barcode, R2 contains mRNA read

source_name: Fetal kidney

extract_protocol:
All tissues were shipped overnight in Belzer’s solution at 4 degrees Celsius and were processed immediately upon arrival to the laboratory, as follows. One kidney was dissected in ice-cold PBS and finely minced in a petri dish on ice using razor blades. About 20 mg of tissue were added to 1 ml of cold active protease solution (PBS, 10 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). The tissue was incubated in a 2 ml reaction tube for 15-20 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 20 seconds every 5 minutes. Single cell dissociation was confirmed with a microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.01%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.01%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 http://mccarrolllab.com/dropseq/). Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluorooctanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on the Illumina HiSeq2500 platform. Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.

tag: fetal age

value: 110 days

value: kidney


title: Run1751

status: Public on May 17 2018

type: SRA

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
Sequence aligned using Star
Next, using the tools embedded in Picard tools (picard-tools-1.115) and the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/), the fastq files were processed and the data matrix table containing the gene expression of the barcoded cells was generated. Individual cells were labeled with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers) in order to determine absolute transcript abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format

molecule: total RNA

organism: Homo sapiens

value: 105 days

tag: tissue


title: Run1824

value: 115 days


title: SPRET_BMDM_RNA_polyA_KLA_6h_rep2

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description:
RNA-Seq
Processed data file:
RNA_Seq_C57_SPRET_INFg_response_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: SPRETEIJ_genome.tar.gz

organism: Mus musculus

source_name: bone marrow derived macropages (BMDM)

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
RNA-Seq: Total RNA was isolated from cells and purified using Quick RNA mini prep columns and RNase- free DNase digestion according to the manufacturer’s instructions (Zymo Research). RNA-seq libraries were prepared from poly(A)-enriched mRNA, as previously described (Oishi et al., 2017). Libraries were sequenced on HiSeq 4000 or NextSeq 500.

tag: strain

value: SPRET/EiJ

value: bone marrow derived macropages (BMDM)

tag: culture protocol

value: 7 day cultured BMDMs

tag: ligands in culture

value: KLA 6h

tag: chip antibody


title: SPRET_BMDM_RNA_polyA_KLA_6h_rep1


title: BALB_BMDM_5GRO_KLA_1h_rep2

description:
5'Gro-Seq
Processed data file:
tss_BALB_5GRO_KLA_1h.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: BALBCJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
GRO-seq and 5'GRO-seq: Nascent transcription was captured by global nuclear run-on sequencing (GRO-seq) (Core et al., 2008) and nascent transcription start sites by 5’GRO-seq (Lam et al., 2013). Nuclei were isolated from BMDMs using hypotonic lysis [10 mM Tris-HCl (pH 7.5), 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL CA-630] and flash frozen in GRO-freezing buffer [50 mM Tris-HCl (pH 7.8), 5 mM MgCl2, 40% Glycerol]. 3-5 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (Duttke et al., 2015) with 3x NRO buffer [15mM Tris-Cl (pH 8.0), 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/μL of SUPERase In, 1.5% Sarkosyl, 366 μM ATP, GTP (Roche), Br-UTP (Sigma Aldrich) and 1.2 μM CTP (Roche, to limit run-on length to ~40 nt)]. Reactions were stopped after five minutes by addition of 500 μL Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer.

value: BALB/cJ

value: KLA 1h


title: SPRET_BMDM_GRO_notx_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: SPRETEIJ_genome.tar.gz

value: no treatment


title: SPRET_BMDM_HiC

description:
Hi-C sequencing
Processed data file:
SPRET_BMDM_HiC_raw_interactions_1MB.txt

library_source: genomic

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Hi-C experiments were further analyzed using HOMER and TADbit
genome build: SPRETEIJ_genome.tar.gz

molecule: genomic DNA

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
In situ Hi-C was performed using the Arima-HiC kit (Arima Genomics Inc) as described by the manufacturer.


title: SPRET_BMDM_p65_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: SPRETEIJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ChIP-Seq: Chromatin immunoprecipitation (ChIP) was performed as described previously (Oishi et al., 2017). In brief, cells were resuspended in swelling buffer (10mM HEPES/KOH (pH7.9), 85mM KCl, 1mM EDTA, 0.5% IGEPAL CA-630) with protease inhibitors for 5min and then spun down and resuspended in 500μl lysis buffer (50mM Tris/HCl (pH7.4), 1% SDS, 0.5% Empigen BB, 10mM EDTA) with protease inhibitors, and chromatin was sheared using the Bioruptor (Diagenode). Lysate was diluted with 750μl dilution buffer (20mM Tris/HCl, 100mM NaCl, 0.5% TritonX-100, 2mM EDTA), 1% was taken as input DNA, and immunoprecipitation was carried out overnight with Dynabeads protein G bound to specific antibodies for PU.1 (Santa Cruz, sc- 352X), C/EBP (Santa Cruz, sc-150), H3K4me2 (Millipore, 07-030), H3K27ac (Active Motif, 39135), CJUN (Santa Cruz, sc-1694), P65 (Santa Cruz, sc-372X), USF2 (Santa Cruz, sc-862X) and RUNX1 (Santa Cruz, sc-365644). Beads were washed twice each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently eluted with elution buffer (TE, 2% SDS). DNA was reverse- crosslinked and purified using ChIP DNA Clean & Concentrator (Zymo Research) according to the manufacturer's instructions. Sequencing libraries were prepared from eluted DNA by blunting, A-tailing, adaptor ligation as previously described (Heinz et al., 2010) using NextFlex barcodes (Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected using PAGE/TBE gels for 200-400bp fragments by gel extraction and single-end sequenced on HiSeq 4000 or NextSeq 500.

value: p65 (Vendor:Santa Cruz, Cat#sc-372X)


title: SPRET_BMDM_RNA_polyA_notx_6h_rep2


title: Monosomy_8 [16792]

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

state: NY

address: 550 First Avenue

institute: NYU School of Medicine

description:
16792
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

data_processing:
STAR/2.5 aligner against hg19 reference.
Gene counting against hg19 reference utilizing featureCounts/1.5.3.
Normalization of raw counts and DE test utilizing DESeq2/3.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SuppTable7-Gene-Expression-Table.xlsx: Excel file includes expression values.

source_name: Monosomy 8 embryo

extract_protocol:
SMARTer v4 Ultra Low kit.
Low Input Library prep, Clontech.

value: blastocyst

tag: genotype/variation

value: Monosomy 8


title: Monosomy_9 [16754]

description:
16754
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 9 embryo

value: Monosomy 9


title: SPRET_BMDM_Bisulfite

description:
Bisulfite sequencing
Processed data file:
SPRET_cytosine_report.txt
Processed data file available in:

data_processing:
Faste files from sequencing experiments were mapped to the custom genome using default parameters for BISMARK and shifted back to reference coordinates. BISMARK was used for further downstream analysis
genome build: SPRETEIJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
Bisulfite-seq: Bisulfite sequencing was performed as described in (Urich et al., 2015). DNA from C57Bl/6J and SPRET/EiJ BMDMs was isolated using the PureLink Genomic DNA Kit (Thermo Fisher Scientific) as described by the manufacturer. 2 μg of gDNA supplemented with 0.5% non-methylated ʎ- DNA (Promega) was used as input. DNA was fragmented to a 200 bp peak size using the Covaris microTube sonicator, size selected, end-repaired, adenylated and methylated adapters ligated exactly as detailed in Urich et al. Cytosine to uracil conversion was performed with the EZ DNA methylation-Gold kit (Zymo Research) with 450ng of adapter-ligated gDNA input as described within. Following bisulfite-treated DNA purification, reactions were amplified with four cycles, purified using one volume of AMPure XP bead solution and sequenced on an Illumina NextSeq 500 for 25 million and 31 million reads for C57Bl/6J and SPRET/EiJ, respectively. Conversion rates were 99.69%.


title: Monosomy_XO [16146]

description:
16146
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy XO embryo

value: Monosomy XO


title: Monosomy_XO [16145]

description:
16145
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_9 [16775]

description:
16775
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SPRET_BMDM_5GRO_KLA_1h_rep1

description:
5'Gro-Seq
Processed data file:
tss_SPRET_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: SPRETEIJ_genome.tar.gz


title: Monosomy_7 [16730]

description:
16730
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 7 embryo

value: Monosomy 7


title: Monosomy_7 [16726]

description:
16726
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SPRET_BMDM_ATAC_notx_rep2

description:
ATAC-seq
Processed data file:
peaks_SPRET_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ATAC-seq: To approximately 150k nuclei in 22.5ul GRO freezing buffer, isolated as described for GRO-seq above, 25ul DNA Tagmentation buffer was added, reaction mixed and 2.5uL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) added. Mixture was incubated at 37°C for 30 minutes and subsequently purified using the Zymogen ChIP DNA purification kit as described by the manufacturer. DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 10 cycles. PCR reactions were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, size selected using PAGE/TBE gels for 160 – 280 bp and DNA eluted as described for GRO-seq.


title: SPRET_BMDM_ATAC_KLA_1h_rep1

description:
ATAC-seq
Processed data file:
peaks_SPRET_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: Monosomy_8 [16781]

description:
16781
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SPRET_BMDM_PLAC_notx

description:
formaldehyde-crosslinked PLAC-Seq
Processed data file:
PLAC_seq_consensus_interactions.txt

data_processing:
Library strategy: PLAC-Seq
Fastq files from sequencing experiments were processed according to the FitHiChIP pipeline
genome build: SPRETEIJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
PLAC-seq libraries were prepared as described in (Fang et al., 2016).

value: H3K4me3 (Vendor:Millipore, Cat#04-745)


title: Monosomy_5 [16750]

description:
16750
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 5 embryo

value: Monosomy 5


title: PWK_BMDM_ATAC_notx_rep1

description:
ATAC-seq
Processed data file:
peaks_PWK_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: PWKPHJ_genome.tar.gz

value: PWK/PhJ


title: PWK_BMDM_5GRO_KLA_1h_rep1

description:
5'Gro-Seq
Processed data file:
tss_PWK_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: PWKPHJ_genome.tar.gz


title: Monosomy_4 [16794]

description:
16794
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 4 embryo

value: Monosomy 4


title: PWK_BMDM_5GRO_notx_rep2

description:
5'Gro-Seq
Processed data file:
tss_PWK_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar


title: Monosomy_4 [16742]

description:
16742
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: NOD_BMDM_PLAC_notx

data_processing:
Library strategy: PLAC-Seq
Fastq files from sequencing experiments were processed according to the FitHiChIP pipeline
genome build: NODSHILTJ_genome.tar.gz

value: NOD/ShiLtJ


title: Monosomy_5 [16741]

description:
16741
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_22 [16616]

description:
16616
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 22 embryo

value: Monosomy 22


title: NOD_BMDM_GRO_KLA_1h_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: NODSHILTJ_genome.tar.gz

value: bone marrow derived macropages (BMDM)

value: 7 day cultured BMDMs


title: Monosomy_22 [16611]

description:
16611
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: NOD_BMDM_ATAC_notx_rep1

description:
ATAC-seq
Processed data file:
peaks_NOD_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: NODSHILTJ_genome.tar.gz


title: Monosomy_21 [16743]

description:
16743
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 21 embryo

value: Monosomy 21


title: Monosomy_21 [16615]

description:
16615
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: NOD_BMDM_ATAC_KLA_1h_rep1

description:
ATAC-seq
Processed data file:
peaks_NOD_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

value: KLA 1h


title: PWK_BMDM_GRO_notx_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: PWKPHJ_genome.tar.gz

value: no treatment


title: Monosomy_20 [16749]

description:
16749
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 20 embryo

value: Monosomy 20


title: F1_C57_SPRET_BMDM_GRO_notx

description:
GRO-Seq
Processed data file:
GRO_Seq_F1_C57_SPRET_notx.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for bowtie2 and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & SPRETEIJ_genome.tar.gz

value: C57BL/6J x SPRET/EiJ


title: Monosomy_2 [16753]

description:
16753
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 2 embryo

value: blastocyst

value: Monosomy 2


title: Monosomy_20 [16739]

description:
16739
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: F1_C57_PWK_BMDM_PU1_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FPC_PWK_C57_PU1_notx.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for bowtie2 and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & PWKPHJ_genome.tar.gz

value: C57BL/6J x PWK/PhJ

value: PU1 (Vendor:Santa Cruz, Cat#sc-352X)


title: Monosomy_6 [16724]

description:
16724
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 6 embryo

value: Monosomy 6


title: NOD_BMDM_5GRO_KLA_1h_rep2

description:
5'Gro-Seq
Processed data file:
tss_NOD_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: NODSHILTJ_genome.tar.gz


title: Monosomy_2 [16722]

description:
16722
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SPRET_BMDM_GRO_KLA_1h_rep2

value: SPRET/EiJ


title: F1_C57_PWK_BMDM_PU1_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FPC_PWK_C57_PU1_KLA.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: Monosomy_19 [16769]

description:
16769
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 19 embryo

value: Monosomy 19


title: NOD_BMDM_GRO_notx_rep1


title: Monosomy_19 [16729]

description:
16729
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_18 [16773]

description:
16773
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 18 embryo

value: Monosomy 18


title: Monosomy_3 [16744]

description:
16744
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 3 embryo

value: Monosomy 3


title: C57_BMDM_PLAC_notx

description:
formaldehyde-crosslinked PLAC-Seq
Processed data file:
PLAC_seq_consensus_interactions.txt
PLAC_seq_consensus_interactions.txt

data_processing:
Library strategy: PLAC-Seq
Fastq files from sequencing experiments were processed according to the FitHiChIP pipeline
genome build: mm10

value: H3K4me3 (Vendor:Millipore, Cat#04-745)


title: C57_BMDM_RNA_polyA_KLA_6h_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_C57_SPRET_INFg_response_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: mm10

value: bone marrow derived macropages (BMDM)

value: KLA 6h


title: Monosomy_18 [16752]

description:
16752
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_17 [16751]

description:
16751
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 17 embryo

value: Monosomy 17


title: Monosomy_17 [16745]

description:
16745
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: C57_BMDM_RNA_polyA_KLA_6h_rep1

value: 7 day cultured BMDMs


title: NOD_BMDM_ATAC_KLA_1h_rep2

description:
ATAC-seq
Processed data file:
peaks_NOD_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

value: NOD/ShiLtJ

value: KLA 1h


title: NOD_BMDM_5GRO_notx_rep2

description:
5'Gro-Seq
Processed data file:
tss_NOD_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar

value: no treatment


title: Monosomy_16 [16723]

description:
16723
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 16 embryo

value: blastocyst

value: Monosomy 16


title: Monosomy_16 [16721]

description:
16721
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: C57_BMDM_Input_cJun_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked input DNA
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: mm10

source_name: bone marrow derived macropages (BMDM)


title: C57_BMDM_HiC

description:
Hi-C sequencing
Processed data file:
C57_BMDM_HiC_raw_interactions_1MB.txt

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Hi-C experiments were further analyzed using HOMER and TADbit
genome build: mm10


title: C57_BMDM_cJun_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_cJun_notx_opt.
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: mm10

value: cJun (Vendor:Santa Cruz, Cat#sc-1694)


title: WT-H3K27me3-ChIP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq and 4C-seq reads were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ChIP-seq, ATAC-seq and 4C-seq

growth_protocol: MOLM13 cells were cultured on RPMI 1640 with 10% FBS.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3 and H3K79me2 antibody.  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    4C seq library samples derived from two enzyme digestion BglII and NlaIII and ligation with T4 ligase.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: cell types

value: Human-derived acute myeloid leukemia cells

value: wild type

value: Anti-H3K27me3, Millipore, Cat No. 07-449


title: Monosomy_15 [16728]

description:
16728
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

data_processing:
STAR/2.5 aligner against hg19 reference.
Gene counting against hg19 reference utilizing featureCounts/1.5.3.
Normalization of raw counts and DE test utilizing DESeq2/3.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SuppTable7-Gene-Expression-Table.xlsx: Excel file includes expression values.

source_name: Monosomy 15 embryo

value: Monosomy 15


title: CBS79KO-H3K4me3-ChIP-seq

value: Anti-H3K4me3,  Millipore,  Cat No. 04-745


title: CBS79KO-H3K27me3-ChIP-seq


title: WT-H3K4me3-ChIP-seq


title: Monosomy_15 [16614]

description:
16614
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: WT_2_RNAseq


title: CBS79KO_1_RNAseq


title: CBS79KO_2_RNAseq


title: C57_BMDM_RNA_polyA_notx_6h_rep1


title: C57_BMDM_RNA_polyA_notx_6h_rep2


title: C57_BMDM_cJun_notx_rep1


title: WT_1_RNAseq


title: C57_BMDM_cJun_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_cJun_KLA_opt.
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: Monosomy_14 [16796]

description:
16796
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 14 embryo

value: Monosomy 14


title: Monosomy_14 [16772]

description:
16772
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: C57_BMDM_Input_cJun_notx_rep2


title: Monosomy_13 [16795]

description:
16795
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 13 embryo

value: Monosomy 13


title: C57_BMDM_Bisulfite

description:
Bisulfite sequencing
Processed data file:
C57_cytosine_report.txt

data_processing:
Faste files from sequencing experiments were mapped to the custom genome using default parameters for BISMARK and shifted back to reference coordinates. BISMARK was used for further downstream analysis
genome build: mm10

value: bone marrow derived macropages (BMDM)


title: C57_BMDM_5GRO_notx_rep1

description:
5'Gro-Seq
Processed data file:
tss_C57_5GRO_notx.
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie and shifted back to reference coordinates2. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: mm10


title: BALB_BMDM_PLAC_notx

description:
formaldehyde-crosslinked PLAC-Seq
Processed data file:
PLAC_seq_consensus_interactions.txt

data_processing:
Library strategy: PLAC-Seq
Fastq files from sequencing experiments were processed according to the FitHiChIP pipeline
genome build: BALBCJ_genome.tar.gz

value: BALB/cJ

value: 8 day cultured BMDMs

value: H3K4me3 (Vendor:Millipore, Cat#04-745)


title: Monosomy_12 [16725]

description:
16725
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 12 embryo

value: Monosomy 12


title: BALB_BMDM_GRO_KLA_1h_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: BALBCJ_genome.tar.gz

value: 7 day cultured BMDMs

value: KLA 1h


title: Monosomy_11 [16720]

description:
16720
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 11 embryo

value: blastocyst

value: Monosomy 11


title: BALB_BMDM_ATAC_notx_rep1

description:
ATAC-seq
Processed data file:
peaks_BALB_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: BALBCJ_genome.tar.gz

value: no treatment


title: Monosomy_10 [16797]

description:
16797
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 10 embryo

value: Monosomy 10


title: C57_BMDM_cJun_KLA_1h_rep1

value: cJun (Vendor:Santa Cruz, Cat#sc-1694)


title: Monosomy_11 [16748]

description:
16748
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_13 [16780]

description:
16780
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_10 [16757]

description:
16757
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Monosomy_1 [16782]

description:
16782
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Monosomy 1 embryo

value: Monosomy 1


title: Trisomy_XXY [16186]

description:
16186
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy XXY embryo

value: Trisomy XXY


title: Monosomy_1 [16756]

description:
16756
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_XXX [16187]

description:
16187
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy XXX embryo

value: Trisomy XXX


title: Trisomy_XXY [16185_asterick]

description:
16185
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: AUS-LTS-5

type: genomic

city: Seoul

first: Chul-Kee

last: Park

address: 101 Daehak-ro, Jongno-gu

department: Department of Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: We filtered the following probes in the Illumina Infinium HumanMethylation450 BeadChip: i) probes with a detection p-value is above 0.01 in more than 5% of samples. According to Illumina, the detection-p-value of a probe is estimated by comparing the measured CpG site intensity (the sum of methylated probe intensity and unmethylated probe intensity) with the intensities of negative control probes., ii) the probes whose bead counts are less than 3 in more than 5% of samples, iii) probes with SNP sites, iv) probes whose sequences align to multiple locations in the reference genome, v) probes associated with the sex chromosomes. The filtering was done by using R package ChAMP (Morris et al. 2014), resulting in 409,307 sites from 485,512 sites.

source_name: Glioblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted by standard methods for formalin-fixed paraffin-embedded tumor tissue. The QIAamp DNA FFPE Tissue Kit (Qiagen) was used to isolate and purify DNA from formalin fixed, paraffin embedded tissue.

value: Glioblastoma

tag: survival group

value: LTS (survival longer than 3 years)

tag: race

value: WHITE

tag: gender


title: AUS-LTS-8


title: SNU-STS-10

value: STS (survival shorter than 1 year)

value: ASIAN

value: Male


title: AUS-LTS-11


title: SNU-STS-9

value: Female


title: SNU-STS-6


title: AUS-LTS-2


title: AUS-LTS-3


title: AUS-LTS-10


title: AUS-LTS-4


title: AUS-LTS-6


title: SNU-STS-12


title: AUS-LTS-1


title: Trisomy_9 [16466]

description:
16466
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 9 embryo

value: Trisomy 9


title: SNU-STS-4


title: SNU-STS-11


title: AUS-LTS-9


title: SNU-STS-7


title: AUS-LTS-7


title: SNU-LTS-33


title: Trisomy_XXX [16147]

description:
16147
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-STS-5


title: Trisomy_9 [16774]

description:
16774
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-LTS-34


title: SNU-STS-2


title: SNU-STS-8


title: Trisomy_8 [16432]

description:
16432
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 8 embryo

value: Trisomy 8


title: SNU-STS-3


title: SNU-LTS-31


title: SNU-STS-1


title: SNU-LTS-29


title: Trisomy_7 [16477]

description:
16477
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 7 embryo

value: blastocyst

value: Trisomy 7


title: CBS79KO-H3K79me2-ChIP-seq

value: Human-derived acute myeloid leukemia cells

value: Anti-H3K79me2,  Abcam,  Cat No. ab3594


title: SNU-LTS-30


title: Trisomy_7 [16732]

description:
16732
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_8 [16420]

description:
16420
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-LTS-27


title: WT-H3K79me2-ChIP-seq

value: wild type


title: U2OS-PLKO.1 DMSO R3

type: RNA

city: Singapore

first: Crasta

last: Karen

state: Singapore

address: 59 Nanyang Drive

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

description: Dmso-treated U2OS cells

hyb_protocol: In vitro transcription (IVT) generated cRNA was then purified and subjected to 2nd-cycle single-stranded sense cDNA synthesis which was later fragmented, labelled, and hybridized to Affymetrix Human Transcriptome 2.0 array for 16 hours at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing:
All CEL files from the 4 total RNA samples hybridized to GeneChip® Human Transcriptome 2.0 arrays were imported into Partek Genomics Suite version 7.0 with the core meta-probe set. The configeration consisted of a pre-background adjustment for GC content and probe sequence, RMA for background correction, quantile normalization and probe set normalization using median computation from the raw data of each file. All signal were log2 transformed. Library files were those specified by Affymetrix (Human gene 2.0 AGCC library file) and the annotation file version was HTA-2_0.na36.hg19.transcript.csv.
The Anova was performed for all samples with contrasts set to type of drug treament. Genes differentially expressed by >2.5 and <-2.5 folds between two biological replicates of Noc vs dmso with an unadjusted p-value of less than 0.05 was selected and examined.

label: Biotin

source_name: U2OS cells

label_protocol: All RNA samples were processed according to the Affymetrix recommended protocols, and Origen Labs’ SOP. Briefly, 100ng of total RNA was reverse transcribed to produce cDNA/mRNA hybrid molecule, which was subsequently used as a template to create double stranded cDNA. This double-stranded cDNA was then amplified via in vitro transcription (IVT) to produce cRNA.

growth_protocol: U2OS cells were maintained at 37oC with 5% CO2 atmosphere with DMEM supplement with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol: Cells were trypsinised, followed by total RNA extraction using RNeasy plus Mini Kit (QIAGEN) according to manufacturer's instructions.

treatment_protocol: U2OS cells were synchronised by 24h of serum starvation, followed by 24h of thymidine treatment and 3h of drug-free media before nocodazole treatment. Cells were then treated with nocodazole or DMSO for 48h.

value: U2OS cells

tag: agent

value: DMSO


title: MOLM13-CBS79KO-4C-seq

data_processing:
library strategy: 4C-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq and 4C-seq reads were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ChIP-seq, ATAC-seq and 4C-seq


title: MOLM13-WT-4C-seq


title: U2OS-PLKO.1 NOC 48h R3

description: Noc-treated U2OS cells

value: nocodazole


title: SNU-LTS-26

value: Glioblastoma


title: Trisomy_6 [16747]

description:
16747
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 6 embryo

value: Trisomy 6


title: U2OS-PLKO.1 DMSO R2

description: Dmso-treated U2OS cells


title: Trisomy_5 [16463]

description:
16463
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 5 embryo

value: Trisomy 5


title: Trisomy_6 [16727]

description:
16727
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: CBS79KO_1_ATAC-seq


title: SNU-LTS-24

value: LTS (survival longer than 3 years)


title: Trisomy_5 [16770]

description:
16770
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-LTS-23

value: ASIAN


title: Trisomy_4 [16746]

description:
16746
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 4 embryo

value: Trisomy 4


title: 017_7_21_SS2_N729S507

city: San Diego

first: Meng

last: Zhao

address: 9420 Athena Cir

institute: La Jolla Institute of Allergy and Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: iNKT cell subsets

extract_protocol:
Sorted cells were lysed in Trizol LS (ThermoFisher), RNA was prepared using miRNeasy micro kit from Qiagen and quantified using real-time PCR
Adapted from the Smart-seq2 protocol, an oligo-based capture of Poly-A tailed mRNA was carried out followed by a high-fidelity reverse transcription using locked nucleic acids (LNA)-oligos to obtain full-length transcripts. mRNA complementary (c)DNA strands were then amplified using a PCR-based method and sequencing adaptors incorporated into the cDNA fragments in a single step using Tn5 transposase technology (Nextera XT reagents and barcoded adaptors kits).

value: Thymus

tag: cell type

tag: genotype/model

value: SKG

tag: background strain

value: BALB/c


title: CBS79KO_2_ATAC-seq


title: U2OS-PLKO.1 NOC 48h R2

description: Noc-treated U2OS cells


title: WT_2_ATAC-seq


title: SNU-LTS-20

value: Female


title: SNU-LTS-25


title: WT_1_ATAC-seq


title: SNU-LTS-22


title: 018_7_21_SS17_N729S508


title: Trisomy_3 [16783]

description:
16783
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 3 embryo

value: blastocyst

value: Trisomy 3


title: Trisomy_4 [16606]

description:
16606
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_3 [16434]

description:
16434
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-LTS-21


title: Trisomy_21 [16001]

description:
16001
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 21 embryo

value: Trisomy 21


title: SNU-LTS-19


title: SNU-LTS-10


title: 014_7_11_WW2_N729S503

value: WT


title: Trisomy_3 [16418]

description:
16418
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: 016_7_21_SS1_N729S506


title: SNU-LTS-13


title: 012_7_11_SS17_N728S511


title: Trisomy_22 [15098]

description:
15098
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 22 embryo

value: Trisomy 22


title: 015_7_11_WW17_N729S505


title: SNU-LTS-2

value: Male


title: SNU-LTS-7


title: Trisomy_22 [15096]

description:
15096
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: SNU-LTS-15


title: 013_7_11_WW1_N729S502


title: Trisomy_21 [15284]

description:
15284
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: 011_7_11_SS2_N728S510


title: SNU-LTS-1


title: EP91

city: Chuo-ku

first: Kohei

last: Fukuoka

address: 5-1-1 Tsukiji

department: Division of Brain Tumor Translational Research

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software was used. Beta values were obtained after background correction and normalization to internal controls.

label: Cy3, Cy5

source_name: Ependymoma

extract_protocol: Genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

value: female

tag: age

tag: tumor location

value: posterior fossa

tag: pathological diagnosis

value: anaplastic ependymoma (G3)

tag: molecular status

value: ependymoma,  posterior fossa group A


title: Trisomy_21 [15283]

description:
15283
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

tag: tissue


title: Trisomy_20 [16605]

description:
16605
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 20 embryo

value: Trisomy 20


title: 010_7_11_SS1_N728S508


title: Trisomy_20 [16481]

description:
16481
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: 009_7_10_SS17_N728S507


title: 008_7_10_SS2_N728S506


title: 007_7_10_SS1_N728S505


title: 006_7_10_WW17_N728S503


title: Trisomy_19 [16478]

description:
16478
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 19 embryo

value: Trisomy 19


title: Trisomy_19 [16791]

description:
16791
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_2 [16740]

description:
16740
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 2 embryo

value: Trisomy 2


title: SNU-LTS-18

value: Glioblastoma

value: LTS (survival longer than 3 years)

value: ASIAN


title: Trisomy_18 [16004]

description:
16004
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 18 embryo

value: Trisomy 18


title: EP95

value: male


title: 004_7_10_WW1_N727S511

value: Thymus

value: BALB/c


title: Trisomy_18 [16003]

description:
16003
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

value: blastocyst


title: EP83

value: ependymoma (G2)

value: ependymoma,  posterior fossa group B


title: Trisomy_2 [16798]

description:
16798
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_18 [16002]

description:
16002
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: 003_7_5_WW17_N727S510

value: WT


title: 002_7_5_WW2_N727S508


title: 005_7_10_WW2_N728S502


title: Trisomy_17 [16731]

description:
16731
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 17 embryo

value: Trisomy 17


title: 001_7_5_WW1_N727S507


title: SGK rep. 2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
SKG-NKTO-2
differential_expression.txt.gz
raw_count_matrix.txt.gz

data_processing:
Reads were aligned using Hisat2 (v.2.1.0) with unstranded default parameters and the primary GRCm38 genome assembly (downloaded 08/26/2016). Reads overlapping exons were enumerated using featureCounts (subread v.1.4.4) requiring a minimum mapping quality of 10 using GRCm38.85 ensembl annotations (downloaded 08/26/2016).
Differential expression was computed using DESeq2 (v1.14.1) using the count data generated by featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Differential expression results as generated by DESeq2 are found in differential_expression.txt. Raw counts per gene generated by featureCounts are supplied in the raw_count_matrix.txt

molecule: polyA RNA

source_name: Stage 0 iNKT cells from thymus

extract_protocol:
Stage 0 iNKT cells (PBS57-CD1d tetramer+, CD44-, CD24+, CD69+, CD4lo/-, CD8-) were sorted from the pooled thymi of 3 BALB/c or SKG mice (about 1000 cells were recovered) directly into Trizol buffer. Three independents samples were generated for each genotype. Stage 0 iNKT cells (PBS57-CD1d tetramer+, CD44-, CD24+, CD69+, CD4lo/-, CD8-) were sorted from the pooled thymi of 3 BALB/c or SKG mice (about 1000 cells were recovered) directly into Trizol buffer. Three independents samples were generated for each genotype. Total RNA for each sample was extracted using the Direct-zol RNA MicroPrep kit from Zymo Research.
Libraries were prepared from polyA+ RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing by Takara. Briefly, purified RNA was reverse transcribed using SMARTScribe Reverse Transcriptase and template switching primers. A preamplification step of 18 PCR cycles was performed using the SeqAmp DNA Polymerase. The PCR product was purified using AMPureXP beads (Beckman Coulter) and 1 ng was further used for library preparation using the Nextera XT LibraryPrep kit (Illumina). Tagmented DNA was amplified with a 12-cycle PCR and again purified with AMPureXP beads. Library size distri- bution and yield were evaluated using the Bioanalyzer high- sensitivity DNA kit. Libraries were pooled at equimolar ratios and sequenced with the rapid run protocol on a HiSEq. 2500 (Illumina) with 50-nt single end cycling.

tag: strain

tag: genotype

value: SKG

value: 8 to 10 weeks

value: Stage 0 iNKT cells


title: Trisomy_16 [16482]

description:
16482
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 16 embryo

tag: genotype/variation

value: Trisomy 16


title: SGK rep. 3

description:
SKG-NKTO-3
differential_expression.txt.gz
raw_count_matrix.txt.gz


title: Trisomy_17 [16480]

description:
16480
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP98

value: posterior fossa

value: Ependymoma (G2)


title: Trisomy_16 [16467]

description:
16467
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP128

value: ependymoma,  posterior fossa group A


title: SGK rep. 1

description:
SKG-NKTO-1
differential_expression.txt.gz
raw_count_matrix.txt.gz


title: Trisomy_15 [15094]

description:
15094
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 15 embryo

value: Trisomy 15


title: BALB/c rep. 3

description:
BALB-NKTO-4
differential_expression.txt.gz
raw_count_matrix.txt.gz


title: Trisomy_15 [15093]

description:
15093
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: BALB/c rep. 2

description:
BALB-NKTO-3
differential_expression.txt.gz
raw_count_matrix.txt.gz


title: BALB/c rep. 1

description:
BALB-NKTO-2
differential_expression.txt.gz
raw_count_matrix.txt.gz


title: Trisomy_15 [15092]

description:
15092
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP115

value: supratentorial

value: anaplastic ependymoma (G3)

value: ependymoma,  RELA fusion


title: EP131

value: female


title: Trisomy_15 [15090]

description:
15090
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

value: blastocyst


title: WT_young_LSKs_WGBS

city: Shanghai

first: Qiuhua

last: Huang

address: 197 ruijin road II

institute: Shanghai Institute of Hematology

data_processing:
Basecalls were performed using CASAVA for RNA-seq and bisulfite-seq.
Reads quality was checked for each sample using FastQC. RNA-seq reads were filtered using Seqtk with following parameters: reads containing adaptor sequence, length of reads less than 25bp, Q value of reads less than 20bp at 3' end, ribosome RNA reads. Reads quality of bisulfite-seq was checked for each sample using FastQC. Trimmomatic software was used to trim low quality reads with following parameters: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLUMINACLIP:adapter.fa:2:30:7:1:true, length of reads less than 36bp, non-paired reads.
RNA-seq reads were aligned to mm10 genome using Hisat2 (version:2.0.4). Bisulfite-seq reads were aligned to the mm10 mouse genome using Bismark software.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of RNA-seq read were calculated using Stringtie (version:1.3.0), trimmed mean of M values and perl script. Bismark was used to detect the DNA methylation site and calculated methylation level with a formula ML=mC/(mC+umC).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_LSKs_RNAseq.txt: Tab-delimited text files include FPKM values for RNA-seq Samples.
Supplementary_files_format_and_content: *_LSKs_Bisulfite-Seq.bw: bigWig files for bisulfite-seq of WT and KO LSKs.

source_name: Bone marrow LSK cells

extract_protocol:
BM LSKs were sorted by BD FACSAria™ III. Total RNA of young and old WT and KO LSKs were harvested using Trizol reagent. Genomic DNA of young WT and KO LSKs were harvested using QIAamp DNA Mini Kit (Cat:51304, Qiagen).
VAHTS Total RNA-Seq (H/M/R) Library PrepKit (Cat:NR603-02, Vazyme) was used with 100ng of total RNA for the construction of sequencing libraries. Accel-NGS® Methyl-Seq DNA Library Kit was used with 100ng of genomic DNA for sequencing libraries.

tag: strain/background

value: Bone marrow LSK cells

value: 4 weeks after pI-pC induction


title: KO_young_LSKs_WGBS

value: Setd2 KO


title: EP108

value: male


title: Trisomy_15 [15091]

description:
15091
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_14 [16604]

description:
16604
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 14 embryo

value: Trisomy 14


title: EP127


title: KO_old_LSKs_RNAseq

value: 8 months after pI-pC induction


title: Trisomy_14 [16479]

description:
16479
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP71

value: ependymoma (G2)

value: ependymoma,  posterior fossa group B


title: WT_old_LSKs_RNAseq

value: WT


title: OX ZFHD10 GFP low blue light _ChIPseq

city: Glasgow

first: Eirini

last: Kaiserli

address: University Avenue

department: Institute of Molecular, Cell & Systems Biology

country: United Kingdom

institute: University of Glasgow

data_processing:
Peak detection, quality trimming and filtering of ChIP
seq reads was performed using sickle and Cutadapt version 1.5 (Martin, 2011,http://dx.doi.org/10.14806/ej.17.1.200) and mapping of the pre-processed reads to the A. thaliana genome (TAIR10) was done using Bowtie version 0.12.7. Only the uniquely aligned reads were used for further analysis. The transcription factor binding site enrichment was determined using SICER version 1.1. Window and gap sizes were set at 50 bp and 200 bp, respectively. An FDR cut-off 0.1 was used and redundant reads were eliminated from analysis. Annotation of ChIP enriched peaks and identification of enriched motifs was done using HOMER (http://homer.ucsd.edu/homer/) . The transcript database required for chromosome coordinate information was created using the transcriptome annotation file in GFF format (TAIR10).

organism: Arabidopsis thaliana

source_name: OX ZFHD10

growth_protocol: Arabidopsis seeds were surfaced sterilized and sown on 0.8% agar plates containing half-strength Murashige and Skoog salts in the  absence of sucrose. Plates were stratified in the dark at 4C for a minimum of 48 hours. Seedlings were grown for 7 d under low blue light before fixation and harvesting.

extract_protocol:
Plants were harvested, fixed via vacuum infiltration with 1% formaldehyde for 15 minutes. The reaction was stopped with 0.125 M glycine. Nuclei were isolated, lysed, and sonicated. Chromatin was immunoprecipitated with anti-GFP antibody.
Sequencing of the ChIP DNA was carried out in the Glasgow Polyomics Facility (University of Glasgow). A DNA library was prepared using the NEB Next Ultra II DNA Library Prep Kit (New England BioLabs Inc.) according to the manufacturer's protocol, which included fragments end repair, adaptor ligation, size selection and PCR amplification. The libraries were prepared from 1ng of ChIP DNA with 12 cycles of PCR giving final libraries of approximately 400bp. Subsequently, the samples were sequenced using an Illumina NextSeq 500 sequencer producing single-end 75 bp long reads

value: OX ZFHD10

tag: developmental stage

value: 7 days old seedlings

tag: light conditions

value: low blue light conditions

tag: antibody

value: anti-GFP


title: KO_young_LSKs_RNAseq


title: Trisomy_13 [16425]

description:
16425
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 13 embryo

value: Trisomy 13


title: WT_young_LSKs_RNAseq


title: Trisomy_12 [16431]

description:
16431
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 12 embryo

value: Trisomy 12


title: Col-0 GFP low blue light _ChIPseq


title: EP104

tag: gender

value: female

value: posterior fossa

value: Ependymoma (G2)

value: ependymoma,  posterior fossa group A


title: EP79

value: anaplastic ependymoma (G3)


title: Trisomy_13 [16433]

description:
16433
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

value: blastocyst


title: Trisomy_11 [16607]

description:
16607
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 11 embryo

value: Trisomy 11


title: EP109

value: male


title: EP29


title: Trisomy_11 [16419]

description:
16419
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: Trisomy_10 [16603]

description:
16603
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 10 embryo

value: Trisomy 10


title: 36_RYj15_wk-4_control

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.20.0.422 was used for demultiplexing.
Reads were aligned to an assembly of Indian Rhesus macaque (Macaca mulatta) (MacaM_Rhesus_Genome_v7.fasta) using STAR software (v2.5.2b)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

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

tag: ID

tag: timepoint

tag: treatment

value: control


title: Trisomy_10 [16465]

description:
16465
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: 34_RNi15_wk-4_control


title: EP75

source_name: Ependymoma

value: ependymoma (G2)

value: ependymoma,  posterior fossa group B


title: EP70


title: Trisomy_1 [16755]

description:
16755
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Trisomy 1 embryo

value: Trisomy 1


title: EP76


title: 33_RAk15_wk-4_control


title: EP55


title: Normal [Yael_17133]

description:
17133
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

source_name: Normal embryo

value: Normal


title: EP30


title: 32_RJl15_wk-4_control


title: Normal [Yael_17132]

description:
17132
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP60


title: 31_RHo15_wk-4_control


title: Normal [15282]

description:
15282
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: EP36

value: supratentorial

value: ependymoma,  RELA fusion


title: EP51


title: EP59


title: OX TZP GFP low blue light _ChIPseq

source_name: OX TZP

value: OX TZP

value: 7 days old seedlings

value: low blue light conditions

value: anti-GFP


title: 29_RHa15_wk-4_IFN

value: IFN


title: EP77

value: anaplastic ependymoma (G3)


title: Normal [15274]

description:
15274
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

value: blastocyst


title: 28_REb16_wk-4_IFN


title: KI-2

city: Tokyo

first: Masahiro

last: Uni

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Hematology and Oncology

institute: Graduate School of Medicine, The University of Tokyo

data_processing:
Fastq files were aligned to UCSC.mm10 (NCBI GRCm38) genome assembles using TopHat.
Expression profiles of assembled transcripts for each sample were calculated by Cufflinks, and Fragments Per Kilobase of transcript per Million Mapped reads (FPKM) values were calculated and normalized.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: KSL

extract_protocol:
2.4×106 of LSK cells isolated from eight Asxl1+/+ mice and eight Asxl1G643fs/+ mice by FACSAria III were subject to total RNA extraction with NucleoSpin RNA (TaKaRa Bio, Kusatsu), then obtained total RNAs were reverse transcribed into cDNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hematopoietic stem cell

value: eight weeks old


title: 30_RHb15_wk-4_IFN


title: KI-1


title: Normal [15275]

description:
15275
Processed data file: SuppTable7-Gene-Expression-Table.xlsx


title: miR-9/9*-124+shREST_Rep 2

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (assembly hg19).
Gene level expression (gene counts) file containing a histogram of the gene CPM values. Import into MS Excel or similar software as tab-delimitted text files or open in a standard text editor
Raw sequence reads generated by the Illumina sequencer for single reads.

source_name: Reprogramming cells_Day7

extract_protocol:
Total RNA was extracted using PureLink RNA mini kit (Thermo Fisher Scientific, 12183018A)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Reprogramming cells Day7

tag: expression

value: shREST


title: WT-2

tag: age


title: miR-9/9*-124+shREST_Rep 1


title: 27_RCy15_wk-4_IFN


title: 26_RBo15_wk-4_IFN


title: EP48

value: male

tag: tumor location

value: posterior fossa

tag: pathological diagnosis

value: ependymoma (G2)


title: WT-1

tag: tissue


title: EP26

value: anaplastic ependymoma(G3)

tag: molecular status


title: miR-9/9*-124+shCTL_Rep 2

value: shCTL


title: miR-9/9*-124+shCTL_Rep 1


title: 24_RYj15_wk34_control

value: control


title: 25_RRe15_wk-4_IFN


title: EP34

value: female

value: ependymoma,  posterior fossa group B


title: FB_shCTL_Replicate 2

source_name: Fibroblasts

value: Fibroblasts


title: FB_shCTL_Replicate 1


title: EP35

value: ependymoma,  posterior fossa group A


title: 23_RWl15_wk34_control


title: Trisomy_1 [16793]

description:
16793
Processed data file: SuppTable7-Gene-Expression-Table.xlsx

data_processing:
STAR/2.5 aligner against hg19 reference.
Gene counting against hg19 reference utilizing featureCounts/1.5.3.
Normalization of raw counts and DE test utilizing DESeq2/3.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SuppTable7-Gene-Expression-Table.xlsx: Excel file includes expression values.

value: Trisomy 1


title: 22_RNi15_wk34_control


title: K562-WKKD-V5chip

city: Nanjing

first: Jia-Yu

last: Chen

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

description: RNA-DNA hybrid

data_processing:
R-ChIP and GRO-seq sequence reads were mapped to the human genome (hg19) via default --local mode of Bowtie2
Repeatedly-mapped reads, reads with low mapping quality (-q 30 for R-ChIP and -q 2 for GRO-seq) and PCR duplicates were discarded according to Samtools
R-ChIP reads were extended to 150 nt (which corresponds to the average size of gel-isolated DNA fragments). We then used MACS2 with default settings to call narrow (or broad when necessary) R-loop peaks. Only confident R-loop peaks with ≥5 folds enrichment and with q-value ≤ 0.001 (or 0.0001 for broad peak) over background were kept for subsequent analyses. GRO-seq reads were extended to 90 nt and were used to estimate the expression level. The expression level in promoter proximal regions was quantified as RPKM in the region -30 to +300 bp from TSS, while the overall gene expression level was defined as RPKM in the downstream region from +300 bp of TSS to gene end.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1X penicillin-streptomycin; K562 cells were cultured in RPMI1640 with 10% FBS, 2mM sodium pyruvate and 1X penicillin-streptomycin.

extract_protocol:
For R-ChIP, cells expressing mutant RNASEH1 were fixed followed by nuclei extraction. Chromatin DNA was sheared to 250-600 bp in size by sonication followed by incubation with magnetic beads conjugated with anti-V5 antibody overnight at 4°C. Beads were sequentially washed in high salt buffers to remove non-specifically bound protein and chromtin complexes. The enriched RNASEH1-RNA/DNA complex was eluted and decrosslinked overnight at 65°C. After sequential RNase A and Proteinase K treatment, the precipitated hybrid was cleaned by phenol and phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. The recovered fragment was subjected to library construction. For GRO-seq, the intact nuclei were extracted and mixed with run-on reaction buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 200 U/ml RNaseOut, 1% Sarkosyl, 500 μM ATP, 500 μM GTP, 500 μM Br-UTP and 2 μM CTP) for in vitro run-on reaction and Br-U labeling for 5 min at 30°C. The reaction was stopped by adding TRIzol LS reagent (Thermo Fisher). RNA was then extracted followed by treatment wtih DNase I (Promega) and antarctic phosphatase (NEB). For immunopurification, equilibrated and blocked anti-BrdU agarose beads (Santa Cruz) were mixed with RNA for 1 hr at 4°C. After binding, beads were thoroughly washed and BrU-incorporated RNAs were eluted. The BrU-RNA end was repaired by T4 PNK (NEB) and then subjected to poly-A tailing reaction. Tailed RNAs were reverse transcribed into cDNA by using superscript III (Thermo Fisher) and the GRO-seq RT primer (5’-pAGATCGGAAGAGCGTCGTGTAG;GCAGAAGACGGCATACGAGATTTTTTTTTTTTTTTTTTTTVN-3’), where p indicates 5’ phosphate; ‘;’ indicates the abasic dSpacer furan, and VN indicates degenerate nucleotides. The cDNA products were treated with Exonuclease I (NEB) for 1 hr at 37°C to eliminate excessive primer. The resultant cDNA was resolved in 10% polyacrylamide TBE-urea gel and the fraction in the size range of 100-400 bp was excised and recovered.
For R-ChIP library construction, DNA from precipitated RNA/DNA hybrids was used as the template to generate dsDNA by random priming using a tail-containing N9 primer (5’- /invddt/CAAGCAGAAGACGGCATACGAGNNNNNNNNN-3’). An “A” base was then added to the 3’ end and the standard Illumina adaptor was ligated to one end of the resultant dsDNA. After purification,PCR were performed and the libraries in the size range of 130-350 bp were gel-isolated and purified. For GRO-seq library construction, cDNA was circularized and re-linearized. the libraries were amplified by PCR reaction. the final products were resolved in a non-denaturing 10% polyacrylamide TBE gel and libraries with the size 130-250 bp were recovered.
R-ChIP and GRO-seq

treatment_protocol: DRB (100 mM) was added to the medium to the final concentration of 100 μM. Cells were incubated for 2 hrs. To wash off DRB, the DRB-containing medium was aspirated, followed by washing with PBS. Fresh medium was then added and the cells were incubated for 30 min before harvest.

tag: rnaseh mutant


title: 21_RAk15_wk34_control


title: MEC1 125nm SD6 at 6 h

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

description:
M1SD6_6_RNA-seq
Transcriptome analysis by RNA-seq

data_processing:
TopHat 2.1.1 was used for mapping sequence reads to the human genome (hg19) with the parameter for Illumina stranded sequencing (--library-type fr-firststrand).
Cuffdiff was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet contains FPKM values for each transcript in all samples.

source_name: Blood

growth_protocol: The CLL cell lines MEC1 and the Epstein-Barr virus (EBV)-positive lymphoblast cell line GM12878 were maintained in RPMI-1640 medium (HyClone, Waltham, MA) supplemented with 10% fetal bovine serum (FBS), and 1× penicillin/streptomycin (P/S) at 37 °C.

extract_protocol:
RNA was extracted using Qiagen Qiazal reagents
Libraries for stranded mRNA sequencing were prepared using KAPA Stranded mRNAseq Kit Illumina platform (Kapa Biosystems) following manufacturer’s instructions.

treatment_protocol: SD6 was prepared in dimethyl sulfoxide (DMSO) as 10 mM stock solution and stored at -80°C until used. Cells were treated with SD6 at 125nm of SD6 for 24 hours. Samples were taken at 0, 2, 6, and 24 hour time point.

value: 125nm SD6 at 6 hr

tag: cell line

value: Blood

tag: cell types

value: CLL B Cell line, EBV(+)

tag: tumorigenicity

value: Leukemia cells


title: MEC1 125nm SD6 at 24 h

description:
M1SD6_24_RNA-seq
Transcriptome analysis by RNA-seq

value: 125nm SD6 at 24 hr


title: EP41

value: supratentorial

value: anaplastic ependymoma (G3)

value: ependymoma,  RELA fusion


title: MEC1 125nm SD6 at 2 h

description:
M1SD6_2_RNA-seq
Transcriptome analysis by RNA-seq

value: 125nm SD6 at 2 hr


title: 19_RHo15_wk34_control


title: 35_RWl15_wk-4_control


title: 18_RHb15_wk33_IFN

value: IFN


title: 20_RJl15_wk34_control


title: GM12878 125nm SD6 at 24 h

description:
GMSD6_24_RNA-seq
Transcriptome analysis by RNA-seq

value: CD19+ B Cell line, EBV(+)

value: Importalized lymhoblast cells


title: GM12878 125nm SD6 at 6 h

description:
GMSD6_6_RNA-seq
Transcriptome analysis by RNA-seq


title: 15_RCy15_wk33_IFN


title: 16_REb16_wk33_IFN


title: GM12878 125nm SD6 at 2 h

description:
GMSD6_2_RNA-seq
Transcriptome analysis by RNA-seq


title: 14_RBo15_wk33_IFN


title: EP46

value: female

value: posterior fossa

value: ependymoma (G2)


title: EP20


title: GM12878 125nm SD6 at 0 hr

description:
GMSD6_0_RNA-seq
Transcriptome analysis by RNA-seq

value: 125nm SD6 at 0 hr


title: High MV Rep 2

city: Daegu

first: Hong Gil

last: Nam

address: Techno jungang-daero

department: Center for Plant Aging Research

institute: IBS

description: Gene expression of high MV group replicate 2

hyb_protocol: cRNA was fragmented for 30 minutes followed by hybridize onto Agilent C. elegans gene expression Microarray containing 43.803 probes at 65 ℃ for 17 hours

scan_protocol: The arrays were scanned on AgilentG3_GX_1color mode using an Agilent Surescan microarray scanner (Agilent Technologies) and then raw data was obtained Feature Extraction software (ver. 11.5.1.1; Agilent Techologies).

data_processing: Processed by quantile normalization method using MATLAB

organism: Caenorhabditis elegans

source_name: N2 worms with high MV

label_protocol: The total RNA was transcribed to double-stranded complementary DNA (cDNA), synthesized into complementary RNA (cRNA), and finally labeled with cyanine-3-CTP.

growth_protocol: Wild type worms (N2) were grown under 20 ℃.

extract_protocol: Total RNA was extracted by using miRNeasy mini kit (Qiagen, Cat No. 217004).

treatment_protocol: Wild type worms (N2) were grown under 20 ℃ on NGM plate. At day 7-8 of adulthood, wild type worms were moved to a physical assay plate with no bacteria to measure the maximum velocity.

tag: strain

value: Whole body

value: Adult day 7-8

tag: physical ability

value: High maximum velocity (MV)


title: MEC1 125nm SD6 at 0 hr

description:
M1SD6_0_RNA-seq
Transcriptome analysis by RNA-seq

value: Blood

value: CLL B Cell line, EBV(+)


title: 11_RWl15_wk33_control

value: control


title: 17_RHa15_wk33_IFN


title: 12_RYj15_wk33_control


title: High MV Rep 1

description: Gene expression of high MV group replicate 1


title: Low MV Rep 1

description: Gene expression of low MV group replicate 1

source_name: N2 worms with low MV

value: Low maximum velocity (MV)


title: Low MV Rep 2

description: Gene expression of low MV group replicate 2


title: 10_RNi15_wk33_control


title: 9_RAk15_wk33_control


title: 8_RJl15_wk33_control


title: V703_Control probes

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Library strategy: ChIRP-Seq
Adapter and quality trimming of ChIRP-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIRP-seq reads were aligned to hg38 with Bowtie2 version 2.0.6, using default parameters
Potential PCR duplicates were removed from aligned ChIP Seq reads files
Peak calling was done with MACS v1.4
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-Seq peak file in Excel format and WIG track and were generated with MACS v.14. WIG track was normalized by dividing the WIG signal in each 25bp genomic bin by the average signal across the whole genome

source_name: Colon cancer cells

growth_protocol: Cells were grown in 2% FBS, at 5% CO2

extract_protocol:
DNA was isolated using a Qiagen DNA isolation kit
DNA libraries were prepared using an Illumina kit

treatment_protocol: No specific treatment

tag: disease state

value: Colon tumor

tag: Stage

value: Tumor stage B

tag: probe

value: Right colon


title: V703_lincDUSP-specific probes

value: lincDUSP-specific probes


title: ATMSC-ODM-c

city: Helsinki

first: Arjen

middle: WH

last: Gebraad

address: Haartmaninkatu 8, PO box 63

department: Department of Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

description: ODM (c)

hyb_protocol: A hybridization cocktail is prepared including the labeled, fragmented target and hybridization controls. The target is then hybridized to the GeneChip array in cartridge format during 16-hour incubation at 45 °C. Immediately following hybridization, the array is washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450, followed by scanning on a GeneChip® Scanner. GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 4, Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with R Statistical Software (R 3.4.0) using the Robust Multichip Average (RMA) algorithm of the oligo package as a normalization method. A modified t-statistics was calculated using the limma package. A false discovery rate (FDR) of < 0.05 was used to filter differentially expressed genes between treatments and control (EV-depleted MM).

label: biotin

source_name: ATMSC-ODM

label_protocol: The starting amount of total RNA was 100 ng. 15 ug of cRNA was used for single-stranded cDNA-synthesis (sscDNA). This single-stranded DNA sample is then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the unnatural dUTP residues and breaks the DNA strand. DNA is labeled by  erminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin. GeneChip® WT Plus Reagent Kit, Manual Target Preparation for GeneChip® Whole Transcript Expression Arrays, P/N  703174 Rev.5, Affymetrix.

growth_protocol: AT-MSCs at passages 4-6 were seeded in 96-well plates at 2.5 * 103 cells/cm2. ls. The cells were cultured for 18 days at 37°C and 5% CO2 in a humidified atmosphere during which the medium was refreshed every 2-3 days. Each time, EVs were freshly added.

extract_protocol: Total RNA was isolated from the AT-MSCs using the miRCURY™ RNA Isolation Kit (Exiqon A/S) according to the manufacturer's instructions.

treatment_protocol: The culture medium was removed, the wells were washed in PBS and the contents were collected for analysis.

tag: gender

value: adipose tissue-derived mesenchymal stem/stromal cells

tag: treatment

value: ODM


title: ATMSC-ODM-b

description: ODM (b)

value: female

tag: cell type


title: ATMSC-ODM-a

description: ODM (a)


title: 7_RHo15_wk33_control

tag: ID

tag: timepoint


title: 4_REb16_wk32_IFN

value: IFN


title: 5_RHa15_wk32_IFN


title: 3_RCy15_wk32_IFN


title: 2_RBo15_wk32_IFN


title: ATMSC-OCHAEV-b

description: OC HA-EVs (b)

source_name: ATMSC-OCHAEV

value: OC HA-EVs


title: ATMSC-OCTCPSEV-c

description: OC TCPS-EVs (c)

source_name: ATMSC-OCTCPSEV

value: OC TCPS-EVs


title: 1_RRe15_wk32_IFN


title: 6_RHb15_wk32_IFN


title: ATMSC-OCHAEV-a

description: OC HA-EVs (a)


title: ATMSC-OCTCPSEV-a

description: OC TCPS-EVs (a)


title: Control_3h_Rep_3

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

data_processing:
Demultiplexing
Quality control Fastq quality trimming using FastX version 0.0.13 and a cut-off value of phred score 20
Size filtering: discarding reads shorter than 15 nt (READemption 0.4.2, Förstner et al., 2014)
Mapping: Reads were mapped toreference genome sequences (NCBI accession no. NC_002976.3 [31 January 2014])using segemehl version 0.2.0-418 (READemption 0.4.2, Förstner et al., 2014)
Coverage calculation, normalization (READemption 0.4.2, Förstner et al., 2014) and differential gene expression profiling (DESeq2 version 1.16.1,  Love et al., 2014)
Genome_build: (NCBI accession no. NC_002976.3 [31 January 2014])
Supplementary_files_format_and_content: abundance measurements: text format, coverage files: wiggle format

organism: Staphylococcus epidermidis RP62A

source_name: S. epidermidis

growth_protocol: Bacterial strain S. epidermidis was grown statically in TSB medium (in a 6-well plate) at 37 degree C.

extract_protocol:
RNA was isolated from all the samples (control and C3-treated), using customized protocol described by (Franca et al., 2012).
Library preparation was performed according to the NEBNext Multiplex Small RNA Library Preparation Guide for Illumina

treatment_protocol: S. epidermidis was either treated with DMSO (final concentration 3.75% on cells) as control or C3 (62.5 µg/ml)

value: S. epidermidis RP62A treated with DMSO


title: EP8

tag: age

tag: tumor location

value: posterior fossa

tag: pathological diagnosis

value: anaplastic ependymoma (G3)

value: ependymoma,  posterior fossa group A


title: D39luxS gene mutant strain in vitro biofilm gene expression with respect to D39 wild type replicate III

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

description: Biological replicate 3 of 3

hyb_protocol: The Cy3 or Cy5-labeled cDNA probes were purified with QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Dried Cy3 or Cy5-labeled cDNA probes were resuspended in hybridization buffer containing 30% formamide, 5X SSC, 0.1% SDS, 0.1mg/ml salmon sperm DNA. The Cy3 or Cy5-labeled cDNA probes were mixed together and hybridized to a microarray slide (Shigella flexneri 2a str. 2457T plus Shigella flexneri 2a str. 301 virulence plasmid pCP301 Oligonucleotide 3x15K microarray) (Mycroarray.com, Ann Arbor, MI). After overnight at 42C, the slide was washed twice with washing solution 1 containing 2X SSC, 0.1% SDS for 5 min at 42C, and once with washing solution 2 containing 0.1X SSC, 0.1% SDS for 10 min at room temperature, and finally four times with 0.1X SSC for 1 min at room temperature. The slide was dried by centrifugation at 650 rpm for 5min.

scan_protocol: Hybridization image on the slide was scanned by Axon 4000B (Axon Instrument, Union City, CA).

data_processing: Hybridization image was analyzed by GenePix Pro 3.0 software (Axon Instrument, Union City, CA) to obtain gene expression ratios (reference vs test sample). Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions, India). Global lowess was used for data analysis with normalization.

organism: Streptococcus pneumoniae D39

source_name: D39 wild type biofilm III

label_protocol: cDNA probes for cDNA microarray analysis were prepared by the reverse-transcription of total RNA (25ug) in the presence of aminoallyl-dUTP and 6ug of random primers (Invitrogen, Carlsbad, CA) for 3 hrs. The cDNA probes were cleaned up using Microcon YM-30 column (Millipore, Bedford, MA) and then followed by coupling of Cy3 dye (for reference) or Cy5 dye (for test sample) (Amersham Pharmacia, Uppsala, Sweden).

growth_protocol: Biofilm were growth in 24 well microtitter plate in brain heart infusin medium for 18 hours at at 37° C. Thereafter washed 2 time to remove growth medium and RNA was extracted

extract_protocol: After washing cells were treated with 100 µl (3mg/ml) lysozyme and incubation for 4 min. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.The integrity of bacterial total RNA was checked by capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and further purified with an RNeasy Mini Kit ( Qiagen, Valencia, CA).

treatment_protocol: D39 wild type strain biofilms

tag: sample type

value: biofilm

source_name: D39 luxS mutant Biofilm cell 3


title: ATMSC-OCHAEV-c

description: OC HA-EVs (c)


title: Control_3h_Rep_2

tag: tissue


title: ATMSC-MCEV-c

description: MC-EVs (c)

source_name: ATMSC-MCEV

value: MC-EVs


title: D39luxS gene mutant strain in vitro biofilm gene expression with respect to D39 wild type replicate II

description: Biological replicate 2 of 3

source_name: D39 wild type biofilm II

source_name: D39 luxS mutant Biofilm cell 2


title: EP2

source_name: Ependymoma

value: supratentorial

tag: molecular status

value: ependymoma,  RELA fusion


title: Control_3h_Rep_1


title: Control_20min_Rep_3


title: D39luxS gene mutant strain in vitro biofilm gene expression with respect to D39 wild type replicate 1

description: Biological replicate 1 of 3

source_name: D39 wild type biofilm I

source_name: D39 luxS mutant Biofilm cell 1

treatment_protocol: 18 hours incubation in 24-well microtiter plate, after 18 h incubation period, non-adherent bacteria were removed by two washes with PBS


title: p_15_t_1E

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from patient N° 15 3 weeks from h-HSCT

hyb_protocol: Samples were hybridized to GeneChip Human Transcriptome Arrays 2.0 (Thermo Scientific) following the Encore Biotin Module user guide (NuGen Technlogies) and Affymetrix's Hybridization procedures

scan_protocol: Arrays were scanned following the GCS 3000 7G User guide (Thermo Scientific)

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray: hta20hsentrezgcdf v21.0.0 custom CDF. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: sorted NK cell subset from human PBMCs of h-HSCT recipient

label_protocol: Samples were amplified an labeled according to Ovation Pico WTA System V2 and Encore Biotin Module user guides (NuGen Technlogies)

extract_protocol: Toral RNAs were isolated following the microRNeasy kit guidelines (Qiagen)

value: PBMC

value: Natural Killer (NK) cells

tag: population


title: ATMSC-MCEV-b

description: MC-EVs (b)


title: ATMSC-MCEV-a

description: MC-EVs (a)


title: ATMSC-MM-c

description: MM (c)

source_name: ATMSC-MM

value: MM


title: Control_20min_Rep_2

tag: strain


title: p_26_t_1E

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from patient N° 26 3 weeks from h-HSCT


title: p_26_t_1A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from patient N° 26 3 weeks from h-HSCT


title: p_17_t_1E

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from patient N° 17 3 weeks from h-HSCT


title: 45min-pH4.5 rep1

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

data_processing:
For the analysis of RNA-Seq data, Bowtie2 was used to align raw reads to the R. tropici CIAT 899 genome (Genbank entry U00096.2) and samtools was used to obtain BAM files.
Differentially expressed genes (DEGs) were obtained via NOISeq 2.14.1 Bioconductor package using local fit and betaPrior parameter set to False.
A false discovery rate (FDR) threshold of 0.95 was set for DEG calling. Sample clustering and principal component analyses were performed upon variance stabilizing transformation of expression data (NOISeq package)
Transcripts were called as differentially expressed when the FDR-Log2FC adjusted p values were below 0.05 and fold-changes over 2 (Tarasona et al., 2011, Tarasona et al., 2015)
Genome_build: R. tropici CIAT 899 genome (Genbank entry U00096.2)
Supplementary_files_format_and_content: tab-delimited text files include read counts of every gene for each Sample

organism: Rhizobium tropici

source_name: Bacteria Strain

growth_protocol: Rhizobium tropici CIAT899 was routinely grown in TY medium (Beringer, 1974) or the minimal medium described by Kingsley and Bohlool (1992), adjusted to pH 6.8 (MM- buffered to pH 6.8 with 20 mM N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) Hepes)) or to pH 4.5 (MAM- buffered to pH 4.5 with 25 mM Homopiperazine-N,N’-bis-2[ethanesulfonic] acid [Homopipes]; Research organics, Cleveland, OH, U.S.A.) at 30° C. MM and MAM were solidified with 0.8% gelrite (Carl Roth GmbH, Karlsruhe, Germany). E. coli strains were grown in Luria-Bertani (LB) medium (Sambrook et al. 1989) at 37° C. Antibiotics were added at the following final concentrations (µg/mL): kanamycin (Km) 50; carbenicillin (Cb) 100; tetracycline (Tc) 10 and nalidixic acid (Nal) 20, if not indicated otherwise.

extract_protocol:
Total RNA was prepared using the RNeasy mini kit (QIAGEN, Hildesheim, Germany) with some modifications. Pellets were resuspended in RLT buffer, with lysozyme (20 mg per mL; QIAGEN, Hildesheim, Germany) containing Zirconium Oxide Beads (0.5 mm, Next Advance). Cells were disrupted using the Bullet Blender Tissue Homogenizer (Next-Advance) in impact-resistant 2 mL tubes. Genomic DNA was digested with RNase free DNase (QIAGEN, Hildesheim, Germany) for 20 minutes at room temperature. Final RNA concentrations were determined using a NanoDrop (Thermo Scientific). The typical OD260 to OD280 ratio of RNA samples was approximately 2.0. The integrity of RNA samples was verified using a TapeStation 2200 instrument (Agilent Technologies) and the RNA integrity number (RINe) was determined
RNA-Seq libraries were prepared using the TruSeq RNA sample Prep kit (Illumina) and sequenced (150 nt per read) by HiSeq 2500 instrument (Illumina) at the Beijing Genomics Institute (BGI, China)

treatment_protocol: For acid shock treatment cells were cultured in MM medium to mid-log phase, then washed with MAM and incubated another 45 minutes in MAM (pH 4.5) (sample CR). Cultures were harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen.

value: CIAT 899


title: 45min-pH4.5 rep2


title: Control_20min_Rep_1


title: p_15_t_1A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from patient N° 15 3 weeks from h-HSCT


title: p_17_t_1A

description: conventional CD56bright CD16neg (cCD56bright) NK cell subset from patient N° 17 3 weeks from h-HSCT


title: pH4.5 rep2


title: 45min-pH4.5 rep3


title: pH4.5 rep3


title: ATMSC-MM-b

description: MM (b)

value: adipose tissue-derived mesenchymal stem/stromal cells


title: C3_3h_Rep_3

value: S. epidermidis RP62A treated with the bioactive compound C3


title: C3_3h_Rep_1


title: pH4.5 rep1


title: HC3_0E

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from healthy donor 3

source_name: sorted NK cell subset from human PBMCs of healthy donor


title: ATMSC-MM-a

description: MM (a)

value: female


title: C3_3h_Rep_2


title: control pH6.8 rep3

value: control pH6.8


title: control pH6.8 rep2


title: control pH6.8 rep1


title: C3_20min_Rep_1


title: C3_20min_Rep_3


title: C3_20min_Rep_2


title: ATMSC-OCTCPSEV-b

description: OC TCPS-EVs (b)

value: OC TCPS-EVs


title: HC2_0E

description: unconventional CD56dim CD16neg (uCD56dim) NK cell subset from healthy donor 2