title: Airway epithelial cells - COPD1 - p7


title: U5_wild type YAP1 rep3

status: Public on Aug 04 2020

type: SRA

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

description: U5 neural stem cells transduced with pLJM1-wtYAP1-PGK-Puro rep 3

library_source: transcriptomic

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: U5_wild type YAP1

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: human neural stem cell line

tag: genotype/variation


title: Airway epithelial cells - COPD2 - p3

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
RNA-seq data analysis was performed separately for each panel (lowly and highly expressed genes), according to the following bioinformatics pipeline.
Reads were aligned to the sequences of the targeted transcript retrieved from the human reference genome (UCSC assembly hg19) using BWA (v.0.7.17).
Samtools (v.1.9) was used to generate, to sort and to index the BAM files. Read counting for each transcript was performed with the GenomicAlignments (v.1.36.0) Bioconductor package.
The geNorm algorithm implemented within the ctrlGene (v.1.0.1). R package was used to identify stably expressed genes among the set of measured housekeeping genes. The selected housekeeping genes were used within the DESeq2 (1.24.0) Bioconductor package in order to compute the size factors associated with each library.
Genome_build: human reference genome (UCSC assembly hg19)
Supplementary_files_format_and_content: normalized-expres-low-panel.csv contains the expression matrix of the low panel after normalisation based on housekeeping genes. normalized-expres-high-panel.csv contains the expression martrix of the high panel after the normalisation based on housekeeping genes.

source_name: Airway epithelial cells

growth_protocol: A large piece of cartilaginous bronchus was selected, located as far as possible from the tumour site and submitted to pronase digestion overnight at 4°C, in order to derive human broncho-epithelial cells (HBEC). HBECs were cultured in flasks in retinoic acid-supplemented Bronchial Epithelial Cell Growth Basal Medium (Lonza, Verviers, Belgium) until confluence. Cells were then detached and seeded at a density of 80,000 cells/well on 24-well polyester filter-type inserts (0.4-µm pore size; Corning, Corning, NY, USA) coated with 0.2 mg/ml collagen IV (Sigma-Aldrich, Saint-Louis, MO, USA) until a confluent monolayer. The culture was then carried out in air/liquid interface (ALI) for 14 to 20 days, according to the experiment. Once in ALI, HBECs were cultured in BEBM:DMEM (1:1) medium supplemented with penicillin (100U/ml), streptomycin (100µg/ml) (Lonza), bovine serum albumin (BSA) (1.5 µg/ml), retinoic acid (30ng/ml) (Sigma, Saint-Louis, MO), and BEGM SingleQuotsTM Supplements and Growth Factors (Lonza), including bovine pituitary extract (52µg/ml), insulin (5µg/ml), hydrocortisone (0.5g/ml), transferrin (10µg/ml), epinephrine (0.5µg/ml), epidermal growth factor (0.5ng/ml) and triiodothyronine (3.25ng/ml)

extract_protocol:
RNA was isolated from ALI-reconstituted airway epithelium cultured cells of smoker, non smoker and COPD patients. RiboPure™ RNA Purification kit from Ambion was used for the RNA extraction using bromochloropropane (BCP) instead of chloroform to avoid DNA contamination
The library preparation was performed using 50ng total RNA follwing TruSeq® Targeted RNA Expression protocol from Illumina. The libraries were single read (1x50 bp) sequenced on MiSeq (Illumina Inc)

value: ALI-reconstituted airway epithelium

tag: phenotype

value: moderate COPD


title: GEP-NETs Patient7_G2

type: RNA

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent microarray scanner (G2565BA, Agilent)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent)  using default parameters.

source_name: Tumor tissue

label_protocol: The miRNA expression levels were assessed using SurePrint G3 Human Microarray Agilent Human 8x60K miRNA Microarray (Agilent Technologies) based on Sanger miRBase release 21, according to the manufacturer’s instructions. Briefly, 100 ng of total RNA isolated from FFPE section of 18 NENs patients were firstly dephosphorylated with a calf intestine alkaline phosphatase treatment for 30 minutes at 37°C before labeling. Samples were diluted with DMSO, denatured for 10 minutes at 100°C, and labeled using pCp-Cy3 in T4 RNA ligation buffer.

growth_protocol: No growth

extract_protocol: Total RNA, including small RNA fraction, was isolated from FFPE section of 5 µm-thickness using miRNeasy FFPE kit (Qiagen) according to the manufacturer’s protocol. Total RNA was then eluted in ribonuclease-free water. The RNA concentration was determined with NanoDrop ND-2000 Spectrophotometer (Nanodrop Technologies).

treatment_protocol: No treatment

tag: disease state

value: Gastroenteropancreatic neuroendocrine tumors (GEP-NETs)

tag: sample tissue

value: FFPE tissue

tag: gender

value: Female

tag: age

tag: tumor grade

tag: tumor localization

value: Small intestine


title: Airway epithelial cells - COPD1 - p5

value: mild COPD


title: Airway epithelial cells - COPD2 - p2


title: Airway epithelial cells - COPD1 - p4


title: GEP-NETs Patient9_G2

value: Pancreas


title: Airway epithelial cells - smoker - p1

value: smoker


title: Airway epithelial cells - Non smoker - p4

value: non smoker


title: Airway epithelial cells - COPD4 - p6

value: very severe COPD


title: U5_wild type YAP1 rep2

description: U5 neural stem cells transduced with pLJM1-wtYAP1-PGK-Puro rep 2


title: Airway epithelial cells - COPD1 - p3


title: U5_wild type YAP1 rep1

description: U5 neural stem cells transduced with pLJM1-wtYAP1-PGK-Puro rep 1


title: GEP-NETs Patient13_G3

value: Male

value: Cecum


title: Airway epithelial cells - Non smoker - p3


title: GEP-NETs Patient6_G2


title: U5_GFP rep3

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 3


title: Airway epithelial cells - COPD4 - p5


title: Airway epithelial cells - COPD1 - p2


title: Airway epithelial cells - COPD4 - p4


title: GEP-NETs Patient3_G1

value: Duodenum


title: GEP-NETs Patient4_G3

value: Stomach


title: Airway epithelial cells - COPD4 - p3


title: Airway epithelial cells - COPD1 - p1


title: Airway epithelial cells - Non smoker - p2


title: GEP-NETs Patient2_G1


title: U5_GFP rep1

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 1


title: A2N rep2

city: Kongens Lyngby

first: Xiaobo

last: Li

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

description: Single copy of 2A23p-nox expressed in E3

data_processing:
Basecalling online_YX BasecallVersion0.5.6.153
Sequenced reads were filtered by removing adaptor sequences and low-quality reads
Sequenced reads were mapped to reference sequence S.erythraea NRRL2338 (Genbank accession number: NC_009142) using Geneious Prime version 2019.1.3.
Genome_build: S.erythraea NRRL2338 (NC_009142)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Saccharopolyspora erythraea

source_name: engineered strain A2N, early exponential phase

growth_protocol: Modified minimal liquid medium was used for liquid culture of S.erythraea. Cells were harvested at two time points, i.e. 4 h in the early exponential phase for total RNA extraction.

extract_protocol:
Total RNA was extracted with an RNAeasy Plus Mini kit (Qiagen, Germany) using glass beads to mechanically disrupting cells with a FastPrep (30 s ×4; M.P. Biomedical, USA). DNase treatment by RNase-Free DNase Set (Qiagen, Germany) aided to digest DNA in samples.
rRNA was removed with Illumina Ribo-zero rRNA removal kit(bacteria) after total RNA was collected. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dATPs,dGTPs,dCTPs,dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adapters. Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute PCR Purification Kit before PCR amplification.

treatment_protocol: The  cells were harvested and resuspended in 2 mL RNAlaterTM solution (Invitrogen, USA).

tag: strain

tag: growth phase

value: early exponential phase (4 h)

tag: genotype


title: R3N rep2

description: Single copy of ermE*p-nox expressed in E3

source_name: engineered strain R3N, early exponential phase


title: R3N rep1


title: Airway epithelial cells - COPD4 - p2


title: Airway epithelial cells - COPD4 - p1


title: Airway epithelial cells - Non smoker - p1


title: A2N rep1


title: GEP-NETs Patient1_G1

value: Rectum


title: Sample 3 treated

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

data_processing:
Raw sequencing files were analyzed with Torrent Suite v.5.0.4, using hg19 Ampliseq transcriptome reference
Genome_build: Hg19
Supplementary_files_format_and_content: Raw gene count matrix in tab separated value file format

source_name: Nasal brushing

growth_protocol: The CRC culture method was adapted (8), and is described in detail below. The major change from this protocol was the use of irradiated NIH3T3 fibroblast (ATCC #CRL-1658) feeder layers. Burst size was defined as the total cells recovered divided by the total number of cells plated. Projected cell amplification was calculated assuming 8x105 cells recovered at passage 1 (P1). The cell yield at P1 was multiplied by the empirically determined burst size to determine the total cells generated at P2. This process was repeated for the following passages.  For ALI differentiation, passage 4 CRC cultured cells were differentiated using the method of Wu et al (5). Briefly, cells were plated  at  a  density  of  90,909  cell/cm2 (12mm  semipermeable  inserts)  in  ALI  expansion  medium containing Y-27632. At confluence the expansion medium was switched to ALI differentiation media. ALI culture was maintained for 28 days.

extract_protocol:
RNA was purified using the Qiagen RNeasy kit as per manufacturer's protocol
Barcoded Ion Ampliseq Transcriptome Gene Expression sequencing libraries were constructed. Libraries were sequenced on an Ion Torrent Proton sequencer to generate quantitative gene expression data for >20,000 RefSeq gene transcripts. Sequencing reads were mapped to the AmpliSeq Transcriptome Gene Expression target regions and quantified with the ampliSeqRNA plugin for Ion Proton System. We removed duplicated sequences from the FASTA file. We used the uniquely mapping reads option of the plugin. We modified the bed file locations for 166 amplicons which were inconsistent with the primer position of these amplicons in the corresponding FASTA sequence.
RNA AmpliSeq

treatment_protocol: The cells from three donors used for this experiment were continuously cultured with Y-27632 (10uM) stimulation before P2. During P2, cells were cultured for 8 days with or without continuous Y-27632 stimulation (10uM).

tag: tissue

value: Nasal airway epithelium

tag: treatment


title: Sample 3 untreated

value: Ctrl


title: Sample 2 treated


title: Donor 2 F5

city: Silver Spring

first: Frederick

middle: C

last: Mills

state: MD

address: Building 52, Room 2108

department: CDER, OPQ, OBP, Division IV

institute: FDA

description:
Donor 2 F5_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 F5_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 F5_12_db-pass.tab (IgA isotype assigned durng data processing)

data_processing:
NGS data were analyzed using the FDA High-Performance Integrated Virtual Environment (HIVE) platform(doi: 10.1093/database/baw022) Reverse and forward reads were combined into a single paired sequence of 500-600 base pairs by matching ≥15 overlaps.
Paired sequences were filtered for quality scores of >30 and length above 350 base pairs. The HIVE Hexagon algorithm was used to sort samples with HC (Heavy Chain) sequences by aligning with the constant region primers.
HC sequences were submitted to IMGT High V-Quest for VDJ assignment ( Rogosch et al., doi: 10.3389/fimmu.2012.00176).
The output from IMGT High V-Quest was parsed via MakeDb from the Change-O Python package(https://changeo.readthedocs.io/en/stable/) to generate the standardized database file. After processing with MakeDb, 18 separate database files were obtained for each donor, corresponding to the combination of 6 cell subsets and 3 Ig isotypes, The MakeDB files are tab delimited text, with rows for each assembled sequence and associated germline human heavy chain V, D, and J sequences
For Donor 1, Ig isotypes were maintained from the beginning of the data analysis pipeline, so for this donor there are 18 processed data files corresponding to 18 R1/R2 pairs of raw data files. For Donor 2, for each B cell subset there is only a single R1/R2 pair, with the Ig isotype for each sequence being assigned during data processing. Therefore for this donor there are 18 processed files derived from 6 R1/R2 pairs of raw data files.
hg19
tab delimited text, sequences and associated germline human heavy chain V, D, and J sequences, scores for identity

source_name: tonsil FCRL4_ FCRL5+

extract_protocol:
RNA was extracted from 3x10^ 5 sorted cells per each subset. RNA integrity and quantity were determined using a bioanalyzer (Agilent, Santa Clara, CA) and high sensitivity chip. Samples with RNA integrity values of >7 were prepared for NGS.
Reverse transcription and PCR were performed with the SMARTer RACE 5’/3’ Kit (Takara, Mountain View, CA) using primers that anneal to the 5’ end of HC constant regions. Primers were (5’-3’): Cμ, CAGGAGACGAGGGGGAAAAG; Cγ, GCCAGGGGGAAGACSGATG; Cα, CTCAGCGGGAAGACCTTG. PCR was performed in 50 µL with cDNA, GeneAmp Gold Buffer (Thermo Fisher), 1.5 mM MgCl2, 0.2 mM dNTP, Universal Primer Mix, 1µM of constant region primer, and 2.5 U of AmpliTaq Gold (Thermo Fisher). PCR cycling conditions were 10 min at 95°C, 30 cycles of (1 min at 95°C, 1 min at 63°C, 1 min at 72°C), 72°C for 10 min. PCR products were ethanol precipitated, excised from 1.8% UltraPure™ agarose gels (Life Technologies) and purified using a NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel, Bethlehem, PA). Illumina adapter sequences were ligated to the amplicons using the NEBNext Ultra Ligation Module (New England Biolabs, Ipswich, MA) according to the manufacturer’s protocol. Full-length amplicons were purified with Agencourt AMPure XP Beads (Beckman Coulter. Brea, CA). Illumina index primers were added using the NEBNext High-Fidelity 2× PCR Master Mix and NEBNext Multiplex Oligos (Index Primers set 1) according to the manufacturer’s instructions. PCR conditions consisted of 30 seconds at 98°C, 15 cycles of (10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C), 5 min at 72°C. Amplicons were purified with Agencourt AMPure XP Beads. Library integrities and amplicon sizes were confirmed on an Agilent Bioanalyzer
5'RACE RNA seq, NGS using Agilent Bioanalyzer prior to Illumina MiSeq 2 x 300 bp sequencing

treatment_protocol: Tonsils from one female 2 year old donor (donor 1) and one 2 year old male donor (donor 2) were obtained from the Mid-Atlantic CHTN following institutionally approved protocols. Lymphocytes were isolated by manual disruption and Ficoll purification, using standard procedures. Lymphocytes were either used fresh or were frozen for later use in liquid nitrogen in 10% DMSO, 50% FBS in RPMI. For sorting, B cells were isolated from ~400x10^6 tonsil cells using the Pan B cell isolation kit (StemCell Tecnologies, Cambridge, MA), then stained with CD19-APC-Cy7, IgD-FITC, CD38-BV421, FCRL4-APC and FCRL5-PE (all from Biolegend, San Diego, CA), and sorted on FACSAria Fusion in buffer containing 7-AAD (BD Bioscience, San Jose, CA).

tag: individual

value: Donor 2

value: 2 years old

value: female

tag: ig isotype

value: tonsil

value: B cells

tag: cell subset


title: Sample 2 untreated


title: E3 rep1

description: high-erythromycin producing strain

source_name: parental strain, early exponential phase


title: Astro_d28_Mat_3: Astrocyte differentiation with matrigel d28_rep3

city: Singapore

first: Uma Sangumathi

last: Kamaraj

state: singapore

address: 8 college road

department: CVMD

country: Singapore

institute: Duke NUS

description: Day 7 of differentiation on matrigel from neural progenitor cells (28 days total). Figure 4F. Replicate 3

data_processing:
Trimmomatic v0.39
STAR v2.7.3
featureCounts v1.6.0
Genome_build: GRCh38

source_name: Astrocyte

growth_protocol: For astrocyte differentiation, cells were seeded onto flasks coated with Matrigel in neural induction medium (NIM) for 14 days (to obtain NPCs). Cells were then expanded for 7 days in NIM and replated at day 21 onto Matrigel or all factor conditions for another 21 days in astrocyte medium. Primary astrocytes were cultured in Astrocyte medium. H9 ESCs were cultured in Essential 8 medium.

extract_protocol:
following the NEB protocol using  NEBNext Ultra II directional RNA library prep kit and   NEBNext Poly(A) mRNA Magnetic: Poly A mRNA isolation, RNA fragmentation, cDNA sythesis, Adaptor ligation, PCR
Poly(A) mRNA enrichment, PCR using dual index primers

treatment_protocol: Astrocyte differentiation cultures were treated with matrigel or all predicted factors

tag: cell type

value: Astrocytes differentiated from neural progenitor cells


title: Donor 2 PB

description:
Donor 2 PB_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 PB_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 PB_12_db-pass.tab (IgA isotype assigned during data processing)

source_name: tonsil PB

value: PB


title: Donor 2 DP

description:
Donor 2 DP_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 DP_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 DP_12_db-pass.tab (IgA isotype assigned during data processing)

source_name: tonsil FCRL4 + FCRL5+

value: DP


title: U5_GFP rep2

description: U5 neural stem cells transduced with pLJM1-GFP-PGK-Puro rep 2

tag: cell line

value: human neural stem cell line

tag: genotype/variation


title: Donor 2 DN

description:
Donor 2 DN_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 DN_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 DN_12_db-pass.tab (IgA isotype assigned during data processing)

source_name: tonsil FCRL4_ FCRL5-

value: DN


title: E3 rep2

description: high-erythromycin producing strain


title: Donor 1 DN IgA

value: Donor 1

value: male

value: IgA


title: Sample 1 treated


title: Donor 1 DN IgG

value: IgG


title: Donor 2 GC

description:
Donor 2 GC_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 GC_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 GC_12_db-pass.tab (IgA isotype assigned during data processing)

source_name: tonsil GC

value: GC


title: Spinal_cord_tRNA_1_DM

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

data_processing:
Processing: cutadapt ver 1.12 was used twice in succession with the following parameters first to remove two degenerate bases encoded in the RT primer (--cut 2), potential 5' adapter (-g TCCAACTGGATACTGGN -e 0.2) and then to remove the 3' CCA + adapter (-a CCAGTATCCAGTTGGAATT -e 0.2).
Mapping: bowtie2 ver 2.3.5 was used to map processed reads to a reference generated from high confidence tRNAs (unique sequences collapsed) defined in GtRNAdb (mm10) using the following parameters: (--quiet --min-score G,1,8 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5).
Downstream analyses: Mapped sam files were converted to bam files using samtools ver 1.9 (samtools view). Further analyses were carried out in Rstudio ver 1.1.463 (R ver 3.5.2 (2018-12-20) -- "Eggshell Igloo"). Read count tables over tRNA genes were generated by using featureCounts from the Rsubread package using the following parameters: strandSpecific = 1,useMetaFeatures=F,minMQS = 10.
mm10; gtRNAdb Release 18
CSV files of variant counts and coverage for every base at the isodecoder level from mouse tissues.

organism: Mus musculus

source_name: Spinal cord

extract_protocol:
All mouse tissue samples were isolated from C57B/6J mice. Samples were received on dry ice, and stored as whole tissue at -80°C. Samples were thawed on ice and 1mL of Trizol was added per 100g of dissected whole tissue. On ice, samples were masticated and passed through successively higher gauges of needles to ensure a homogeneous mixture. Samples were stored at -80°C until further processing. RNA was isolated according to manufacturer’s suggested conditions with the addition of a second ethanol precipitation step with two 75% ethanol washes following isopropanol precipitation. Samples were resuspended in distilled H2O and stored at -80°C until library preparation.
Total RNA samples were quantified using a nanodrop spectrophotometer (ThermoFisher) prior to library preparation and RNA integrity was checked on a 1.2% denaturing formaldehyde agarose gel. To remove 3’ conjugated amino acids, total RNA was deacylated in deacylation buffer (final concentration 20mM Tris-HCL pH=9.0) at a final concentration of 1ug/uL. 1 ug of deacylated total RNA from each sample was subject to demethylase treatment (rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit, ArrayStar) followed by library preparation. 10 pmol of the 3’ and 10 pmol of the 5’ single-stranded adapter mix (2.5 pmol of each adapter 5’-TGrGrA-3’, 5’-TGrGrT-3’, 5’-TGrGrG-3’, 5’-TGrGrC-3’; Table 1) were added to a 200uL thin-walled amplification tube and denatured at 95°C for 2 minutes. Then annealing buffer was added to a final concentration of 5mM Tris-HCl (pH 8.0), 0.5mM ethylenediaminetetraacetic acid (EDTA) and 10mM MgCl2 and incubated at 37°C for 15 minutes hybridizing the annealed double-stranded adapter to the total RNA. The ligation reaction was catalyzed by 5U/uL of RNA ligase 2 (NEB) with manufacturers suggested conditions at 37°C for 60 minutes then 4°C at 60 minutes. All reactions were ethanol precipitated with glycoblue (Thermo Fisher) with two 75% ethanol washes, then suspended in 10ul of dH2O. Following ligation, synthesis of cDNA began with hybridization of the reverse transcriptase primer to the ligated total RNA with a final concentration of 0.5pmol/uL. The samples were incubated at 70°C for 2 minutes and temperature was reduced to 37°C by 0.1°C/sec. Synthesis of cDNA was achieved using Superscript IV at 55°C for 60 minutes. To remove DNA-RNA dimers following cDNA synthesis, we hydrolyzed RNA with a final concentration of 0.1N NaOH in dH2O at 98°C for 20 minutes. All reactions were ethanol precipitated with glycoblue (ThermoFisher) with two 75% ethanol washes, then suspended in 12ul of dH2O. cDNA libraries were separated using 7M urea 6% denaturing polyacrylamide gels. Gels were stained with 1X SYBR gold (Thermo Fisher) in 1X TBE for 15 minutes and regions of interest (60-200 nucleotides) were excised on a UV light box. Gel slices were sheared through the bottom of a 0.5 mL tube nested in a 1.7 mL tube by centrifugation then suspended in 400uL of DNA elution buffer (300mM NaCl, 10mM Tris (pH=8.0, 1mM EDTA), incubated on dry ice for 30 minutes, and allowed to incubate at room temperature overnight on a standing rotator. Libraries were isopropanol precipitated with glycoblue followed by two 75% ethanol washes. Linear cDNA libraries were then suspended in 12ul of dH2O. Circularization of cDNA libraries was performed with CircLigase (Epicentre) with 0.5U/uL using manufacturer’s suggested conditions at 37°C for 1 hour. The reaction was terminated with incubation at 80°C for 20 minutes. All reactions were ethanol precipitated with glycoblue with two 75% ethanol washes, then suspended in 12.5ul of dH2O. cDNA libraries were amplified using the NEBnext Ultra II Q5 next-generation master mix (NEB) with manufacturer’s suggested conditions. HEK293 libraries were amplified for 7 cycles and mouse tissue libraries amplified for 7-9 cycles. Amplified libraries were gel purified from 2% agarose gels stained with 0.05mg/ml Ethidium Bromide. Regions of interest (100-250bp) were excised on a UV light box and purified using the Qiaquick (Qiagen) gel extraction kit using all optional steps. All libraries were ethanol precipitated with glycoblue (thermo) with two 75% ethanol washes, then suspended in 10ul of dH2O before sequencing.

tag: passages


title: Spinal_cord_tRNA_2_DM


title: Sample 1 untreated

value: Nasal airway epithelium


title: Donor 2 naïve

description:
Donor 2 N_10_db-pass.tab (IgM isotype assigned during data processing)
Donor 2 N_11_db-pass.tab (IgG isotype assigned during data processing)
Donor 2 N_12_db-pass.tab (IgA isotype assigned during data processing)

source_name: tonsil naïve B

value: naïve


title: Donor 1 F5 IgA


title: Donor 1 DN IgM

value: IgM


title: Donor 1 F5 IgM

value: 2 years old


title: Heart_tRNA_2_DM

source_name: Heart


title: SUMO_HS_siz1_RNA_rep3

city: Guangzhou

first: Danlu

last: Han

state: Guangdong

address: No. 55, West of Yat-sen Avenue

department: School of Life Science

country: China

institute: South China Normal University

data_processing:
RNA-seq reads were aligned to the TAIR10 genome assembly using HISAT2 (Galaxy Version 2.1.0+galaxy5) with the minimum and maximum intron length setting being 20 bp and 2000bp, respectively.
Mapped reads were assembled according to TAIR10 version of genome annotation using Cufflinks ((Galaxy Version 2.2.1.2)
Assembled transcripts from three independent biological replicates in Col and acc1-5 were included and compared by using cuffdiff version 2.1.1
Cufflinks-generated gtf files
Genome_build: TAIR10
Supplementary_files_format_and_content: gtf files were generated using  Cufflinks ((Galaxy Version 2.2.1.2) with Max Intron Length = 4000.

organism: Arabidopsis thaliana

growth_protocol: The Arabidopsis thaliana seeds of Col-0 (wild-type) and siz1-2 (SALK_065397, obtained from Arabidopsis Stock Center, were used in the experiments. Seeds were sterilized for 2 min in 70% ethanol, then 10min in 2.5% bleach solution and 0.05 % Triton X-100, rinsed five times with sterile water, next sown on the half-concentration Murashige and Skoog (MS) medium with 1.5% sucrose and 8 % agar and stratified at 4°C in the dark for 2 days, before transferred into a 23°C greenhouse with a long day  (16 h light / 8 h dark) condition.

extract_protocol: Total RNA was extracted from 10-day-old seedlings using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. Genomic DNA was removed by treating with DNase TURBO (Ambion).  Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacture’s protocol

treatment_protocol: 10-day-old seeding grown on the medium in petri dishes (90 × 15 mm) were incubated at 37°C for 30 min in a circulating water bath. During recovery 37°C treatment, the petri dishes containing seedlings were removed from the water bath and kept at 23°C for 90 min in the greenhouse under previous growth condition(Charng et al., 2006). The seedlings were collected at the indicated time points for further experiments

tag: developmental stage

value: 10 days atfer germination

value: seedings

value: HS


title: Donor 1 DP IgA

tag: gender

value: tonsil

value: B cells


title: SUMO_HS_siz1_RNA_rep2


title: Donor 1 DP IgG

tag: age

value: DP


title: Donor 1 F5 IgG


title: Heart_tRNA_1_DM


title: SUMO_HS_siz1_RNA_rep1


title: Donor 1 DP IgM


title: Donor 1 PB IgA

value: PB


title: SUMO_RT_siz1_RNA_rep3

value: RT


title: SUMO_RT_siz1_RNA_rep2


title: Donor 1 PB IgG

value: Donor 1


title: Donor 1 GC IgA

value: male


title: Donor 1 PB IgM


title: KO Lo+A 2

city: Hannover

first: Jaba

last: Gamrekelashvili

address: Carl-Neuberg-Str. 1

department: Nephrology

country: Germany

institute: Medizinische Hochschule Hannover

data_processing:
Illumina bcl2fastq conversion software (v2.20.0.422) was used for demultiplexing
Pre-processing of FASTQ inputs, alignment of the reads and quality control was conducted by nfcore/rnaseq (version 1.5dev) analysis pipeline (The National Genomics Infrastructure, SciLifeLab Stockholm, Sweden).
Nextflow tools from analysis pipeline included TrimGalore (version 0.4.4_dev), STAR (version STAR_2.5.3a_modified) and Feature counts (version 1.6.1).
Normalization was performed with DESeq2 (Galaxy Tool Version 2.11.39) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: GRCm38.p6 release M17 (GENCODE.org)
Supplementary_files_format_and_content: comma-separated values (csv) file includes mRNA count values for each sample

source_name: KO Lo+A_peripheral blood

growth_protocol: Sham or Imiquimod (IMQ) treated animals were maintained in specific pathogen free conditions and water and food was given ad libidum.

extract_protocol:
FACS sorted monocytes were collected on ice, washed in PBS and RNA was isolated using RNeasy micro kit (Qiagen).
Libraries were constructed from total RNA with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (Takara/Clontech) according to manufacturer’s recommendations, barcoded by dual indexing approach and amplified with 11 cycles of PCR. Fragment length distribution was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (Agilent Technologies) and quantified by ‘Qubit® dsDNA HS Assay Kit’ (ThermoFisher Scientific).

treatment_protocol: 50mg/mouse/day Aldara (containing 5% IMQ) or Sham crème (Vaseline) were applied on depilated skin of the mice for 4-5 consecutive days. On day 5 mice were euthanized, peripheral blood cells were purified using density gradient centriffugation and monocyte subsets were FACS sorted.

tag: strain background

value: Notch2 mutant

value: 8-10 weeks

value: Lo+A

value: Peripheral blood


title: KO Lo+A 1


title: Donor 1 GC IgG

value: IgG

value: GC


title: Donor 1 naïve IgA

value: 2 years old

value: IgA

value: naïve


title: WT Lo+A 4

source_name: WT Lo+A_peripheral blood

value: wild type


title: Donor 1 naïve IgM

value: IgM

value: tonsil


title: Donor 1 naïve IgG

value: B cells


title: SUMO_RC_WT_RNA_rep3

value: 10 days atfer germination

value: seedings

value: WT

value: RC


title: KO Lo+A 4

value: Notch2 mutant


title: SUMO_RC_WT_RNA_rep2


title: WT Lo+A 2

value: 8-10 weeks


title: WT Lo+A 1

value: Lo+A


title: C3

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

data_processing:
Zebracall process Version 0.5.0.13875 used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for bulks C and D were aligned to the reference genome using TopHat v2.0.9
Genome_build: GCF_000226075.1
Supplementary_files_format_and_content: csv file reporting abundance measurements

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: Potato plants were planted in plastic pots filled with soil. Plants grew in greenhouse from May to October.

extract_protocol:
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using Dynabeads®mRNA Purification Kit for mRNA enrichment (Ambion, 61006), and cDNA libraries were prepared using using MGIEasy RNA Directional Library Prep Set (MGI, 1000006386). The established cDNA libraries were sequenced on the BGISEQ-500 sequencing platform (BGI Genomics, China) to generate 100-bp paired-end reads (PE100).

treatment_protocol: At stage of full anthesis, leaves were collected, ground in liquid nitrogen and freezed in -80°C untill use.

tag: population

value: Diploid hybrid 15-1

value: Full anthesis

tag: phenotype

value: Low glycoalkaloids, high phytotoxic potential

value: untreated

value: leaf


title: NB4 cells TanI treated rep3

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
The sequencing reads were aligned to the human GRCh38 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts for each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurements and Deseq2 results

source_name: NB4 cells TanI treated

growth_protocol: NB4 cells were cultured in RPMI-1640 medium supplemented with 10% FBS in 5% CO2 and humidified atmosphere at 37℃.

extract_protocol:
Total RNAs from embryos was extracted using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NB4 cells treated with DMSO or 10 μM Tan I  for 3 days.

tag: tissue source

value: human promyelocytic leukemia

value: 10 μM Tan I  for 3 days


title: C1


title: KO Hi+A 4

source_name: KO Hi+A_peripheral blood

tag: genotype

value: Hi+A

value: Peripheral blood


title: D2

value: Low glycoalkaloids, low phytotoxic potential

tag: tissue


title: D1

tag: treatment


title: SUMO_RC_WT_RNA_rep1

value: 10 days atfer germination


title: WT Lo+A 3

value: wild type


title: NB4 cells TanI treated rep2


title: C2


title: Donor 1 GC IgM

tag: individual

value: Donor 1

value: 2 years old

value: male

value: IgM

value: tonsil

value: B cells

value: GC


title: SUMO_HS_WT_RNA_rep1

value: seedings

value: WT

value: HS


title: SUMO_RT_WT_RNA_rep3

value: RT


title: SUMO_HS_WT_RNA_rep2


title: NB4 cells DMSO treated rep2

source_name: NB4 cells DMSO treated

value: human promyelocytic leukemia

value: DMSO for 3 days


title: NB4 cells DMSO treated rep3


title: NB4 cells DMSO treated rep1


title: SUMO_HS_WT_RNA_rep3


title: D3

value: Diploid hybrid 15-1

value: Full anthesis

value: untreated

value: leaf


title: SUMO_RT_WT_RNA_rep2

value: 10 days atfer germination


title: KO Hi+A 1

value: Notch2 mutant

value: 8-10 weeks

value: Hi+A

value: Peripheral blood


title: pat 9 tumor [HDV_9A_S6]

city: BALTIMORE

first: Luigi

last: Ferrucci

address: 251 BAYVIEW BLVD.

department: Translational Gerontology Branch

institute: National Institute on Aging, National Institutes of Health

data_processing:
140 RNA-seq samples from 70 HCC tumors and matched nontumor tissue were pooled and sequenced on NovaSeq using Illumina TruSeq Stranded Total RNA Kit RS-122-2201 and paired-end sequencing.
The sequencing quality of the reads was assessed using FastQC (version 0.11.5), Preseq (version 2.0.3)32, Picard tools (version 1.119), and RSeQC (version 2.6.4).
Reads were trimmed using Cutadapt (version 1.14)33 to remove sequencing adapters, prior to mapping to the human reference genome hg38 using STAR (version 2.5.2b) in two-pass mode34.
Across the samples, the median percentage of mapped reads was 95.4%.  Expression levels were quantified using RSEM version 1.3.035 with GENCODE annotation version 2136.
The RSEM counts were then normalized using the voom algorithm37 from the Limma R package (version 3.40.6)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text data matrices with genes as rows and samples as columns: RSEM_GeneCounts.txt is an integer matrix of transcript counts, voom_GeneExpression.txt is the voom-normalized gene expression.

source_name: liver tissue

extract_protocol:
Frozen liver samples were homogenized using 2.8mm ceramic beads (Mo Bio cat.no.13114-50) and RNA was extracted using Trizol reagent, treated with DNase, quality control was checked using Agilent Nano chip.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subject status

value: hepatocellular carcinoma patient

tag: tumor/non-tumor

value: tumor


title: pat 8 non-tumor [HDV_8B_S33]

value: non-tumor


title: KO Lo+A 3

value: Lo+A


title: pat 9 non-tumor [HDV_9B_S26]


title: NB4 cells TanI treated rep1

value: 10 μM Tan I  for 3 days


title: WT Hi+A 4

source_name: WT Hi+A_peripheral blood

value: wild type


title: Treated with resveratrol  25 µM day 12 Jurkat screen

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

country: Canada

institute: University of Montreal

description: processed data file: Jurkat_sgRNA_read_counts.txt

library_source: genomic

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed.
Read counts from all control samples and time-points from each experiment were summed.
Genome_build: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library. For Jurkat screens: TKOv3 sgRNA library (Hart et al. 2017,PMID:28655737).
Supplementary_files_format_and_content: Tab-separated sgRNA read counts per sample

molecule: genomic DNA

growth_protocol: Nalm-6 and Jurkat cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Genomic DNA was extracted and purified using the Gentra Cell Puregene kit (QIAGEN, cat. # 158388).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol:
(NALM-6) A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 8 days (see Bertomeu et al., 2018 for details). The pooled EKO library was split in different T-75 flasks and compounds were added (16 µM resveratrol, 16 µM pterostilbene, 100 µM hydroxyurea, or DMSO 0.1% v/v). Fresh media and compound was added at each cell passage.
(Jurkat) The genome-wide screen in Jurkat cells was performed by transduction of cells with the lentiviral TKOv3 library as described (Hart et al., 2017) with modifications as described. Cells were treated with 16 µM resveratrol or 0.1% DMSO v/v/ for 12 days. Fresh media and compound was added at each cell passage.

tag: cell line background

value: Jurkat cell line

tag: sample type

value: pooled sgRNA library

tag: molecule subtype

value: sgRNAs PCR-amplified from genomic DNA


title: KO Hi+A 3


title: pat 8 tumor [HDV_8A_S55]


title: pat 7 tumor [HDV_7A_S28]


title: WT Hi+A 3


title: WT Hi+A 2


title: 0.1% DMSO day 12 control for resveratrol Jurkat screen


title: pat 70 non-tumor [HDV_70B_S67]


title: pat 70 tumor [HDV_70A_S53]


title: 0.1% DMSO day 6 control for resveratrol Jurkat screen


title: WT Hi+A 1


title: Day 0 control for resveratrol Jurkat screen


title: pat 6 tumor [HDV_6A_S29]


title: pat 69 non-tumor [HDV_69B_S48]


title: KO Hi+A 2


title: SUMO_RT_WT_RNA_rep1

value: seedings

value: WT

value: RT


title: pat 69 tumor [HDV_69A_S8]


title: pat 6 non-tumor [HDV_6B_S29]


title: KO Hi 4

source_name: KO Hi_peripheral blood

value: Hi


title: Treated with hydroxyurea 100 µM day 8 Nalm-6 screen

description: processed data file: Nalm6_sgRNA_read_counts.txt

value: Nalm-6 pre-B lymphoid cell line


title: KO Hi 3

value: Notch2 mutant

value: 8-10 weeks


title: pat 68 non-tumor [HDV_68B_S5]


title: pat 68 tumor [HDV_68A_S50]


title: 0.1% DMSO day 8 control for hydroxyurea Nalm-6 screen


title: pat 67 non-tumor [HDV_67B_S56]


title: KO Hi 2

value: Peripheral blood


title: pat 7 non-tumor [HDV_7B_S54]

value: hepatocellular carcinoma patient


title: Untreated day 8 control for hydroxyurea Nalm-6 screen


title: pat 66 non-tumor [HDV_66B_S24]


title: pat 67 tumor [HDV_67A_S4]

value: tumor


title: KO Hi 1


title: WT Hi 4

source_name: WT Hi_peripheral blood


title: pat 65 non-tumor [HDV_65B_S19]

value: non-tumor


title: pat 65 tumor [HDV_65A_S46]


title: pat 64 non-tumor [HDV_64B_S14]


title: WT Hi 3


title: pat 64 tumor [HDV_64A_S43]


title: pat 63 non-tumor [HDV_63B_S53]


title: Untreated day 6 control for hydroxyurea Nalm-6 screen (spinner flask)


title: pat 63 tumor [HDV_63A_S40]


title: pat 66 tumor [HDV_66A_S49]


title: Untreated day 2 control for hydroxyurea Nalm-6 screen (spinner flask)


title: Untreated day 4 control for hydroxyurea Nalm-6 screen (spinner flask)


title: pat 62 non-tumor [HDV_62B_S9]


title: WT Hi 1


title: pat 62 tumor [HDV_62A_S36]


title: Day 0 control for hydroxyurea Nalm-6 screen


title: pat 61 tumor [HDV_61A_S32]


title: pat 61 non-tumor [HDV_61B_S1]


title: pat 60 non-tumor [HDV_60B_S47]


title: pat 60 tumor [HDV_60A_S27]


title: Untreated day 8 control for hydroxyurea Nalm-6 screen (spinner flask)


title: Tibialis_tRNA_2

description: Mouse_tissue_anticodon_raw_counts.csv; Mouse_tissue_isodecoder_raw_counts.csv; Mouse_tissue_variant_counts.csv

data_processing:
Processing: cutadapt ver 1.12 was used twice in succession with the following parameters first to remove potential 5' adapter (-g ^ACTGGATACTGG) and then to remove the 3' CCA + adapter (-a CCAGTATCCAGTTGGAATT).
Mapping: bowtie2 ver 2.3.5 was used to map processed reads to a reference generated from high confidence tRNAs (unique sequences collapsed) defined in GtRNAdb (mm10) using the following parameters: --quiet --min-score L,1,0 --local -D 20 -R 3 -N 1 -L 10 -i S,1,0.5.
Downstream analyses: Mapped sam files were converted to bam files using samtools ver 1.9 (samtools view). Further analyses were carried out in Rstudio ver 1.1.463 (R ver 3.5.2 (2018-12-20) -- "Eggshell Igloo"). Read count tables over tRNA genes were generated by using featureCounts from the Rsubread package using the following parameters: strandSpecific = 1,useMetaFeatures=F,minMQS = 10.
genome build: mm10; gtRNAdb Release 18
CSV files of raw counts at the anticodon and isodecoder levels. Also, variant counts and coverage for every base at the isodecoder level from mouse tissues.

source_name: Tibialis

extract_protocol:
All mouse tissue samples were isolated from C57B/6J mice. Samples were received on dry ice, and stored as whole tissue at -80°C. Samples were thawed on ice and 1mL of Trizol was added per 100g of dissected whole tissue. On ice, samples were masticated and passed through successively higher gauges of needles to ensure a homogeneous mixture. Samples were stored at -80°C until further processing. RNA was isolated according to manufacturer’s suggested conditions with the addition of a second ethanol precipitation step with two 75% ethanol washes following isopropanol precipitation. Samples were resuspended in distilled H2O and stored at -80°C until library preparation.
Total RNA samples were quantified using a nanodrop spectrophotometer (ThermoFisher) prior to library preparation and RNA integrity was checked on a 1.2% denaturing formaldehyde agarose gel. To remove 3’ conjugated amino acids, total RNA was deacylated in deacylation buffer (final concentration 20mM Tris-HCL pH=9.0) at a final concentration of 1ug/uL. 1 ug of deacylated total RNA from each sample was subject to library preparation. 40 pmol of the 3’ and 40 pmol of the 5’ single-stranded adapter mix (10 pmol of each adapter 5’-TGrGrA-3’, 5’-TGrGrT-3’, 5’-TGrGrG-3’, 5’-TGrGrC-3’; Table 1) were added to a 200uL thin-walled amplification tube and denatured at 95°C for 2 minutes. Then annealing buffer was added to a final concentration of 5mM Tris-HCl (pH 8.0), 0.5mM ethylenediaminetetraacetic acid (EDTA) and 10mM MgCl2 and incubated at 37°C for 15 minutes hybridizing the annealed double-stranded adapter to the total RNA. The ligation reaction was catalyzed by 5U/uL of RNA ligase 2 (NEB) with manufacturers suggested conditions at 37°C for 60 minutes then 4°C at 60 minutes. All reactions were ethanol precipitated with glycoblue (Thermo Fisher) with two 75% ethanol washes, then suspended in 10ul of dH2O. Following ligation, synthesis of cDNA began with hybridization of the reverse transcriptase primer to the ligated total RNA with a final concentration of 0.5pmol/uL. The samples were incubated at 70°C for 2 minutes and temperature was reduced to 37°C by 0.1°C/sec. Synthesis of cDNA was achieved using Superscript IV at 55°C for 60 minutes. To remove DNA-RNA dimers following cDNA synthesis, we hydrolyzed RNA with a final concentration of 0.1N NaOH in dH2O at 98°C for 20 minutes. All reactions were ethanol precipitated with glycoblue (ThermoFisher) with two 75% ethanol washes, then suspended in 12ul of dH2O. cDNA libraries were separated using 7M urea 6% denaturing polyacrylamide gels. Gels were stained with 1X SYBR gold (Thermo Fisher) in 1X TBE for 15 minutes and regions of interest (60-200 nucleotides) were excised on a UV light box. Gel slices were sheared through the bottom of a 0.5 mL tube nested in a 1.7 mL tube by centrifugation then suspended in 400uL of DNA elution buffer (300mM NaCl, 10mM Tris (pH=8.0, 1mM EDTA), incubated on dry ice for 30 minutes, and allowed to incubate at room temperature overnight on a standing rotator. Libraries were isopropanol precipitated with glycoblue followed by two 75% ethanol washes. Linear cDNA libraries were then suspended in 12ul of dH2O. Circularization of cDNA libraries was performed with CircLigase (Epicentre) with 0.5U/uL using manufacturer’s suggested conditions at 37°C for 1 hour. The reaction was terminated with incubation at 80°C for 20 minutes. All reactions were ethanol precipitated with glycoblue with two 75% ethanol washes, then suspended in 12.5ul of dH2O. cDNA libraries were amplified using the NEBnext Ultra II Q5 next-generation master mix (NEB) with manufacturer’s suggested conditions. HEK293 libraries were amplified for 7 cycles and mouse tissue libraries amplified for 7-9 cycles. Amplified libraries were gel purified from 2% agarose gels stained with 0.05mg/ml Ethidium Bromide. Regions of interest (100-250bp) were excised on a UV light box and purified using the Qiaquick (Qiagen) gel extraction kit using all optional steps. All libraries were ethanol precipitated with glycoblue (thermo) with two 75% ethanol washes, then suspended in 10ul of dH2O before sequencing.

value: Tibialis

tag: strain

value: C57BL/6J wild-type


title: pat 5 non-tumor [HDV_5B_S25]


title: pat 5 tumor [HDV_5A_S24]


title: Tibialis_tRNA_1


title: pat 59 non-tumor [HDV_59B_2_S69]


title: WT Hi 2

value: wild type


title: Heart_tRNA_3

value: Heart


title: CRL7250_V5-SSX1_aa1-188-full-length_RNA-Seq_Rep1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2a Only uniquely mapping reads with at most two mismatches were retained.
Genome_build: hg19
Supplementary_files_format_and_content: Gene count tables were output from STAR quantMode

molecule: polyA RNA

source_name: CRL7250 (FIbroblast)

growth_protocol: CRL7250 cells were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), 1% HEPES (Gibco), 1% NEAA (Gibco), 1% sodium pyruvate (Gibco) and 1% penicillin-streptomycin (Gibco).Synovial sarcoma cell lines Aska and SYO-1 was grown in DMEM without sodium pyruvate (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).

extract_protocol:
One million cells of each condition were harvested using Qiagen RNeasy kit and 1 ug was used in NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) kit followed by NEBNext® Ultra™ II kit (New England BioLabs)
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: CRL7250 cells were lentivirally infected with V5-tagged overexpression constructs, selected with puromycin for 48h, and then cultured for 5 days. SYO-1 and Aska cells were lentivirally infected with either shControl or shSSX vector, selected with puromycin for 48h, and then cultured for 5 days.  Cells were harvested for RNA-seq 7 days post infection.

tag: cell type

value: FIbroblast

tag: cell line


title: CRL7250_V5-SSX1_aa111-188-78aa-tail_RNA-Seq_Rep2


title: pat 59 tumor [HDV_59A_S47]


title: pat 58 non-tumor [HDV_58B_S51]


title: CRL7250_V5-SSX1_aa111-188-78aa-tail_RNA-Seq_Rep1


title: CRL7250_N106_Blank_RNA-Seq_Rep2


title: Heart_tRNA_2


title: pat 57 non-tumor [HDV_57B_S3]


title: CRL7250_V5-SSX1_aa1-188-full-length_RNA-Seq_Rep2


title: Tibialis_tRNA_3


title: pat 57 tumor [HDV_57A_S65]


title: Heart_tRNA_1


title: pat 56 tumor [HDV_56A_S51]


title: pat 55 non-tumor [HDV_55B_S45]


title: CRL7250_N106_Blank_RNA-Seq_Rep1


title: pat 56 non-tumor [HDV_56B_S68]


title: CRL7250_V5-SS18-SSX_L168A-mut-SSX-Tail_RNA-Seq_Rep2


title: Liver_tRNA_3

source_name: Liver

value: Liver


title: Liver_tRNA_2


title: pat 55 tumor [HDV_55A_S22]


title: pat 54 non-tumor [HDV_54B_S43]


title: Liver_tRNA_1


title: pat 54 tumor [HDV_54A_S50]


title: CRL7250_V5-SS18-SSX_L168A-mut-SSX-Tail_RNA-Seq_Rep1


title: pat 53 non-tumor [HDV_53B_S21]


title: CRL7250_V5-SS18-SSX_W164A-mut-SSX-Tail_RNA-Seq_Rep2


title: pat 58 tumor [HDV_58A_S44]


title: Spinal_cord_tRNA_3

value: Spinal cord


title: pat 52 non-tumor [HDV_52B_S41]


title: CRL7250_V5-SS18-SSX_33aa-SSX-Tail_repeat_RNA-Seq_Rep2


title: pat 52 tumor [HDV_52A_S12]


title: Spinal_cord_tRNA_1


title: CRL7250_V5-SS18-SSX_W164A-mut-SSX-Tail_RNA-Seq_Rep1


title: pat 53 tumor [HDV_53A_S17]


title: pat 51 tumor [HDV_51A_S7]


title: pat 51 non-tumor [HDV_51B_S39]


title: CRL7250_V5-SS18-SSX_33aa-SSX-Tail_repeat_RNA-Seq_Rep1


title: Medulla_oblongata_tRNA_3

source_name: Medulla oblongata

value: Medulla oblongata


title: pat 50 tumor [HDV_50A_S3]


title: pat 4 tumor [HDV_4A_S23]


title: Medulla_oblongata_tRNA_2


title: pat 50 non-tumor [HDV_50B_S36]


title: pat 4 non-tumor [HDV_4B_S20]


title: CRL7250_V5-SS18-SSX_78aa-SSX-Tail_RNA-Seq_Rep2


title: CRL7250_V5-SS18-SSX_78aa-SSX-Tail_RNA-Seq_Rep1


title: pat 49 tumor [HDV_49A_S70]


title: pat 49 non-tumor [HDV_49B_S66]


title: Medulla_oblongata_tRNA_1


title: pat 48 non-tumor [HDV_48B_S32]


title: pat 48 tumor [HDV_48A_S69]


title: Cortex_tRNA_3

source_name: Cortex

value: Cortex


title: CRL7250_V5-SS18-SSX_33aa-SSX-Tail_RNA-Seq_Rep2


title: pat 47 non-tumor [HDV_47B_S28]


title: Cortex_tRNA_2


title: Spinal_cord_tRNA_2

source_name: Spinal cord


title: CRL7250_V5-SS18-SSX_33aa-SSX-Tail_RNA-Seq_Rep1


title: pat 47 tumor [HDV_47A_S41]


title: pat 46 non-tumor [HDV_46B_S23]


title: pat 46 tumor [HDV_46A_S37]


title: Cortex_tRNA_1


title: CRL7250_V5-SS18-SSX_23aa-SSX-Tail_RNA-Seq_Rep1


title: Cerebellum_tRNA_3

source_name: Cerebellum

value: Cerebellum


title: pat 45 tumor [HDV_45A_S63]


title: Cerebellum_tRNA_2


title: CRL7250_V5-SS18-SSX_6aa_BasicDel_RNA-Seq_Rep2


title: pat 43 non-tumor [HDV_43B_S13]


title: pat 43 tumor [HDV_43A_S67]


title: CRL7250_V5-SS18-SSX_6aa_BasicDel_RNA-Seq_Rep1


title: CRL7250_V5-SS18-SSX_7aa_AcidicDel_RNA-Seq_Rep2


title: pat 44 tumor [HDV_44A_S61]


title: Cerebellum_tRNA_1


title: pat 42 non-tumor [HDV_42B_S8]


title: pat 42 tumor [HDV_42A_S25]


title: CRL7250_V5-SS18-SSX_23aa-SSX-Tail_RNA-Seq_Rep2


title: CRL7250_GFP_RNA-Seq_Rep2


title: Splenic EAE B cell

city: Harbin

first: Shenyue

last: Wang

address: NO.157 Baojian Road

institute: Harbin Medical University

data_processing:
Illumina novaseq6000 used for basecalling.
Sequencing reads were processed by software called Cell Ranger (version 3.0.2) into FASTQs Files.
Then, the FASTQs files were aligned to the mouse reference genome (GRCm38) with default parameters
After quality control and downstream analysis, the data were generated to gene-cell digital expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: BC.filtered.matrix table include expression genes and UMIs of each cell.

source_name: Spleen

extract_protocol:
Spleen was removed and placed in ice-cold RPMI 1640 medium, ground and filtered with 40 μm nylon mesh strainers.The splenic cells were incubated in RPMI-1640 (2×106cells/mL) with rMOG (10ng/mL) in a humidified incubator at 37°C with 5 % CO2 for 24h.After the B-cell sorting,the splenic cell suspension was generated to single-cell gel beads in the emulsion with the Chromium single-cell controller.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

tag: condition

value: EAE


title: pat 41 non-tumor [HDV_41B_S2]


title: pat 45 non-tumor [HDV_45B_S18]


title: 190239A_C1

city: Tianjin

first: Qiang

last: Liu

state: Tianjin

address: No.154 Anshan Road, Heping District

department: Neurology

institute: Tianjin Medical University General Hospital

description: NK cells in the normal blood

data_processing:
Single-cell RNA-seq libraries were constructed using BD Rhapsody WTA Amplification Kit.
The libraries were finally sequenced using an Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.
The BD Rhapsody analysis pipeline was used to process sequencing data (.fastq files).
Cell labels and molecular indices were identified, and gene identity was determined by alignment against the GRCm38 Genome Reference
Supplementary_files_format_and_content: csv and raw counts for the genes

source_name: NK in C57BL/6 mice after intracerebral hemorrhage (ICH)

extract_protocol:
CD3-NK1.1+NKp46+ cells were isolated at 4°C using fluorescence-activated cell sorting (FACS) and cell viability was no less than 90% for all samples by CountStar® Rigel.
The cDNA was generated and then amplified using 22 cycles of PCR, and quality assessed using an Agilent 4200.

treatment_protocol: Single cell suspension was prepared from pooled mouse blood and brain tissues at 12 h after ICH induced by autologous blood injection or sham-operations.

value: NK cells


title: WT_induction_37C_rep3

city: Umea

first: Maria

last: Fallman

address: Petrus Laestadius väg

department: Molecular Biology

country: Sweden

institute: Umea university

data_processing:
Reads were trimmed from 5' and 3' ends until all the adapter and low-quality bases were removed and the sequences passed QC checking by FastQC
Reads were aligned to a reference genome of Y. pseudotuberculosis (accession number NC_010465) using bowtie2 with the unique-mapping option.
Post-mapped read quality checking was done using RseQC, and the numbers of reads for each gene were counted using HTseq
Aligned reads were converted to BAM and wig by SAMtool and custom script
Differential gene expression was determined using DEseq2, using the shrinkage estimation of dispersion option (lfcSrink =True) to generate more accurate estimates of differential expression in fold changes
Genome_build: NC_010465
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized counts and differential expression statistics for every gene and every sample

organism: Yersinia pseudotuberculosis

source_name: In vitro growing

growth_protocol: All strains were routinely grown at 26ºC in LB medium containing kanamycin (50 µg/ml) to the desired OD600.

extract_protocol:
For isolation and purification of RNA, the Trizol method (Ambion Life Technologies, Carlsbad, CA) and the Direct-zol RNA kit (Zymo Research, USA) were used. To remove unwanted DNA, purified RNA was treated with DNAse for 30 min at room temperature according to the manufacturer’s instructions. RNA quantity was measured by Qubit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To reach the virulence induction condition, overnight bacterial cultures were diluted to OD600 0.05 in LB and grown at 26ºC. After 1 h, calcium was depleted by adding EGTA to 5 mM and MgCl2 to 20 mM , and cultures were shifted to 37ºC

value: YPIII

tag: growth phase

value: induction

value: Wild type


title: WT_induction_37C_rep2


title: CRL7250_GFP_RNA-Seq_Rep1


title: pat 41 tumor [HDV_41A_S19]

value: hepatocellular carcinoma patient

value: tumor


title: pat 44 non-tumor [HDV_44B_S65]

value: non-tumor


title: SUMO_RT_siz1_RNA_rep1

tag: developmental stage

value: 10 days atfer germination

value: seedings

value: RT


title: pat 40 non-tumor [HDV_40B_S44]


title: WT_induction_37C_rep1


title: rpoN_induction_37C_rep3

value: Mutant


title: SYO1_shCt_H2AK119Ub_ChIP-Seq

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 2.1.0, reporting only the highest scoring alignment for each sequence.
To create ChIP-seq coverage plots, bedGraph plots were created using MACS2 callpeak, sorted and then converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig script downloaded from UCSC

source_name: SYO1 (Synovial Sarcoma)

extract_protocol:
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA).  Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C.   After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody.
ChIP-sequencing libraries were prepared with the NEBNext® Ultra™ II kit (New England BioLabs )

treatment_protocol: CRL7250 cells were lentivirally infected with V5-tagged overexpression constructs, selected with puromycin for 48h, and then cultured for 5 days. SYO-1 and Aska cells were lentivirally infected with either shControl or shSSX vector, selected with puromycin for 48h, and then cultured for 5 days.  Cells were harvested for ChIP-seq 7 days post infection.

value: Synovial Sarcoma

tag: chip antibody

value: CST (D27C4)


title: pat 40 tumor [HDV_40A_S14]


title: pat 3 non-tumor [HDV_3B_S15]


title: CRL7250_V5-SS18-SSX_7aa_AcidicDel_RNA-Seq_Rep1

value: FIbroblast


title: rpoN_induction_37C_rep2


title: Aska_shCt_H3K36me3_ChIP-Seq

source_name: Aska (Synovial Sarcoma)

value: Aska

value: Abcam (ab9050)


title: Aska_shCt_H2AK119Ub_ChIP-Seq


title: NTR-expressing cells 100 nM negativ control of LSD1 inhibitor treated - rep3

city: Freiburg

first: Manfred

last: Jung

address: Albertstr. 25

department: Institut für Pharmazeutische Wissenschaften

institute: University Freiburg

description:
BN_191017_THP1NTR100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a negative control (structurally related to OG86, but inactive on LSD1)

hyb_protocol: 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ S Assay. (according to user manual Affymetrix WT PLUS Reagent Kit)

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: biotin

label_protocol: The Applied Biosystems™ WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 500ng total RNA

growth_protocol: cells were incubated at 37 °C, 5 % CO2 atmosphere, 95 % humidity

extract_protocol: Qiagen RNeasyMini Kit with ß-Mercaptoethanol in RLT-buffer according to the manufacturer instructions

treatment_protocol: cells were treated with inhibitors with a final DMSO (vehicle)-concentration of 0,1 % for 24 hours.

value: NfsB-positive THP1 cells

value: stably NfsB expressing AML cell line


title: pat 3 tumor [HDV_3A_S18]


title: SYO1_shCt_H3K36me3_ChIP-Seq


title: rpoN_induction_37C_rep1

value: YPIII


title: NTR-expressing cells 50 nM NTR prodrug treated - rep3

description:
BL_191017_THP1NTR50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with NTR prodrug of LSD1 inhibitor

value: NTR prodrug of LSD1 inhibitor


title: NTR-expressing cells vehicle treated - rep3

description:
BP_191017_THP1NTRDMSO_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with vehicle DMSO

source_name: NTR-expressing cells vehicle treated

value: vehicle DMSO


title: NTR-expressing cells 100 nM negativ control of NTR prodrug treated - rep3

description:
BO_191017_THP1NTR100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)


title: CRL7250_WT_H4K16ac_ChIP-Seq

value: CST (E2B8W)


title: pat 39 non-tumor [HDV_39B_S42]

source_name: liver tissue

value: hepatocellular carcinoma patient


title: WT_Stationary_26C_rep3

value: Stationary

value: Wild type


title: NTR-expressing cells 50 nM LSD1 inhibitor treated - rep3

description:
BJ_191017_THP1NTR50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86

value: LSD1 inhibitor OG86


title: CRL7250_WT_H4K12ac_ChIP-Seq

value: CST (D2W60)


title: pat 39 tumor [HDV_39A_S59]

value: tumor


title: NTR-expressing cells 100 nM LSD1 inhibitor treated - rep3

description:
BK_191017_THP1NTR100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86


title: WT_Stationary_26C_rep2


title: NTR-expressing cells 100 nM NTR prodrug treated - rep3

description:
BM_191017_THP1NTR100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1NTR+ cells treated with NTR prodrug of LSD1 inhibitor


title: wild-type cells vehicle treated - rep3

description:
BI_191017_THP1wtDMSO_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with vehicle DMSO

source_name: wild-type cells vehicle treated

value: THP1 wild-type cells

value: AML cell line


title: CRL7250_WT_RING1B_ChIP-Seq

value: FIbroblast

value: CST (D22F2)


title: wild-type cells 100 nM negativ control of LSD1 inhibitor treated - rep3

description:
BG_191017_THP1wt100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a negative control (structurally related to OG86, but inactive on LSD1)


title: CRL7250_WT_Input_ChIP-Seq


title: WT_Stationary_26C_rep1


title: pat 38 tumor [HDV_38A_S9]


title: rpoN_Stationary_26C_rep3

value: Mutant


title: rpoN_Stationary_26C_rep2


title: pat 37 non-tumor [HDV_37B_S38]

value: non-tumor


title: pat 37 tumor [HDV_37A_S5]


title: CRL7250_V5-SSX1_aa1-188-full-length_V5_ChIP-Seq

value: CST (D3H8Q)


title: wild-type cells 50 nM NTR prodrug treated - rep3

description:
BE_191017_THP1wt50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor


title: wild-type cells 100 nM NTR prodrug treated - rep3

description:
BF_191017_THP1wt100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor


title: CRL7250_V5-SSX1_aa1-188-full-length_Input_ChIP-Seq


title: pat 36 non-tumor [HDV_36B_S35]


title: CRL7250_V5-SSX1_aa111-188-78aa-tail_V5_ChIP-Seq


title: rpoN_Stationary_26C_rep1

value: YPIII


title: pat 38 non-tumor [HDV_38B_S40]


title: pat 36 tumor [HDV_36A_S20]


title: pat 35 non-tumor [HDV_35B_S16]


title: Non-IPF LF-derived EVs

city: San Francisco

first: Tsukasa

last: Kadota

state: CA

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

description: Total RNA extracted form extracellular vesicles, and 20 ng of RNA for analysis

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: EVs collected from LFs from non-IPF individuals

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

growth_protocol: Primary lung fibroblasts (LFs) were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) with 10% fetal bovine serum and 100 μg/ml penicillin/streptomycin and 0.5 mM sodium pyruvate (Sigma-Aldrich, MO, USA).

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: The IPF and non-IPF LFs were washed with phosphate-buffered saline (PBS), and the culture medium was replaced with serum-free advanced DMEM medium contained antibiotic and antifungal drugs. After incubation, the conditioned medium (CM) was collected and centrifuged at 2,000 x g for 10 min at 4°C. To thoroughly remove cellular debris, the supernatant was filtered through a 0.22-mm filter (Millipore). The CM was then used for EV isolation. To prepare EVs, CM was ultracentrifuged at 35,000 rpm using a SW41Ti rotor for 70 min at 4°C. The pellets were washed with PBS, ultracentrifuged at 35,000 rpm using the SW41Ti rotor for 70 min at 4°C and resuspended in PBS.

value: non-idiopathic pulmonary fibrosis (non-IPF) individual

value: Primary lung fibroblast (LFs)

value: Extracellular vesicles (EVs)

value: miRNA


title: SYO1_shRING1A_shRING1B_H2AUb1K119_ChIP-Seq

description: SYO1_shRING1A_shRING1B_H2AUb1 K119_ChIP-Seq

value: Synovial Sarcoma

value: CST (D27C4)


title: NTR-expressing cells vehicle treated - rep2

description:
BB_191011_THP1NTRDMSO_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with vehicle DMSO

value: NfsB-positive THP1 cells

value: stably NfsB expressing AML cell line

value: vehicle DMSO


title: SYO1_shCt_H2AUb1K119_ChIP-Seq

description: SYO1_shCt_H2AUb1 K119_ChIP-Seq


title: ZIKV_H41R_3

city: Los Angeles

first: Zhifei

last: Luo

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

data_processing:
Primary sequences data were checked by FastQC version 0.11.7 for quality control purpose. To increase accuracy, reads have N base were removed by cutadapt version 1.16 (Martin, 2011) (--max-n 0). Trimmed reads were mapped to human genome GRCh38 using Bowtie version 1.2.2 (Langmead et al., 2009) with option -n 0 -l 17 -a --best --strata to find the best aligned reads. Seed length for alignment was set as 17 and no mismatch was allowed in seed region. PCA analysis of each group was performed as computed by prcomp function in R and shown by scatterolit3d package. Reads counts for genes were summarized by featureCounts v1.6.4 based on a merged annotation files containing miRNA information from miRbase 22 and sequence for other genes (non-coding RNA, tRNA, repeat elements, protein coding genes etc) from UCSC. The read counts for each gene were normalized by total aligned reads for each sample. All mapped reads were normalized to 1 million (RPM), and differentially expressed genes were picked by two-way t-test based on normalized read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_read_counts.txt

source_name: neural stem cells (NSCs)

growth_protocol: Human fetal NSCs were maintained as neurospheres in DMEM/F12 supplemented with StemPro Neural Supplement (Thermo Fisher) using suspension culture dishes (Corning, Acton, MA). NSCs stably expressing ZIKV viral proteins were generated using a standard selection protocol with puromycin (2 µg/ml).

extract_protocol:
total RNA was isolated by Qiagen Rneasy mini kit
Library was constructed using QIAseq miRNA Library Kit  (Cat # 331505) by UCLA Technology Center for Genomics & Bioinformatics (TCGB), followed by deep sequenced using Illumina HiSeq3000, as previously reported (Li et al., 2013). Briefly, the workflow consists of 3’ ligation, primer hybridization, 5’ ligation, first strand synthesis and PCR amplification. Different adapters were used for multiplexing samples in one lane. AMPure XP Beads were used for dual size selection. Library quality was checked with Bioanalyzer (Agilent) and Qubit (Life Technologies).

treatment_protocol: 1x106 NSCs were infected with ZIKV-WT or ZIKV-H41R at MOI: 1 and total RNA was extracted with at 2 dpi.

value: Infected

value: H41R ZIKV


title: wild-type cells 100 nM negativ control of NTR prodrug treated - rep3

description:
BH_191017_THP1wt100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)

value: THP1 wild-type cells

value: AML cell line


title: wild-type cells 50 nM LSD1 inhibitor treated - rep3

description:
BC_191017_THP1wt50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86

value: LSD1 inhibitor OG86


title: ZIKV_H41R_2


title: IPF LF-derived EVs

source_name: EVs collected from LFs from patients with IPF

value: idiopathic pulmonary fibrosis (IPF) patients


title: pat 35 tumor [HDV_35A_S15]

value: hepatocellular carcinoma patient

value: tumor


title: SYO1_shRING1A_shRING1B_SUZ12_ChIP-Seq

value: CST (D39F6)


title: pat 34 non-tumor [HDV_34B_S64]

value: non-tumor


title: SYO1_shCt_SUZ12_ChIP-Seq


title: ZIKV_H41R_1


title: pat 34 tumor [HDV_34A_S35]


title: CRL7250_V5-SSX1_aa111-188-78aa-tail_Input_ChIP-Seq

source_name: CRL7250 (FIbroblast)

value: FIbroblast


title: ZIKV_WT_3

value: wild type ZIKV


title: pat 33 non-tumor [HDV_33B_S63]


title: SYO1_shRING1A_shRING1B_RING1B_ChIP-Seq

value: Synovial Sarcoma

value: CST (D22F2)


title: wild-type cells 100 nM LSD1 inhibitor treated - rep3

description:
BD_191017_THP1wt100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86


title: NTR-expressing cells 100 nM negativ control of LSD1 inhibitor treated - rep2

description:
AZ_191011_THP1NTR100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a negative control (structurally related to OG86, but inactive on LSD1)

value: NfsB-positive THP1 cells


title: ZIKV_WT_2


title: pat 33 tumor [HDV_33A_S68]


title: SYO1_shCt_RING1B_ChIP-Seq


title: ZIKV_WT_1


title: NTR-expressing cells 50 nM NTR prodrug treated - rep2

description:
AX_191011_THP1NTR50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with NTR prodrug of LSD1 inhibitor

value: stably NfsB expressing AML cell line

value: NTR prodrug of LSD1 inhibitor


title: NTR-expressing cells 100 nM LSD1 inhibitor treated - rep2

description:
AW_191011_THP1NTR100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86


title: SYO1_shRING1A_shRING1B_RING1A_ChIP-Seq

value: CST (D2P4D)


title: NTR-expressing cells 100 nM negativ control of NTR prodrug treated - rep2

description:
BA_191011_THP1NTR100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)


title: SYO1_shCt_RING1A_ChIP-Seq


title: pat 32 tumor [HDV_32A_S52]


title: pat 32 non-tumor [HDV_32B_S31]


title: Mock_3

value: Control

value: NO ZIKV


title: SYO1_shRING1A_shRING1B_BAF155_ChIP-Seq

value: CST (D7F8S)


title: Mock_2


title: NTR-expressing cells 100 nM NTR prodrug treated - rep2

description:
AY_191011_THP1NTR100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1NTR+ cells treated with NTR prodrug of LSD1 inhibitor


title: pat 31 non-tumor [HDV_31B_S70]


title: Mock_1


title: pat 31 tumor [HDV_31A_S66]


title: wild-type cells vehicle treated - rep2

description:
AU_191011_THP1wtDMSO_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with vehicle DMSO

value: THP1 wild-type cells

value: AML cell line

value: vehicle DMSO


title: gMDSC_Rep2_KO-oxBS

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

data_processing:
Raw reads of mRNA-seq were first trimmed to remove adapters and low-quality bases by using the trim_galore (v0.4.4_dev) program with parameters: “--paired --illumina”. Trimmed reads were then aligned to the mouse reference genome (mm9) by using the tophat (v2.1.1) program with default parameters. The mouse reference genome and gene annotations were download from the UCSC genome website (http://www.genome.ucsc.edu). The cufflinks (v2.2.1) program to calculate FPKM (Fragments Per Kilobase Million) to estimate the abundance of a given mRNA. The cuffdiff (v2.2.1) program was used to identify differentially expressed genes.
Raw reads of BS-seq and OxBS-seq were trimmed using Trim-Galore to remove low quality bases and adaptor sequences. The trimmed reads were mapped onto the reference genome (mm9) using bsmap (v2.74), followed by removal of PCR duplicates. We extracted methylation signals using methratio.py, a script in the bsmap package (v3.4.2) (40). An R-script was generated to maintain chromosome coordinates consistent for methylation sites between each pair of BS and OxBS samples, allowing to identify 5mC and 5hmC signal in these common sites with the mlml script in methpipe using the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The mRNA-seq processed files containing FPKM value for each gene were genes.fpkm_tracking that was generated by the cuffinks. The OxBS-seq processed files contain methylation level at base-resolution, with five columns: chromosome, position, strand, seq-context, methylated-percentage, and seq-depth.

source_name: mice with tumor challenge (Hepa1-6)

growth_protocol: Hepa1-6_Tu and Py8119_Tu were derived from C57BL/6-derived Hepa1-6 syngeneic tumor and C57BL/6-derived Py8119 syngeneic tumor. The syngeneic tumors were cut in pre-cooling PBS, and the tissue pieces were ground by mechanical grinding. Filter the cells with a 70um cell strainer. The filtered single cells were washed with PBS twice. Isolation of G-MDSCs was performed with the Myeloid-Derived Suppressor Cell Isolation Kit, mouse (130-094-538, Miltenyi Biotec).

extract_protocol:
All isolated cells (Hepa1-6_Tu and Py8119_Tu, G-MDSCs) were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The DNA of G-MDSCs were extracted using a DNA extraction kit (56504, QIAamp DNA Investigator Kit).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used to construct the libraries of mRNA-seq. TrueMethyl Seq protocol recommended by Cambridge Epigenetix (CEGX, Cambridge, UK) was used to prepare the libraries for oxidative bisulfite sequencing (OxBS-seq).

treatment_protocol: All isolated cells (Hepa1-6_Tu and Py8119_Tu, G-MDSCs) were washed once with PBS and immediately used for RNA extraction OR DNA extraction.

tag: age

value: 8 weeks

tag: genotype/variation

tag: tissue source

value: Spleen

tag: tissue/cell type

value: granulocytic myeloid-derived suppressor cells (G-MDSCs)


title: pat 30 non-tumor [HDV_30B_S62]

value: hepatocellular carcinoma patient

value: non-tumor


title: SYO1_shRING1A_shRING1B_SS18_ChIP-Seq

value: Synovial Sarcoma

value: CST (D6I4Z)


title: SYO1_shCt_BAF155_ChIP-Seq


title: gMDSC_Rep2_KO-BS


title: wild-type cells 100 nM negativ control of LSD1 inhibitor treated - rep2

description:
AS_191011_THP1wt100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a negative control (structurally related to OG86, but inactive on LSD1)

tag: treatment


title: NTR-expressing cells 50 nM LSD1 inhibitor treated - rep2

description:
AV_191011_THP1NTR50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86

value: NfsB-positive THP1 cells

value: LSD1 inhibitor OG86


title: pat 30 tumor [HDV_30A_S2]

tag: subject status

value: tumor


title: wild-type cells 100 nM NTR prodrug treated - rep2

description:
AR_191011_THP1wt100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor

value: NTR prodrug of LSD1 inhibitor


title: SYO1_shCt_SS18_ChIP-Seq


title: gMDSC_Rep2_WT-oxBS

value: wild type


title: SYO1_shRING1A_shRING1B_Input_ChIP-Seq


title: SYO1_shCt_Input_ChIP-Seq


title: CLR7250_V5-SS18-SSX_33aa-SSX-Tail_repeat_V5_ChIP-Seq

value: FIbroblast

value: CST (D3H8Q)


title: pat 29 non-tumor [HDV_29B_S61]

tag: tumor/non-tumor


title: wild-type cells 100 nM negativ control of NTR prodrug treated - rep2

description:
AT_191011_THP1wt100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)

value: THP1 wild-type cells


title: gMDSC_Rep1_KO-oxBS


title: wild-type cells 50 nM NTR prodrug treated - rep2

description:
AQ_191011_THP1wt50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor

value: AML cell line


title: wild-type cells 50 nM LSD1 inhibitor treated - rep2

description:
AO_191011_THP1wt50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86


title: gMDSC_Rep2_WT-BS


title: gMDSC_Rep1_KO-BS


title: wild-type cells 100 nM LSD1 inhibitor treated - rep2

description:
AP_191011_THP1wt100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86


title: CLR7250_V5-SS18-SSX_33aa-SSX-Tail_repeat_Input_ChIP-Seq


title: NTR-expressing cells vehicle treated - rep1

description:
AN_191009_THP1NTRDMSO_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with vehicle DMSO

value: stably NfsB expressing AML cell line

value: vehicle DMSO


title: gMDSC_Rep1_WT-oxBS

value: 8 weeks

value: Spleen


title: pat 29 tumor [HDV_29A_S64]

value: hepatocellular carcinoma patient


title: CLR7250_V5-SS18-SSX_L169A-mut-SSX-Tail_V5_ChIP-Seq


title: pat 28 non-tumor [HDV_28B_S60]

value: non-tumor


title: NTR-expressing cells 100 nM negativ control of NTR prodrug treated - rep1

description:
AM_191009_THP1NTR100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)


title: NTR-expressing cells 100 nM negativ control of LSD1 inhibitor treated - rep1

description:
AL_191009_THP1NTR100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with a negative control (structurally related to OG86, but inactive on LSD1)


title: pat 2 non-tumor [HDV_2B_S10]


title: pat 28 tumor [HDV_28A_S48]


title: gMDSC_Rep1_WT-BS

value: granulocytic myeloid-derived suppressor cells (G-MDSCs)


title: pat 2 tumor [HDV_2A_S38]


title: CLR7250_V5-SS18-SSX_L169A-mut-SSX-Tail_Input_ChIP-Seq


title: CLR7250_V5-SS18-SSX_W164A-mut-SSX-Tail_V5_ChIP-Seq


title: 2nd_gMDSC_KO_H


title: pat 27 non-tumor [HDV_27B_S59]


title: pat 27 tumor [HDV_27A_S57]


title: pat 26 non-tumor [HDV_26B_S27]


title: NTR-expressing cells 100 nM NTR prodrug treated - rep1

description:
AK_191009_THP1NTR100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1NTR+ cells treated with NTR prodrug of LSD1 inhibitor


title: CLR7250_V5-SS18-SSX_78aa-SSX-Tail_V5_ChIP-Seq


title: NTR-expressing cells 50 nM LSD1 inhibitor treated - rep1

description:
AH_191009_THP1NTR50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86


title: pat 26 tumor [HDV_26A_S10]


title: 2nd_gMDSC_WT_H


title: NTR-expressing cells 50 nM NTR prodrug treated - rep1

description:
AJ_191009_THP1NTR50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with NTR prodrug of LSD1 inhibitor


title: 2nd_gMDSC_KO

source_name: mice without tumor challenge


title: 2nd_gMDSC_WT


title: CLR7250_V5-SS18-SSX_78aa-SSX-Tail_Input_ChIP-Seq


title: 1st_gMDSC_KO_H


title: Aska_shSSX_H3K9ac_ChIP-Seq

description: Aska _shSSX_H3K9ac_ChIP-Seq

value: Synovial Sarcoma

value: Aska

value: CST (C5B11)


title: pat 25 non-tumor [HDV_25B_S22]


title: 1st_gMDSC_WT_H


title: Aska_shCt_H3K9ac_ChIP-Seq

description: Aska _shCt_H3K9ac_ChIP-Seq


title: pat 25 tumor [HDV_25A_S62]

value: tumor


title: 1st_gMDSC_KO


title: Aska_shSSX_H3K14ac_ChIP-Seq

description: Aska _shSSX_H3K14ac_ChIP-Seq

value: CST (D4B9)


title: wild-type cells 100 nM negativ control of LSD1 inhibitor treated - rep1

description:
AE_191009_THP1wt100nM-JSF57_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a negative control (structurally related to OG86, but inactive on LSD1)


title: wild-type cells vehicle treated - rep1

description:
AG_191009_THP1wtDMSO_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with vehicle DMSO


title: Aska_shCt_H3K14ac_ChIP-Seq

description: Aska _shCt_H3K14ac_ChIP-Seq


title: CLR7250_V5-SS18-SSX_W164A-mut-SSX-Tail_Input_ChIP-Seq


title: NTR-expressing cells 100 nM LSD1 inhibitor treated - rep1

description:
AI_191009_THP1NTR100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1-NTR+ cells treated with LSD1 inhibitor OG86

value: NfsB-positive THP1 cells

value: LSD1 inhibitor OG86


title: 1st_gMDSC_WT

value: wild type


title: wild-type cells 100 nM NTR prodrug treated - rep1

description:
AD_191009_THP1wt100nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor

value: THP1 wild-type cells

value: NTR prodrug of LSD1 inhibitor


title: pat 24 tumor [HDV_24A_S45]


title: wild-type cells 50 nM NTR prodrug treated - rep1

description:
AC_191009_THP1wt50nM-DA2_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with NTR prodrug of LSD1 inhibitor

value: AML cell line


title: Py8119_Tu_KO-2

source_name: mice with tumor challenge

value: 18 days after tumor cell injection

value: C57BL/6-derived Py8119 breast cancer cell

value: syngeneic tumor


title: wild-type cells 100 nM negativ control of NTR prodrug treated - rep1

description:
AF_191009_THP1wt100nM-EH184_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with a NTR prodrug of negative control (structurally related to OG86, but inactive on LSD1)


title: Aska_shSSX_H4K12ac_ChIP-Seq

description: Aska _shSSX_H4K12ac_ChIP-Seq

value: CST (D2W60)


title: pat 23 non-tumor [HDV_23B_S58]

value: hepatocellular carcinoma patient

value: non-tumor


title: Aska_shCt_H4K12ac_ChIP-Seq

description: Aska _shCt_H4K12ac_ChIP-Seq

value: Synovial Sarcoma


title: Py8119_Tu_WT-2


title: Py8119_Tu_KO-1


title: wild-type cells 100 nM LSD1 inhibitor treated - rep1

description:
AB_191009_THP1wt100nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86


title: SE-4

city: BOTHELL

first: Hailing

last: Lu

institute: Seattle Genetics

description: SE-treated mouse 4

hyb_protocol: following instructions for the panCancer Immune profiling panel

scan_protocol: nanostring nCounter

data_processing: nSolver software

label: nanostring probes

source_name: SE-treated tumor 4

growth_protocol: A20 lymgphoma cells were maintained in RPMI with 10% FBS.  Cells were washed twice before subcutaneous implantation into Balb/c mice (5 million cells/mouse).

extract_protocol: RNA was extracted using the Qiagen DNA/RNA Allprep kit

treatment_protocol: Mice with established A20 tumors (~7 days post implantation) were assigned to PBS, GLA-SE, or SE treatment groups (N=4/group).  Intratumoral injections with PBS, GLA-SE (10 ug GLA in 50ul of 2% stable emulsion) or SE alone was administered every other day for a total of three times.  Tumor were collected at two hours after the last injection.

value: Balb/c

value: A20 lymgphoma cells

tag: Sex

value: Female


title: pat 22 tumor [HDV_22A_S31]

value: tumor


title: Py8119_Tu_WT-1


title: Aska_shCt_H4K16ac_ChIP-Seq

description: Aska _shCt_H4K16ac_ChIP-Seq

value: Aska

value: CST (E2B8W)


title: SE-3

description: SE-treated mouse 3

source_name: SE-treated tumor 3

label_protocol: following instructions for the panCancer Immune profiling panel


title: SE-2

description: SE-treated mouse 2

source_name: SE-treated tumor 2


title: pat 21 non-tumor [HDV_21B_S52]


title: pat 24 non-tumor [HDV_24B_S17]


title: pat 21 tumor [HDV_21A_S26]


title: CRL7250_V5-SS18-SSX_23aa-SSX-Tail_V5_ChIP-Seq

value: FIbroblast

value: CST (D3H8Q)


title: Hepa1-6_Tu_KO-3

value: C57BL/6-derived Hepa1-6 hepatoma carcinoma cell


title: Hepa1-6_Tu_KO-4


title: SE-1

description: SE-treated mouse 1

source_name: SE-treated tumor 1


title: wild-type cells 50 nM LSD1 inhibitor treated - rep1

description:
AA_191009_THP1wt50nM-EH7_(Clariom_S_Human).mean
Gene expression data from THP1 cells treated with LSD1 inhibitor OG86

value: THP1 wild-type cells

value: AML cell line

value: LSD1 inhibitor OG86


title: Hepa1-6_Tu_WT-4

value: 18 days after tumor cell injection

value: wild type

value: syngeneic tumor


title: GLA-SE-4

description: GLA-SE treated mouse 4

source_name: GLA-SE-treated tumor 4


title: CRL7250_V5-SS18-SSX_6aa_BasicDel_V5_ChIP-Seq


title: pat 20 tumor [HDV_20A_S60]

value: hepatocellular carcinoma patient


title: Hepa1-6_Tu_WT-3


title: pat 20 non-tumor [HDV_20B_S57]

value: non-tumor


title: pat 23 tumor [HDV_23A_S42]


title: pat 1 non-tumor [HDV_1B_S4]


title: Aska_shSSX_H4K16ac_ChIP-Seq

description: Aska _shSSX_H4K16ac_ChIP-Seq

value: Synovial Sarcoma


title: CRL7250_V5-SS18-SSX_7aa_AcidicDel_V5_ChIP-Seq


title: Hepa1-6_Tu_KO-2


title: pat 22 non-tumor [HDV_22B_S55]


title: Hepa1-6_Tu_KO-1


title: Hepa1-6_Tu_WT-2


title: Nut3_Spt5-pSer666_rep1

city: Bronx

first: PABITRA

middle: K

last: PARUA

state: NY

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
ChIP-seq: Single-end (75-nt reads) or paired-end (40-nt reads) sequencing was performed on an Illumina NextSeq 500.
ChIP-seq: ‘FastQC Read Quality Reports’ (Galaxy Version 0.72) and ‘Trimmomatic Flexible Read Trimming Tool’ (Galaxy Version 0.36.6) were used to check quality of the sequencing reads and for barcode trimming, respectively.
ChIP-seq: Trimmed sequencing reads were aligned to the human genome (version b37, hg19) using Bowtie2 in Galaxy (Galaxy Version 2.3.4.2). Normalization of the aligned reads was done using ‘bamCoverage’ (Galaxy Version 3.1.2.0.0) by 1) computing and applying scaling factor obtained using aligned sequencing reads of the spike-in reference genome (Saccharomyces cerevisiae, for spike-in samples) and 2) by computing RPKM (reads per kilobase per million) (for the samples without spike-in control).
ChIP-seq: Aligned sequences of each biological replicate were processed separately to identify enriched binding sites using MACS2 callpeak program (Galaxy Version 2.1.1.20160309.6). The resulting bedgraph files were converted to bigwig using ‘Wig/BedGraph-to-bigWig converter’ (Galaxy Version 1.1.1), replicates were combined using ‘Concatenate datasets’ (Galaxy Version 1.0.0).
ChIP-seq: Matrix was computed using ‘computeMatrix’ (Galaxy v.2.3.6.0) in DeepTools to prepare data for plotting heat maps and/or profiles of given regions. The genome-wide distributions, heat maps and metagene plots were created using ‘plotHeatmap’ (Galaxy Version 3.1.2.0.1) and ‘plotProfile’ (Galaxy Version 3.1.2.0.0) tools, respectively. The phospho-over-total signal ratios (log2-ratio) were calculated using ‘bigwigCompare’ (Galaxy Version 3.1.2.0.0). To generate principal component analysis (PCA) plots ‘plotPCA’ (Galaxy Version 3.1.2.0.0) was used.
Genome_build: ChIP-seq: Feb 2009 GRCh37/hg19
Genome_build: ChIP-seq: Skip-in control Saccharomyces cerevisiae (April 2011, sacCer3)
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format (n = 2 biological replicates combined). There are 15-bigWig files in total. .

growth_protocol: ChIP-seq: HCT116 cells cultured in McCoy’s 5A medium with L-glutamine (10-050-CV, Corning) supplemented with 10% Fetal Bovine Serum (FBS, 10437-028, Gibco) and 1x Penicillin-Streptomycin (30-002-Cl, Corning). Drug treatments were performed at 50-60% confluence by substituting the growth medium with fresh medium containing either DMSO, 250 nM (except where noted) NVP-2 (provided by N.S. Gray), 10 μM RO-3306 (S7747, Selleckchem) and 5 μM nutlin-3 (10004372, Cayman Chemical Company).

extract_protocol:
ChIP-seq: HCT116 cells grown to 50-60% confluence were crosslinked with 1% formaldehyde (BP-531, Fisher Scientific) for 10 min at 25°C. Crosslinking was quenched with 125 mM glycine for 5 min at 25°C. Cells were washed twice with ice-cold PBS and collected into 1 ml of RIPA buffer supplemented with protease and phosphatase inhibitors for each 150-mm dish. Cells were lysed and chromatin sheared by sonication in a Bioruptor at high power, for 5 x 10 min with cycles of 30 sec ON and 30 sec OFF. Lysates were clarified by centrifugation at 20,000 x gav for 20 min at 4°C. Before immunoprecipitation, lysates (~5 x 106 cells per experiment) were pre-cleared with PierceTM Protein A Agarose (20333, Thermo Scientific) for 2 hr at 4°C. Beads were separated by centrifugation at 4000 x gav for 1 min at 4°C. The resulting supernatant was incubated with antibodies for 4 hr at 4°C with constant nutation. In spike-in control experiments, 10% (w/w) of the crosslinked Saccharomyces cerevisiae chromatin was added to the immunoprecipitation reaction.
ChIP-seq: Preparation of multiplexed ChIP-seq libraries from purified immunoprecipitated chromatin and sequencing were performed as described. In brief, the NEBNext Ultra II DNA Library Preparation kit (E7103S) was used to generate libraries using 5-10 ng of input or immunoprecipitated DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina (Set 1, E7335 and Set 2, E7500)).

treatment_protocol: ChIP-seq: Drug treatment was performed at 50-60% confluence by substituting the growth medium with fresh medium containing either DMSO or 5 μM nutlin-3 (10004372, Cayman Chemical Company) for 2 hour.

tag: temperature

tag: drug treatiment

value: Nutlin-3 (10004372, Cayman Chemical Company)

tag: drug dose

value: 5 μM

tag: time of treatiment (hour)

value: 2 hour

tag: antibody

value: rabbit anti-Spt5-pSer666 (21st Century Biochemicals)

tag: assay

value: ChIP-seq


title: Nut3_Spt5_rep1

tag: cell line

value: rabbit anti-Spt5 (A300-868A, Bethyl Laboratories)


title: GLA-SE-2

description: GLA-SE treated mouse 2

source_name: GLA-SE-treated tumor 2

tag: strain

value: Balb/c

tag: cell type

value: A20 lymgphoma cells

value: Female


title: CRL7250_V5-SS18-SSX_33aa-SSX-Tail_V5_ChIP-Seq

value: FIbroblast

tag: chip antibody

value: CST (D3H8Q)


title: GLA-SE-1

description: GLA-SE treated mouse 1

source_name: GLA-SE-treated tumor 1


title: GLA-SE-3

description: GLA-SE treated mouse 3

source_name: GLA-SE-treated tumor 3


title: pat 1 tumor [HDV_1A_S13]

source_name: liver tissue

value: tumor


title: pat 18 non-tumor [HDV_18B_S49]


title: pat 19 non-tumor [HDV_19B_S12]


title: PBS-4

description: control PBS mouse 4

source_name: control tumor 4


title: pat 19 tumor [HDV_19A_S30]


title: WT_input_control_rep2

data_processing:
The quality of raw reads generated from Hiseq 2500 was checked using FastQC. Raw reads were trimmed by 5 nt at both the 5’ and 3’ ends by Trimmomatic
Trimmed reads were aligned with the reference Y. pseudotuberculosis genome YPIII (NC_010465) using BWA
Aligned reads were converted to BAM files using SAMtool and duplicate reads were removed with picard
Before peak calling, two biological replicates for each sample and the input (control) were merged using SAMtool
Peak calling was done using MACS (2.1.2) with the following custom settings: log2FC>1 over input, --broad –g, --broad-cutoff = 0.1
Genome_build: NC_010465
Supplementary_files_format_and_content: wig files were generated using custom script.
Supplementary_files_format_and_content: peak text files

source_name: in vitro growing cell

extract_protocol:
Sonicated lysates were purified with antibody.
Y. pseudotuberculosis ∆rpoN expressing RpoN::V5 in trans under the inducible araBAD promoter (YPIII, ∆rpoN/pIBX, prpoN::V5 ) as well as Y. pseudotuberculosis expressing RpoN:V5 in cis under its native promoter (YPIII, rpoN::V5/pIBX ) were grown overnight in LB, diluted to OD600 0.05, and grown for 4 h at 26ºC, at which point the prpoN::V5 plasmid was induced with 0.005% arabinose for 30 min. Virulence-induced cultures were shifted to 37ºC after 1 h at 26ºC and incubated for 75 min in calcium-depleted conditions.. Non-tagged WT Y. pseudotuberculosis grown at 26ºC for 4 h was used as a negative control. Cultures were cross-linked with 1% formaldehyde at room temperature for 10 min. For subsequent ChIP-seq, 10 OD600 were used for each biological replicate. Chromatin immunoprecipitation was performed as described previously, with slight modifications (Bonocora et al., 2013). The 1 ml samples were sonicated in AFA milli-tubes using a Covaris E220 sonicator with the following settings: peak power, 140W; duty factor, –5%; cycles/burst, 200; time, 16 min. Immunoprecipitation was done using 90 μL Anti-V5 Agarose Affinity Gel (Sigma A 7345) overnight at 4ºC. ChIP DNA was eluted in 100 μl elution buffer, treated with RNase A and proteinase K, and purified using a ChIP DNA clean & Concentrator Kit (Zymo Research, USA). AMPure XP magnetic beads (Beckman Coulter) 1.5 and 0.8 were used to remove adapters and clean and concentrate the DNA. Failsafe polymerase (Nordic Biolabs AB, Sweden) was used for efficient library amplification.

value: YPIII

value: none (input)

tag: genotype

value: WT


title: PBS-3

description: control PBS mouse 3

source_name: control tumor 3


title: PBS-1

description: control PBS mouse 1

source_name: control tumor 1


title: PBS-2

description: control PBS mouse 2

source_name: control tumor 2


title: WT_input_control_rep1

treatment_protocol: prpoN::V5 plasmid was induced with 0.005% arabinose for 30 min.


title: Nut3_Pol II-pSer2_rep1

value: rabbit anti-Rpb1 CTD pSer2 (ab5095, Abcam)


title: DMSO_Spt5-pThr806_rep1

value: DMSO

value: rabbit anti-Spt5-pThr806 (21st Century Biochemicals)


title: Nut3_Spt5-pThr806_rep1

value: Nutlin-3 (10004372, Cayman Chemical Company)

value: 5 μM


title: Nut3_Pol II_rep1

value: 2 hour

value: rabbit anti- Rpb1 (sc-899; Santa Cruz Biotechnology)


title: pat 17 non-tumor [HDV_17B_S11]

value: hepatocellular carcinoma patient

value: non-tumor


title: pat 18 tumor [HDV_18A_S21]


title: RpoN-V5_logarithmic_phase_rep2

value: Anti-V5 Agarose Affinity Gel (Sigma A 7345)


title: pat 17 tumor [HDV_17A_S16]


title: RpoN-V5_logarithmic_phase_rep1


title: DMSO_Spt5-pSer666_rep1

value: rabbit anti-Spt5-pSer666 (21st Century Biochemicals)

value: ChIP-seq


title: DMSO_Spt5_rep1

value: rabbit anti-Spt5 (A300-868A, Bethyl Laboratories)


title: pat 16 non-tumor [HDV_16B_S7]


title: Hepa1-6_Tu_WT-1

tag: age

value: 18 days after tumor cell injection

tag: genotype/variation

value: wild type

tag: tissue source

value: C57BL/6-derived Hepa1-6 hepatoma carcinoma cell

value: syngeneic tumor


title: DMSO_Pol II-pSer2_rep1

value: rabbit anti-Rpb1 CTD pSer2 (ab5095, Abcam)


title: RpoN-V5_pBAD_overexpression_rep2

value: YPIII

value: delta_rpoN/pIBX, prpoN::V5


title: pat 16 tumor [HDV_16A_S58]

tag: subject status

value: tumor


title: RpoN-V5_induction_condition_rep2


title: RpoN-V5_induction_condition_rep1


title: pat 15 non-tumor [HDV_15B_S34]

tag: tumor/non-tumor


title: Spt5-pThr806_rep2

value: rabbit anti-Spt5-pThr806 (21st Century Biochemicals)


title: PC-3 Transfected + 1 uM iCRT14 rep3

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

department: Chemical & Biological Engineering

institute: Villanova University

data_processing:
Data processed using Excel, raw data normalized for FPKM and synthesized using vLookup function.
Supplementary_files_format_and_content: FPKM, DEG

source_name: Prostate Cancer Cells

growth_protocol: PC-3 cells were grown using RPMI 1640 media supplemented with 10% FBS and 1% P/S and passaged every 2-5 days (PC-3).

extract_protocol:
Small sample of cells evaluated using flow cytometry for transfection efficiency at 24 hours post-transfection, and then the remaining sample was lysed and extracted according to the Qiagen RNeasy kit instructions.
Samples sent off for sequencing with BGI for mRNA sequencing. (polyA capture)

treatment_protocol: PC-3 cells were seeded in T-75 well plates and grown in RPMI-1640 media. Transfections with Lipofectamine® LTX were performed according to the manufacturer’s protocol using Lipofectamine LTX, Plus Reagent, and pEF-GFP.

tag: treatment

value: pEF-GFP + 1 uM Icrt14


title: pat 15 tumor [HDV_15A_S11]


title: PC-3 Transfected + 1 uM iCRT14 rep2


title: DMSO_Pol II_rep1

tag: temperature

value: DMSO

value: 2 hour

value: rabbit anti- Rpb1 (sc-899; Santa Cruz Biotechnology)


title: DMSO_Input_rep1

tag: drug treatiment


title: pat 14 non-tumor [HDV_14B_S30]

value: hepatocellular carcinoma patient

value: non-tumor


title: PC-3 Transfected + 1 uM iCRT14 rep1