title: PG2_rna_muscle

description: Total RNAseq from adult tissue

source_name: homogenised adult skeletal muscle


title: Batch2 Saikosaponin C 2uM rep1

status: Public on Aug 19 2021

type: SRA

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description:
Saikosaponin C 2uM rep1
Batch2

library_source: transcriptomic

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to human genome assembly GRCh38 (hg38) via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with human gene annotation GRCh38.84.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human lung cancer A549 cell line (CCL-185) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in RPMI1640 (Gibco, Grand Island, NY, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco), 100 IU/mL penicillin/100 mg/mL streptomycin (P/S; Gibco).

extract_protocol:
Total RNA was isolated from tissue using Maxwell (Promega) based method.
One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.   The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

treatment_protocol: We obtained lyophilized powder of water extract of Bupleuri Radix (W-BR; 3-10-0054) and ethanol extract of Bupleuri Radix (E-BR; 3-10-0097) from Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM; Naju, Korea). Each powder was dissolved in 2% dimethyl sulfoxide (DMSO; Sigma, St Louis, MO, USA) to a final concentration of 10 mg/mL, filtered, and stored at -20°C until use.

tag: treatment

value: Saikosaponin C

tag: treatment dose


title: PG3_rna_liver

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

description: Total RNAseq from adult tissue

data_processing:
RNAseq reads were mapped to MZ_UMD2a and gene expression values were calculated using kallisto (see SUPP methods)
WGBS reads were mapped to mapped to SNP-corrected genomes (based on MZ_UMD2a) and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see SUPP Methods). Methylation at CG sites with ≥5 ≤100 non-clonal seq reads averaged across 50bp-long non-slidding windows per species were performed to produce bw files.
Species-specific high-confidence SNP-corrected genome (fa file) was generated for each of the species studied in this study by using published whole genome sequencing dataset (Malinsky et al 2018); see Methods.
DMRs were called using DSS (see SUPP Methods). P<0.05, minimal overall methylation difference across any DMR between any species was >25% (d25pc), ≥4 CpG, ≥50bp and pvalue<0.05 (p005). For DMR calling, all CG sites were used independent of sequencing coverage following DSS recommandations (improved DMR calling).
Genome_build: Maylandia zebra MZ_UMD2a  and SNP-corrected genomes
Supplementary_files_format_and_content: tpm for RNAseq (tsv) generated using kallisto, mCG/CG (bigwig) generated using bismark, SNP-corrected genomes (fa)

organism: Petrotilapia genalutea

source_name: homogenised adult liver tissue

extract_protocol:
total RNA extracted using phenol/chlorophorm approach (see SUPP methods)
ribosomal RNA depletion (RiboZero Illumina) followed by Illumina RNAseq stranded library kit, according to manusfacturer's instructions

tag: tissue

value: liver

tag: Sex

value: male

tag: type

value: wild-caught


title: iMEFB_inhib_rep1

city: Paris

first: Daniel

last: Holoch

state: Cedex 05

address: 26 rue d'Ulm

department: Genetics and Developmental Biology Unit

country: France

institute: Institut Curie, Centre de Recherche

data_processing:
Adapter trimming (Trim Galore! 0.4.4 wrapper with default settings)
Discard reads aligning to complete mouse rRNA sequence (Bowtie 2.2.9)
Alignment to mouse genome (Tophat 2.1.1 & Bowtie 2.2.9)
Gene counts (FeatureCounts 1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.txt files contain gene counts
Supplementary_files_format_and_content: read_counts.txt files contain wild-type and mutant read counts for targeted experiments

organism: Mus musculus

source_name: Immortalized mouse embryonic fibroblast line B

growth_protocol: MEF cells were grown in DMEM supplemented with 10% FCS, 100 mM nonessential amino acids, 2 mM L-glutamine.

extract_protocol:
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions
Truseq Stranded mRNA

tag: cell type

value: c-myc-immortalized mouse embryonic fibroblasts

tag: genotype/treatment

value: wild-type + 2 uM UNC1999 + 4 uM A395

tag: fraction

value: total RNA


title: iMEFB_washout_rep1

value: wild-type after washout of  2 uM UNC1999 + 4 uM A395


title: iMEFB_inhib_rep2


title: PG2_rna_liver

description: Total RNAseq from adult tissue


title: Batch2 Saikosaponin C 10uM rep1

description:
Saikosaponin C 10uM rep1
Batch2


title: Batch2 Saikosaponin B4 10uM rep2

description:
Saikosaponin B4 10uM rep2
Batch2

value: Saikosaponin B4


title: Batch2 Saikosaponin C 10uM rep2

description:
Saikosaponin C 10uM rep2
Batch2


title: PG1_rna_muscle

description: Total RNAseq from adult tissue

value: skeletal muscle


title: Batch2 Saikosaponin B4 0.4uM rep1

description:
Saikosaponin B4 0.4uM rep1
Batch2


title: iMEFB_mock_rep2

value: wild-type


title: iMEFB_mock_rep1


title: PG1_rna_liver

description: Total RNAseq from adult tissue


title: zinc basal treat (donor #2), IL15

city: Belfast

first: Imre

last: Lengyel

state: English

address: 97 Lisburn Road, Centre for Experimental Medicine, Queens Un

country: United Kingdom

institute: Queens University Belfast

data_processing:
FastQ QC using Qualimap was performed with first alignment
Counts data was generated from the bam file following the protocol: https://htseq.readthedocs.io/en/release_0.9.1/count.html
Genome_build: hs; genome build 37
Supplementary_files_format_and_content: tab-delimited text raw gene counts for every gene and every sample

source_name: primary retinal pigment epithelial cells

extract_protocol:
total RNA was extracted from snap-frozen transwell inserts using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) following manufacturers’ instructions.
Libraries were prepared following the KAPA HyperPrep kit
Libraries were quantified, normalized and pooled in equimolar amounts for RNA sequencing based on Sanger/Illumina 1.9 on Illumina NextSeq 500 (strand-specific-reverse)

treatment_protocol: Primary human fetal RPE cells (ScienCell, Carlsbad, USA) from three donors with unknown clinical or genetic background were used for our experiments at passage number three (P3). Cells were seeded onto Corning 6-well transwell inserts (10 µm thick polyester inserts with 0.4 µm pore size, 4*10e6/cm2 pore density) in epithelial cell medium (EpiCM, ScienCell Carlsbad, USA). After seven days, cell culture media was replaced with Miller medium for an additional four weeks in the absence or presence of 125 µM externally added zinc (as zinc sulphate; Merck, Darmstadt, Germany),

tag: individual

value: donor #2

value: fetal eye

tag: age

value: 5 weeks

value: zinc basal treat


title: zinc basal treat (donor #3), IL13

value: donor #3

value: primary retinal pigment epithelial cells


title: zinc basal treat (donor #1), IL16

value: donor #1


title: Batch2 Saikosaponin B4 2uM rep1

description:
Saikosaponin B4 2uM rep1
Batch2


title: shAU021063-4T1 cells_shRNA3_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: hAU021063-4T1 knockdown 4T1 cells

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: hAU021063-4T1 knockdown 4T1 cells

extract_protocol:
An RNeasy Mini Kit (Qiagen) was used to isolate total RNA.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cell line

value: murine breast cancer 4T1 cells


title: 15-070_Mild_24_W.P.I. [3F6]

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description:
P3F6
15-070_Female_Mild_24_W.P.I._Total RNA

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts per gene counts

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.
Total RNA-Seq 2x150 bp paired-end reads.

value: Female

tag: disease severity

value: Mild

tag: rin

value: Peripheral blood

tag: timepoint


title: Batch2 Saikosaponin B4 10uM rep1

description:
Saikosaponin B4 10uM rep1
Batch2


title: shAU021063-4T1 cells_shRNA3_rep1

description: hAU021063-4T1 knockdown 4T1 cells


title: zinc apical treat (donor #2), IL12

value: zinc apical treat


title: Batch2 Saikosaponin C 0.4uM rep1

description:
Saikosaponin C 0.4uM rep1
Batch2

value: Saikosaponin C


title: 15-066_Mild_24_W.P.I. [3A8]

description:
P3A8
15-066_Female_Mild_24_W.P.I._Total RNA


title: Batch2 Saikosaponin B3 0.4uM rep3

description:
Saikosaponin B3 0.4uM rep3
Batch2

value: Saikosaponin B3


title: zinc apical treat (donor #1), IL11


title: Batch2 Saikosaponin B3 2uM rep3

description:
Saikosaponin B3 2uM rep3
Batch2


title: shAU021063-4T1 cells_shRNA1_rep2

description: hAU021063-4T1 knockdown 4T1 cells


title: 15-065_Mild_16_W.P.I. [3F4]

description:
P3F4
15-065_Female_Mild_16_W.P.I._Total RNA


title: shAU021063-4T1 cells_shRNA1_rep1

description: hAU021063-4T1 knockdown 4T1 cells


title: zinc apical treat (donor #2), IL10


title: 15-065_Mild_24_W.P.I. [3C7]

description:
P3C7
15-065_Female_Mild_24_W.P.I._Total RNA


title: Batch2 Saikosaponin B3 10uM rep3

description:
Saikosaponin B3 10uM rep3
Batch2


title: zinc apical treat (donor #3), IL08


title: control (donor #2), IL07

value: control


title: WT_cells_rep2

description: mock transfected 4T1 cells

source_name: mock transfected 4T1 cells


title: 15-064_Mild_24_W.P.I. [3H7]

description:
P3H7
15-064_Female_Mild_24_W.P.I._Total RNA


title: control (donor #1), IL06


title: WT_cells_rep1

description: mock transfected 4T1 cells


title: Batch2 Saikosaponin B2 2uM rep3

description:
Saikosaponin B2 2uM rep3
Batch2

value: Saikosaponin B2


title: 15-064_Mild_16_W.P.I. [3A5]

description:
P3A5
15-064_Female_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B2 10uM rep3

description:
Saikosaponin B2 10uM rep3
Batch2


title: 15-059_Mild_24_W.P.I. [3E8]

description:
P3E8
15-059_Male_Mild_24_W.P.I._Total RNA

value: Male


title: HA_Arid5_w_IL-6_rep2

description: HA-tagged Arid5a-overexpressing 4T1 cells following stimulation with IL-6 (100 ng/ml)

library_source: genomic

data_processing:
Prepared libraries were sequenced using a NovaSeq 6000 platform (Illumina), and 101 bp paired-end reads were obtained.
After adapter trimming by Cutadapt ver2.7, the trimmed reads were mapped to  the mouse reference genome sequences (mm10) using Bowtie2 ver. 2.3.5.1. Peak  calling was performed with MACS2 ver. 2.2.7.1
Genome_build: Sequence reads were aligned to the mouse genome (mm10).
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions

molecule: genomic DNA

extract_protocol:
Briefly, cells were cultured in 20 cm dishes and stimulated using IL-6. Chromatin (5 μg) was prepared using 4 rounds of sonication (30 sec on and 30 sec off) in precooled conditions. DNA disrupted into fragments of 200-1000 bp was immunoprecipitated using Protein-G Dynabeads (Novex) bound with an anti-HA antibody to detect Arid5a (4 μg each). Normal IgG (4 μg) was used as a control, and libraries were constructed from immunoprecipitated DNA.
The ChIP-Seq library of precipitated DNAs was prepared using KAPA Library Preparation Kits for Illumina (Kapa Biosystems).


title: control (donor #3), IL04


title: 15-059_Mild_16_W.P.I. [3D4]

description:
P3D4
15-059_Male_Mild_16_W.P.I._Total RNA


title: 15-069_Moderate_24_W.P.I. [3E6]

description:
P3E6
15-069_Male_Moderate_24_W.P.I._Total RNA

value: Moderate


title: control (donor #2), IL03

value: donor #2

value: fetal eye


title: HA_Arid5_w_IL-6_rep1


title: 15-058_Mild_16_W.P.I. [3E4]

description:
P3E4
15-058_Female_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B3 0.4uM rep2

description:
Saikosaponin B3 0.4uM rep2
Batch2


title: Batch2 Saikosaponin B3 2uM rep2

description:
Saikosaponin B3 2uM rep2
Batch2


title: 15-058_Mild_24_W.P.I. [3D8]

description:
P3D8
15-058_Female_Mild_24_W.P.I._Total RNA


title: control (donor #3), IL01

value: 5 weeks


title: Batch2 Saikosaponin B3 10uM rep2

description:
Saikosaponin B3 10uM rep2
Batch2


title: Input_w_IL-6_rep2


title: Input_w_IL-6_rep1


title: Batch2 Saikosaponin B2 0.4uM rep3

description:
Saikosaponin B2 0.4uM rep3
Batch2


title: LA1-5s Normoxia R1 (RNA-seq)

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a human genome (hg19 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Calculate weighted coverage and CG density (used an in house script)
Calculate h-density (used an in house script)
Genome_build: hg19
Supplementary_files_format_and_content: "h_density" bedGraph files contain hmTOP-seq h-density values for each CG; "uTOPseq" coverage file contain coverage values for all identified CG sites; "RNAseq" file contain average RNA expression values for protein-coding genes

molecule: polyA RNA

growth_protocol: 1:1 mixture of MEM medium with nonessential amino acids and Ham's F12 nutrient mixture; 15% FBS (SK-N-BE(2)), 15% heat-inactivated FBS (BE(2)-C and BE(2)-M17), 10% FBS (LA-N-1, LA1-5s and LA1-55n); 37°C; 5% CO2.

extract_protocol:
DNA - standard phenol-chloroform extraction. RNA - isolation with RNAzol RT reagent.
DNA TOP-seq libraries were constructed according to uTOP-seq (Staševskij et al., 2017) and hmTOP-seq (Gibas et al., 2020) protocols. Briefly, sonicated gDNA was labeled with azide moieties using Ado-6-azide (for uCG analysis) or UDP-6-azide-glucose (for 5hmC analysis) cofactors. After ligation of adapters, the alkyne-bearing oligodeoxyribonucleotides (ODNs) with (5hmC) or without (uCG) biotin were attached to the azide-modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads. Purified DNA after ODN conjugation (uCG) or biotin-enrichment (5hmC) was subsequently used in a DNA priming reaction. The products were amplified, size-selected and subjected to Ion Proton sequencing. For RNA-seq mRNA was enriched from the total RNA with Dynabeads mRNA Purification Kit (Invitrogen) and ribosomal RNA was depleted using RiboCop rRNA Depletion Kit (Lexogen). RNA-seq libraries were prepared with Ion Total RNA-Seq Kit v2 (Ion Torrent) and subjected to Ion Proton sequencing.

treatment_protocol: Normoxia - 72 h in atmospheric O2 concentration; hypoxia - 72 h in 1% O2

value: normoxia


title: HA_Arid5_wo_IL-6_rep2

description: HA-tagged Arid5a-overexpressing 4T1 cells following stimulation without IL-6 (100 ng/ml)


title: LA1-5s Hypoxia R1 (RNA-seq)

value: hypoxia


title: Batch2 Saikosaponin B2 0.4uM rep2

description:
Saikosaponin B2 0.4uM rep2
Batch2


title: 15-055_Mild_24_W.P.I. [3B7]

description:
P3B7
15-055_Male_Mild_24_W.P.I._Total RNA


title: LA1-55n Normoxia R1 (RNA-seq)


title: Batch2 Saikosaponin B2 2uM rep2

description:
Saikosaponin B2 2uM rep2
Batch2


title: Input_wo_IL-6_rep2


title: 15-052_Mild_16_W.P.I. [3B4]

description:
P3B4
15-052_Female_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B2 10uM rep2

description:
Saikosaponin B2 10uM rep2
Batch2


title: Batch2 Saikosaponin B3 0.4uM rep1

description:
Saikosaponin B3 0.4uM rep1
Batch2


title: Input_wo_IL-6_rep1


title: LA1-55n Hypoxia R1 (RNA-seq)


title: Negative_control


title: Batch2 Saikosaponin B3 2uM rep1

description:
Saikosaponin B3 2uM rep1
Batch2


title: 15-052_Mild_24_W.P.I. [3A7]

description:
P3A7
15-052_Female_Mild_24_W.P.I._Total RNA


title: SKmel254P_Priming_Meki_PDL1_D7_TCR

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

country: USA

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #10

data_processing:
The reads are first mapped to Grch38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat
The normalized count from the Seurat object after NormalizeData step are provided as processed data file
Subsequent clustering analyses are descibed in the full manuscript
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level expression matrix

source_name: Nf1mutated syngeneic mouse model

extract_protocol:
10x Genomics single cell 5' RNA-Seq and V(D)J sequencing
Single Cell 5' Gene Expression Libraries v1.1; Single Cell V(D)J Libraries v1.1

value: V(D)J sequencing

tag: molecule subtype

value: V(D)J mRNA


title: 15-051_Mild_16_W.P.I. [3A4]

description:
P3A4
15-051_Male_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B3 10uM rep1

description:
Saikosaponin B3 10uM rep1
Batch2


title: Batch2 Saikosaponin B2 0.4uM rep1

description:
Saikosaponin B2 0.4uM rep1
Batch2


title: SKmel254P_Priming_Meki_D7_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #8

value: Anti-PD-L1 lead-in+Trametinib


title: SKmel254P_Priming_Meki_PDL1_D3_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #9


title: BE(2)-M17 Hypoxia R3 (RNA-seq)


title: 15-046_Mild_16_W.P.I. [3A6]

description:
P3A6
15-046_Female_Mild_16_W.P.I._Total RNA

value: Female

value: Mild


title: 15-049_Moderate_24_W.P.I. [3G6]

description:
P3G6
15-049_Female_Moderate_24_W.P.I._Total RNA

value: Peripheral blood


title: BE(2)-M17 Hypoxia R4 (RNA-seq)


title: HA_Arid5_wo_IL-6_rep1

value: murine breast cancer 4T1 cells


title: SKmel254P_Priming_Meki_D3_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #7


title: 15-053_Mild_16_W.P.I. [3C4]

description:
P3C4
15-053_Male_Mild_16_W.P.I._Total RNA


title: 15-045_Mild_16_W.P.I. [3D5]

description:
P3D5
15-045_Male_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B2 2uM rep1

description:
Saikosaponin B2 2uM rep1
Batch2


title: BE(2)-M17 Hypoxia R2 (RNA-seq)


title: Batch2 Saikosaponin B2 10uM rep1

description:
Saikosaponin B2 10uM rep1
Batch2


title: BE(2)-M17 Hypoxia R1 (RNA-seq)


title: BE(2)-M17 Normoxia R2 (RNA-seq)


title: 15-043_Mild_16_W.P.I. [3H4]

description:
P3H4
15-043_Female_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B1 0.4uM rep3

description:
Saikosaponin B1 0.4uM rep3
Batch2

value: Saikosaponin B1


title: 15-038_Mild_16_W.P.I. [3H5]

description:
P3H5
15-038_Female_Mild_16_W.P.I._Total RNA


title: SKmel254P_Meki_PDL1_D7_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #5


title: BE(2)-M17 Normoxia R1 (RNA-seq)


title: SKmel254P_Priming_D0_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #6

value: Anti-PD-L1 lead-in


title: 15-038_Mild_24_W.P.I. [3G8]

description:
P3G8
15-038_Female_Mild_24_W.P.I._Total RNA


title: SKmel254P_Meki_PDL1_D3_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #4


title: Batch2 Saikosaponin B1 10uM rep3

description:
Saikosaponin B1 10uM rep3
Batch2


title: Batch2 Saikosaponin B1 2uM rep3

description:
Saikosaponin B1 2uM rep3
Batch2


title: BE(2)-C Normoxia R1 (RNA-seq)


title: 15-035_Critical_12_W.P.I. [3G3]

description:
P3G3
15-035_Female_Critical_12_W.P.I._Total RNA

value: Critical


title: BE(2)-C Hypoxia R4 (RNA-seq)


title: Batch2 Saikosaponin A 0.4uM rep3

description:
Saikosaponin A 0.4uM rep3
Batch2

value: Saikosaponin A


title: 15-034_Mild_24_W.P.I. [3C8]

description:
P3C8
15-034_Female_Mild_24_W.P.I._Total RNA


title: BE(2)-C Hypoxia R3 (RNA-seq)


title: BE(2)-C Hypoxia R2 (RNA-seq)


title: Batch2 Saikosaponin A 2uM rep3

description:
Saikosaponin A 2uM rep3
Batch2


title: SKmel254P_ctrl_D0_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #1

value: no


title: Batch2 Saikosaponin A 10uM rep3

description:
Saikosaponin A 10uM rep3
Batch2


title: BE(2)-C Hypoxia R1 (RNA-seq)


title: 15-033_Mild_16_W.P.I. [3G5]

description:
P3G5
15-033_Female_Mild_16_W.P.I._Total RNA


title: LA1-5s Normoxia R2 (uTOP-seq)

data_processing:
Library strategy: uTOP-seq
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a human genome (hg19 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Calculate weighted coverage and CG density (used an in house script)
Calculate h-density (used an in house script)
Genome_build: hg19
Supplementary_files_format_and_content: "h_density" bedGraph files contain hmTOP-seq h-density values for each CG; "uTOPseq" coverage file contain coverage values for all identified CG sites; "RNAseq" file contain average RNA expression values for protein-coding genes


title: SKmel254P_Priming_Meki_PDL1_D7

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #10

value: 5' gene expression sequencing

value: 5' mRNA


title: SKmel254P_Priming_Meki_PDL1_D3

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #9


title: 15-032_Mild_16_W.P.I. [3D6]

description:
P3D6
15-032_Female_Mild_16_W.P.I._Total RNA


title: BE(2)-C Normoxia R2 (RNA-seq)


title: 15-032_Mild_24_W.P.I. [3B8]

description:
P3B8
15-032_Female_Mild_24_W.P.I._Total RNA


title: LA1-5s Normoxia R1 (uTOP-seq)


title: SKmel254P_Meki_D7_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #3

value: Trametinib


title: SKmel254P_Priming_Meki_D7

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #8


title: Batch2 Saikosaponin B1 0.4uM rep2

description:
Saikosaponin B1 0.4uM rep2
Batch2


title: Batch2 Saikosaponin B1 10uM rep2

description:
Saikosaponin B1 10uM rep2
Batch2


title: 15-031_Mild_12_W.P.I. [3F2]

description:
P3F2
15-031_Female_Mild_12_W.P.I._Total RNA


title: Batch2 Saikosaponin A 0.4uM rep2

description:
Saikosaponin A 0.4uM rep2
Batch2


title: LA1-55n Normoxia R2 (uTOP-seq)

value: normoxia


title: 15-030_Mild_24_W.P.I. [3D7]

description:
P3D7
15-030_Male_Mild_24_W.P.I._Total RNA

value: Male


title: SKmel254P_Meki_D3_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #2

value: V(D)J sequencing


title: SKmel254P_Priming_Meki_D3

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #7


title: 15-034_Mild_16_W.P.I. [3C5]

description:
P3C5
15-034_Female_Mild_16_W.P.I._Total RNA


title: SKmel254P_Priming_D0

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #6


title: Batch2 Saikosaponin A 2uM rep2

description:
Saikosaponin A 2uM rep2
Batch2


title: SKmel254P_Meki_PDL1_D7

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #5


title: 15-030_Mild_16_W.P.I. [3B5]

description:
P3B5
15-030_Male_Mild_16_W.P.I._Total RNA


title: 15-029_Mild_24_W.P.I. [3G7]

description:
P3G7
15-029_Female_Mild_24_W.P.I._Total RNA


title: Batch2 Saikosaponin A 10uM rep2

description:
Saikosaponin A 10uM rep2
Batch2


title: LA-N-1 Normoxia R2 (uTOP-seq)


title: LA-N-1 Normoxia R1 (uTOP-seq)


title: SKmel254P_Meki_PDL1_D3

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #4


title: 15-029_Mild_16_W.P.I. [3F5]

description:
P3F5
15-029_Female_Mild_16_W.P.I._Total RNA


title: Batch2 Saikosaponin B1 0.4uM rep1

description:
Saikosaponin B1 0.4uM rep1
Batch2


title: SKmel254P_Meki_D7


title: Batch2 Saikosaponin B1 2uM rep1

description:
Saikosaponin B1 2uM rep1
Batch2


title: 15-028_Mild_24_W.P.I. [3E7]

description:
P3E7
15-028_Male_Mild_24_W.P.I._Total RNA


title: LA1-55n Normoxia R1 (uTOP-seq)


title: BE(2)-C Normoxia R1 (uTOP-seq)


title: Batch2 Saikosaponin B1 10uM rep1

description:
Saikosaponin B1 10uM rep1
Batch2


title: SKmel254P_Meki_D3


title: SKmel254P_ctrl_D0

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #1


title: 15-027_Critical_12_W.P.I. [3C3]

description:
P3C3
15-027_Male_Critical_12_W.P.I._Total RNA


title: Batch2 Saikosaponin A 0.4uM rep1

description:
Saikosaponin A 0.4uM rep1
Batch2


title: Batch2 Saikosaponin A 2uM rep1

description:
Saikosaponin A 2uM rep1
Batch2


title: BE(2)-M17 Normoxia R1 (uTOP-seq)


title: 15-028_Mild_16_W.P.I. [3C6]

description:
P3C6
15-028_Male_Mild_16_W.P.I._Total RNA


title: 15-025_Mild_12_W.P.I. [3F3]

description:
P3F3
15-025_Female_Mild_12_W.P.I._Total RNA


title: SK-N-BE(2) Normoxia R2 (uTOP-seq)


title: BE(2)-M17 Normoxia R2 (uTOP-seq)


title: KO2

city: xiamen fujian

first: Nengming

last: Xiao

address: xiangan south road

country: China

institute: School of Life Sciences, Xiamen University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters -x faindex -p 4 --dta -t --phred33 -1 _1.clean.fq.gz -2 *1.unmap.fq.gz --un-conc-gz .unmap.fq.gz
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

growth_protocol: Donor SMARTA CD4+ T cells from Ddb1-TaKO SMARTA mice (CD45.1+) and WT SMARTA mice (CD45.1+ CD45.2+) were mixed in a 1:1 ratio, and cells were adoptively transferred into WT mice (CD45.2+), follow by LCMV Armstrong infection. Donor cells were sorted from recipients mice at day5 after LCMV Armstrong infection.

extract_protocol:
RNA was harvested using Rneasy Plus Mini Kit from QIAGEN. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: cells

value: activated CD4+ T cells

value: post infection day 5

tag: genotype


title: KO1


title: Batch2 Saikosaponin A 10uM rep1

description:
Saikosaponin A 10uM rep1
Batch2

tag: treatment

tag: treatment dose


title: 15-023_Moderate_12_W.P.I. [3B3]

description:
P3B3
15-023_Female_Moderate_12_W.P.I._Total RNA

tag: Sex

value: Female

value: Moderate

tag: tissue


title: Batch2 Wortmannin 1.95uM rep3

description:
Wortmannin 1.95uM rep3
Batch2

value: Wortmannin


title: 15-022_Critical_12_W.P.I. [3B2]

description:
P3B2
15-022_Male_Critical_12_W.P.I._Total RNA

value: Peripheral blood


title: C2posTAM_pos_BISULFIT_2EME

data_processing:
Alignment to mouse genome (Bismark Mapper 0.22.1 with default parameters)
Removal of PCR duplicates (Bismark Deduplicate 0.22.1)
Extraction of per-base methylation metrics (MethylDackel 0.3.0.1 with the following parameters: --OT 4,0,0,94 --OB 3,100,8,0  --keepSingleton --keepDiscordant -q 10 -p 5 -D 2000 --minOppositeDepth 0 --maxVariantFrac 1.0 -d 1 --ignoreFlags 3840 --requireFlags 0 -fraction)
Conversion to bigWig format (Wig/BedGraph-to-bigWig converter from Galaxy)
Genome_build: mm10
Supplementary_files_format_and_content: .bw files contain alignments (per-base cytosine methylation)

source_name: Immortalized mouse embryonic fibroblast line A

extract_protocol:
Genomic DNA was bisulfite-converted using the EZ DNA Methylation-Gold kit (Zymo Research)
Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences)

tag: cell type

value: c-myc-immortalized mouse embryonic fibroblasts


title: SK-N-BE(2) Normoxia R1 (uTOP-seq)


title: BE(2)-C Normoxia R2 (uTOP-seq)


title: 15-024_Mild_12_W.P.I. [3C2]

description:
P3C2
15-024_Female_Mild_12_W.P.I._Total RNA

value: Mild


title: 15-021_Mild_12_W.P.I. [3F1]

description:
P3F1
15-021_Female_Mild_12_W.P.I._Total RNA


title: WT2

value: WT


title: Batch2 Vehicle  rep2

description:
Vehicle  rep2
Batch2

value: Vehicle


title: 20 week +dox experimental 2 female [TC44982_CTTGTA]

city: Houston

first: Thomas

middle: A

last: Cooper

state: TX

address: One Baylor Plaza

department: Pathology & Immunology

institute: Baylor College of Medicine

description:
total RNA; polyA selected
TC44982_CTTGTA

data_processing:
Low-quality nucleotides were trimmed from both ends of the sequence reads and reads were mapped to the mouse genome (UCSC mm10) using Tophat
Alternative splicing events, including skipped exons, alternative 5’/3’ splice sites, alternative first or last exons, mutually exclusive exons and retained introns, were analyzed using MISO
Alternative splicing was quantified by PSI value, indicating the fraction of transcripts that include a given exon. Events with DPSI >10%, when comparing the treatment group with the controls with a Bayes factor >5, were considered significant.
events that changed when comparing CTG960 –dox with TREþdox controls were filtered out of the analysis to rule out any events that were altered owing to the presence of doxycycline when repeats were not expressed.
Alternative splicing was reproducible between biological replicates at both six weeks and 12 weeks (Figure S5)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: for more details PMID: 29771332

source_name: Quad

extract_protocol:
Tissue was isolated and immediately flash frozen. Total RNA was isolated from individual skeletal muscles using TRIzol reagent (Invitrogen) with a Bullet Blender (Next Advance). RNeasy fibrous tissue mini-kit (Qiagen) was used for RNA extraction of skeletal muscle tissues used in RNA-seq experiments according to the manufacturer's protocol. RNA was resuspended in RNase-free water (Ambion) and treated with DNaseI (Ambion).
The Genomic and RNA Profiling Core (GARP) at Baylor College of Medicine (BCM) performed HiSeq library preparation and Illumina sequencing of 100-bp paired-end reads on a HiSeq 2500 sequencer. RNA was poly-A selected, barcoded and run in eight lanes.

value: plus doxycycline (experimental)

tag: genotype/variation

value: TREDT960I-HOM; MDAFrtTA

tag: time point

value: 20 week


title: Batch2 Vehicle  rep3

description:
Vehicle  rep3
Batch2


title: 20 week -dox control 1 female [TC44983_AGTCAA]

description:
total RNA; polyA selected
TC44983_AGTCAA

value: no doxycycline (not induced)


title: Batch2 Wortmannin 1.95uM rep1

description:
Wortmannin 1.95uM rep1
Batch2


title: 20 week +dox experimental 1 female [TC44766_TAGCTT]

description:
total RNA; polyA selected
TC44766_TAGCTT

source_name: Gastroc


title: 12 week +dox experimental 2 female [TC43836_TGACCA]

description:
total RNA; polyA selected
TC43836_TGACCA

value: 12 week


title: Batch2 Wortmannin 1.95uM rep2

description:
Wortmannin 1.95uM rep2
Batch2


title: Batch1 E-BR 5.32ug/mL rep3

description:
E-BR 5.32ug/mL rep3
Batch1

value: Ethanol extract of Bupleuri Radix (E-BR)


title: WT1


title: 12 week +dox experimental 1 female [TC43835_TTAGGC]

description:
total RNA; polyA selected
TC43835_TTAGGC


title: C2posTAM_pos_BISULFIT_1ER


title: C2pos_BISULFIT_2EME

value: wild-type


title: 15-020_Mild_12_W.P.I. [3H1]

description:
P3H1
15-020_Male_Mild_12_W.P.I._Total RNA

value: Male


title: 15-014_Mild_24_W.P.I. [3F8]

description:
P3F8
15-014_Male_Mild_24_W.P.I._Total RNA


title: 20 week -dox control 2 female [TC44984_AGTTCC]

description:
total RNA; polyA selected
TC44984_AGTTCC


title: 15-019_Mild_24_W.P.I. [3H6]

description:
P3H6
15-019_Female_Mild_24_W.P.I._Total RNA


title: 12 week -dox control 2 female [TC45061_ATGTCA]

description:
total RNA; polyA selected
TC45061_ATGTCA


title: Foxa1_WT_mock_rep2

data_processing:
Adapter trimming (Trim Galore! 0.4.4 wrapper with default settings)
Discard reads aligning to complete mouse rRNA sequence (Bowtie 2.2.9)
Alignment to mouse genome (Bowtie 2.2.9)
Gene counts (FeatureCounts 1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.txt files contain gene counts

extract_protocol:
Truseq Stranded mRNA
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions
described in an additional column

treatment_protocol: DD-dCas9-VPR; sgRNA-Foxa1, uninduced

value: DD-dCas9-VPR; sgRNA-Foxa1

value: uninduced

tag: fraction

value: total RNA


title: 12 week -dox control 1 female [TC43838_GCCAAT]

description:
total RNA; polyA selected
TC43838_GCCAAT


title: C2pos_BISULFIT_1ER


title: 15-019_Mild_16_W.P.I. [3H3]

description:
P3H3
15-019_Female_Mild_16_W.P.I._Total RNA

tag: age

value: Female


title: Nr2f1_WT_washout_rep2

treatment_protocol: DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction

value: DD-dCas9-VPR; sgRNA-Nr2f1

value: after transient induction


title: Batch2 Vehicle  rep1

description:
Vehicle  rep1
Batch2


title: Foxa1_WT_washout_rep1

treatment_protocol: DD-dCas9-VPR; sgRNA-Foxa1, after transient induction

value: c-myc-immortalized mouse embryonic fibroblasts


title: Nr2f1_WT_washout_rep1


title: 15-015_Mild_12_W.P.I. [3E3]

description:
P3E3
15-015_Female_Mild_12_W.P.I._Total RNA

value: Mild

value: Peripheral blood


title: Foxa1_WT_washout_rep2


title: 20 week +dox control female [TC43903_GATCAG]

description:
total RNA; polyA selected
TC43903_GATCAG

value: plus doxycycline control


title: 12 week +dox control female [TC43539_ATCACG]

description:
total RNA; polyA selected
TC43539_ATCACG


title: Batch1 E-BR 133ug/mL rep3

description:
E-BR 133ug/mL rep3
Batch1


title: 15-014_Mild_12_W.P.I. [3D3]

description:
P3D3
15-014_Male_Mild_12_W.P.I._Total RNA


title: 6 week +dox experimental 1 female [TC43900_ACTTGA]

description:
total RNA; polyA selected
TC43900_ACTTGA

value: plus doxycycline (experimental)

value: TREDT960I-HOM; MDAFrtTA

value: 6 week


title: 15-011_Mild_12_W.P.I. [3D1]

description:
P3D1
15-011_Female_Mild_12_W.P.I._Total RNA


title: Nr2f1_WT_mock_rep1

treatment_protocol: DD-dCas9-VPR; sgRNA-Nr2f1, uninduced


title: Foxa1_WT_mock_rep1


title: 15-014_Mild_16_W.P.I. [3B6]

description:
P3B6
15-014_Male_Mild_16_W.P.I._Total RNA


title: 15-010_Mild_12_W.P.I. [3E1]

description:
P3E1
15-010_Male_Mild_12_W.P.I._Total RNA


title: Batch1 W-BR 20ug/mL rep3

description:
W-BR 20ug/mL rep3
Batch1

value: Water extract of Bupleuri Radix (W-BR)


title: Batch1 W-BR 100ug/mL rep3

description:
W-BR 100ug/mL rep3
Batch1


title: Batch1 E-BR 26.6ug/mL rep3

description:
E-BR 26.6ug/mL rep3
Batch1

value: Ethanol extract of Bupleuri Radix (E-BR)


title: 15-009_Mild_12_W.P.I. [3H2]

description:
P3H2
15-009_Female_Mild_12_W.P.I._Total RNA


title: 15-013_Mild_12_W.P.I. [3B1]

description:
P3B1
15-013_Male_Mild_12_W.P.I._Total RNA


title: 6 week +dox experimental 2 female [TC44981_GGCTAC]

description:
total RNA; polyA selected
TC44981_GGCTAC


title: Batch1 W-BR 500ug/mL rep3

description:
W-BR 500ug/mL rep3
Batch1


title: ES_E14_washout_rep1

source_name: Mouse embryonic stem cells

growth_protocol: mouse embryonic stem cells were grown in N2B27 medium supplemented with 3 µM CT-99021, 1 µM PD0325901 and 10 ng/mL LIF, on 0.1% gelatin-coated flasks.

treatment_protocol: wild-type after washout of 2 µM UNC1999 + 4 µM A395

value: Mouse embryonic stem cells E14

value: wild-type

value: after washout of 2 uM UNC1999 + 4 uM A395


title: Batch1 W-BR 20ug/mL rep2

description:
W-BR 20ug/mL rep2
Batch1


title: ES_E14_inhib_rep2

treatment_protocol: wild-type + 2 µM UNC1999 + 4 µM A395


title: ATAC_C2-T-Ezh2_replicate_2

data_processing:
Alignment to mouse genome allowing an insert size of up to 2 kb (Bowtie 2.2.9 with the following parameters: '--reorder -p 8 -D 70 -R 3 -N 0 -L 20 -i S,1,0.50 -X 2000')
Filtering of reads to exclude reads mapping to mitochondria or common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of RPKM values per 50bp bin and conversion to bigWig format (DeepTools bamCoverage)
Peak calling was performed on each replicate using SEACR (Meers et al., 2019, PMID 31300027) with a threshold of 0.006 and “stringent” mode, and Intersect (Galaxy v1.0.0) was used to identify overlapping pieces of intervals.
Genome_build: mm10
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)
Supplementary_files_format_and_content: .bed file contains peak coordinates

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2015, PMID 25559105) with transposition on 50,000 whole cells rather than nuclei in order to minimize mitochondrial DNA contamination as recommended by Karabacak Cakviello et al., 2019 (PMID 30791920).
Buenrostro et al., 2015, PMID 25559105

treatment_protocol: Ezh2 -/- , retroviral pMSCV-Ezh2

value: retroviral pMSCV-Ezh2 rescue


title: Batch2 Saikosaponin B1 2uM rep2

description:
Saikosaponin B1 2uM rep2
Batch2

value: Saikosaponin B1


title: 15-012_Mild_12_W.P.I. [3A3]

description:
P3A3
15-012_Female_Mild_12_W.P.I._Total RNA

value: Female


title: Nr2f1_WT_mock_rep2

value: DD-dCas9-VPR; sgRNA-Nr2f1

value: uninduced

value: total RNA


title: Batch1 E-BR 5.32ug/mL rep2

description:
E-BR 5.32ug/mL rep2
Batch1


title: 6 week +dox control female [TC43899_CAGATC]

description:
total RNA; polyA selected
TC43899_CAGATC


title: ATAC_C2-T_replicate_2

value: c-myc-immortalized mouse embryonic fibroblasts


title: Batch1 E-BR 26.6ug/mL rep2

description:
E-BR 26.6ug/mL rep2
Batch1


title: 15-009_Mild_16_W.P.I. [3G4]

description:
P3G4
15-009_Female_Mild_16_W.P.I._Total RNA

value: Mild

value: Peripheral blood


title: ES_E14_washout_rep2


title: 6 week -dox control 1 female [TC43678_CGATGT]

description:
total RNA; polyA selected
TC43678_CGATGT

value: no doxycycline (not induced)


title: Batch1 E-BR 133ug/mL rep2

description:
E-BR 133ug/mL rep2
Batch1


title: Batch1 W-BR 500ug/mL rep2

description:
W-BR 500ug/mL rep2
Batch1


title: ATAC_C2_replicate_2

treatment_protocol: wild-type


title: Batch1 E-BR 5.32ug/mL rep1

description:
E-BR 5.32ug/mL rep1
Batch1


title: Batch1 W-BR 100ug/mL rep2

description:
W-BR 100ug/mL rep2
Batch1


title: 15-007_Critical_12_W.P.I. [3G2]

description:
P3G2
15-007_Female_Critical_12_W.P.I._Total RNA

value: Critical


title: ATAC_C2-T-Ezh2_replicate_1


title: 15-009_Mild_24_W.P.I. [3F7]

description:
P3F7
15-009_Female_Mild_24_W.P.I._Total RNA


title: 6 week -dox control 2 male [TC43837_ACAGTG]

description:
total RNA; polyA selected
TC43837_ACAGTG

value: TREDT960I-HOM; MDAFrtTA

value: 6 week


title: Batch1 E-BR 26.6ug/mL rep1

description:
E-BR 26.6ug/mL rep1
Batch1

value: Ethanol extract of Bupleuri Radix (E-BR)


title: 15-008_Mild_12_W.P.I. [3G1]

description:
P3G1
15-008_Male_Mild_12_W.P.I._Total RNA

value: Male


title: ES_E14_mock_rep2

value: Mouse embryonic stem cells E14

value: wild-type


title: ES_E14_mock_rep1


title: 15-005_Severe_12_W.P.I. [3D2]

description:
P3D2
15-005_Male_Severe_12_W.P.I._Total RNA

value: Severe


title: 15-006_Mild_12_W.P.I. [3E2]

description:
P3E2
15-006_Female_Mild_12_W.P.I._Total RNA


title: ES_E14_inhib_rep1


title: C2_EZH2-H3K36me3_rep2

data_processing:
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)

source_name: Immortalized mouse embryonic fibroblast line A, Ezh2 -/-

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. For CUT&RUN permeabilized cells were incubated with specific antibodies followed by incubation with pA-MNAse. Digested DNA fragments were subsequently recovered in the supernatant.
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

tag: chip antibody

value: H3K36me3 (Abcam, polyclonal, catalog# ab9050)


title: ATAC_C2_replicate_1


title: 15-004_Mild_12_W.P.I. [3A2]

description:
P3A2
15-004_Male_Mild_12_W.P.I._Total RNA

tag: disease severity


title: NPC_H3K27me3_washout_rep1

data_processing:
Library strategy: Cut&Run
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)

source_name: Neural progenitor cells, wild-type after washout of  2 µM UNC1999 + 4 µM A395

growth_protocol: neural progenitor cells were grown in N2B27 medium supplemented with EGF and FGF2 (10ng/ml each), on 0.1% gelatin-coated flasks.

value: ES-derived neural progenitor cells

value: washout of  2 µM UNC1999 + 4 µM A395

value: H3K27me3 (Cell Signaling Technology, clone C36B11), catalog# 9733


title: Batch1 W-BR 20ug/mL rep1

description:
W-BR 20ug/mL rep1
Batch1

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to human genome assembly GRCh38 (hg38) via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with human gene annotation GRCh38.84.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

value: Water extract of Bupleuri Radix (W-BR)


title: Batch1 E-BR 133ug/mL rep1

description:
E-BR 133ug/mL rep1
Batch1


title: 15-002_Mild_16_W.P.I. [3E5]

description:
P3E5
15-002_Male_Mild_16_W.P.I._Total RNA

tag: rin


title: C2_EZH2-H3K4me3_rep2

value: c-myc-immortalized mouse embryonic fibroblasts

value: H3K4me3 (Cell Signaling Technology, clone C42D8), catalog# 9751


title: CD45+ tumorinfiltrating immune cells_NL-_and_L-PM

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

description: mRNA from single cells

data_processing:
Processing of raw reads was done using the BD Rhapsody WTA Analysis Pipeline v1.0 which  takes the FASTQ files, a reference genome file (GRCm38) and a transcriptome annotation (genecodevM19) file for alignment. Molecular counts per cell generated by the pipeline were used for data analysis in Partek Flow.
Raw paired sequencing data consist of R1 and R2 file. Sample demultiplexing is done based on information from R1 that contain cell label and R2 reads that contain mRNA sequences and tag sequences. Each of R1 reads sequenced contain the cell label although not every corresponding R2 read contain tag sequence. To demultiplex samples, firstly the cell labels are annotated in order to determine putative cells. After determination of putative cells, each of cells have assigned cluster of reads R1 and associated R2 reads. Based on tag sequence in group of R2 reads assigned to cell, each cell is assigned to sample tag.    Detailed description on annotation of cell labels (step 2) and determination of putative cells (step 6) followed by determination of sample of origin (step 7) can be found in BD Single Cell Genomics Bioinformatics Handbook (GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf) Available tag sequences used for sample multiplexing can be found in Attachement_B2_SampleTagSequences_MusMusculus_ver1.fasta for Mous
Genome_build: reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: CD45+ tumorinfiltrating immune cells

extract_protocol:
At day 15 single cell suspensions were prepared from excised whole tumors by tissue digestion using murine tumor dissociation kit and gentleMACS dissociator (Miltenyi Biotec). CD45+ cells were enriched by murine CD45 (TIL) MicroBeads (Miltenyi Biotec) using MACS technology. To enrich purity viable CD45+ cells were sorted using AriaIII flow cytometer (BD Bioscience).
Cells derived from 3 independent experiments per group (3x NL-PM and 3x L-PM) were "labeled" by Sample Tags 3,4,5 (NL-PM) and 6,7,9 (L-PM) and then together loaded on the Rhapsody cartridge. After capturing of single cells RNA molecules bound to magnetic beads, libraries were generated following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation protocol (BD Biosciences). Barcoding of RPE and Sample Tag library was done by Library Reverse Primer 1 (Illumina i7 Index): 5'-GCTACGCT-3'

treatment_protocol: B6J mice were subcutanously inoculated with B16F10-OVA Tumor cells. Starting from day 4 after inoculation tumors were peritumorally (at the tumor site) injected with either empty (NL-PM) or adenylat cyclase MDL-12.330A-loaded Nanopartclies (polypept(o)id micelles).

value: CD45+ tumor infiltrating immune cells

value: WT

value: mixed sample:empty or MDL-12.330A-loaded Particles (non-demultiplexed)


title: Batch1 W-BR 500ug/mL rep1

description:
W-BR 500ug/mL rep1
Batch1


title: NPC_H3K27me3_inhibitors_rep2

data_processing:
Library strategy: Cut&Run
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Peak calling on combined replicates using MACS2 (2.1.1.20160309) with parameters -f BAMPE --gsize mm --broad --broad-cutoff 0.1 --bdg
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)

source_name: Neural progenitor cells, wild-type + 2 µM UNC1999 + 4 µM A395


title: 15-002_Mild_12_W.P.I. [3C1]

description:
P3C1
15-002_Male_Mild_12_W.P.I._Total RNA

value: Mild

value: Peripheral blood

tag: timepoint


title: NPC_H3K27me3_inhibitors_rep1


title: Batch1 Vorinostat 10uM rep3

description:
Vorinostat 10uM rep3
Batch1

value: Vorinostat


title: Batch1 W-BR 100ug/mL rep1

description:
W-BR 100ug/mL rep1
Batch1


title: 15-001_Severe_12_W.P.I. [3A1]

description:
P3A1
15-001_Male_Severe_12_W.P.I._Total RNA

value: Male


title: 2102Ep_HiC

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

data_processing:
Reads were aligned using PAtChER (https://github.com/MBrancoLab/PAtChER), with -d 20000 for human data and -d 10000 for mouse data.
Read pairing information was removed using PAtChER's unpair tool.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: BigWig tracks

growth_protocol: E14 ESCs were grown in DMEM GlutaMAX supplemented with 15% FBS, non-essential amino acids, 50μM 2-mercaptoethanol, antibiotic-antimycotic and 1,000 U/ml LIF. MCF7 and 2102Ep cells were grown in DMEM GlutaMAX supplemented with 10% FBS, penicillin-streptomycin and non-essential amino acids.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. To match the HiChIP protocol, DNA was heat denatured, followed by purification, isolation of ligated fragments using streptavidin beads, and library amplification.
Libraries were prepared using the NEBNext ultra II DNA library prep kit.

tag: cell line


title: NPC_H3K27me3_mock_rep2

source_name: Neural progenitor cells, wild-type

value: untreated


title: ATAC_C2-T_replicate_1


title: Batch1 Trichostatin A 0.64uM rep3

description:
Trichostatin A 0.64uM rep3
Batch1

extract_protocol:
Total RNA was isolated from tissue using Maxwell (Promega) based method.
One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.   The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

value: Trichostatin A


title: NPC_H3K27me3_mock_rep1

value: wild-type


title: C2_EZH2-H3K36me3_rep1

value: H3K36me3 (Abcam, polyclonal, catalog# ab9050)


title: C2_EZH2-H3K4me3_rep1


title: MCF7_HiC


title: NPC_H3K27me3_washout_rep2

value: ES-derived neural progenitor cells


title: C2_EZH2-Pol2_rep1

value: RNA Polymerase II (Santa Cruz Biotechnology clone N-20), catalog# sc-899


title: 2102Ep_HiMeDIP

data_processing:
Library strategy: HiChIP
Reads were aligned using PAtChER (https://github.com/MBrancoLab/PAtChER), with -d 20000 for human data and -d 10000 for mouse data.
Read pairing information was removed using PAtChER's unpair tool.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation.
Normalised bigWig tracks were generated by dividing the HiChIP tracks by the corresponding Hi-C tracks, using bigwigCompare (deeptools) with --pseudocount 0.01 --skipZeroOverZero.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: BigWig tracks

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. After heat denaturation, methylated DNA was immunoprecipitated using an anti-5mC antibody (Active Motif 61479). Immunoprecipitated DNA was purified, followed by isolation of ligated fragments using streptavidin beads, and library amplification.
Libraries were prepared using the NEBNext ultra II DNA library prep kit.

tag: antibody

value: anti-5-methylcytosine (Active Motif 61479)


title: Batch1 Vehicle  rep3

description:
Vehicle  rep3
Batch1

value: Vehicle


title: NPC_washout_rep2

extract_protocol:
Truseq Stranded mRNA
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions

value: after washout of  2 uM UNC1999 + 4 uM A395

value: total RNA


title: K27me3_C26-Ezh2-Flp_Michel

source_name: Immortalized mouse embryonic fibroblast line B, Ezh2 endogenous rescue

value: c-myc-immortalized mouse embryonic fibroblasts

value: Ezh2 endogenous rescue

value: H3K27me3 (Cell Signaling Technology, clone C36B11), catalog# 9733


title: Batch1 No treatmenet  rep3

description:
No treatmenet  rep3
Batch1

value: No treatment


title: C2_EZH2-Pol2_rep2


title: NPC_inhibitors_rep2


title: MCF7_HiMeDIP


title: C2_EZH2_input


title: K27me3_C26-Ezh2-Flp_Daniel


title: tissue of a giant cell tumor of bone

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

description: not collected

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V4.0.0
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: Tumor tissue

extract_protocol:
After removing the fat, visible vessels and surrounding necrotic area, a small fragment tumor tissues were cut and rinsed with clod Dulbecco’s phosphate-buffered saline (DPBS, Gibco, C14190500BT). Then, we cut the tissues into approximately 1 mm3 pieces on ice and transferred into DPBC and washed twice. We used collagenase 2 to digest the tissues into single cells for 45 min at 37℃. After filtered by 100 μm cell strainer in the DPBS with 1% fetal bovine serum (FBS) (Gibco, 10091148), the suspended cells were centrifuged at 300 g for 5 min. After discarding the supernatant, we removed red blood cells using 1×RBC lysis buffer (10× diluted to 1×, BioLegend, B250015) for 5 min and passed the cells through a 40μm cell strainer. The final single cell suspension were re-suspended in DPBS with 1% FBS after washing twice with DPBS. Viability was confirmed to be > 80% in all samples via trypan blue (0.4%, Gibco, 420301) and the cell suspensions were kept on ice to prepare for 10× Genomics.
The final single cells from each sample were loaded on a 10× Genomics Chromium Single-Cell Chip along with the single cell master mix and single cell 3’ gel beads (10× Genomics) to generate single-cell gel bead-in-emulsions (GEMs). According to the manufacturer’s instructions the samples were processed by 10× Genomics V3 barcoding chemistry kits. mRNA in drops were undergo the reverse transcription reactions and then the cDNA amplification was followed by the instructions. And the single cell libraries were sequenced on an Illumina HiSeq X Ten instrument.

value: giant bone cell tumor


title: Batch1 Wortmannin 1.95uM rep3

description:
Wortmannin 1.95uM rep3
Batch1

value: Wortmannin


title: NPC_inhibitors_rep1


title: Batch1 Wortmannin 1.95uM rep2

description:
Wortmannin 1.95uM rep2
Batch1


title: K27me3_C26_Ezh2_Michel

data_processing:
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Peak calling on combined replicates using MACS2 (2.1.1.20160309) with parameters -f BAMPE --gsize mm --broad --broad-cutoff 0.1 --bdg
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)

source_name: Immortalized mouse embryonic fibroblast line B, Ezh2 -/- (reversible)

value: Ezh2 -/- (reversible)


title: Patient 6 tissue of an osteosarcoma

value: tumor


title: Batch1 Trichostatin A 0.64uM rep2

description:
Trichostatin A 0.64uM rep2
Batch1

value: Trichostatin A


title: K27me3_C26_Michel

source_name: Immortalized mouse embryonic fibroblast line B, wild-type

value: wild-type


title: Batch1 No treatmenet  rep2

description:
No treatmenet  rep2
Batch1


title: LGEs, Meis2-CKO-4

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
The raw data were filtered and processed by FastQC software (Version 0.11.5, available online at the website: http://www. bioinformatics.babraham.ac.uk/projects/fastqc)
Low-quality RNA-Seq reads were removed if they had a Phred quality score of less than 20 or had less than 50 nucleotides
The filtered reads were mapped onto the mouse reference genome (GRCm38.p2.genome, released on 12/10/2013) using HISAT2 software (Version 2.1.0).
Assembly and quantification of the transcripts were accomplished with StringTie software (Version 1.3.1) using the mouse genome annotation file as the reference (gencode.vM2. annotation, available at the GENCODE website)
The number of FPKM was used for the measurement of the relative abundances of the transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: gene count

source_name: Lateral ganglionic eminence

extract_protocol:
The LGEs from E14.5 Meis2-CKO mutant and Control brains (n = 4 per group) were dissected, and RNA was isolated with the Direct-zol RNA Miniprep kit (Zymo, catalog #R2050) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lateral ganglionic eminence

tag: strain

value: a mixed genetic background of C57BL/6J and CD1

value: Embryonic day 14.5

tag: group

value: Meis2-CKO brain


title: NPC_mock_rep2

value: ES-derived neural progenitor cells

tag: genotype

tag: treatment

value: untreated


title: Patient 5 tissue of an osteosarcoma


title: Batch1 Vehicle  rep2

description:
Vehicle  rep2
Batch1

value: Vehicle

tag: treatment dose


title: NPC_mock_rep1

value: total RNA


title: Patient 4 tissue of an osteosarcoma

tag: tissue


title: K27me3_C2plusTplusE2_Michel

source_name: Immortalized mouse embryonic fibroblast line A, Ezh2 -/- , retroviral pMSCV-Ezh2

tag: cell type

value: c-myc-immortalized mouse embryonic fibroblasts

value: Ezh2 -/- , retroviral pMSCV-Ezh2


title: K27me3_C2plusT_Michel

value: H3K27me3 (Cell Signaling Technology, clone C36B11), catalog# 9733


title: NPC_washout_rep1

value: after washout of  2 uM UNC1999 + 4 uM A395


title: Patient 2 tissue of an osteosarcoma


title: Patient 3 tissue of an osteosarcoma


title: LGEs, Meis2-CKO-3


title: Batch1 Vorinostat 10uM rep2

description:
Vorinostat 10uM rep2
Batch1

value: Vorinostat


title: Patient 1 tissue of an osteosarcoma


title: Batch1 Wortmannin 1.95uM rep1

description:
Wortmannin 1.95uM rep1
Batch1

value: Wortmannin


title: Batch1 Vorinostat 10uM rep1

description:
Vorinostat 10uM rep1
Batch1


title: Batch1 Trichostatin A 0.64uM rep1

description:
Trichostatin A 0.64uM rep1
Batch1


title: LGEs, Meis2-CKO-1


title: K27me3_C26_Daniel


title: CAD-89

city: Guangzhou

first: guodong

last: he

address: zhongshan road No.102

institute: Guangdong Provincial People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie hisat2 with parameters -p 12 -5 5 -3 5 --rna-strandness RF
HTseq was used to calculate the counts of the Reads mapped the genome.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with Htseq-counts

source_name: exosome from plasma

extract_protocol:
2mL of venous blood from patients were collected into Ethylene Diamine Tetraacetic Acid (EDTA) routine blood tubes. Plasma was separated by centrifugation at 3000 rpm for 10 min at 4℃ and collected into cryogenic vials and stored at −80℃. The exoRNeasy Serum/Plasma kit (Qiagen) was applied to extract the exosomal total RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: exosome from plasma

value: 66 years old

tag: disease state

value: stable coronary artery disease


title: LGEs, Ctrl-4

value: Lateral ganglionic eminence

value: littermate control


title: K27me3_C26_Ezh2_Daniel

value: Ezh2 -/- (reversible)


title: K27me3_C2plusTplusE2_Daniel


title: CAD-88

value: 45 years old


title: LGEs, Ctrl-3

value: a mixed genetic background of C57BL/6J and CD1

value: Embryonic day 14.5


title: CAD-86


title: Batch1 No treatmenet  rep1

description:
No treatmenet  rep1
Batch1

value: No treatment


title: LGEs, Ctrl-2


title: LGEs, Ctrl-1


title: K27me3_C2_Daniel

source_name: Immortalized mouse embryonic fibroblast line A, wild-type

value: wild-type


title: K27me3_C2plusT_Daniel

value: c-myc-immortalized mouse embryonic fibroblasts


title: CAD-85

value: 55 years old


title: K27me3_C2_Michel

value: H3K27me3 (Cell Signaling Technology, clone C36B11), catalog# 9733


title: LGEs, Meis2-CKO-2

value: Meis2-CKO brain


title: CAD-84

value: 52 years old


title: Nascent_C26-Ezh2-Flp_Michel

extract_protocol:
Truseq Stranded Total RNA
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions

value: Ezh2 endogenous rescue

value: nascent RNA


title: del rqcH RqcP-FLAG3 vs total tRNA rep2

type: RNA

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Biological replicate 2 of 2

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

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

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

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: cultivated cells

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

growth_protocol:
Cells were pre-grown on LB plates overnight at 30 °C. Fresh individual colonies were used to inoculate 3000 mL LB cultures. The cultures were grown until OD600 of 0.8 at 37 °C.
Cell were grown independently for each biological experiment.

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

value: trpC2 rqcP-FLAG3 spcR rqcH::cmR

tag: molecule subtype

value: total RNA IP


title: CAD-81

value: exosome from plasma

value: 56 years old

value: stable coronary artery disease


title: Batch1 Vehicle  rep1

description:
Vehicle  rep1
Batch1

value: Vehicle


title: Nascent_C26_Michel

tag: fraction


title: Nascent_C26-Ezh2_Michel

value: Ezh2 -/- (reversible)


title: RqcP_FLAG3 vs total tRNA rep2

description: Biological replicate 2 of 2

value: trpC2 rqcP-FLAG3 spcR rplK::cmR


title: goat retina OD D

city: Wenzhou City

first: Yu

last: Zhonghao

state: Zhejiang Province, China

address: 270 Xueyuan West Road

institute: The Eye Hospital, School of Ophthalmology & Optometry

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS1 (Capra hicus) genome using Tophat2 software
Cufflinks are used for assemble transcripts and remap and quantity gene-expression level which is estimate by FPKM value.
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample.
Supplementary_files_format_and_content: known_lncRNA.result.txt (includes our known lncRNA)
Supplementary_files_format_and_content: LncRNA.fa (contains the sequences of unknown genes)

organism: Capra hircus

source_name: retina

extract_protocol:
Total RNA of each sample was extracted following the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: Left pre-chiasmatic optic nerve was crushed one day before collected samples.

value: right retina

value: retina

tag: breed

value: Saanen dairy goat

value: uninjured


title: CAD-80

tag: age

value: 53 years old


title: CAD-82

value: 38 years old


title: Nascent_C2plusTplusE2_Michel

value: c-myc-immortalized mouse embryonic fibroblasts

value: Ezh2 -/- , retroviral pMSCV-Ezh2


title: del rqcH RqcP-FLAG3 vs total tRNA rep1

description: Biological replicate 1 of 2


title: goat optic nerve OD #1 D

source_name: optic nerve

value: right retrobulbar optic nerve

value: optic nerve


title: RqcP_FLAG3 vs total tRNA rep1

description: Biological replicate 1 of 2

value: total RNA IP


title: goat optic nerve OS #3 D

value: left pre-chiasmatic optic nerve

value: injured


title: goat optic nerve OS #1 D

value: left retrobulbar optic nerve


title: Total_C26-Ezh2_Michel

value: total RNA


title: goat retina OS D

value: left retina


title: Nascent_C2plusT_Michel

value: nascent RNA


title: goat optic nerve OD #3 D

value: right pre-chiasmatic optic nerve


title: goat retina OD 3

value: right retina

value: retina


title: RqcH-HTF vs total tRNA rep1

description: Biological replicate 1 of 3

value: tBulk

value: Purfied RqcH-HTF and tBulk

value: tBulk IP


title: Total_C26_Michel

value: c-myc-immortalized mouse embryonic fibroblasts

value: wild-type


title: RqcH-HTF vs total tRNA rep2

description: Biological replicate 2 of 3


title: Nascent_C2_Michel


title: goat optic nerve OD #3 3

value: Saanen dairy goat

value: uninjured


title: goat retina OS 3


title: del_rplK_RqcH-FLAG3 vs total tRNA rep2

description: Biological replicate 2 of 3

value: trpC2 rqcH-FLAG3 spcR rplK::cmR

value: total RNA IP


title: del_rplK_RqcH-FLAG3 vs total tRNA rep3

description: Biological replicate 3 of 3


title: del_rqcP_RqcH-FLAG3 vs total tRNA rep3

description: Biological replicate 3 of 3

value: trpC2 rqcH-FLAG3 spcR rqcP::cmR


title: del_rplK_RqcH-FLAG3 vs total tRNA rep1

description: Biological replicate 1 of 3


title: RqcH-HTF vs total tRNA rep3

description: Biological replicate 3 of 3


title: goat optic nerve OS #1 3

value: left retrobulbar optic nerve

value: optic nerve


title: Total_C2plusT_Michel

value: total RNA


title: Nascent_C26-Ezh2_Daniel

value: Ezh2 -/- (reversible)

value: nascent RNA


title: Total_C2plusTplusE2_Michel

value: Ezh2 -/- , retroviral pMSCV-Ezh2


title: RqcH DR-HTF vs total tRNA rep2

description: Biological replicate 2 of 3

value: Purfied RqcHDR-HTF and tBulk


title: goat optic nerve OD #1 3

value: right retrobulbar optic nerve


title: Total_C26-Ezh2-Flp_Michel

value: Ezh2 endogenous rescue


title: goat retina OD 2

value: right retina

value: retina


title: del_rqcP_RqcH-FLAG3 vs total tRNA rep2

description: Biological replicate 2 of 3


title: Total_C2_Michel

value: c-myc-immortalized mouse embryonic fibroblasts

value: wild-type


title: Nascent_C26-Ezh2-Flp_Daniel


title: del_rqcP_RqcH-FLAG3 vs total tRNA rep1

description: Biological replicate 1 of 3


title: goat optic nerve OD #3 2

value: right pre-chiasmatic optic nerve

value: Saanen dairy goat

value: uninjured


title: goat retina OS 2

value: left retina


title: Nascent_C2plusTplusE2_Daniel


title: Nascent_C26_Daniel


title: ACS-30

value: exosome from plasma

value: 58 years old

value: acute myocardial infarction


title: goat optic nerve OD #1 2

value: optic nerve


title: ACS-31

value: 73 years old


title: ACS-33

value: 55 years old


title: goat optic nerve OS #3 2

value: left pre-chiasmatic optic nerve

value: injured


title: RqcH DR-FLAG3 vs total tRNA rep3

description: Biological replicate 3 of 3

value: trpC2 rqcH::spcR thrC::(Physpank-rqcHDR-FLAG3 kmR)

value: total RNA IP


title: RqcH DR-HTF vs total tRNA rep1

description: Biological replicate 1 of 3

value: tBulk

value: Purfied RqcHDR-HTF and tBulk

value: tBulk IP


title: ACS-29

value: 77 years old


title: Nascent_C2_Daniel

value: c-myc-immortalized mouse embryonic fibroblasts

value: wild-type

value: nascent RNA


title: goat optic nerve OS #3 3

value: Saanen dairy goat


title: RqcH DR-HTF vs total tRNA rep3

description: Biological replicate 3 of 3

value: Purfied RqcH-HTF and tBulk


title: RqcH DR-FLAG3 vs total tRNA rep2

description: Biological replicate 2 of 3


title: goat optic nerve OS #1 2

value: left retrobulbar optic nerve

value: uninjured


title: RqcH DR-FLAG3 vs total tRNA rep1

description: Biological replicate 1 of 3


title: Nascent_C2plusT_Daniel


title: ACS-28

value: exosome from plasma

value: 57 years old

value: acute myocardial infarction


title: Total_C26-Ezh2-Flp_Daniel

value: Ezh2 endogenous rescue

value: total RNA


title: ACS-27

value: 56 years old


title: goat retina OD 1

value: right retina

value: retina


title: ACS-26

value: 46 years old


title: goat optic nerve OD #3 1

value: right pre-chiasmatic optic nerve

value: optic nerve


title: Total_C26_Daniel

value: c-myc-immortalized mouse embryonic fibroblasts

value: wild-type


title: goat retina OS 1

value: left retina

value: Saanen dairy goat


title: Total_C26-Ezh2_Daniel

value: Ezh2 -/- (reversible)


title: Total_C2plusTplusE2_Daniel

value: Ezh2 -/- , retroviral pMSCV-Ezh2


title: goat optic nerve OD #1 1

value: right retrobulbar optic nerve

value: uninjured


title: ACS-24

value: exosome from plasma

value: 73 years old

value: acute myocardial infarction


title: LAK cell

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University

hyb_protocol: Following labeling, 5.2 ug of cDNA were hybridized for 16 hr at 45 degree C on Clariom S Human Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G system.

data_processing: The data analysis were used Transcriptome Analysis Console Ver.4.0. Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA). Expression Analysis was performed using ebayes ANOVA.

label: biotin

source_name: LAK cell

label_protocol: The fragmented 5.2 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent that is covalently linked to biotin. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

growth_protocol: PBMCs were obtained from 16 mL heparinized peripheral blood from healthy volunteers (31- and 41-year-old men). The CD3 fraction of the PBMCs was depleted by the RosetteSepTM Human CD3 Depletion Cocktail (STEMCELL Technologies, Vancouver, Canada). The CD3-depleted PBMCs were placed in a T25 culture flask (Corning, Steuben, NY, USA) containing AIM V medium (Life Technologies) supplemented with 10% autologous plasma, 50 ng/mL recombinant human IL-18 (rhIL-18, Medical & Bio-logical Laboratories Co., Ltd., Nagoya, Japan), and 3000 IU/mL rhIL-2 (Novartis, Basel, Switzerland) at 37 °C in a humidified atmosphere containing 5% CO2 for 14 days. The AIM V medium containing 3000 IU/mL rhIL-2 was replenished as necessary. LAK (Lymphocyte Activated Killer) cells were obtained the PBMCs which were cultured in AIM-V medium supplemented with 5% autologous plasma and 3000 IU/mL rhIL-2 at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA of spheroids derived from 5 × 10^3 GBM cells cultured for 3 days, human primary NK cells, and LAK cells was extracted by using NucleoSpin RNA (Takara Bio, Shiga, Japan).

value: LAK cell


title: goat optic nerve OS #1 1

value: left retrobulbar optic nerve


title: U251MG

source_name: spheroid derived from conventional glioma cell line

growth_protocol: T98G, U87MG, LN-18, and U251 cells were seeded onto nonadherent V-shape bottom 96-well plates (PrimeSurface 96U, MS-9096V, Sumitomo Bakelite Co., Ltd., To-kyo, Japan) in 10% FBS-supplemented DMED at a density of 2,500 to 5,000 cells/well and cultured for 3 days at 37C in a humidified atmosphere containing 5% CO2.

tag: sample type


title: Total_C2_Daniel

value: total RNA


title: NK cell

source_name: primary human NK cell

value: Primary human NK cell


title: Total_C2plusT_Daniel

source_name: Immortalized mouse embryonic fibroblast line A, Ezh2 -/-


title: goat optic nerve OS #3 1

value: left pre-chiasmatic optic nerve

value: injured


title: ACS-7

value: 63 years old


title: ACS-25

value: 70 years old


title: Control rep1

status: Public on Aug 18 2021

city: Shijiazhuang

first: Zong

middle: mao

last: Zhao

address: 215 West Heping Road

institute: The Second Hospital of Hebei Medical University

hyb_protocol: Each slide was hybridized with  1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: Non-small cell lung cancer

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: A total of 17 squamous cell carcinoma (age range, 41-76) and 23 adenocarcinoma tissues (age range, 32-71) were collected in our hospital between February 2019 and September 2019. None of the patients had received radiotherapy or chemotherapy prior to surgery. Samples were immediately frozen in liquid nitrogen and then stored at -80˚C until required for further use.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: Lung tumor tissue

value: Non-small cell lung cancer without bone metastasis


title: T98G

value: spheroid derived from conventional glioma cell line


title: The patient 2

city: Shinjuku-ku

first: Shigeki

last: Ohta

state: Tokyo

address: 6N1 35 Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University

description: Gene expression of pretreatment tumor cells

hyb_protocol: Total RNA was amplified using Ovation PicoSL WTA System V2 (NuGEN Technologies, Inc.Cat #3312-48) according to the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using SureTag DNA Labeling Kit (Agilent Technologies, Cat.5190-4240) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

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

source_name: melanoma cell

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. RNA quantity and quality were determined using a NanodropOne spectrophotometer (Thermo Fisher Scientific Inc.) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), as recommended.

treatment_protocol: Melanoma cells were digested using collagenase type IV from resected metastatic tumors and then stained with anti-CD146 antibody（Clone; P1H12）and anti-melanoma antibody (Clone; HMB45 + M2-7C10 + M2-9E3 + T311) (Abcam) to purify tumor cells.

value: LN metastasis

tag: gender

value: male


title: The patient 3

value: Subcutaneous metastasis


title: Control rep3

treatment_protocol: Samples were immediately frozen in liquid nitrogen and then stored at -80˚C until required for further use.


title: experimental rep2

value: Non-small cell lung cancer with bone metastasis


title: experimental rep3


title: Patient-derived stromal cell 1 (PDS1)

city: Okayama

first: Hotaka

last: Kawai

state: Okayama

address: Shikata

department: Oral pathology and medicine

institute: Okayama University

description: Tumor tissue was collected from tongue OSCC patient with endophytic type.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x fragmentation buffer and 10x GE blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37℃ Agilent Gene Expression Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction ver.12.0.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw data (.txt format file) was imported into GeneSpring ver.14.9, and the signal value was normalized.
Import configuration was that threshold raw signals was 1.0 and normalization algorithm was 75th percentile shift.

source_name: Patient-derived stromal cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color RNA Spike-In Kit (Agilent, #5188-5282) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN, #74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The fresh tissue specimens were obtained from two oral squamous cell carcinoma patients. The enzymatic digestion of tissue specimens by collagenase II and dispase was performed, and primary stromal cells mixed with cancer cells were separated by the difference in the adherence ability between fibroblasts and cancer cells. We named isolated stromal cells as patient-derived stromal cells (PDS1, 2). PDS1, PDS2, and HDF were grown in minimum essential medium-alpha (α-MEM) (Gibco, Life Technologies, Carlsbad, CA, USA) with 10% fetal bovine serum (FBS) (Gibco, Life Technologies, Carlsbad, CA, USA) and 1% antibiotic/antimycotic (Gibco, Life Technologies, Carlsbad, CA, USA) in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, #74104) following the manufacturer's recommendations.

tag: subject status

value: Oral squamous cell carcinoma (OSCC) patient

value: female

value: OSCC tumor tissue

value: Stromal cells


title: Adult human adult dermal fibroblast (HDF)

description: HDF cell line was purchased from Lonza Walkersville, Inc.

tag: cell line

value: HDF

value: Adult human adult dermal fibroblast


title: LN-18


title: experimental rep1


title: Control rep2


title: E04_Bl001_BAC_E04

type: genomic

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description:
Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Single blastomere WGA product (Bl001) from the embryo E04 in the pedigree BAC_E04

hyb_protocol: According to the manufacturer's protocol of Infinium HD Assay for BovineHD BeadChip arrays.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA) according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA)

data_processing:
Samples were genotyped using the BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA. The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently analysed these data with haplarithmisis adapted for bovine (Zamani Esteki et al. 2015, AJHG).
Genotypes: AA,AB,BB or NC (No Call); BAF: B-allele frequency; logR: log2ratio

organism: Bos taurus

source_name: Blastomere

label_protocol: 200 ng of gDNA and 600 ng of whole-genome amplified DNA was used as input for processing the samples according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA).

growth_protocol: Embryos were in vitro produced according to previously described methods (Catteeuw et al., 2017).

extract_protocol: Extraction of gDNA from sperm and ovarian tissue was performed using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer's protocol (sperm: user-developed protocol for purification of total DNA from animal sperm using the DNeasy® Blood & Tissue Kit; protocol 2). Single blastomere and whole-embryo DNA was whole-genome amplified using the REPLI-g SC kit (Qiagen) according to the manufacturer's instructions with full or half reaction volumes and a 3 h incubation reaction.

treatment_protocol: Single blastomeres of bovine preimplantation embryos were dissociated and whole genome amplified as described previously (Destouni et al., 2016)). Briefly, zona pellucida was removed by pronase treatment and single blastomeres were disassociated and picked individually.

value: Embryonic


title: Affected_BAC_E04

description:
WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Sibling embryo WGA product in the pedigree BAC_E04

source_name: Embryo


title: Patient-derived stromal cell 2 (PDS2)

description: Tumor tissue was collected from tongue OSCC patient with exophytic type.


title: E04_Bl003_BAC_E04

description:
Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Single blastomere WGA product (Bl003) from the embryo E04 in the pedigree BAC_E04


title: miR-150 fl/fl_LV_Sham_rep2

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

description:
MiR-150fl-Sham-2
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). Each labeled cRNA was then fragmented, and the mixture was heated at 60°C for 30min. Lastly, labeled cRNAs were loaded into gasket slides and assembled to microarray slides. The slides were then incubated for 17h at 65°C in the SureHyb Hybridization Chamber (Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: LV_Sham_4 week

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit).

extract_protocol: Total RNAs from LVs were prepared using Qiagen RNeasy Plus kit. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: age upon harvesting

value: 14 week age

tag: genotype/variation

value: miR-150 floxed/floxed [miR-150 fl/fl]

value: sham

value: left ventricles (LVs)


title: The patient 1


title: Mother_BAC_E04

description:
Genomic DNA extracted from cow ovarian tissue was genotyped using BovineHD BeadChip arrays (Illumina).
Cow gDNA in the pedigree BAC_E04

source_name: Cow ovarian tissue pedigree BAC_E04

value: Ovarian


title: E03_Bl001_Family6225

description:
Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Single blastomere WGA product (Bl001) from the embryo E03 in the pedigree Family6225


title: miR-150 fl/fl_LV_Sham_rep3

description:
MiR-150fl-Sham-3
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

tag: strain

value: 13 week age


title: miR-150 fl/fl_LV_MI_rep2

description:
MiR-150fl-Ml-2
Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

source_name: LV_MI_4 week

value: myocardial infarction [MI]


title: U87MG

value: spheroid derived from conventional glioma cell line


title: E03_Bl002_Family6225

description:
Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).
Single blastomere WGA product (Bl002) from the embryo E03 in the pedigree Family6225


title: EY006_MPP3_ERlow_ST

city: Yuseong-gu

first: Hyojung

last: Paik

state: Daejeon

address: 245 Daehak-ro

institute: KISTI

data_processing:
All of droplet-based single-cell RNA seq data are processed using the Cell Ranger Single-Cell Software Suite (version 2.0, 10xGenomics) against the Mus musculus genome (GRCm38) provided by Cell Ranger.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count mtx

source_name: Multipotent progenitor 3 ER volume low_6hr cultured_ w/ LPS and Pam3CSK4 stimulation

extract_protocol:
For bulk RNA-seq, cells (5,000 to 7,000 per sample) were directly sorted into 350 μl RLT lysis buffer containing 1% b-mercaptoethanol from the RNeasy Plus Micro Kit (Qiagen, 74034) and RNA was isolated according to the manufacturer’s instructions.
For bulk RNA-seq, libraries were prepared using Trio RNA-seq Library Preparation Kit (NuGen, 0507) and for single cell RNA-seq, libraries were prepared using a Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics).

value: Bone marrow

value: 6hr cultured_LPS (100 ng/ml) and Pam3CSK4 (1 μl/ml) stimulation

tag: sequencing method

value: droplet-based sing-cell RNA seq (10X Genomics, Illumina Hiseq 4000)


title: EY007_MPP3_ERhigh_US

source_name: Multipotent progenitor 3 ER volume high_6hr cultured_ w/o LPS and Pam3CSK4 stimulation

tag: treatment

value: 6hr cultured


title: EY008_MPP3_ERhigh_ST

source_name: Multipotent progenitor 3 ER volume high_6hr cultured_ w/ LPS and Pam3CSK4 stimulation


title: EY002_MPP3ST

source_name: Multipotent progenitor 3_6hr cultured_ w/ LPS and Pam3CSK4 stimulation


title: EY004_MPP3BA

source_name: Multipotent progenitor 3_Scl-tTA:TRE-BCR/ABL_freshly isolated

value: untreated


title: EY001_MPP3US

source_name: Multipotent progenitor 3_6hr cultured_ w/o LPS and Pam3CSK4 stimulation


title: EY003_MPP3Control

source_name: Multipotent progenitor 3_Control_freshly isolated

value: Scl-tTA, TRE-BCR/ABL, or WT C57BL/6