title: pTH15804.2_HK_8mer

type: protein

city: Toronto

first: Isaac

last: Yellan

state: Ontario

address: 160 College St.

department: Molecular Genetics

institute: University of Toronto

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. VALUE - median kmer intensity; Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.  Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: Crocodylus porosus

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector.

tag: dbd

value: Unknown

tag: platform_id_id design

value: HK


title: pTH15805.2_HK_8mer

status: Public on Feb 09 2021

country: Canada

label_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.


title: pTH15805.1_ME_8mer

value: ME


title: PAX-BJ-165-post-methy

type: genomic

city: Beijing

first: Wenbo

last: Guo

state: Beijing

address: Haidian

country: China

institute: Tsinghua University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.   Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.

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

data_processing: Arrays were imported and quality control. Methylation score of each CpG is represented as AVG_beta value.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PDX model of pancreatic cancer patient PAX-BJ-165 after gemcitabine treatment

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions.

tag: patient id

tag: tissue

value: patient-derived xenograft


title: pTH15804.1_ME_8mer


title: MA_2_p13

type: SRA

city: Budapest

first: János

middle: Miklós

last: Réthelyi

address: Balassa utca 6.

country: Hungary

institute: Semmelweis University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for short or low-quality sequence using Trimgalore! With parameters: s -5, -q 20, -l 50, then mapped to hg19 reference genome using hisat2 v.2.1.0
Mapped reads were annotated to genes using featureCounts
After exclusion of all X and Y chromosome genes, differential expression analysis (SZ-HU-PROB compare to SZ-HU-MO and SZ-HU-PROB compare to SZ-HUFA) was performed by using DESeq2 program
Rlog normalization was performed by DESeq2 analysing all the sample
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file containing read counts of genes per sample

molecule: total RNA

source_name: Neuronal progenitor cell

growth_protocol: We used the dentate gyrus differentiation protocol (Yu et al, Stem Cell Reports, 2014)

extract_protocol:
Total RNA was isolated from NPCs using TRIzol™ reagent.
RNA libraries were prepared for sequencing using standard Illumina NextSeq 500 protocols
Sequencing was performed after library preparation on the NextSeq500 platform using 75 bp reads.

treatment_protocol: NO specific treatment was applied.

tag: cell type

value: IPSC-derived neural progenitor cells

tag: passage

tag: cell line

tag: phenotype

value: control


title: MA_2_p12


title: pTH15803.2_HK_8mer


title: pTH15803.1_ME_8mer


title: pTH15802.1_ME_8mer

organism: Latimeria chalumnae


title: pTH15802.2_HK_8mer


title: MA_2_p11


title: pTH15801.2_HK_8mer


title: T419R_rep_5 [GC079643]

city: Leuven

first: Rik

last: Schrijvers

address: Herestraat 49 bus 1023

department: Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology

country: Belgium

institute: KU Leuven

description:
GC079643
mRNA

data_processing:
Single-end reads of 50 bp length were produced with a minimum of 1.5M reads per sample.
Adapters were filtered with ea-utils fastq-mcf (https://github.com/ExpressionAnalysis/ea-utils).
Splice-aware alignment was performed with STAR v2 against the human reference genome hg37 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM alignment files were handled with Samtools v1.5. Quantification of reads per gene was performed with HT-Seq Count v2.7.14.
Differential expression analysis was performed with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.
Genome_build: hg37 (GRCh37)
Supplementary_files_format_and_content: *_plus_differential_expression.csv: Differential expression analysis was performed with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.

source_name: U3A cells

growth_protocol: U3A cells were grown in DMEM 10% serum.

extract_protocol:
Total mRNA was isolated using AurumTM total RNA mini kit (Biorad, REF 7326820).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Each sample was either left unstimulated or stimulated for 4h with IFNγ (1U/µl).

value: fibrosarcoma

tag: complement

value: STAT1 T419R

tag: ifngamma stimulation

value: no


title: PROB_2_p13

value: schizophrenia


title: pTH15800.2_HK_8mer


title: pTH15799.2_HK_8mer


title: pTH15801.1_ME_8mer


title: pTH15800.1_ME_8mer


title: T419R_rep_4 [GC079642]

description:
GC079642
mRNA


title: blood_201_female_T0

type: RNA

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

country: France

institute: INRA

description: Gene expression T0

hyb_protocol: For each sample, 1.65 μg of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 minutes in a volume of 55 μl containing 25× Agilent Fragmentation Buffer and 10× Agilent Blocking Agent. Subsequently, 55 μl of 2× Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array, in accordance with the recommended protocol. After hybridization, the microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37 °C using GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 4X44K slides

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).

organism: Equus caballus

source_name: blood, 201, female, T0

label_protocol: Cyanine-3 (Cy3)-labelled cRNAs were prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). Specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Scientific, USA).

extract_protocol: Total RNAs were isolated using the Preserved Blood RNA Purification Kit I (Norgen Biotek Corp., Ontario, Canada), according to the manufacturer’s instructions. RNA yield and purity were measured using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA)

treatment_protocol: Twenty pure-breed or half-breed Arabian horses (7 females, 3 male, and 10 geldings; mean ± SD age: 10 ± 1.69) were selected from the cohort used by Plancade et al, 2019 (PMID: 31270376).Among the 20 horses selected for this study, 16 horses were enrolled for the 160 km category and four for the 120 km category.

value: blood

tag: individual

tag: Sex

value: female

tag: time of sampling


title: T419R_rep_2 [GC079640]

description:
GC079640
mRNA


title: T419R_rep_3 [GC079641]

description:
GC079641
mRNA


title: pTH15797.2_HK_8mer

organism: Acanthochromis polyacanthus


title: pTH15799.1_ME_8mer


title: pTH15798.1_ME_8mer


title: T419R_rep_1 [GC079639]

description:
GC079639
mRNA


title: pTH15798.2_HK_8mer


title: T419R_rep_1 [GC079644]

description:
GC079644
mRNA

value: yes


title: pTH15797.1_ME_8mer


title: E411A_rep_5 [GC079638]

description:
GC079638
mRNA

value: STAT1 E411A


title: pTH15796.2_HK_8mer


title: pTH15796.1_ME_8mer


title: E411A_rep_4 [GC079637]

description:
GC079637
mRNA


title: pTH15795.2_HK_8mer


title: pTH15795.1_ME_8mer


title: Patient 9b

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: BAL cells from a COVID-19 ICU patient

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.1.0 was used for demultiplexing, barcode processing and assembly of the BCR/TCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. fasta: high-confidence contig sequences of immune receptors (TCR or BCR) with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor (TCR or BCR), cellular barcode and contig-id.

source_name: CD45+ cells from BAL

extract_protocol:
CD45+ cells were enriched from bronchoalveolar lavage samples by MACS using CD45 Microbeads. Live CD45 cells were subsequently sorted by FACS. These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 13 cycles of PCR and then used for both 5’ gene expression (GEX), TCR and BCR library preparation. TCR and BCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells and Enrichment Kit for Human B cells, respectively. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX, TCR and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for TCR and BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).

value: Bronchoalveolar lavage (BAL)

value: BAL cells

tag: disease

value: COVID-19 ICU patient


title: E411A_rep_2 [GC079635]

description:
GC079635
mRNA


title: E411A_rep_1 [GC079634]

description:
GC079634
mRNA


title: pTH15794.2_HK_8mer

organism: Hofstenia miamia

source_name: Hmiamia_HMIM010378-RA:0-186,HK design

value: Unknown


title: pTH15794.1_ME_8mer

source_name: Hmiamia_HMIM010378-RA:0-186,ME design


title: pTH15793.1_ME_8mer

organism: Acyrthosiphon pisum


title: pTH15792.1_ME_8mer

organism: Rhodnius prolixus

source_name: hAT-1_RPr_1p_repbase:0-195,ME design


title: Cord Blood_TD110

city: Tokyo

first: Kohei

last: Kashima

address: 7-3-1 Hongo Bunkyo-ku

department: Pediatrics

country: Japan

institute: The University of Tokyo Hospital

hyb_protocol: The resultant cRNAs were fragmented for 30 min at 60°C in dark. The fragmented cRNAs (600 ng) were hybridized on the microarray at 65°C for 17 h.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

data_processing: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

source_name: CBMC

label_protocol: Starting with 100  ng of the isolated RNA for each sample, double stranded cDNA and cyanine 3 labeled cRNA were synthesized using low input quick amp labeling kit, one-color and RNA spike-in kit, one-color (Agilent).

extract_protocol: DNA extracted by Qiagen AllPrep kit.

treatment_protocol: Mononuclear cells were separated by gradient centrifugation using Ficoll-Hypaque from cord blood and postnatal peripheral blood samples within 24 h of the sample collection.

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: gestational age

tag: birthweight sdscore


title: Patient 1

description: BAL cells from a COVID-19 ICU patient

tag: tissue

tag: cell type


title: Patient 11  (Activated B cells, Set 2)

description: Activated B cells from a COVID-19 ICU patient

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.1.0 was used for demultiplexing, barcode processing and assembly of the TCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. Fasta: high-confidence contig sequences of immune receptors annotated with the corresponding cellular barcode and contig-id; csv: results from the signle cell immune profiling comprising including the receptor type, VDJ-Genes annotation, CDR3 nucleotide and amino acid sequense as well as the count for the corresponding cellular barcode and contig.

source_name: CD38high CD27high activated B cells

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMCs) were isolated with density gradient seperation and and stored at -80°C. Cells were thawed and live CD3- CD14- CD16- CD38high CD27high cells were subsequently sorted by FACS. These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 14 or 16 cycles of PCR and then used for both 5’ gene expression (GEX) and BCR library preparation. BCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human B cells. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).

value: peripheral blood

value: Activated B cells


title: Measles

description: Measles-reactive memory T cells from a healthy donor

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-hg19-1.2.0 as reference and expected-cells number of 3000 for each sample; polymorphisms removed.
For immune profiling Cell Ranger Single Cell Software Suite 3.1.0 was used for demultiplexing, barcode processing and assembly of the TCR sequences, using the vdj command and refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcodes for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. fasta: high-confidence contig sequences of immune receptors with the corresponding cellular barcode and contig-id; csv: results from single cell immune profiling, comprising the annotation of the immune receptor, cellular barcode and contig-id.

source_name: Measles-reactive memory T cells

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMCs) were isolated with density gradient seperation and stimulated for 6 hours with anti-CD28 and measles lysate in presence of anti-CD40. Live CD19- CD14- CD3+ CD4+ CD45RO+ CD154+ cells were subsequently sorted by FACS. These were then pooled and applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 13 cycles of PCR and then used for both 5’ gene expression (GEX) and TCR library preparation. TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX and TCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).

value: Measles-reactive memory T cells

value: healthy donor


title: pTH15792.2_HK_8mer

source_name: hAT-1_RPr_1p_repbase:0-195,HK design

tag: dbd

tag: platform_id_id design

value: HK


title: pTH15791.3_ME_8mer

organism: Locusta migratoria

source_name: hAT-4_LMi_1p_repbase:0-198,ME design

value: ME


title: E411A_rep_5 [GC079633]

description:
GC079633
mRNA

tag: cell line

value: fibrosarcoma

tag: complement

tag: ifngamma stimulation


title: pTH15791.4_ME_8mer


title: pTH15791.1_ME_8mer


title: Patient 10  (Activated B cells, Set 2)

tag: disease


title: E411A_rep_3 [GC079631]

description:
GC079631
mRNA

value: no


title: NSCs, Gal4 DamPr Set7

city: Singapore

first: Hongyan

last: Wang

state: Singapore

address: 8 College Rd

country: Singapore

institute: Duke-NUS

library_source: genomic

data_processing:
Library strategy: DamID-seq
Basecalls performed using Illumina's bcl2fastq v2.19.0.316
DamID-seq reads were aligned to the dm6 genome assembly using Bowtie version 2.2.6 with the option --very-fast
peaks were called using MACS version 1.4.2 with the option -g dm
Genome_build: dm6
Supplementary_files_format_and_content: peak file (bed format)

organism: Drosophila melanogaster

source_name: Drosophila NSCs at 24h after larval hatching

growth_protocol: UAS-Dam or UAS-Dam-Pr-set7 was expressed under the control of grh-Gal4 driver. Eggs were collected within a 6h period and raised at 25 °C for 24h till larvae hatched out. Hatched larvae were transferred to 29 °C for 24 hours before dissection.

extract_protocol:
Genomic DNA was extracted and digested by DpnI (targets only methylated GATC sites). After that, methylated DNA was amplified by PCR
The Illumina TruSeq DNA PCR-free library preparation kit were used according to the manufacturer’s protocol. Briefly, DNA was fragmented and end-repaired first. Then an adenine (A) nucleotide was added to the 3ʹ ends of the fragments to prevent self-ligation. After that, index adaptors were ligated and followed by quantifying. normalizing and pooling of libraries. The libraries were sequenced on the illumina MiSeq equipment.

tag: developmental stage

value: 24h after larval hatching

value: Neural stem cells (NSCs)

tag: genotype

value: UAS-Dam-Pr-set7 (pUASTattB-LT3-NDam-Pr-set7) induced by grh-Gal4


title: E411A_rep_4 [GC079632]

description:
GC079632
mRNA


title: Patient 8  (Activated B cells, Set 2)


title: pTH15790.2_HK_8mer

organism: Chrysemys picta


title: Patient 9a

description: BAL cells from a COVID-19 ICU patient


title: E411A_rep_3 [GC079636]

description:
GC079636
mRNA

value: yes


title: pTH15790.1_ME_8mer


title: blood_213_gelding_T0

description: Gene expression T0

source_name: blood, 213, gelding, T0

value: blood

tag: individual

tag: Sex

value: gelding

tag: time of sampling


title: Patient 3 (Activated B cells, Set 2)


title: E411A_rep_2 [GC079630]

description:
GC079630
mRNA

value: STAT1 E411A


title: pTH15793.2_HK_8mer


title: pTH15789.2_HK_8mer


title: pTH15791.2_HK_8mer

source_name: hAT-4_LMi_1p_repbase:0-198,HK design


title: pTH15788.2_HK_8mer

organism: Salarias fasciatus


title: Healthy Control 3

description: Activated B cells from a healthy donor

extract_protocol:
CD19+ cells were enriched from the peripheral blood by MACS using StraightFrom Blood CD19 Microbeads. Live CD3- CD14- CD16- CD38high CD27high cells were subsequently sorted by FACS. These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 13 or 14 cycles of PCR and then used for both 5’ gene expression (GEX) and BCR library preparation. BCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human B cells. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq500 device (Illumina) using High Output v2 Kits (150 cycles) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: n.a.) and Mid Output v2 Kits (300 cycles) for BCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).


title: Healthy Control 2

description: Activated B cells from a healthy donor


title: R321S_rep_5 [GC079628]

description:
GC079628
mRNA

value: STAT1 R321S


title: Healthy Control 1

description: Activated B cells from a healthy donor


title: pTH15787.1_ME_8mer

organism: Hippocampus comes

value: Unknown


title: pTH15786.1_ME_8mer

organism: Kryptolebias marmoratus


title: Patient 9

value: peripheral blood

value: COVID-19 ICU patient


title: pTH15787.2_HK_8mer


title: pTH15786.2_HK_8mer


title: pTH15788.1_ME_8mer


title: R321S_rep_2 [GC079625]

description:
GC079625
mRNA


title: E411A_rep_1 [GC079629]

description:
GC079629
mRNA


title: pTH15785.1_ME_8mer

organism: Fundulus heteroclitus


title: pTH15789.1_ME_8mer


title: pTH15784.2_HK_8mer

organism: Mola mola


title: Patient 7

value: Activated B cells


title: pTH15785.2_HK_8mer


title: Patient 8


title: R321S_rep_5 [GC079623]

description:
GC079623
mRNA


title: R321S_rep_3 [GC079626]

description:
GC079626
mRNA


title: R321S_rep_1 [GC079624]

description:
GC079624
mRNA


title: pTH15784.1_ME_8mer


title: R321S_rep_4 [GC079627]

description:
GC079627
mRNA


title: pTH15783.3_HK_8mer

organism: Rhizophagus irregularis


title: Patient 6


title: pTH15783.1_ME_8mer


title: R321S_rep_3 [GC079621]

description:
GC079621
mRNA


title: pTH15782.1_ME_8mer


title: Patient 5


title: pTH15782.2_HK_8mer


title: R321S_rep_2 [GC079620]

description:
GC079620
mRNA


title: pTH15781.1_ME_8mer

organism: Rhipicephalus appendiculatus


title: N574I_rep_5 [GC079653]

description:
GC079653
mRNA

organism: Homo sapiens

value: STAT1 N574I


title: pTH15781.2_HK_8mer

value: HK


title: Patient 4


title: R321S_rep_1 [GC079619]

description:
GC079619
mRNA


title: pTH15780.1_ME_8mer

organism: Erpetoichthys calabaricus

value: ME


title: pTH15779.2_HK_8mer


title: Patient 3


title: pTH15783.2_HK_8mer


title: pTH15780.2_HK_8mer


title: R274W_rep_5 [GC079618]

description:
GC079618
mRNA

value: fibrosarcoma

value: STAT1 R274W


title: pTH15778.2_HK_8mer


title: R321S_rep_4 [GC079622]

description:
GC079622
mRNA

value: no


title: pTH15778.1_ME_8mer


title: pTH15779.1_ME_8mer


title: Patient 2


title: R274W_rep_4 [GC079617]

description:
GC079617
mRNA


title: Patient 1b


title: pTH15777.2_HK_8mer

organism: Amphiprion percula


title: Patient 1a


title: R274W_rep_3 [GC079616]

description:
GC079616
mRNA


title: pTH15777.1_ME_8mer


title: pTH15776.2_HK_8mer

organism: Amphiprion ocellaris


title: pTH15776.1_ME_8mer


title: R274W_rep_2 [GC079615]

description:
GC079615
mRNA


title: scRNA_E16_NZC

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

country: USA

institute: University of Southern California

description: single cell RNA-Seq

data_processing:
10x Genomics cellranger
Genome_build: mm10
Supplementary_files_format_and_content: 10x Genomics cellranger output

molecule: polyA RNA

organism: Mus musculus

source_name: nephrogenic zone cells

extract_protocol: 10x Genomics Chromium v1

tag: strain

tag: embryonic day

value: nephrogenic zone cells


title: pTH15775.1_ME_8mer

organism: Acanthochromis polyacanthus


title: R274W_rep_1 [GC079614]

description:
GC079614
mRNA


title: pTH15774.2_HK_8mer


title: pTH15773.2_HK_8mer


title: pTH15773.3_HK_8mer


title: R274W_rep_4 [GC079612]

description:
GC079612
mRNA


title: CUT&RUN Utx-/- CD8+ T cells Rep 2

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
P14_D15_K27me3_KO_merge.bw
P14_D15_K27me3_KO_merge_hidden_mapq_10_analysis.bed
P14_D15_K27me3_KO_merge_hidden_mapq_10_vis.bed
P14_D15_K27me3_KO_merge_macs2_broadPeaks.bed

data_processing:
Library strategy: CUT&RUN
Initial processing and basecalling was done using Genome Analyzer Pipeline Software
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
RNA-seq alignment to the mm9 genome was performed using Tophat2
RNA-seq reads were counted at mm9 genes using HTseq-count
CUT&RUN aligment to the mm9 genome was performed using Bowtie2
CUT&RUN peaks called with MACS2 and hiddenDomains
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with reads per gene (RNA-seq) or peak (CUT&RUN)

source_name: Utx-/- CD8+ T cells

extract_protocol:
RNA was extracted using TRIZOL reagent, followed by mRNA purification
Libraries were generated using KAPA mRNA HyperPrep Kit (KK8580) for RNA-seq or KAPA HyperPrep Kit (KK8504) for CUT&RUN

treatment_protocol: WT or Utx-/- P14+CD8+ T cells were transferred to C57BL/6 recipient mice, CD4+ T cells were depleted prior to LCMV-A22 infection, and donor P14+CD8+ T cells were sorted from spleens at day 21 post-infection (RNA-Seq) or 15 days post-infection (CUT&RUN).

tag: time point

value: 15 days post infection

tag: agent

value: chronic lymphocytic choriomeningitis virus

value: Utx-/- knock-out

tag: antibody


title: CUT&RUN Utx-/- CD8+ T cells Rep 3


title: CUT&RUN Utx-/- CD8+ T cells Rep 4


title: pTH15772.2_HK_8mer

organism: Austrofundulus limnaeus


title: R274W_rep_3 [GC079611]

description:
GC079611
mRNA

tag: cell type


title: R274W_rep_5 [GC079613]

description:
GC079613
mRNA


title: R274W_rep_2 [GC079610]

description:
GC079610
mRNA


title: CUT&RUN WT CD8+ T cells Rep 4

description:
P14_D15_K27me3_WT_merge.bw
P14_D15_K27me3_WT_merge_hidden_mapq_10_analysis.bed
P14_D15_K27me3_WT_merge_hidden_mapq_10_vis.bed
P14_D15_K27me3_WT_merge_macs2_broadPeaks.bed

source_name: WT CD8+ T cells

value: wild-type


title: pTH15772.1_ME_8mer

tag: dbd


title: pTH15771.1_ME_8mer

organism: Latimeria chalumnae

tag: platform_id_id design


title: CUT&RUN WT CD8+ T cells Rep 3


title: pTH15775.2_HK_8mer


title: pTH15774.1_ME_8mer


title: pTH15773.1_ME_8mer


title: CUT&RUN WT CD8+ T cells Rep 2


title: pTH15769.2_HK_8mer

organism: Cyprinus carpio


title: R274W_rep_1 [GC079609]

description:
GC079609
mRNA

source_name: U3A cells

tag: cell line


title: wt_rep_5 [GC079608]

description:
GC079608
mRNA

tag: complement

value: STAT1 WT

value: yes


title: CUT&RUN WT CD8+ T cells Rep 1


title: pTH15770.1_ME_8mer

value: Unknown


title: CUT&RUN Utx-/- CD8+ T cells Rep 1


title: wt_rep_4 [GC079607]

description:
GC079607
mRNA

tag: ifngamma stimulation


title: pTH15771.2_HK_8mer


title: pTH15767.8_HK_8mer


title: wt_rep_2 [GC079605]

description:
GC079605
mRNA


title: pTH15767.3_ME_8mer


title: pTH15767.9_HK_8mer


title: pTH15770.2_HK_8mer


title: pTH15767.6_ME_8mer


title: pTH15767.2_HK_8mer


title: pTH15767.10_HK_8mer


title: pTH15767.1_ME_8mer


title: wt_rep_4 [GC079602]

description:
GC079602
mRNA


title: wt_rep_1 [GC079604]

description:
GC079604
mRNA


title: pTH15765.2_HK_8mer


title: pTH15766.1_ME_8mer


title: wt_rep_5 [GC079603]

description:
GC079603
mRNA


title: pTH15765.1_ME_8mer


title: wt_rep_3 [GC079601]

description:
GC079601
mRNA


title: pTH15769.1_ME_8mer


title: wt_rep_2 [GC079600]

description:
GC079600
mRNA


title: pTH15768.1_ME_8mer

organism: Anabarilius grahami


title: pTH15768.2_HK_8mer


title: pTH15767.5_ME_8mer


title: wt_rep_3 [GC079606]

description:
GC079606
mRNA


title: wt_rep_1 [GC079599]

description:
GC079599
mRNA


title: pTH15764.1_ME_8mer

organism: Sparus aurata


title: pTH15764.2_HK_8mer


title: pTH15763.9_HK_8mer

organism: Paramormyrops kingsleyae


title: pTH15766.2_HK_8mer


title: pTH15763.5_ME_8mer


title: pTH15763.8_HK_8mer


title: nt_rep_5 [GC079598]

description:
GC079598
mRNA

value: nt


title: Control siRNA

first: Lin

last: He

address: Xueyuan Road 38

institute: Peking University

description: Control

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of raw data was examined by FastQC, and sequencing adapter and low-quality reads, i.e. those with more than five ‘N’ bases and mean Phred quality score less than 15, were removed through fastp.
Spliced Transcripts Alignment to a Reference (STAR) software was utilized to align clean reads to the unmasked human reference genome (GRCh37, hg19). Raw counts of the reads mapped to genes were selected to analyze differentially expressed genes using DESeq2 Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: HepG2 cells

growth_protocol: HepG2 cells were maintained according to the ATCC’s recommendation.

extract_protocol:
Total mRNAs were isolated with Trizol reagents (Invitrogen) for cDNA synthesis, library construction, and sequencing using HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HepG2 cells were transfected with vector or FLAG-JFK or treated with control siRNA or ING5 siRNA.

tag: tissue

value: Liver

tag: transfection

value: Control siRNA


title: Vector

description: Control

value: Vector


title: nt_rep_4 [GC079597]

description:
GC079597
mRNA


title: ING5 siRNA

description: ING5 knockdown

value: ING5 siRNA


title: nt_rep_3 [GC079596]

description:
GC079596
mRNA


title: pTH15763.2_HK_8mer

value: HK


title: pTH15763.3_ME_8mer

value: ME


title: pTH15763.1_ME_8mer


title: pTH15763.11_ME_8mer


title: pTH15763.6_ME_8mer


title: pTH15762.1_ME_8mer

organism: Hucho hucho


title: pTH15761.2_HK_8mer


title: pTH15762.2_HK_8mer


title: JFK

description: JFK overexpression

value: JFK


title: tNetSeq WT pol II Rep2 (re-analyzed)

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description:
nascent nuclear RNA
Anti-pol II nascent RNA

data_processing:
Library strategy: tNET-Seq
Paired-end 150 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome hisat2
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: Data sets were processed into Bedgraph files.  tNet-MaP seq, tNetPIP seq and tNET-seq edits were processed using  pipelines available at https://github.com/rnabioco/rnastruct. Putative protein footprints were subtracted in files labelled no FP. Structure score files that include reads mapped to repetitive elements are labelled non-unique. DMS files were background subtracted (bgsub).

molecule: nuclear RNA

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

growth_protocol: Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

extract_protocol:
[tNet_MaPseq]  IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). Precipitated RNA was was purified by Trizol extraction and random primed.  DMS and DMSO treated RNA was reverse transcribed under MaP conditions.  All tNetSeq and tNetMaP-Seq libraries were constructed using the KAPA stranded RNAseq kit.
[tNet_PIPseq]  Following RNAase digestion, samples with treated with Proteinase K at 1mg/ml  for 15mins at 37º and then 65 º for 30mins to reverse crosslinks.  RNA was purifed with trizol extraction and RNA fragments were convereted into sequencing libraries with lexogen small RNA kit.

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

tag: growth conditions

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: treatment

value: untreated


title: pTH15763.10_HK_8mer


title: tNetSeq R749H slow pol II Rep1 (re-analyzed)

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.


title: tNetSeq WT pol II Rep3 (re-analyzed)


title: tNetSeq R749H slow pol II Rep3 (re-analyzed)


title: pTH15761.1_ME_8mer


title: nt_rep_2 [GC079595]

description:
GC079595
mRNA

value: fibrosarcoma


title: tNetSeq WT pol II Rep1 (re-analyzed)


title: nt_rep_1 [GC079594]

description:
GC079594
mRNA


title: nt_rep_3 [GC079591]

description:
GC079591
mRNA

value: no


title: nt_rep_5 [GC079593]

description:
GC079593
mRNA


title: pTH15759.2_HK_8mer


title: pTH15760.1_ME_8mer

organism: Sphaeramia orbicularis


title: pTH15760.2_HK_8mer


title: Input_pooled_OPC

city: Heidelberg

first: Daniel

last: Haag

state: Baden-Wuerttemberg

address: INF 580

department: Pediatric Neurooncology

institute: German Cancer Research Cernter (DKFZ)

data_processing:
Sequence Analysis and Filtering: 50-nt sequence reads generated by Illumina sequencing (using a HiSeq 2000 V4) were mapped to the genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed.
Determination of Fragment density: 5´-ends of aligned reads (“tags”) were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. This information (“signal map”; histogram of fragment densities) was stored in a bigWig file.
Peak Finding: The generic term “Interval” was used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used were MACS (Zhang et al., Genome Biology 2008, 9:R137) for H3K4me3 marks and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009) for H3K27me3 marks. Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random  background).
Standard Normalization: For standard normalization, the tag number of all samples (within a comparison group) was reduced by random sampling to the number of tags present in the smallest sample.
Spike-in adjustment: Spike-in adjustment of Drosophila chromatin was performed for H3K27me3 ChIP-seq. The number of test tags were adjusted (by down-sampling) by a factor that would result in the same number of spike-in Drosophila tags for each sample.
Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping Intervals were grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample had an Interval, this Interval defined the Merged Region. The use of Merged Regions was necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples.
Annotations: After defining the Intervals and Merged Regions, their genomic locations along with their proximities to gene annotations and other genomic features were determined and presented in Excel spreadsheets. In addition, average and peak (i.e. at “summit”) fragment densities within intervals and merged regions were compiled.
Genome_build: human reference genome assembly hg19, GRCh37
Supplementary_files_format_and_content: Excel file listing all Merged Regions (genomic regions containing 1 or multiple overlapping intervals) for HA-, H3K4me3-, and H3K27me3-reads from all samples. Merged Region = Unique identifier assigned to each Merged Region; Chromosome = Chromosome number; Start = Nucleotide position on chromosome where Merged Region starts (if on + strand) or ends (if on – strand); End = Nucleotide position on chromosome where gene ends (if on +strand) or starts (if on – strand); Length = Length of Merged Region in base pairs; IntervalCount = Number of Intervals that make up the Merged Region; [Sample x] Avg Value = Average of fragment densities of all the bins within the Merged Region; [Sample x] Peak Value = Peak fragment density of the Merged Region (Value at “Summit”); CGIslandCount = Number of UCSC-annotated CpG Islands within a set distance of each Merged Region; PromoterCount = Number of Promoters (-7500 to +2500 bp relative to gene starts) overlapping with each Merged Region; GeneCount = Number of NCBI annotated genes within a set distance (GeneMargin) of each Merged Region; Gene List = Names (symbols) of genes found within a set distance (GeneMargin) of Merged Region; Dist to Start = Distance of midpoint of Merged Region to gene start; Position = Location of midpoint of Merged Region relative to gene; UCSC Link = Link to display Merged Region +/- 0.5 kb flanking sequence in browser (only for tables with <65,530 rows); [Sample x] Present = Presence of an Interval from [Sample x] in an Merged Region is denoted by "1" and absence is denoted by "0". These columns are useful for sorting data to determine patterns between samples.
Supplementary_files_format_and_content: USCS bigWig URL File. The bigWig track file will show peak shapes in the form of a signal histogram. Both files are uploaded through the “URL or data” window of the UCSC browser.

source_name: iPSC line established from PBMCs

extract_protocol:
Cells were fixed by adding 1/10 volume of freshly-prepared formaldehyde solution (11% formaldehyde, 0.1 M NaCl,  1 mM EDTA pH 8.0, 50 mM HEPES pH 7.9) to the existing media in each cell culture plate. Plates with added formaldehyde solution were agitated 15 minutes at room temperature. Fixation was stopped by adding 1/20 volume a 2.5 M glycine solution and incubating at room temperature for 5 minutes. Subsequently, cells were scraped off the culture dish surface and washed by transferring to a 50 ml conical tube on ice and pelleting at 800 x g in a refrigerated centrifuge for 10 minutes. Supernatant was removed and cells were re-suspended cells in 10 ml chilled PBS-Igepal (1x PBS pH 7.4, 0.5% Igepal CA-630). Cells were centrifuged again, supernatant was removed, and 10 ml chilled PBS-Igepal supplemented with 1 mM PMSF was added and the cell pellet was resuspemded. Cells were pelleted again at 800 x g, supernatant removed completely, and the cell pellet was snap-frozen on dry ice. Frozen cell pellets were kept at -80C and shipped to Active Motif (AM, commercial service provider) for further processing (chromatin extraction, fragmentation, antibody-precipitation and library preparation) according to AM’s standard procedure.
Libraries were prepared by Active Motif (Carlsbad, CA) for sequencing using standard Illumina protocols

treatment_protocol: NSCs and OPCs were infected with lentivirus expressing either Cre-GFP or Flp-GFP to induce the H3.3-K27M mutation or maintain the wildtype allele, respectively. Cells were harvested approximately 3 weeks after infection.

value: iPSC line established from PBMCs

value: oligodendroglial progenitor cell

tag: genotype

value: mixed H3.3-wildtype/H3.3-K27M

tag: chip antibody

value: none (input)

value: Grown on matrigel in OPC medium (DMEM/F12, GlutaMax, non-essential amino acids, β-ME, N2, B27, PDGF, IGF, HGF, NT3, insulin, biotin, cAMP, T3)


title: nt_rep_4 [GC079592]

description:
GC079592
mRNA

value: nt


title: pTH15756.2_HK_8mer

value: Unknown


title: pTH15756.3_ME_8mer


title: pTH15758.2_HK_8mer


title: pTH15758.1_ME_8mer


title: pTH15757.2_HK_8mer

organism: Nematostella vectensis


title: pTH15759.1_ME_8mer


title: Input_iPSC

value: induced pluripotent stem cell

value: Grown on matrigel in mTeSR1 medium


title: nt_rep_1 [GC079589]

description:
GC079589
mRNA


title: pTH15757.1_ME_8mer


title: Input_pooled_NSC

value: neural stem cell

value: Grown on matrigel in NeuroCult NS-A Human Proliferation medium


title: nt_rep_2 [GC079590]

description:
GC079590
mRNA


title: pTH15756.1_ME_8mer

value: ME


title: OPC_H3.3wt_K27me3

value: Active Motif, cat # 39155


title: pTH15755.2_HK_8mer

value: HK


title: OPC_H3.3wt_K4me3

value: Active Motif, cat # 39159


title: OPC_H3.3K27M_K27me3


title: OPC_H3.3K27M_K4me3


title: NSC_H3.3wt_K27me3


title: NSC_H3.3wt_K4me3


title: MTA-treated CD8 T cell -rep2

city: Bethesda

first: Xin Wei

state: Maryland

address: 37 Convent Drive, Bldg 37 Rm 3050

department: Center for Cancer Research

institute: National Institutes of Health

data_processing:
Raw ATAC-seq reads were trimmed and filtered with Cutadapt v1.18 and  aligned to hg38 using Bowtie2 v2.2.6.
Uniquely aligned reads were identified using picard v2.18.26 MarkDuplicates utility with 72 to 79% non-duplicates mapped reads among all the samples.
Peak from individual samples was called using Genrich (https://github.com/jsh58/Genrich) with the argument -j -y -r -v -d 150 -m 5 -e chrM, chrY -E blacklist_regions.bed to exclude reads from mitochondria and reads from regions on chrY or those that intersected ENCODE blacklisted regions.
Genome_build: hg38
Supplementary_files_format_and_content: narrow peak files

source_name: MTA-treated CD8 T cell

growth_protocol: TexMACS medium (Miltenyi Biotec) supplement with 10% FBS and IL-2.

extract_protocol:
We used the OMNI ATAC-seq protocol introduced by Corces et al  for library preparation. In brief, 50,000 viable cells were pelleted (500 RCF, 4°C, 5 minutes), and lysed by resuspending in 50ul cold ATAC-Resuspension Buffer with detergents (10mM Tris-HCl; 10mM NaCl; 3mM MgCl2; 0.1% NP40; 0.1% Tween-20 and 0.01% Digitonin) and incubating for 3 minutes, followed by washing with the same buffer, but without NP40 and Digitonin. The nuclei were pelleted (500 RCF, 4°C, 10 minutes) and resuspended in 50ul transposition mix (1xTD buffer Illumina cat# 15027866), 100nM transposase (Illumina cat# 15027865), 1xPBS, 0.01% digitonin, 0.1% Tween-20).
Transposition was performed at 37°C for 30 minutes in a thermomixer with shaking at 1000 r.p.m. After purification of DNA by Zymo DNA Clean and Concentrator-5 kit (cat#D4014), amplification was performed for seven cycles using NEBNext 2x MasterMix (New England Biolabs cat# M0541S). The PCR reaction was purified by double size selection with SPRI beads, to remove any primer dimers (1.3x ratio) and large fragments over 1000bp (0.5x ratio). Additional cleanups were performed to remove primer dimers, as needed.

treatment_protocol: CD8+ T cells were isolated from peripheral blood mononuclear cells and stimulated with CD2/3/28 beads and incubated with/without SAM 100 µM or MTA 100 µM for seven days.

value: blood cell

tag: cell subtype

value: CD8+ T cell

value: CD2/CD3/CD28 activated

value: MTA 100 µM


title: mock-treated CD8 T cell -rep3

source_name: mock-treated CD8 T cell

value: untreated


title: SAM-treated CD8 T cell -rep1

source_name: SAM-treated CD8 T cell

value: SAM 100 µM


title: SAM-treated CD8 T cell -rep3


title: MTA-treated CD8 T cell -rep1


title: MTA-treated CD8 T cell -rep3


title: SAM-treated CD8 T cell -rep2


title: pTH15755.1_ME_8mer

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector.


title: pTH15754.2_HK_8mer


title: pTH15751.2_HK_8mer

organism: Aedes aegypti


title: pTH15752.2_HK_8mer

organism: Acipenser ruthenus


title: pTH15754.1_ME_8mer


title: pTH15749.2_HK_8mer


title: pTH15752.1_ME_8mer


title: pTH15753.2_HK_8mer


title: pTH15749.1_ME_8mer


title: pTH15753.1_ME_8mer


title: pTH15750.2_HK_8mer


title: NSC_H3.3wt_HA

organism: Homo sapiens

value: iPSC line established from PBMCs

value: Abcam, cat # ab9110


title: OPC_H3.3wt_HA

value: oligodendroglial progenitor cell

value: Grown on matrigel in OPC medium (DMEM/F12, GlutaMax, non-essential amino acids, β-ME, N2, B27, PDGF, IGF, HGF, NT3, insulin, biotin, cAMP, T3)


title: pTH15748.2_HK_8mer

organism: Culex quinquefasciatus

value: Unknown


title: pTH15751.1_ME_8mer


title: NSC_H3.3K27M_K27me3

value: neural stem cell


title: pTH15750.1_ME_8mer


title: mock-treated CD8 T cell -rep1


title: pTH15748.1_ME_8mer


title: mock-treated CD8 T cell -rep2


title: non-activated CD8 T cell -rep3

source_name: non-activated CD8 T cell


title: pTH15747.2_HK_8mer


title: NSC_H3.3K27M_K4me3

value: Grown on matrigel in NeuroCult NS-A Human Proliferation medium


title: iPSC_H3.3wt_K4me3

value: induced pluripotent stem cell

value: Grown on matrigel in mTeSR1 medium


title: non-activated CD8 T cell -rep2


title: pTH15746.2_HK_8mer

value: HK


title: pTH15747.1_ME_8mer

value: ME


title: iPSC_H3.3wt_HA


title: iPSC_H3.3wt_K27me3

value: Active Motif, cat # 39155


title: non-activated CD8 T cell -rep1

value: blood cell

value: CD8+ T cell


title: pTH15745.2_HK_8mer


title: pTH15746.1_ME_8mer


title: pTH15743.2_HK_8mer


title: pTH15744.1_ME_8mer


title: pTH15742.2_HK_8mer

organism: Salmo salar


title: pTH15742.1_ME_8mer


title: pTH15741.2_HK_8mer


title: pTH15740.2_HK_8mer


title: pTH15741.1_ME_8mer


title: pTH15744.2_HK_8mer


title: pTH15740.1_ME_8mer


title: pTH15739.2_HK_8mer


title: pTH15743.1_ME_8mer


title: INFG_HIRE_026

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: blood

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes.

tag: Sex

value: male

tag: status

value: HIV


title: INFG_HIRE_032


title: INFG_HIRE_031


title: INFG_HIRE_029


title: INFG_HIRE_028

value: female


title: pTH15739.1_ME_8mer

data_processing: We provide several scores for each 8-mer in each experiment. VALUE - median kmer intensity; Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.  Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.


title: INFG_HIRE_024


title: pTH15738.2_HK_8mer


title: pTH15737.2_HK_8mer

organism: Labeo rohita


title: pTH15738.1_ME_8mer


title: INFG_HIRE_023


title: HG2_Control_R2

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

description: HepG2 treated with 0.1%DMSO during 48h

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized, independently for each cell line, with Bioconductor software using RMA algorithm.

label: biotin

source_name: HepG2, hepatocellular carcinoma cell line, ATCC® HB-8065™

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Treatment with CM272 inhibitor at 400nM during 48hours. Control cells were treated with the correspondig vehicle alone (0.1% DMSO) during 48 hours.

extract_protocol: Total RNA from cell lines was extracted using the automated Maxwell system from Promega (Madison, WI, USA) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 200000 cells / well in 6-well plates. After overnight incubation, cells were treated for 48 h with vehicle alone (0.1% DMSO) or with CM272 at 400nM in culture medium supplemented with 10% FBS (HepG2) or 2% FBS (LX2) and 100 U/ml penicillin-streptomycin in both cases.


title: pTH15736.2_HK_8mer


title: pTH15737.1_ME_8mer


title: HG2_CM272_R1

description: HepG2 treated with CM272 400nM during 48h

source_name: HepG2, hepatocellular carcinoma cell line, ATCC® HB-8065™, treated with CM272

value: CM272 at 400nM during 48 hours


title: INFG_HIRE_027


title: pTH15736.1_ME_8mer


title: INFG_HIRE_021


title: pTH15745.1_ME_8mer


title: INFG_HIRE_020


title: pTH15735.1_ME_8mer


title: pTH15735.2_HK_8mer


title: INFG_080


title: INFG_078


title: pTH15733.1_ME_8mer


title: pTH15734.1_ME_8mer


title: INFG_076


title: pTH15733.2_HK_8mer


title: TCDD_male_biorep3_technicalrep2

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
7-TCDD-MALE_CAGATC_L004

data_processing:
Illumina HiSeq 2500 system used for base calling
Reads were initially evaluated by FastQC v0.11.9 to detect major sequencing problems, and then trimmed for quality control with two rounds of Skewer v0.2.2 to remove ends of reads with low mean Phred quality score (Skewer round 1 options: ‑x  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -‑mode pe -‑max 100 -‑cut3 -‑format auto -‑compress -‑threads 9; Skewer round 2 options: ‑x Mouse_adapters.fa -‑mode pe -‑end-quality 30 -‑mean-quality 30 -‑min 30 -‑format auto -‑compress -‑threads 9; where "Mouse_adapters.fa" represents a fasfa file containing the following sequences: >Illumina Multiplexing Adapter 1  GATCGGAAGAGCACACGTCT  >Illumina_TruSeq_Adapter_Index_1  GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACG  >Illumina_TruSeq_Adapter_Index_2  GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT  >Illumina_TruSeq_Adapter_Index_3  GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGC  >Illumina_TruSeq_Adapter_Index_3a  ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGC  >Illumina_TruSeq_Adapter_Index_4  GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA  >Illumina_TruSeq_Adapter_Index_5  GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG  >Illumina_TruSeq_Adapter_Index_6  GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT  >Illumina_TruSeq_Adapter_Index_7  GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC  >Illumina_TruSeq_Adapter_Index_8  GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGA  >Illumina_read2_adapter_segment  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG  >Illumina_read2_adapter_segment01  GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG  >Illumina Multiplexing Index Read Sequencing Primer  GATCGGAAGAGCACACGTCTGAACTCCAGTCAC  >Illumina_read_adapter_segment_1  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  >Illumina_read_adapter_segment_2  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
RNA-seq alignment and quantification proceeded with Bowtie2 v2.4.1 being used to build HISAT2 v2.1.0 genome index files from the Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6) genome downloaded from Ensembl (release 100; ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz). To enhance the genome index files, the HISAT2 scripts, hisat2_extract_splice_sites.py and hisat2_extract_exons.py, were used to extract splice site and exon information, respectively, from the Ensembl 100 gene transfer format (GTF) file (ftp://ftp.ensembl.org/pub/release-100/gtf/mus_musculus/Mus_musculus.GRCm38.100.gtf.gz). The extracted genomic information was incorporated into HISAT2 index files, using the hisat2-build command.
After building enhanced genome index files, trimmed reads were aligned with HISAT2 v2.1.0 and then piped through SAMtools v1.10 to convert aligned reads to binary alignment style (BAM) and then to sort BAM reads by position, using the following command: hisat2  q - phred33 - rna-strandness RF - no-mixed - no-discordant - new-summary - threads 9  x GENOME_INDEX  1 PAIR1_FILE.fastq.gz  2 PAIR2_FILE.fastq.gz | samtools view  u  @9 | samtools sort  n  O bam  o OUTPUT_FILE_sorted_byName.bam  @9.
Gene counts were estimated using the htseq-count command from HTSeq v0.12.4 with the GRCm38.p6 Ensembl 100 GTF annotation (options: - format=bam - order=name - stranded=reverse - type=exon - idattr=gene_id - additional attr=gene_name - mode=intersection-nonempty).
Analysis of gene counts was conducted using R v4.0.2 and Bioconductor v3.11 packages in the RStudio v1.3.959 integrated development environment. Counts from technical replicates split across sequencing lanes were averaged, and initial exploratory data analysis (i.e. gene variance heatmaps and PCA plots) revealed an outlier TCDD sample, which was removed (TCDD_male_biorep1). The Bioconductor package, edgeR v3.30.3, was used to normalize gene counts and determine differential expression. Briefly, genes were filtered using their filterByExpr function to exclude those with low counts in a minimum number of samples across libraries. Filtered genes were then normalized across samples using the trimmed mean of M values (TMM) method to minimize composition bias between libraries. Differential expression of genes was determined using functions from edgeR, which uses the negative binominal generalized linear model extended by quasi-likelihood methods to fit the count data, the Cox-Reid profile-adjusted likelihood method to calculate dispersions, empirical Bayes quasi-likelihood F-tests, and differential expression above a logarithmic fold change threshold of log2(1.5) between experimental and control samples was subsequently determined using a version of the TREAT (t-tests relative to a threshold) method. The ‘robust=TRUE’ option was used to protect the empirical Bayes estimates against the possibility of outlier genes with wide ranging individual dispersions. Genes with a Benjamini-Hochberg (BH) adjusted p ≤ 0.05 were considered significantly differentially expressed.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: xlsx files containing the combined HTSeq-count gene estimations of aligned reads and edgeR differential gene expression

organism: Mus musculus

source_name: urogenital sinus

growth_protocol: All procedures were approved by the University of Wisconsin Animal Care and Use Committee and conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals. All mice were purchased from Jackson Laboratories (Bar Harbor, ME) and maintained on a C57BL/6J genetic background (mouse stock number 000664). Mice were housed in Innovive® HDPE plastic microisolator cages in a room maintained on a 12-h light and dark cycle, ambient temperature of 20.5 ± 1°C, and relative humidity of 30-70%. Mice were fed a 5015 Diet (PMI Nutrition International, Brentwood, MO). Feed and water were available ad libitum, and cages contained corncob bedding. Mice were time-mated by pairing males and females overnight. The morning of definitive copulatory plug identification was considered E0.

extract_protocol: Total RNA was purified from each UGE using the RNeasy® system (Qiagen) and analyzed using the Agilent Bioanalyzer 2100 and an Agilent RNA 6000 PicoKit (Agilent Technologies).

treatment_protocol: Pregnant C57BL/6J mice were treated orally with either 5 mL/kg corn oil (vehicle control) or 5 µg/kg TCDD on E13.5. Dams were euthanized at E16.75 via CO2 asphyxiation, and urogenital sinuses (UGSs) were dissected from fetuses and immediately placed into 300 µL of 1% trypsin (Difco, 215240) in PBS and incubated on ice for 30 min. Collagenase (Sigma, C9891) was added to a final concentration of 1 mg/mL, followed by an additional 30-45 min incubation on ice. A dissecting microscope was used to mechanically separate UGS mesenchyme from UGS epithelium (UGE) and excise bladder and distal urethra leaving only the portion of UGE from which the prostate derives. Each treatment group consisted of 4 biological replicates and each replicate contained 5 or 6 individual UGEs that were pooled for RNA isolation.

tag: strain

tag: developmental stage

value: TCDD


title: TCDD_male_biorep4_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
9-TCDD-MALE_ACTTGA_L004


title: TCDD_male_biorep4_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
9-TCDD-MALE_ACTTGA_L003


title: HG2_CM272_R2


title: TCDD_male_biorep3_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
7-TCDD-MALE_CAGATC_L003


title: LX2_Control_R2

description: LX2 treated with 0.1%DMSO during 48h

source_name: LX-2 Human Hepatic Stellate Cell Line (SCC064, Millipore, Merk)


title: HG2_Control_R1

description: HepG2 treated with 0.1%DMSO during 48h


title: LX2_CM272_R2

description: LX2 treated with CM272 400nM during 48h

source_name: LX-2 Human Hepatic Stellate Cell Line (SCC064, Millipore, Merk), treated with CM272


title: LX2_CM272_R1

description: LX2 treated with CM272 400nM during 48h


title: INFG_073


title: LX2_Control_R1

description: LX2 treated with 0.1%DMSO during 48h


title: INFG_075


title: pTH15730.2_HK_8mer

first: Isaac

institute: University of Toronto


title: pTH15731.1_ME_8mer


title: pTH15730.1_ME_8mer


title: pTH15731.2_HK_8mer


title: pTH15732.1_ME_8mer


title: pTH15732.2_HK_8mer


title: TCDD_male_biorep2_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
6-TCDD-MALE_GCCAAT_L004


title: pTH15734.2_HK_8mer


title: TCDD_male_biorep2_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
6-TCDD-MALE_GCCAAT_L003


title: pTH15729.2_HK_8mer


title: pTH15729.1_ME_8mer


title: TCDD_male_biorep1_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
5-TCDD-MALE_ACAGTG_L004


title: INFG_072


title: pTH15728.1_ME_8mer


title: pTH15727.1_ME_8mer


title: pTH15727.2_HK_8mer


title: INFG_068


title: INFG_070


title: Control_male_biorep4_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
4-CTL-MALE_TGACCA_L004

value: Control


title: pTH15725.2_HK_8mer


title: pTH15726.1_ME_8mer


title: Control_male_biorep4_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
4-CTL-MALE_TGACCA_L003


title: INFG_067


title: INFG_066


title: pTH15726.2_HK_8mer


title: INFG_065


title: INFG_064


title: Control_male_biorep3_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
3-CTL-MALE_TTAGGC_L003


title: pTH15724.2_HK_8mer


title: pTH15724.1_ME_8mer


title: pTH15728.2_HK_8mer


title: pTH15725.1_ME_8mer


title: Control_male_biorep2_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
2-CTL-MALE_CGATGT_L004


title: INFG_063


title: pTH15723.2_HK_8mer


title: tNetSeq R749H slow pol II Rep2 (re-analyzed)

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: untreated


title: TCDD_male_biorep1_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
5-TCDD-MALE_ACAGTG_L003


title: pTH15723.1_ME_8mer

tag: dbd

value: Unknown


title: INFG_062


title: pTH15721.2_HK_8mer

tag: platform_id_id design


title: Control_male_biorep2_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
2-CTL-MALE_CGATGT_L003


title: pTH15721.1_ME_8mer


title: pTH15720.2_HK_8mer


title: pTH15720.1_ME_8mer


title: INFG_061


title: pTH15722.1_ME_8mer


title: Control_male_biorep1_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
1-CTL-MALE_ATCACG_L004


title: INFG_060


title: pTH15719.2_HK_8mer


title: pTH15722.2_HK_8mer


title: Control_male_biorep1_technicalrep1

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
1-CTL-MALE_ATCACG_L003


title: INFG_059


title: Control_male_biorep3_technicalrep2

description:
exposed in utero E13.5
Combined_HTSeq_gene_counts.xlsx
edgeR_differential_expression.xlsx
3-CTL-MALE_TTAGGC_L004


title: pTH15718.8_HK_8mer


title: pTH15718.4_ME_8mer


title: INFG_056


title: pTH15718.2_HK_8mer


title: pTH15718.1_ME_8mer


title: INFG_055


title: pTH15718.10_ME_8mer


title: con_2

city: Xi'an

first: Li

middle: hui

last: chen

address: No.169 Changlexi Road

department: Biochemistry and Molecular Biology

institute: Fourth Military Medical University

description: untreated

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data was handled by Perl and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/). The read length was 2X  150 bp.
The principle of STAR software is to divide the entire sequence into multiple seed sequences to align genome sequences. Some sequence alignments are continuous, and some sequence alignments are non-continuous. Among them, the matching parameter requirements are set to --twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5, and the rest are default, and RSEQC is used to compare the statistics.
For the forward and reverse complementary strands of the new transcripts assembled by StringTie for gene interval prediction, the Transdecoder program is used to predict the potential of the transcript based on the Markov model (log likelihood ratio, based on the log likelihood ratio between encoding and non-coding) Protein coding region (CDS), according to the standard codon table, the coding region sequence is translated into amino acid sequence, and the potential coding protein sequence in the transcript is obtained. For the potential multiple protein sequences of the transcript, the longest sequence is adopted as the prediction of the new transcript Protein sequence. The Blastp program was compared with the Uniprot-Swissprot protein sequence database, and the Evalue was set to 1E-3. The GO annotation information of the Uniprot-Swissprot protein target sequence in the comparison result performs GO functional classification annotation to the encoded protein sequence of the new transcript. The KEGG database was used to annotate the coding protein sequence of the new transcript with KEGG Pathway. The Interpro database was used to predict the protein structure and functional domain of the new transcript encoding protein sequence.
Supplementary_files_format_and_content: FPKM

source_name: liver

growth_protocol: TAMs from mice bearing miR-144 or miR-451a overexpression in HCC cells and control .

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: orthotopic HCC

tag: cell type

value: TAM

value: control HCC


title: pTH15717.2_HK_8mer

city: Toronto

last: Yellan

address: 160 College St.

value: HK


title: con_3

description: untreated


title: INFG_053


title: con_4

description: untreated


title: pTH15717.1_ME_8mer

value: ME


title: S_144_1

description: untreated

value: miR-144 overexpression in HCC


title: pTH15716.2_HK_8mer


title: pTH15716.1_ME_8mer


title: INFG_051


title: pTH15719.1_ME_8mer


title: INFG_052


title: pTH15715.2_HK_8mer


title: INFG_050


title: pTH15714.2_HK_8mer


title: pTH15718.5_ME_8mer


title: pTH15718.7_HK_8mer


title: S_144_3

description: untreated


title: INFG_048


title: S_144_4

description: untreated


title: S_144_2

description: untreated


title: con_1

description: untreated


title: pTH15714.1_ME_8mer


title: pTH15715.1_ME_8mer


title: pTH15718.11_HK_8mer


title: con_5

description: untreated


title: pTH15713.2_HK_8mer


title: pTH15712.1_ME_8mer


title: pTH15712.2_HK_8mer


title: S_144_5

description: untreated


title: pTH15711.2_HK_8mer


title: S_451_1

description: untreated

value: miR-451a overexpression in HCC


title: pTH15711.1_ME_8mer


title: INFG_044

value: male


title: pTH15710.1_ME_8mer


title: INFG_045

value: HIV


title: pTH15709.2_HK_8mer


title: INFG_043


title: S_451_2

description: untreated


title: pTH15710.2_HK_8mer


title: S_451_3

description: untreated


title: INFG_042


title: pTH15709.1_ME_8mer


title: S_451_4

description: untreated


title: pTH15442.2_HK_8mer

source_name: ENSLACP00000005761,HK design


title: pTH15442.1_ME_8mer

source_name: ENSLACP00000005761,ME design


title: INFG_036

value: female


title: INFG_037


title: pTH15441.2_HK_8mer

source_name: ENSLACP00000011201,HK design


title: INFG_046


title: WT_PA2_E100_5

city: Kansas City

first: Irina

last: Pushel

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Reads were demultiplexed allowing up to one mismatch using Illumina bcl2fastq2 v2.18
Reads were aligned to mm10 (Ensembl91) GTF using Tophat 2.1.1 with parameters --no-novel-juncs -g 1.
Reads were counted using the summarizeOverlaps method from the GenomicAlignments v1.8.4 in R 3.3.2.
Data were filtered to remove genes with low counts (total CPM <= 2).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of counts per million reads (CPM) for each gene in each sample.

source_name: embryo pharyngeal arch

extract_protocol:
Pharyngeal arches 1 and 2 were manually dissected from embryos in ice-cold PBS and flash frozen in liquid nitrogen. RNA was extracted using TRIzol and purified using the Zymo Research Direct-zol mini-prep kit (Cat#R2052).
Libraries were prepared using the Takara Clontech SMART-seq v4 ultra low input RNA kit (Cat#634891) to generate cDNA, and Illumina Nextera XT Library prep kit (Cat#FC-131-1096) and Illumina Nextera XT Index kit (Cat#FC-131-2001) for library construction according to standard protocols.

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2

value: wildtype


title: pTH15713.1_ME_8mer


title: pTH15440.2_HK_8mer

source_name: ENSLACP00000005873,HK design


title: pTH15441.1_ME_8mer

source_name: ENSLACP00000011201,ME design


title: INFG_035


title: pTH15440.1_ME_8mer

source_name: ENSLACP00000005873,ME design


title: WT_PA1_E100_5

value: pharyngeal arch 1


title: pTH15439.1_ME_8mer

source_name: ENSLACP00000001072,ME design


title: pTH15439.2_HK_8mer

source_name: ENSLACP00000001072,HK design


title: WT_PA2_E100_4


title: pTH15438.2_HK_8mer

source_name: ENSLACP00000002738,HK design


title: pTH15438.1_ME_8mer

source_name: ENSLACP00000002738,ME design


title: INFG_032

source_name: blood


title: INFG_031


title: INFG_033


title: pTH15437.2_HK_8mer

source_name: ENSLACP00000013575,HK design


title: WT_PA2_E100_3


title: pTH15436.2_HK_8mer

source_name: ENSLACP00000010221,HK design


title: pTH15437.1_ME_8mer

source_name: ENSLACP00000013575,ME design


title: INFG_030


title: pTH15436.1_ME_8mer

source_name: ENSLACP00000010221,ME design


title: pTH15435.2_HK_8mer

organism: Gallus gallus

source_name: CGGBP1-201,HK design


title: WT_PA1_E100_3


title: pTH15434.2_HK_8mer

source_name: ENSLACP00000018122,HK design


title: WT_PA2_E100_2


title: INFG_028


title: pTH15434.1_ME_8mer

source_name: ENSLACP00000018122,ME design


title: pTH15432.2_HK_8mer

source_name: ENSLACP00000010284,HK design


title: WT_PA1_E100_2

source_name: embryo pharyngeal arch


title: pTH15433.2_HK_8mer

source_name: ENSLACP00000009796,HK design


title: pTH15433.1_ME_8mer

source_name: ENSLACP00000009796,ME design


title: WT_PA2_E100_1


title: INFG_027


title: pTH15431.2_HK_8mer

source_name: ENSLACP00000002619,HK design


title: pTH15432.1_ME_8mer

source_name: ENSLACP00000010284,ME design


title: S_451_5

description: untreated

source_name: liver


title: WT_PA1_E100_4


title: INFG_026


title: pTH15431.1_ME_8mer

source_name: ENSLACP00000002619,ME design


title: WT_PA1_E100_1


title: INFG_023


title: INFG_024


title: pTH15429.2_HK_8mer

source_name: ENSLACP00000007780,HK design


title: pTH15435.1_ME_8mer

source_name: CGGBP1-201,ME design


title: INFG_029

source_name: blood


title: INFG_022


title: a2KO_PA1_E105_3


title: pTH15429.1_ME_8mer

source_name: ENSLACP00000007780,ME design


title: a2KO_PA2_E105_2


title: pTH15428.2_HK_8mer

source_name: ENSLACP00000006171,HK design


title: pTH15428.1_ME_8mer

source_name: ENSLACP00000006171,ME design


title: a2KO_PA1_E105_2


title: pTH15427.2_HK_8mer

organism: Anabas testudineus

source_name: ENSATEP00000024877,HK design


title: INFG_020


title: a2KO_PA2_E105_1


title: a2KO_PA2_E105_3


title: pTH15427.1_ME_8mer

source_name: ENSATEP00000024877,ME design


title: INFG_021


title: pTH15426.2_HK_8mer

organism: Latimeria chalumnae

source_name: ENSLACP00000010249,HK design


title: INFG_019


title: pTH15430.2_HK_8mer

source_name: ENSLACP00000001536,HK design


title: pTH15426.1_ME_8mer

source_name: ENSLACP00000010249,ME design


title: pTH15430.1_ME_8mer

source_name: ENSLACP00000001536,ME design


title: a2KO_PA2_E100_5

source_name: embryo pharyngeal arch


title: pTH15424.1_ME_8mer

organism: Petromyzon marinus

source_name: CGGBP1-201|ENSPMAP00000006497,ME design


title: pTH15424.2_HK_8mer

source_name: CGGBP1-201|ENSPMAP00000006497,HK design


title: pTH15425.1_ME_8mer

source_name: ENSLACP00000006137,ME design


title: INFG_014


title: INFG_015


title: pTH14290.1_ME_8mer

source_name: CGGBP1.FL,ME design


title: L_GF_DM_3

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
4-week-old male mouse
TGACAT

data_processing:
Library strategy: tRNA-seq
Remove de-multiplexing, adapters, primers, and low-quality sequences for the raw sequencing data
Mapping using Geneious prime (version 2019.2.3) with appropriate parameters
Modification-related analyses based on the mutation fractions of main methylations at the Watson–Crick face of each tRNA
Counting of the following statistical values: (a) mapped tRNA reads; (b) mapped paired-end tRNA reads
Calculation of the mapped tRNA molecules ((including full-length tRNA molecules and partial tRNA fragments)
Calculation of the fragments per kilobase per million (FPKM) values of tRNAs
Expression-related analyses based on the FPKM values in the tRNA isodecoder/isoacceptor/isotype level
Genome_build: Construction of reference cytosolic (GtRNAdb, https://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/) and mitochondrial tRNA datasets of Mus musculus (GenBank accession no. NC005089)
Supplementary_files_format_and_content: Tab-delimited text files include the RPKM values of each sample;  Microsoft Excel (.xls) files include the sequencing read counts and mapping results of each sample, and include the list of all the used tRNA genes in the two datasets

source_name: Liver tissue

growth_protocol: SPF mice were housed under specific pathogen free conditions and the mice had been tested free of designated pathogens. GF mice were housed in tightly controlled and monitored isolators to prevent contamination. GF mice are microbiologically sterile and no living organisms can be cultured from them

extract_protocol:
Experiments were carried out according to previously published protocols for DM-tRNA-seq (Zheng et al. Nat Methods. 2015;12:835–7). Dissected tissues were homogenized with glass beads using tissue homogenizer and total RNAs of them were isolated using TRIzol reagent (Ambion) following the manufacturer's protocol. RNA samples were dissolved in RNase-free water, and the concentration and purity of total RNAs were spectrophotometrically measured at 260 nm using a NanoDrop 2000 (Thermo Scientific). Total RNAs were firstly deacylated with Tris-HCl (pH = 9.0) at 37°C for 30 mins and then gel purified using 10% urea denaturing gel as standard procedures. The tRNA bands from each sample were cut off under the UV shadowing, and isolated total tRNAs (approximately 3 μg, 60 pmol) were dissolved in RNase-free water. About 1.5 μg total tRNA from each sample was treated with a 3× molar ratio of wild-type AlkB (180 pmol) and a 4× molar ratio of D135S mutant (240 pmol) to remove Watson–Crick face methylations on tRNAs that can impede the processivity of reverse transcription while another 1.5 μg total tRNA extracted from the same sample was untreated. Afterward, we performed reverse transcription of 150 ng of demethylase-treated (+DM) and untreated (−DM) tRNA with a thermophilic reverse transcriptase (TGIRT, InGex). We purified and eluded cDNAs on a 10% urea denaturing gel by using linear acrylamide (AM9520, Thermo Scientific) as the carrier. The purified cDNAs were circularized with CircLigase II (Epicentre) at 60°C overnight following the manufacturer's protocol and then extracted with phenol-chloroform-isoamyl alcohol (25: 24: 1) followed by ethanol precipitation
For library construction, the circularized cDNAs were amplified with Phusion-HF (NEB) by PCR amplification of 12 cycles using Illumina multiplex (5'–AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC–3') and barcode (5'–CAAGCAGAAGACGGCATACGAGAT [Index] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT–3'). The PCR products were purified with AMPure XP beads (Beckman Coulter) and sequenced on an Illumina HiSeq system

treatment_protocol: Four tissues (brain, intestine, kidney, and liver) were dissected from the 4-week-old male C57BL/6 SPF and GF mice and freshly frozen on dry ice and stored at −80°C

tag: gender

value: Male

value: Liver

tag: mouse

value: GF

value: Demethylase-treated

tag: replicate

tag: sequenced molecule

value: Total tRNA


title: a2KO_PA2_E100_4

tag: tissue


title: INFG_012


title: INFG_013


title: a2KO_PA1_E100_4


title: L_GF_DM_2

description:
4-week-old male mouse
CTGATC

tag: treatment


title: a2KO_PA1_E100_5

tag: genotype


title: INFG_011


title: L_GF_DM_1

description:
4-week-old male mouse
TCAAGT


title: a2KO_PA1_E105_1


title: pTH15425.2_HK_8mer

source_name: ENSLACP00000006137,HK design

value: Unknown


title: INFG_010

source_name: blood


title: L_GF_UT_3

description:
4-week-old male mouse
GCCTAA

value: Untreated


title: pTH14290.2_HK_8mer

source_name: CGGBP1.FL,HK design

value: HK


title: tNet-MaPseq R749H slow pol II - untreated control (DMSO)

description:
nascent nuclear RNA
Anti-pol II nascent RNA  treated with DMSO

data_processing:
Library strategy: tNet-MaPseq
Paired-end 150 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome hisat2
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: Data sets were processed into Bedgraph files.  tNet-MaP seq, tNetPIP seq and tNET-seq edits were processed using  pipelines available at https://github.com/rnabioco/rnastruct. Putative protein footprints were subtracted in files labelled no FP. Structure score files that include reads mapped to repetitive elements are labelled non-unique. DMS files were background subtracted (bgsub).

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 2% DMSO for 5mins at 37C followed by 30% final mercaptoethanol.
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: R749H slow pol II

value: DMSO

tag: cell line


title: L_GF_UT_2

description:
4-week-old male mouse
ACATCG


title: L_SPF_DM_3

description:
4-week-old male mouse
TTTCAC

value: SPF


title: a2KO_PA1_E100_2

value: CBA/Ca/J x C57BL/10


title: a2KO_PA2_E100_2

value: pharyngeal arch 2


title: L_SPF_UT_3

description:
4-week-old male mouse
ATTGGC


title: L_GF_UT_1

description:
4-week-old male mouse
CGTGAT


title: tNet-MaPseq WT pol II - untreated control (DMSO)

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with DMSO

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

value: WT pol II


title: L_SPF_DM_2

description:
4-week-old male mouse
GCGGAC


title: tNet-MaPseq R749H slow pol II Rep1

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with DMS

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 2% DMS for 5mins at 37C followed by 30% final mercaptoethanol.
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

value: DMS


title: L_SPF_DM_1

description:
4-week-old male mouse
GGACGG

value: Male


title: L_SPF_UT_2

description:
4-week-old male mouse
CACTGT

value: Liver


title: K_GF_DM_3

description:
4-week-old male mouse
CGAAAC

source_name: Kidney tissue

value: Kidney

value: GF


title: tNet-MaPseq WT pol II Rep1


title: L_SPF_UT_1

description:
4-week-old male mouse
TGGTCA

value: Total tRNA


title: a2KO_PA1_E100_1

value: pharyngeal arch 1


title: a2KO_PA2_E095_5


title: a2KO_PA2_E100_1


title: K_GF_DM_2

description:
4-week-old male mouse
GGCCAC

value: Demethylase-treated


title: K_GF_UT_3

description:
4-week-old male mouse
GTAGCC

value: Untreated


title: K_GF_DM_1

description:
4-week-old male mouse
CTCTAC


title: a2KO_PA2_E100_3


title: K_GF_UT_2

description:
4-week-old male mouse
AAGCTA


title: a2KO_PA1_E095_5


title: a2KO_PA1_E100_3


title: K_SPF_DM_3

description:
4-week-old male mouse
GCTACC


title: K_GF_UT_1

description:
4-week-old male mouse
GATCTG


title: K_SPF_DM_2

description:
4-week-old male mouse
CCACTC


title: K_SPF_DM_1

description:
4-week-old male mouse
CGTACG


title: a2KO_PA2_E095_4


title: a2KO_PA1_E095_4


title: SNS-032_3

city: Shanghai

first: xia

last: jing

address: 1678 Dongfang Road

institute: Shanghai Children’s Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCh38 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
The gene expression level (FPKM) was calculated according to the RSEM
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: celllines

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: REH cells were seeded at a density of 1× 106 cells/ml and treated with 200nm SNS_032 or DMSO for 24h.

value: REH cells

tag: agent

value: SNA-032 treated


title: SNS-032_2


title: K_SPF_UT_3

description:
4-week-old male mouse
GGAACT


title: a2KO_PA2_E095_3


title: K_SPF_UT_2

description:
4-week-old male mouse
TTGACT


title: a2KO_PA1_E095_3


title: psoriasis lesional epidermis_Human_rep3

city: guangzhou

first: dan

last: hong

address: 107 Yanjiang Rd W, Guangzhou, China

department: Department of Dermatology

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

description: Gene expression data from psoriasis lesional epidermis

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip human genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Command Console® Software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: skin epidermis

label_protocol: The double-stranded DNA reverse transcribed from total RNA was used as templates to synthesize cRNA and in the presence of biotin.

extract_protocol: Skin sections were incubated in  0.3% dispase II overnight at 4℃ to separate epidermis.Total RNA was extracted from epidermis using the RNAiso Plus reagent (Takara, #9109)

value: skin epidermis

tag: diagnosis

value: psoriasis


title: DMSO_3

value: DMSO treated


title: a2KO_PA2_E095_2

tag: strain

value: CBA/Ca/J x C57BL/10


title: I_GF_DM_3

description:
4-week-old male mouse
ATTGGC

source_name: Intestine tissue

value: Intestine


title: a2KO_PA1_E095_2

tag: developmental stage


title: psoriasis lesional epidermis_Human_rep2


title: healthy control epidermis_Human_rep3

description: Gene expression data from healthy control epidermis

value: healthy control


title: SNS-032_1


title: psoriasis lesional epidermis_Human_rep1


title: healthy control epidermis_Human_rep4


title: healthy control epidermis_Human_rep2


title: a2KO_PA2_E095_1

value: pharyngeal arch 2


title: I_GF_DM_1

description:
4-week-old male mouse
TGGTCA

value: Male


title: T cells +MSCshCHI3L1-2 #2

first: Yan

last: Xu

address: No. 600 Tianhe Road

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
For sample 1-sample 10, the sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12).
For sample 11-sample 16,data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:   Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%. Using String Tie for readcount and FPKM calculation. Differential expression analyses were performed using the limma package.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

source_name: CD3+T cells

growth_protocol: MSCs were cultured in L-DMEM (Gibco) supplemented with 10% FBS, 1% glutamine, 1% penicillin/streptomycin, 2 ng/mL bFGF. For co-culture, MSCs (1×105 cells) were plated into 24-well plate (Corning) and cultured 24 h before co-culture with lymphocytes. The next day, human peripheral blood mononuclear cells were collected from healthy donors and red blood cells were removed by ammonium chloride lysis buffer for 5 min at room temperature, and then centrifuged at 300 g for 5 min. After washed twice with PBS (containing 3% FCS), cells were incubated with an anti-mouse CD3 antibody (Catalog # 100204, Biolegend ) at 4 ℃ for 30 min. CD3+ T cells were sorted by CD3 MicroBeads (Catalog # 130-050-101, Miltenyi Biotec, Germany) and suspended in RPMI1640 at 2.5×106 cells/mL and add 1mL to the 24-well plates in the presence or absence of MSCs.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
For sample 1-sapmle 10, Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China.    For sample 11-sample 16, a total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: T cell activation was induced by phytohaemagglutinin (PHA, Sigma-Aldrich) at the final concentration of 5 μg/mL. After co-culture for 48 hours, CD3+ T cells were collected and sequenced.

value: PBMC

value: PHA for 48 hours

tag: co-culture

value: co-culture with MSCshCHI3L1-2


title: DMSO_2


title: psoriasis lesional epidermis_Human_rep4


title: a2KO_PA1_E095_1


title: T cells +MSCshCHI3L1-2 #1


title: K_SPF_UT_1

description:
4-week-old male mouse
TACAAG

value: Kidney

value: SPF

value: Total tRNA


title: I_GF_DM_2

description:
4-week-old male mouse
CACTGT

value: GF

value: Demethylase-treated


title: a2KO_PA2_E090_4


title: I_GF_UT_3

description:
4-week-old male mouse
TGACAT

value: Untreated


title: a2KO_PA1_E090_4

value: pharyngeal arch 1


title: a2KO_PA2_E090_3


title: T cells +MSCshCHI3L1-1 #2

value: co-culture with MSCshCHI3L1-1


title: I_GF_UT_2

description:
4-week-old male mouse
CTGATC


title: I_SPF_DM_3

description:
4-week-old male mouse
TTTCAC


title: I_GF_UT_1

description:
4-week-old male mouse
TCAAGT


title: T cells +MSCshCHI3L1-1 #1


title: DIPG-H3.3K27M-2

hyb_protocol: 3’ target hybridization was performed for cartridge arrays on a GeneChip Fluidics Station 450 (Affymetrix) using a GeneChip Hybridization, Wash and Stain Kit (Affymetrix) following the manufacturer’s protocols.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (GCS3000) controlled by the AGCC 4.0  standard processing workflow for  GeneChip cartridges (Affymetrix).

data_processing: Raw data was processed by the internal analysis pipeline of Genomics and Proteomics Core Facility of the German Cancer Research center (DKFZ)

source_name: human iPSC-NSC-derived tumor

label_protocol: PolyA RNA was reverse transcribed into double-stranded cDNA for generation of biotin-labeled cRNA by in vitro transcription and production of fragmented labeled cRNA for hybridization using the GeneChip 3’ IVT Plus Reagent Kit Assay following the manufacturer’s protocol.

growth_protocol: iPSCs were grown on matrigel in mTeSR1 medium, iPSC-derived neural stem cells were grown on matrigel in NeuroCult NS-A Human Proliferation medium including FGF, EGF, and hLIF.

extract_protocol: Total RNA  was extracted using the Rneasy Mini Kit from Qiagen following the manufacturer's standard protocol and included on-column Dnase I digest.

treatment_protocol: iPSC and NSCs were infected with lentivirus expressing either Cre-GFP or Flp-GFP to induce the H3.3-K27M mutation or maintain the wildtype allele, respectively.

value: human iPSC-NSC-derived tumor

tag: timepoint


title: a2KO_PA2_E090_2

source_name: embryo pharyngeal arch

value: CBA/Ca/J x C57BL/10


title: I_SPF_DM_1

description:
4-week-old male mouse
GGACGG

value: Intestine


title: T cells +MSCshNTC #2

value: co-culture with MSCshNTC


title: I_SPF_UT_3

description:
4-week-old male mouse
GCCTAA


title: a2KO_PA1_E090_3


title: I_SPF_DM_2

description:
4-week-old male mouse
GCGGAC


title: NSC-H3.3K27M-3

source_name: human iPSC-derived NSC

value: human iPSC-derived NSC

value: 26 days after lentiviral infection


title: T cells  #1

value: PBMC


title: T cells +MSCshNTC #1

value: PHA for 48 hours


title: NSC-H3.3K27M-4

value: 29 days after lentiviral infection


title: NSC-H3.3wt-3


title: NSC-H3.3wt-4


title: T cells  #2


title: healthy control epidermis_Human_rep1

value: skin epidermis

value: healthy control


title: DIPG-H3.3K27M-1


title: I_SPF_UT_2

description:
4-week-old male mouse
ACATCG

value: Male

value: SPF

value: Total tRNA


title: B_GF_DM_3

description:
4-week-old male mouse
CGAAAC

source_name: Brain tissue

value: Brain

value: GF

value: Demethylase-treated


title: naïve T cells #2

value: untreated


title: NSC-H3.3wt-2

value: 18 days after lentiviral infection


title: a2KO_PA2_E090_1

value: CBA/Ca/J x C57BL/10

value: pharyngeal arch 2


title: a2KO_PA1_E090_1

value: pharyngeal arch 1


title: naïve T cells #1


title: a2KO_PA1_E090_2


title: B_GF_DM_1

description:
4-week-old male mouse
CTCTAC


title: iPSC-H3.3wt-2

source_name: human iPSC line C6-a

value: human iPSC line C6-a

value: 6 days after lentiviral infection


title: F1-Gamma2_nmbu_sncRNA_3

city: Oslo

first: Leonardo

middle: Martin

last: Martin

address: Ullevålsveien 72

department: Basic Sicences and Aquatic medicine

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7
Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt
Length filtered reads were mapped, classified into genomic features, and counted using Unitas (v1.5.2) under default settings
miRNAs were quantified with miRDeep2 v0.0.5  using the built-in script quantifier.pl
piRNA clusters were predicted using proTRAC (v4.2.4) under default values
Genome_build: GRCz10
Supplementary_files_format_and_content: matrix of raw read counts (abundances) as comma separated values

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads (Roche Diagnostics, Germany), and total RNA was isolated using Trizol following the instructions of manufacturer (Thermo Fisher Scientific, USA).
sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina®,( New England Biolabs® inc, USA) from each sample 1 μg of total RNA was used as input material.

tag: develomental stage

value: 5.5 hpf (50 percent  epiboly)

value: AB

value: wild type

tag: group

value: F1 from exposed parents


title: WT_PA2_E105_2

value: wildtype


title: iPSC-H3.3K27M-2

tag: cell type


title: WT_PA2_E105_3


title: NSC-H3.3K27M-1

value: human iPSC-derived NSC

value: 10 days after lentiviral infection


title: NSC-H3.3K27M-2


title: F1_Control3_nmbu_sncRNA_3

value: F1 from control parents


title: F1-Gamma2_nmbu_sncRNA_2


title: B_GF_UT_2

description:
4-week-old male mouse
AAGCTA

tag: gender

value: Male

value: Brain

tag: mouse

value: GF

value: Untreated

value: Total tRNA


title: F1_Control2_nmbu_sncRNA_2


title: WT_PA1_E105_1

value: CBA/Ca/J x C57BL/10


title: WT_PA1_E105_3

value: pharyngeal arch 1


title: Pediatric Patient 41

city: Richmond

first: Maren

middle: Lydia

last: Smith

state: Virginia

address: 1217 E Marshall St

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to GRC38.91 using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.
Count data was corrected for batch effects using ComBat (Johnson et al. PMID: 16632515) and transformed to positive whole numbers.
Genome_build: GRC38.91
Supplementary_files_format_and_content: Tab-deliminted text files countaining count values for each sample after batch correction by ComBat and transformation to positive, whole numbers.

source_name: whole blood

extract_protocol:
Whole blood (2 mL) was collected from study participants in Tempus Blood RNA tubes at the time of diagnosis or flareup. RNA was extracted from blood using the Tempus Spin RNA Isolation Kit (Thermo Fisher), and polyA enrichment was conducted using the NEBNEXT Poly(A) mRNA magnetic isolation kit (New England BioSciences).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole blood

tag: disease state

value: ANCA-associated vasculitis

tag: rna-cluster

value: cluster 2

tag: anca status

value: NEG


title: B_GF_UT_1

last: Wang

description:
4-week-old male mouse
GATCTG

tag: tissue

tag: treatment

tag: replicate

tag: sequenced molecule


title: Pediatric Patient 40

value: outlier 2

value: MPO