title: mrWT, biological replicate 1

source_name: 769-P cells transduced with the rescue of the canonical form of STAT3 cloned in pLX304-blast vector

value: Normal activity of STAT3


title: cf-s-6-1

status: Public on Nov 15 2023

type: SRA

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

country: China

institute: School of Medicine, Southeast University

library_source: transcriptomic

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
Slam-seq:The flow ofslamdunkis to first map your reads, filter your alignments, call variants on your final alignments and use these to calculate conversion rates, counts and various statistics for your 3’UTRs.
Slam-seq:SLAM-DUNK was used to  map reads, filter   alignments, call variants on  final alignments and use these to calculate conversion rates, counts and various statistics for 3’UTRs.Extract and summarize the count results of tcount files into a count table.
Slam-seq:Differential gene expression analysis was performed using the DESeq2 R-package.
Slam-seq:GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
Assembly: mm10
Supplementary files format and content: TcReadfpkm.xls
Library strategy: Slam-seq

molecule: total RNA

organism: Mus musculus

source_name: primary neonatal mouse fibroblasts

extract_protocol:
Pulse labeling: Seed cells the day before the labelling experiment in a density that allows exponential growth for the duration of the experiment.Pulse/chase labeling: After pulse labeling, remove s4U -containing media from the cells.  IAA treatment (Protect samples from light) .
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: primary neonatal mouse fibroblasts

tag: treatment


title: CNS-tumor_pediatric-LGG_64487

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: CNS tumor

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from fresh frozen or FFPE tumor samples was carried out using the Maxwell RSC Tissue DNA kit or the Maxwell RSC DNA FFPE kit, respectively.

tag: Sex

value: Male

tag: age

tag: location

value: hemispheric, cortical

tag: tumor subgroup

value: low grade glioma

tag: tissue

value: CNS tumor


title: SA, biological replicate 1

type: RNA

city: Barcelona

first: Anna

last: Meseguer

address: Paseo Vall d'Hebron 119-129

country: Spain

institute: VHIR

description: Gene expression data from cells overexpressing STAT3 carrying the p.Ser727Ala mutation

hyb_protocol: Following fragmentation, 5,5ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Clariom S human array plate. Array plate was washed and stained in the Affymetrix GeneTitan MultiChannel System

scan_protocol: Array plate was scanned using the Gene Titan MultiChannel System

data_processing: Raw expression values were obtained directly from .CEL files and were processed using the RMA method in oligo R package to get normalized expression values (log2 scale) summarized at the gene level.  Different quality checks (boxplots, hierarchical clustering and principal component analyses (PCAs)) were performed before and after normalization to ensure that samples were suitable for differential expression analysis. A complete quality report was obtained using arrayQualityMetrics R package. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis.  P-values are adjusted to obtain strong control over the false discovery rate using the Benjamini and Hochberg method. Statistical language R (version 3.6.0) and Bioconductor associated packages were used to process and analyze the data.

label: biotin

source_name: 769-P cells transduced with the rescue STAT3 vector with the phosphoablative mutation p.Ser727Ala (c.2179T>G)

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 200 ng total RNA (GeneChip WT Plus Kit Manual Workflow, user guide).

growth_protocol: Human-derived ccRCC cell lines 769-P (CRL-1933), as well as lentiviruses producer HEK293T/17 (CRL-11268) cell line were cultured in Dulbecco’s Modified Eagle Medium medium supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate [100 mM], 1% antibiotic/antimycotic, and 0.2% plasmocin at 37°C with 5% CO2. Culture medium was also supplemented with antibiotics puromycin and blasticidin to select and maintain cell lines transduced with silencing and overexpression vectors, respectively.

extract_protocol: Total RNA was isolated using TRIzol reagent, following the supplier’s instructions

treatment_protocol: Cells were treated with 10 ng/ml IL6 for 48 h and then RNA was isolated as indicated below

tag: phenotype

value: Ser727 cannot be phosphorylated, free Tyr705


title: RAM015_Prox_Tubules_replicate1

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

country: USA

institute: University of Washington

description: 2023-DSP-SLU-006-RAM015 - 003.png

library_source: other

data_processing:
Illumina BaseSpace FASTQ Generation 2022-02-08 18:10:56Z
Nanostring GeoMx NGS Pipeline Version 2.3.3.10
Assembly: Not applicable, sequences mapped to Nanostring directory of probe-gene associations
Supplementary files format and content: .dcc, digital count files for input into GeoMx DSP. Each .dcc file represents counts from one region of interest (ROI)
Supplementary files format and content: ROI reports.zip: zip file containing .pngs for each ROI, a .png overview of the entire slide and an .html file for navigation. There is one ROI report.zip file for each slide scanned in the experiment
Library strategy: Nanostring GeoMx DSP readout

molecule: other

source_name: Kidney

growth_protocol: Not applicable

extract_protocol:
Nanostring pretreatment for GeoMx DSP = HIER + proteinase K 1µg/ml
Nanostring GeoMx DSP SeqCode A
(2x27bp with standard 8bp indexes)

treatment_protocol: Not applicable

value: Kidney

tag: donor id

tag: roi histology

tag: geomx dsp_probe_set

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: cf-s-24-2


title: RAM015_Glomerulus_replicate2

description: 2023-DSP-SLU-006-RAM015 - 002.png

value: Glomerulus


title: CNS-tumor_pediatric-LGG_57304

value: supratentorial, midline


title: cf-s-24-1


title: RAM015_Glomerulus_replicate1

description: 2023-DSP-SLU-006-RAM015 - 001.png


title: WholeRoot_625µMP_0d_rep2 [sP0d.2]

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

institute: IPK Gatersleben

description: Gene expression after 0 days of 625 µM posphate treatment

hyb_protocol: RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 021169_D_F_20140929) to obtain background subtracted and spatially detrended Processed Signal intensities. Analysis of microarray data was performed with the R package limma. Raw feature intensities were background corrected using “normexp”, and “quantile” normalization method was used to normalize between arrays.

organism: Arabidopsis thaliana

source_name: Whole root, 625 µM P, 0 days, replicate 2

growth_protocol: Seeds of Arabidopsis thaliana (Columbia-0, CS60000) were surface sterilized in 70% (v/v) ethanol and 0.05% (v/v) Triton X-100. Seedlings were first germinated for seven days on agar plates containing 0.5% (w/v) sucrose and 1% (w/v) agar before seedlings of similar sizes were transferred to treatments containing identical sucrose and agar concentrations. The nutrient composition was half-strenght Murashige and Skoog and Difco agar (Becton Dickinson; cat. number 214541;) was used as gelling agent. In the preculture, 625 µM P was supplied as KH2PO4. In treatment plates, the solid half-strength MS medium contained 625 µM P (sufficient P) or 100 µM P (deficient P), with 525 µM K being supplied as KCl. Each treatment plate contained 10 seven-day-old seedling. Each replicate was composed of 5 plates containing 10 seven-day-old seedling each (i.e., 50 plants pooled as one replicate). Agar plates were sealed with Leukopor tape (Smith & Nephew) and placed vertically in a randomized block design within a growth cabinet (Percival Scientific) with 22°C day and 19°C night temperatures and a 10-h light period with a light intensity of 120 µmol photons m-2 s-1.

extract_protocol: RNA was extracted from whole roots (roots of 50 plants pooled togeher to form one replicate) using an RNeasy plant mini kit (Qiagen) with on-column DNase treatment according to the manufacturer’s instructions. cDNA was prepared using  random hexamer primers and SuperScript II reverse transcriptase (Life Technologies)  according to the manufacturer’s protocol.

treatment_protocol: Seven-day-old seedlings precultured on sufficient phosphorus were transferred to fresh solid half-strength Murashige and Skoog medium containing 625 µM KH2PO4 (sufficient P) or 100 µM KH2PO4 (deficient P). The missing potassium in the P-deficient medium was supplied as  KCl.

value: whole root

value: 625 µM P

tag: time after treatment

value: 0 days


title: CNS-tumor_pediatric-LGG_18320

value: Female


title: cf-s-18-2


title: RAM013_Outer_medulla_inner_stripe_replicate1

description: 2023-DSP-SLU-006-RAM013 - 009.png


title: CNS-tumor_pediatric-LGG_10826

value: infratentorial


title: pLKO, biological replicate 1

description: Gene expression data from cells used as a control of silencing

source_name: 769-P cells transduced with the empty pLKO.1-puro vector

value: Normal expression of endogenous STAT3


title: CNS-tumor_pediatric-LGG_32475


title: CNS-tumor_pediatric-LGG_53271


title: cf-s-18-1


title: cf-s-12-2


title: RAM013_Distal_Tubules_replicate1

description: 2023-DSP-SLU-006-RAM013 - 005.png


title: RAM013_Prox_Tubules_replicate2

description: 2023-DSP-SLU-006-RAM013 - 004.png


title: RAM013_Distal_Tubules_replicate2

description: 2023-DSP-SLU-006-RAM013 - 006.png


title: RAM013_Glomerulus_replicate2

description: 2023-DSP-SLU-006-RAM013 - 002.png


title: RAM013_Prox_Tubules_replicate1

description: 2023-DSP-SLU-006-RAM013 - 003.png


title: cf-s-0-2


title: RAM013_Glomerulus_replicate1

description: 2023-DSP-SLU-006-RAM013 - 001.png


title: RAM012_Outer_medulla_inner_stripe_replicate2

description: 2023-DSP-SLU-006-RAM012 - 012.png


title: cf-s-0-1


title: RAM012_Outer_medulla_outer_stripe_replicate2

description: 2023-DSP-SLU-006-RAM012 - 010.png


title: RAM013_Outer_medulla_inner_stripe_replicate2

description: 2023-DSP-SLU-006-RAM013 - 010.png


title: CNS-tumor_pediatric-LGG_46313


title: RAM012_Outer_medulla_inner_stripe_replicate1

description: 2023-DSP-SLU-006-RAM012 - 011.png


title: RAM013_Outer_medulla_outer_stripe_replicate2

description: 2023-DSP-SLU-006-RAM013 - 008.png


title: RAM012_Medullary_ray_replicate2

description: 2023-DSP-SLU-006-RAM012 - 008.png


title: RAM012_Outer_medulla_outer_stripe_replicate1

description: 2023-DSP-SLU-006-RAM012 - 009.png


title: CNS-tumor_pediatric-LGG_78245


title: cf-A-6-2


title: RAM012_Medullary_ray_replicate1

description: 2023-DSP-SLU-006-RAM012 - 007.png


title: RAM013_Outer_medulla_outer_stripe_replicate1

description: 2023-DSP-SLU-006-RAM013 - 007.png


title: cf-A-6-1


title: cf-s-12-1


title: RAM012_Distal_Tubules_replicate2

description: 2023-DSP-SLU-006-RAM012 - 006.png


title: CNS-tumor_pediatric-LGG_17885


title: RAM012_Prox_Tubules_replicate2

description: 2023-DSP-SLU-006-RAM012 - 004.png


title: RAM012_Prox_Tubules_replicate1

description: 2023-DSP-SLU-006-RAM012 - 003.png


title: cf-A-24-2


title: RAM012_Distal_Tubules_replicate1

description: 2023-DSP-SLU-006-RAM012 - 005.png


title: cf-A-24-1


title: RAM012_Glomerulus_replicate2

description: 2023-DSP-SLU-006-RAM012 - 002.png


title: CNS-tumor_pediatric-LGG_28057


title: CNS-tumor_pediatric-LGG_59607


title: RAM012_Glomerulus_replicate1

description: 2023-DSP-SLU-006-RAM012 - 001.png


title: biventricular heart, CON, ZT08, biol rep 2

city: Birmingham

first: Lamario

middle: J

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using bcl2fastq v2.18.12 for NextSeq output.
Raw FASTQ files were uploaded to Qiagen's GeneGlobe website for their default microRNA analysis and differential expression analysis.
Assembly: mm10
Supplementary files format and content: raw UMIs values for each microRNA in each sample

source_name: biventricular heart

extract_protocol:
RNA was harvested using miRNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Small RNA sequencing libraries were prepared using the QIAseq miRNA library kit.

tag: strain

value: male

value: biventricular heart

tag: genotype

value: CON

tag: time


title: cf-A-18-2

value: primary neonatal mouse fibroblasts


title: biventricular heart, CON, ZT04, biol rep 2


title: CNS-tumor_pediatric-LGG_98661

value: low grade glioma


title: CNS-tumor_pediatric-LGG_32314

value: Male

value: CNS tumor


title: CNS-tumor_pediatric-LGG_62911


title: cf-A-18-1


title: biventricular heart, CBK, ZT12, biol rep 1

value: CBK


title: cf-A-12-2


title: cf-A-12-1


title: biventricular heart, CBK, ZT08, biol rep 4


title: No Template Control

value: Kidney

value: Not applicable

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: CNS-tumor_pediatric-LGG_86570


title: CNS-tumor_pediatric-LGG_35816

value: hemispheric, cortical


title: biventricular heart, CON, ZT12, biol rep 3


title: CNS-tumor_pediatric-LGG_62041


title: cf-A-0-2


title: CNS-tumor_pediatric-LGG_94136


title: biventricular heart, CON, ZT12, biol rep 2


title: CNS-tumor_pediatric-LGG_14328


title: biventricular heart, CON, ZT12, biol rep 4


title: cf-A-0-1


title: biventricular heart, CON, ZT08, biol rep 1


title: sgNTC_4_day7

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST Array. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: sgNTC OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were sort-purified in the sgRNA transduced OT-I cells from B16-OVA tumors 7 days after adoptive transfer

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: transduced with

value: sgNTC


title: CNS-tumor_pediatric-LGG_93441

value: supratentorial, midline


title: Asp+Pep, c57b6l mice,repeated1 [S8_1_S]

city: Shanghai

first: chen

last: xingxing

address: nanchen road 381

institute: Shanghai University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequences reads were mapped to mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchworl
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delinited text files include FPKM values for each Sample

source_name: leg muscles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1 µg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: leg muscles

tag: mouse model

value: hindlimb suspension ischemia

value: WT

value: peptide hydrogel combined with aspirin


title: biventricular heart, CON, ZT08, biol rep 4

value: male

value: biventricular heart


title: CNS-tumor_pediatric-LGG_27455


title: Asp+Pep, c57b6l mice,repeated2 [S8_3_S]


title: sgIrf1_4_day7

source_name: sgIrf1 OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer

tag: cell type


title: CNS-tumor_pediatric-LGG_21652

value: Female

value: infratentorial


title: sgNTC_3_day7

value: OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer


title: Asp+Pep, c57b6l mice,repeated3 [S8_5_S]

tag: treatment


title: sgIrf1_3_day7


title: CNS-tumor_pediatric-LGG_52504

tag: Sex

value: low grade glioma

value: CNS tumor


title: biventricular heart, CBK, ZT16, biol rep 1

value: CBK


title: Asp, c57b6l mice,repeated3 [S10_4_S]

value: aspirin


title: Asp, c57b6l mice,repeated2 [S7_3_S]


title: CNS-tumor_pediatric-LGG_60840

value: Male

tag: age


title: biventricular heart, CBK, ZT12, biol rep 4


title: Asp, c57b6l mice,repeated1 [S7_1_S]


title: CNS-tumor_pediatric-LGG_63003

tag: location


title: biventricular heart, CBK, ZT12, biol rep 3


title: sgNTC_1_day7


title: Control, c57b6l mice,repeated3 [S9_5_S]

value: untreated


title: sgIrf1_2_day7


title: sgIrf1_1_day7


title: CNS-tumor_pediatric-LGG_73731

tag: tumor subgroup


title: sgRbpj+ sgIrf1_3_day 7

source_name: sgRbpj+ sgIrf1 OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer

value: sgRbpj+ sgIrf1


title: sgNTC_2_day7

value: sgNTC


title: biventricular heart, CBK, ZT04, biol rep 1

tag: tissue


title: CNS-tumor_pediatric-LGG_73721


title: CNS-tumor_pediatric-LGG_98678

value: hemispheric, cortical


title: biventricular heart, CBK, ZT08, biol rep 1


title: biventricular heart, CBK, ZT16, biol rep 4


title: sgRbpj+ sgIrf1_1_day 7


title: Control, c57b6l mice,repeated1 [S9_2_S]

value: leg muscles

value: hindlimb suspension ischemia


title: sgRbpj+ sgIrf1_2_day 7


title: biventricular heart, CON, ZT04, biol rep 1

value: CON


title: biventricular heart, CON, ZT04, biol rep 4

value: male


title: 6-months-old c57b6l mice,repeated3

first: fei

last: sun

state: Shanghai

address: Laboratory of Biotechnology, School of Life Science, Baoshan Campus, Shanghai University, Dachang Town, Baoshan District, Shanghai

source_name: aorta

value: aorta

value: WT

value: 6 months-old


title: CNS-tumor_pediatric-LGG_80652

value: supratentorial, midline


title: cm-A-6-2

source_name: Primary neonatal mouse cardiomyocytes

value: Primary neonatal mouse cardiomyocytes


title: CNS-tumor_pediatric-LGG_42033

value: low grade glioma

value: CNS tumor


title: 6-months-old c57b6l mice,repeated2


title: biventricular heart, CBK, ZT08, biol rep 3

value: biventricular heart

value: CBK


title: 6-months-old c57b6l mice,repeated1


title: biventricular heart, CON, ZT08, biol rep 3


title: CNS-tumor_pediatric-LGG_56290

value: Female

value: infratentorial


title: sgRbpj_4_day 7

source_name: sgRbpj OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer

value: sgRbpj


title: sgRbpj_3_day 7

value: OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer


title: 6-weeks-old c57b6l mice,repeated3

value: 6 weeks-old


title: Wild type mouse lung BAL, HTO-derived DNA

city: New Orleans

first: Guoshun

last: Wang

state: LA

address: 533 Bolivar Street

department: Microbiology, Immunology and Parasitology

institute: Louisiana State University Health Sciences Center

description: 10x Genomics

data_processing:
10x Cellranger V.6.0.0 were used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting and aggregation.
Seurat v4.2.1 for scRNA QC and further analysis
Assembly: mm10-2020-A
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

molecule: protein

source_name: Lung

extract_protocol:
mRNA was extracted from mouse BAL single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and hashtag antibody-derived oligos (HTO) were reverse-transcribed and indexed with a shared cellular barcode. mRNA derived cDNA and HTO DNA were constructed to libraries according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics). mRNA derived cDNA library and HTO library were pooled and sequenced at 4:1 ratio.

value: Lung

value: Lung BAL

value: Wild type mouse

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI:d1/TotalSeq-B0301; d3/TotalSeq-B0302; d5/TotalSeq-B0303


title: Control, c57b6l mice,repeated2 [S9_4_S]

value: leg muscles

value: hindlimb suspension ischemia

value: WT

value: untreated


title: Mac-CF mouse lung BAL, HTO-derived DNA

description: 10x Genomics

value: Mac-CF mouse


title: 6-weeks-old c57b6l mice,repeated2

value: aorta


title: biventricular heart, CBK, ZT20, biol rep 2

value: male

value: biventricular heart

value: CBK


title: biventricular heart, CON, ZT20, biol rep 4

value: CON


title: Wild type mouse lung BAL, mRNA-derived cDNA

description: 10x Genomics

library_source: transcriptomic single cell

value: mRNA


title: sgRbpj_2_day 7

value: OT-I TILs isolated from B16-OVA tumors 7 days after adoptive transfer

value: sgRbpj


title: CNS-tumor_pediatric-LGG_87168

value: Female

value: infratentorial

value: low grade glioma

value: CNS tumor


title: rpoS complement in strain HKE9-M-rpoS, rep3

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

institute: Xi'an Jiaotong University

description:
Biological replicate 3 of 3 K. pneumoniae strain HKE9-C-M-rpoS in LB medium, 12h culture cells
HKE9-C-M-rpoS3

data_processing:
Transcriptome sequencing was performed at Novaseq 6000 in Gene Denovo Co. Ltd. Quality trimmed reads were mapped to the HKE9 using Bowtie2 (version 2.2.8), reads mapped to ribosome RNA were removed. Retained reads were aligned with reference genome to identify known genes and calculated gene expression by RSEM. To evaluate reproducibility between samples, the correlation coefficient among replicas was calculated. Values closer to one indicated better reproducibility.
Principle component analysis (PCA) was performed with the R package gmodels (http://www.r-project.org) to reveal the relationship between samples. The gene expression level was further normalized by using the fragments per kilobase of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression. The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05. DEGs were then subjected to an enrichment analysis of GO functions (http://www.geneontology.org) and KEGG pathways (http://www.genome.jp/kegg), and q values < 0.05 were using as threshold.
Assembly: CP089768（Klebsiella pneumoniae HKE9）
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Klebsiella pneumoniae

extract_protocol:
A fresh culture of HKE9, HKE9-M-rpoS, and HKE9-C-M- rpoS strains were grown to OD600 of 0.6. Total RNA was extracted using RNAprotect Bacteria Reagent and RNeasy minikit (Qiagen, DE). RNA quality was monitored on 1% agarose gels. RNA purity (OD260/OD280, OD260/OD230) was checked using the NanoPhotometer® spectrophotometer (Implen, USA). RNA integrity was measured using Bioanalyzer 2100 (Agilent, CA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: gene rpoS complement

value: ESBL-HvKP


title: rpoS complement in strain HKE9-M-rpoS, rep2

description:
Biological replicate 2 of 3 K. pneumoniae strain HKE9-C-M-rpoS in LB medium, 12h culture cells
HKE9-C-M-rpoS2


title: CNS-tumor_pediatric-LGG_72513

value: supratentorial, midline


title: CNS-tumor_pediatric-LGG_43926

value: hemispheric, cortical


title: CNS-tumor_pediatric-LGG_57937

value: Male


title: biventricular heart, CON, ZT20, biol rep 1


title: biventricular heart, CBK, ZT16, biol rep 2


title: biventricular heart, CBK, ZT20, biol rep 1


title: Mac-CF mouse lung BAL, mRNA-derived cDNA

description: 10x Genomics

value: Lung

value: Lung BAL

value: Mac-CF mouse


title: sgRbpj_1_day 7


title: rpoS complement in strain HKE9-M-rpoS, rep1

description:
Biological replicate 1 of 3 K. pneumoniae strain HKE9-C-M-rpoS in LB medium, 12h culture cells
HKE9-C-M-rpoS1


title: biventricular heart, CON, ZT16, biol rep 1

value: male

value: biventricular heart


title: CNS-tumor_pediatric-LGG_726


title: rpoS knockout strain HKE9-M-rpoS in hypervirulent K. pneumoniae strain HKE9, rep3

description:
Biological replicate 3 of 3 K. pneumoniae strain HKE9-M-rpoS in LB medium, 12h culture cells
HKE9-M-rpoS3

value: gene rpoS knock out


title: CNS-tumor_pediatric-LGG_36718


title: MIN6_shNT_2_batch2

city: Cleveland

first: Sisi

last: Lai

state: Ohio

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
RNA-seq reads were filtered for quality and trimmed for adaptor sequences.
Reads were alighed to reference genome assembly for mouse (mm10) and human (hg19) using HISAT2 with default parameters.
Read count tables were generated with FeatureCounts.
Normalized and differential expression analysis was performed with DESeq2.
Assembly: mm10 and hg19
Supplementary files format and content: Tab-delimited text file with normalized read couns over all genes.

molecule: polyA RNA

growth_protocol: MIN6 cells were cultured in high glucose DMEM with 10% heat-inactivated Fetal Bovine Serum (Gibco), 2 mM GlutMAX (Gibco), 1 mM sodium pyruvate, 50 μM β-mercaptoethanol. EndoC-βH3 were cultured in DMEM containing 5.6 mM glucose, 2% fatty acid free BSA fraction V, 10 mM nicotinamide, 5.5 mg/ml transferrin, 6.7 ng/ml sodium selenite, Penicillin (100 units/ml)/ Streptomycin (100 mg/ml). Cells were passaged and seeded onto matrigel- and fibronectin- coated cell culture dishes.

extract_protocol:
Trizol used to extract RNA from MIN6 cells. Quick-RNA™ Microprep Kit used for EndoC-bH3 RNA extraction.
Illumina TruSeq stranded mRNA kit for MIN6. mRNA-seq Lib Prep Kit (ABclonal) used for EndoC-bH3 cells.

tag: cell line

value: shNT


title: rpoS knockout strain HKE9-M-rpoS in hypervirulent K. pneumoniae strain HKE9, rep2

description:
Biological replicate 2 of 3 K. pneumoniae strain HKE9-M-rpoS in LB medium, 12h culture cells
HKE9-M-rpoS2


title: 6-weeks-old c57b6l mice,repeated1

value: aorta

value: WT

value: 6 weeks-old


title: MIN6_shNT_774_batch3


title: CNS-tumor_pediatric-LGG_74559

value: low grade glioma


title: MIN6_shPdia6#3_774_batch3


title: MIN6_shPdia6#2_2_batch2


title: MIN6_shNT_1_batch1


title: rpoS knockout strain HKE9-M-rpoS in hypervirulent K. pneumoniae strain HKE9, rep1

description:
Biological replicate 1 of 3 K. pneumoniae strain HKE9-M-rpoS in LB medium, 12h culture cells
HKE9-M-rpoS1


title: biventricular heart, CON, ZT00, biol rep 3

value: CON


title: CNS-tumor_pediatric-LGG_13911

value: infratentorial

value: CNS tumor


title: CNS-tumor_pediatric-LGG_87207


title: MIN6_shPdia6#1_1_batch1


title: hypervirulent K. pneumoniae strain HKE9,rep3

description:
Biological replicate 3 of 3 K. pneumoniae strain HKE9 in LB medium, 12h culture cells
HKE9-3

value: wild type

value: ESBL-HvKP


title: biventricular heart, CON, ZT00, biol rep 1


title: CNS-tumor_pediatric-LGG_37648

value: Male

value: hemispheric, cortical


title: biventricular heart, CBK, ZT00, biol rep 4

value: CBK


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0007]

city: Nashville

first: Jonathan

middle: A

last: Kropski

institute: Vanderbilt University Medical Center

data_processing:
Parse_pipeline
MORE DETAILES REQUESTED
Assembly: mm10
Supplementary files format and content: DGE_filtered

source_name: lung

extract_protocol:
Single-cell suspensions were generated from lung dissue with a collagenase/dispase digest.
Parse Evercode

value: lung

tag: strain background

value: WT or Ytdel

value: saline or IT Bleo


title: CNS-tumor_pediatric-LGG_97607


title: hypervirulent K. pneumoniae strain HKE9,rep1

description:
Biological replicate 1 of 3 K. pneumoniae strain HKE9 in LB medium, 12h culture cells
HKE9-1


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0008]


title: biventricular heart, CBK, ZT04, biol rep 4

value: male

value: biventricular heart


title: CNS-tumor_pediatric-LGG_78221


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0006]


title: hypervirulent K. pneumoniae strain HKE9,rep2

description:
Biological replicate 2 of 3 K. pneumoniae strain HKE9 in LB medium, 12h culture cells
HKE9-2


title: biventricular heart, CON, ZT00, biol rep 4


title: biventricular heart, CON, ZT00, biol rep 2


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0005]


title: mub1Δ, rep3

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). CGD Gene Ontology Term Finder (http://www.candidagenome.org/cgi-bin/GO/goTermFinder).
Assembly: C. auris B8441 (GCA_002759435.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Candidozyma auris

extract_protocol:
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)

value: Untreated


title: CNS-tumor_pediatric-LGG_33328


title: mub1Δ, rep2


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0003]


title: biventricular heart, CBK, ZT00, biol rep 3


title: biventricular heart, CBK, ZT20, biol rep 4


title: CNS-tumor_pediatric-LGG_54806

value: Female


title: mub1Δ, rep1


title: biventricular heart, CON, ZT20, biol rep 3


title: ubr2Δ, rep3


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0002]


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0004]


title: biventricular heart, CON, ZT20, biol rep 2


title: ubr2Δ, rep2


title: WT_Ytdel_saline_Bleo mixed sample [9301-CT-0001]


title: CNS-tumor_pediatric-LGG_28779

value: supratentorial, midline


title: biventricular heart, CON, ZT16, biol rep 2


title: biventricular heart, CBK, ZT20, biol rep 3


title: ubr2Δ, rep1


title: CNS-tumor_pediatric-LGG_80372

value: low grade glioma


title: CNS-tumor_pediatric-LGG_96907


title: TMEM WT GRN WT SAM24407694

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
GSNAP was used to align reads to GRCm38.
The HTSeqGenie Bioconductor package was used to count genes.
Gene models were obtained from an internal database.
Assembly: GRCm38
Supplementary files format and content: Tab-delimeted text files with raw counts, width, and rpkm normalized values for each gene.

source_name: Microglia

extract_protocol:
RNA was extracted from the cell pellet using the RNeasy Plus Micro Kit (Qiagen).
Smart-Seq V4 Ultra Low Input RNA Kit (Takara) and Nextera XT DNA Sample Preparation Kit (Illumina)

value: TMEM WT GRN WT

value: Microglia

value: F

tag: dissection

value: Hemi


title: TMEM WT GRN HET SAM24407692

value: TMEM WT GRN HET

value: M


title: TMEM WT GRN WT SAM24407693

value: Entire


title: biventricular heart, CON, ZT12, biol rep 1

tag: strain

value: CON


title: WT, rep2

source_name: WT

value: WT

tag: genotype


title: CNS-tumor_pediatric-LGG_47015

source_name: CNS tumor

value: CNS tumor


title: CNS-tumor_pediatric-LGG_78102

value: infratentorial


title: CNS-tumor_pediatric-LGG_55399

value: Male


title: CNS-tumor_pediatric-LGG_63778

value: hemispheric, cortical


title: TMEM WT GRN HET SAM24407691


title: biventricular heart, CBK, ZT00, biol rep 2

value: male

value: biventricular heart

value: CBK

tag: time


title: BEAS-2B cells,PM2.5 (12.5 μg/mL)+H3N2 (MOI=1),4+24h,rep2 [PM25H3N22]

city: XinXiang

first: WeiDong

last: Wu

address: JinSuiStreet

institute: XinXiangMedicalUniversity

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
After the counts are obtained from the comparison, the protein coding genes need to be filtered to remove the genes with zero reads.
Then clean reads for each sample were retained for subsequent analyses.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: counts.xsl file include counts of each sample
Supplementary files format and content: FPKM.xsl file include FPKM of each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

value: lung

value: bronchial epithelium


title: BEAS-2B cells,PM2.5 (12.5 μg/mL)+H3N2 (MOI=1),4+24h,rep3 [PM25H3N23]


title: CNS-tumor_pediatric-LGG_82532

value: Female

value: supratentorial, midline

value: low grade glioma


title: biventricular heart, CBK, ZT00, biol rep 1


title: TMEM WT GRN HET SAM24407689

value: TMEM WT GRN HET

value: Microglia

value: F

value: Hemi


title: BEAS-2B cells,PM2.5 (12.5 μg/mL)+H3N2 (MOI=1),4+24h,rep1 [PM25H3N21]


title: CNS-tumor_pediatric-LGG_14971


title: BEAS-2B cells,serum-free medium+H3N2 (MOI=1),4+24h,rep3 [H3N23]

value: serum-free medium+H3N2 (MOI=1),4+24h


title: biventricular heart, CBK, ZT08, biol rep 2


title: TMEM WT GRN KO SAM24407687

value: TMEM WT GRN KO

value: Entire


title: biventricular heart, CBK, ZT04, biol rep 3


title: CNS-tumor_pediatric-LGG_24971

value: infratentorial

value: CNS tumor


title: biventricular heart, CBK, ZT04, biol rep 2

value: male


title: BEAS-2B cells,serum-free medium+H3N2 (MOI=1),4+24h,rep2 [H3N22]


title: BEAS-2B cells,serum-free medium+H3N2 (MOI=1),4+24h,rep1 [H3N21]


title: TMEM WT GRN KO SAM24407686


title: CNS-tumor_pediatric-LGG_82549


title: TMEM WT GRN HET SAM24407690


title: BEAS-2B cells,PM2.5 (12.5 μg/mL),28h,rep3 [PM253]


title: TMEM WT GRN KO SAM24407684


title: TMEM WT GRN HET SAM24407688


title: biventricular heart, CBK, ZT16, biol rep 3

value: biventricular heart


title: biventricular heart, CON, ZT16, biol rep 4

value: CON


title: TMEM WT GRN KO SAM24407683

value: M


title: CNS-tumor_pediatric-LGG_28


title: CNS-tumor_pediatric-LGG_83370

value: hemispheric, cortical


title: CNS-tumor_pediatric-LGG_50581

value: Female


title: BEAS-2B cells,PM2.5 (12.5 μg/mL),28h,rep2 [PM252]

value: lung

value: bronchial epithelium


title: biventricular heart, CON, ZT16, biol rep 3


title: TMEM HET GRN WT SAM24407682

value: TMEM HET GRN WT


title: TMEM HET GRN WT SAM24407680

value: Microglia


title: CNS-tumor_pediatric-LGG_7428

value: Male

value: low grade glioma


title: TMEM HET GRN HET SAM24407677

value: TMEM HET GRN HET


title: TMEM HET GRN WT SAM24407681

value: Hemi


title: BEAS-2B cells,serum-free medium,28h,rep2 [MOCK2]

value: serum-free medium,28h


title: bovine fetal testis (mixed samples)

city: Davis

first: Maci

last: Mueller

state: CA

address: One Shields Ave

department: Animal Sciences

institute: University of California, Davis

description:
90d KO bovine testis, sample_1
90d KO bovine testis, sample2
90d ctrl bovine testis, sample_3
90d ctrl bovine testis, sample_4
280d KO bovine testis, sample_5
280d ctrl bovine testis, sample_6
README.tsv
DGE.mtx
all_genes.csv
cell_metadata.csv
sample_well_IDs.tsv
metadata_6samples.xlsx

data_processing:
Sequences were aligned to the bovine reference genome (ARS-UCD1.2-Ensembl version 105) and demultiplexed using the ParseBiosciences pipeline (v0.9.6p) at default settings for each individual sublibrary using the `split-pipe --mode all` and `--samp_list sample-list.txt` to demultiplex the samples (sample/well-ID pairs are noted in the file `sample_well_IDs.tsv`); the output of the eight sublibraries was then combined using `split-pipe --mode combine`.
Downstream analysis was performed using the R package Seurat (v4.1.0) as described in the methods section of the corresponding manuscript.
Assembly: bosTau9
Supplementary files format and content: all_genes.csv, cell_metadata.csv, and DGE.mtx represent the output of the Parse Biosciences pipeline after combining the output of all eight sublibraries and can be imported into Seurat.
Supplementary files format and content: sample_well_Ids.tsv indicates the well-sample combinations for library generation.

organism: Bos taurus

source_name: testis

extract_protocol:
Testis tissue was dissociated using a two-step enzymatic digestion with collagenase-IV and trypsin-EDTA.
Single cell samples were processed using the cell fixation (SB1001) and single-cell whole-transcriptome (SB2001) kits from Parse Biosciences (Seattle, WA). This scRNA-Seq approach is based on combinatorial barcoding, which enables multiplexing of samples.

treatment_protocol: The bovine testes samples were collected from fetuses derived from CRIPSR/Cas9 NANOS3 knockout (NANOS3 -/-) or wildtype control (NANOS3 +/+) embryos.

value: testis

value: 90 days or 280 days of  fetal  age

value: NANOS3 -/- or NANOS3 +/+


title: CNS-tumor_pediatric-LGG_87682

value: supratentorial, midline

value: CNS tumor


title: TMEM HET GRN WT SAM24407678

value: F

value: Entire


title: CNS-tumor_pediatric-LGG_61835

value: hemispheric, cortical


title: Output3

first: Mireia

last: Seuma

state: Barcelona

address: Carrer de Baldiri Reixac, 10, 12

institute: Institute for Bioengineering of Catalonia

description: PCR DNA amplicon from plasmid library

data_processing:
FastQ files from paired-end sequencing of the Aß42 library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Supplementary files format and content: Spreadsheet file with columns indicating aa_seq = amino acid sequence, ID= Fingerprint mutation identifier, lib= Query mutation identifier, mut_type= Mutation type, mean_count= mean read count of the input replicates, nscore[1,2,3]_c= Nucleation score for [1,2,3] replicates, nscore_c= Merged nucleation score centered to WT Abeta 42, sigma= Merged error over nucleation score, fAD= Associated pathogenicity of query mutation
Library strategy: DNA-seq

organism: Saccharomyces cerevisiae

source_name: single cell eukaryotic microorganism

growth_protocol: Yeast cells were transformed in 3 biological replicas (1,2,3) with a Aβ42 synthetic plasmid library with 10,000 unique nucleotide sequences. A minimum of 380,000 yeast transformants were used for each replicate to ensure the coverage of the full library and reaching therefore a >38x coverage of each variant. Once the culture reached the exponential phase, cells were resuspended in 200mL protein inducing medium (-URA, 20% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed for each biological replica. After 24h 25ml input pellets were collected and stored at -20C for later DNA extraction (input pellets). In parallel, 1 million cells/replicate were plated on -ADE-URA selection medium in 145cm2 plates. Plates were incubated at 30 C for 6 days inside an incubator. Finally colonies were scraped off the plates with PBS 1x, harvested by centrifugation and stored at -20C for later DNA extraction (output pellets).

extract_protocol:
The input and output pellets (3 biological, 6 tubes in total) were thawed and resuspended in 2ml extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris pH 8, 1mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62C (10min).  Samples were then vortexed together with 1.5ml of phenol:chloroform:isoamyl 25:24:1 and 1.5g of glass beads (sigma). The aqueous phase was recovered by centrifugation and mixed again with 1.5ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10V of 3M NaOAc and 2.2V of 100% cold ethanol to the aqueous phase and incubating the samples at -20C for 1h. After a centrifugation step, pellets were dried overnight at room temperature. Pellets were resuspended in 1ml resuspension buffer (10mM Tris pH 8, 1mM EDTA pH 8) and treated with 7.5ul RNase A (Thermo Scientific) for 30min at 37C. The DNA was finally purified using 75ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 375ul elution buffer.
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 50 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Ilumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. The three input samples were pooled together equimolarly, and the same for the three output samples. The two final pools were purified from a 2% agarose gel using a silica beads extraction kit (QIAEX II Gel Extraction Kit, Qiagen).

value: single cell eukaryotic microorganism

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: protein expression


title: Output2

description: PCR DNA amplicon from plasmid library


title: Output1

description: PCR DNA amplicon from plasmid library


title: Input3

description: PCR DNA amplicon from plasmid library


title: TMEM HET GRN HET SAM24407676

value: Microglia


title: CNS-tumor_pediatric-LGG_81988

first: Martin

last: Sill

value: Male

value: infratentorial


title: CNS-tumor_pediatric-LGG_2305

value: Female

value: low grade glioma


title: CNS-tumor_pediatric-LGG_41082


title: BEAS-2B cells,PM2.5 (12.5 μg/mL),28h,rep1 [PM251]

value: lung

value: bronchial epithelium


title: TMEM HET GRN HET SAM24407673

value: TMEM HET GRN HET

value: M


title: WT, rep3

value: WT

value: Untreated


title: PND21 WT Male Room Air

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
To generate the metadata files. We first converted the cellranger output to a Seurat v4.1.1 object. Then we performed data filtering using SoupX v1.6.1,  doublet removal using DoubletFinder v 2.0.3. We used Seurat's PercentageFeatureSet to get percent of mitochondrial genes in each cell. Resulting cells were filtered using >= 500 molecular identifiers (nUMI >= 500), removing upper number of UMI outliers (nUMI <= outlier_threshold_nUMI), >250 detectable genes (nGene >= 250), removing upper number of gene outliers (nGene <= outlier_threshold_nGene), log10GenesPerUMI > 0.80, < 5% of transcripts coming from mitochondrial genes (mitoRatio < 0.05). Genes were filtered, only keeping those genes expressed in more than 10 cells. Genes 'Gm42418', 'S100a8', 'S100a9' were removed from Seurat object. We ran SCTransformV2 and Get clusters, resolution 0.6 was chosen. We integrated PND 1 and PND 21 respectively using Seurat's integration method. We got clusters again for the integrated object choosing a resolution of 0.6 and labeled each cluster based on markers given by Seurat's FindMarkers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Comma-separated metadata table.

growth_protocol: WT C57BL/6N mice were subjected to timed mating. Neonatal mouse pups from different litters were randomized to the treatment (hyperoxia) or control (room air) conditions. Mice were transitioned to room air on PND5.

extract_protocol:
The right ventricle was perfused with ice cold PBS and the lungs were harvested quickly and homogenized and dissociated using the Miltenyi MACS lung dissociation kit (Miltenyi Biotec, cat # 130-095-927), using the GentleMacs program m-Lung-1 on the AUTO MaCs. The lungs were incubated for 20min at 37 ◦C under continuous rotation and then run on the gentleMACS m-Lung-2 program on the gentleMACS (Miltenyi Biotec, Cat #130-095-937). This was followed by brief centrifugation and the passage of cells through the 70-uM filter, washed, centrifuged again and the pellet was treated with ACK lysis buffer, centrifuged, and resuspended in sorting buffer and passed through an 40uM filter. Live cells were sorted and subjected to single-cell RNA sequencing.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

treatment_protocol: C57BL/6N neonatal mice were exposed to room air or hyperoxia from PND1-5 to 95% FiO2 or mainatined in room air. Mice were euthanized at PND21.

value: Lung

value: PND 21

value: Mixed

value: Room Air


title: CNS-tumor_pediatric-LGG_60909

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

extract_protocol: Extraction of high molecular weight DNA from fresh frozen or FFPE tumor samples was carried out using the Maxwell RSC Tissue DNA kit or the Maxwell RSC DNA FFPE kit, respectively.

value: supratentorial, midline

value: CNS tumor


title: TMEM HET GRN KO SAM24407671

value: TMEM HET GRN KO

value: Microglia

value: Hemi


title: CNS-tumor_pediatric-LGG_92530

value: Female

value: infratentorial


title: PND 21 WT Female Room AIr

description: 10x Genomics


title: PND21 WT Male Oxygen

description: 10x Genomics

value: Hyperoxia

value: Male


title: ST2-U3C,interferon alpha,72h,STAT2,rep2

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

library_source: genomic

data_processing:
Quality assessment of raw reads was performed with FastQC
Alignment to the GRCh38.106 human genome assembly was done with Bowtie2 v2.4.1 and BAM files were sorted by SAMTools v1.6. PCR duplicates were removed using BamUtil v1.0.15
Peaks were called with MACS v2.2.6 with the significance cut-off q-value 0.01 and -nomodel -call-summits options. For peak annotation and motif enrichment (GAS and ISRE) HOMER v4.11 was used
In order to generate STAT1, STAT2, IRF9, pSTAT1 and pSTAT2 binding profiles upon IFN alpha treatment matrices were computed across 4 kb region centered on ChIP-Seq peak summits with deepTools v3.5.0 (reference-point TSS, upstream region 3000 bp, downstream region 1000 bp). Further steps were performed with profileplyr_1.10.0 R package
Data processing steps described above are valid for 2fTGH and ST2-U3C cell lines. Huh7.5 STAT1 K.O. has been processed in the same way as Huh7.5 wild-type cells submitted previously as part of GSE222668 SuperSeries
Assembly: hg38
Supplementary files format and content: narrowPeak for 2fTGH and ST2-U3C cell lines; regionPeak for Huh7.5 STAT1 K.O. (high-confidence peaks obtained after IDR evaluation between biological replicates - optimal output peak set; https://www.encodeproject.org/data-standards/terms/)

source_name: Human fibrosarcoma

growth_protocol: DMEM; 10% fetal bovine serum (FBS); 2mM L-glutamine; 100 IU/ml penicillin,100 µg/ml streptomycin,250 ng/ml amphotericin B. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were cross-linked with DSG for 30 min (or 45min for Huh STAT1KO) and then with formaldehyde for 10 min. After fixation chromatin was sonicated with a Diagenode Bioruptor Plus to generate 200–1000 bp fragments
ChIP-Seq libraries were performed using TruSeq ChIP Library Preparation Kit or NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina. 5-10ng of DNA was used as starting material. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 200-800bp using gel extraction (TruSeq) or 200bp using Agencourt AMPure XP beads (NEBNext). Libraries were then quantified using Qubit dsDNA HS assay kit and quality was assessed by the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: Cells were starved with medium containing 1% FBS and subsequently treated with 1000U/mL of IFN alpha up to 72h

value: Human fibrosarcoma

tag: chip antibody

value: STAT2 (SantaCruz, #sc-839)


title: CNS-tumor_pediatric-LGG_10929

city: Heidelberg

value: hemispheric, cortical

value: low grade glioma


title: TMEM HET GRN KO SAM24407670

value: F

value: Entire


title: Input1

city: Barcelona

description: PCR DNA amplicon from plasmid library

value: single cell eukaryotic microorganism

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: protein expression


title: PND 1 WT Male Room Air

description: 10x Genomics

value: Lung

value: PND 1

value: Mixed

value: WT

value: Room Air


title: TMEM HET GRN KO SAM24407668

value: TMEM HET GRN KO

value: Microglia


title: ST2-U3C,interferon alpha,2h,STAT2,rep2


title: CNS-tumor_pediatric-LGG_31232

value: Male

value: supratentorial, midline

value: CNS tumor


title: CNS-tumor_pediatric-LGG_50287

value: infratentorial


title: biventricular heart, CBK, ZT12, biol rep 2

value: male

value: biventricular heart

value: CBK


title: TMEM WT GRN WT SAM24407695

value: TMEM WT GRN WT

value: M

value: Entire


title: ST2-U3C,interferon alpha,2h,STAT2,rep1

value: Human fibrosarcoma

value: STAT2 (SantaCruz, #sc-839)


title: TMEM KO GRN WT SAM24407665

value: TMEM KO GRN WT


title: Sp, Fo_pos, 4h stim, scRNAseq

first: Gudrun

middle: Fiona

last: Debes

state: PA

address: 233 South 10th Street

department: Microbiology and Immunology

institute: Thomas Jefferson University

description: 10X genomics

data_processing:
Raw sequencing reads were processed using the Cell Ranger v5.0 pipeline from 10X Genomics. Sequenced BCL files were converted to fastq using Cellranger ‘mkfastq’ function, and reads were demultiplexed between the appropriate samples. For V(D)J BCR, cellranger ‘vdj’ function was used to generate annotated single cell V(D)J sequences for identification of CDR3 sequence and the rearranged V(D)J gene.  Clonotype file from CellRanger was further processed to perform a downstream analysis. First, clonotypes were filtered to remove any sequenced cell that expresses T-cell markers CD3G and CD3D. Further, we excluded cells expressing IL-10 transcript from IL-10– samples. Finally, clonotypes and related CDR3 sequences of IL-10+ and IL-10– B-1a, MZ, and FO samples was compared individually and in groups. The filtering and plotting was performed using R programming language.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files

source_name: spleen

extract_protocol:
Total splenocytes from sIgM-/-IL10GFP mouse were isolated by mechanical disruption through a 70um filter, red blood cells were lysed, and individual live cells counted. Cells were were stimulated at a concentration of 4x10^6/ml with 10 ng/ml PMA, 0.5 ug/ml Iono, and 10 ug/ml LPS for 4-h at 37C, 5% CO2, 13% O2. At end of stimulation, B cells were enriched using CD19 microbeads (Miltenyi 130-121-301) following the manufacturer’s protocol then stained for B cell subset markers and FACS sorted on BD FACSAriaII for IL-10+ and IL-10- B1a, Mz, and Fo B cells subsets. Positive GFP expression (IL-10) was based on a GFP negative wildtype mouse control.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, sorted B cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent. Full-length V(D)J segments (10X barcoded) were enriched from amplified cDNA via PCR amplification with primers specific to Ig constant regions.  During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: spleen

value: B cell

value: 4h PMA/Ionomycin/LPS


title: ST2-U3C,interferon alpha,72h,STAT2,rep1


title: CNS-tumor_pediatric-LGG_44215

value: hemispheric, cortical

value: low grade glioma


title: PND 21 WT Female Oxygen

description: 10x Genomics

value: Lung

value: PND 21

value: Mixed

value: WT

value: Hyperoxia

value: Female


title: ST2-U3C,interferon alpha,72h,IRF9,rep1

value: IRF9 (SantaCruz, #sc-10793)


title: CNS-tumor_pediatric-LGG_49682

value: infratentorial

value: CNS tumor


title: ST2-U3C,interferon alpha,24h,IRF9,rep2

value: Human fibrosarcoma


title: TMEM KO GRN WT SAM24407664

value: Microglia

value: M

value: Hemi


title: Sp, Fo_neg, 4h stim, scRNAseq

description: 10X genomics

value: spleen

value: B cell


title: TMEM KO GRN WT SAM24407663

value: TMEM KO GRN WT

value: F

value: Entire


title: Sp, Mz_pos, 4h stim, scRNAseq

description: 10X genomics

value: 4h PMA/Ionomycin/LPS


title: CNS-tumor_pediatric-LGG_3664

value: low grade glioma


title: ST2-U3C,untreated,IRF9,rep1


title: Saline SAM24380935

source_name: Brain

extract_protocol:
RNA was extracted from the cell pellet using the RNeasy Plus Micro Kit (Qiagen).
Truseq Stranded mRNA Kit (Illumina).

value: saline

tag: group

value: Saline

value: Brain


title: Sp, Mz_neg, 4h stim, scRNAseq

description: 10X genomics

tag: cell type


title: SAM24380911

tag: treatment


title: Sp, B1a_pos, 4h stim, scRNAseq

description: 10X genomics


title: BCL6_cl.7 (Tn+15y)

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v.1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v.0.11.1).
Remaining reads were further filtered for low complexity with reaper (v.15-065).
Reads were aligned against Homo sapiens.GRCh38.92 genome using STAR (v.2.5.3a).
The number of read counts per gene locus was summarized with htseq-count (v.0.9.1) using Homo sapiens.GRCh38.92 gene annotation.
Assembly: GRCh38
Supplementary files format and content: FASTQ

source_name: CD8 T cells

extract_protocol:
Total RNA from the ex vivo sorted cells (between 300 and 8000 cells) was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using the Clontech SMART Seq v4 Ultra Low RNA kit (Clontech Laboratories, Inc.)

treatment_protocol: CD8-enriched from PBMCs were stained with CMV/pp65-specific multimers followed by cell surface marker APC-A750, FITC or APC anti-CD8 (Beckman Coulter) and antibodies against the different identified TRBV families. CMV/pp65/TRBV-specific CD8 T cells were then sorted on a FACSAria (BD Biosciences) flow cytometer in RNAlater Stabilization Solution (Invitrogen).

tag: subject status

value: HLA-A2-positive healthy individuals latently infected with the CMV virus

value: CD8 T cells

tag: avidity

value: low avidity

tag: time-point


title: BCL6_cl.5/6 (Tn+15y)

value: high avidity


title: SAM24380906


title: CNS-tumor_pediatric-LGG_95843

tag: Sex

value: Male

tag: age

tag: location

value: hemispheric, cortical

tag: tumor subgroup

value: CNS tumor


title: Sp, B1a_neg, 4h stim, scRNAseq

description: 10X genomics

tag: tissue

value: spleen


title: SAM24380912


title: CNS-tumor_pediatric-LGG_91810


title: CNS-tumor_pediatric-LGG_51131


title: BKO_Rep4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2018_1 were also provided

source_name: cultured cells

growth_protocol: All cells were maintained with basic DC medium (RPMI-1640 with 10% decomplemented FBS, 1 mM sodium pyruvate, 10 mM HEPES, and 1x Pen/Strep was used. β-mercaptoethanol (at a final concentration of 50 microM) and recombinant GM-CSF (at a final concentration of 10 ng/mL)), in the presence of Dex/Dox (dexamethasone at 100 nM + doxycycline  at 2 μM) to maintain proliferation

extract_protocol: Total RNA was extracted from cultured de-iniDCs (~5x107 cells) with the RNeasy Plus Mini Kit (Qiagen) following the manufacturers’ instructions.

treatment_protocol: Before treatment, Dex/Dox was removed from the culure for 4 days to let cells differentiate into primary-like DCs, which were treated with Venetoclax at a concentration of 5 microM or equivalent DMSO for 18 hours before total RNA extraction

value: cultured cells

tag: cell line

value: inducible immortalized DC

value: DMSO


title: BKO_Rep3


title: CNS-tumor_pediatric-LGG_76033

value: Female

value: infratentorial


title: ASO 1 SAM24380939

value: ASO 1


title: BCL4_cl.2 (Tn+15y)


title: CNS-tumor_pediatric-LGG_35305

value: low grade glioma


title: SAM24380921


title: BKO_Rep2


title: SAM24380918


title: BKO_Rep1


title: CNS-tumor_pediatric-LGG_33751


title: BCL4_cl.4 (Tn+15y)


title: BEAS-2B cells,serum-free medium,28h,rep3 [MOCK3]

value: lung

value: bronchial epithelium

value: serum-free medium,28h


title: BCL4_cl.1 (Tn+15y)

value: HLA-A2-positive healthy individuals latently infected with the CMV virus

value: CD8 T cells


title: SAM24380941

value: Brain


title: WT_Ven_Rep4

value: WT

value: Venetoclax


title: BCL6_cl.5/6 (Tn)

value: high avidity

value: Tn


title: TMEM KO GRN WT SAM24407666

value: TMEM KO GRN WT

value: Microglia

value: M

tag: dissection

value: Entire


title: CNS-tumor_pediatric-LGG_14254

value: Male

value: infratentorial

value: CNS tumor


title: BCL4_cl.3 (Tn+15y)

value: low avidity


title: Saline SAM24380934

value: saline

value: Saline


title: BCL4_cl.2 (Tn)

value: HLA-A2-positive healthy individuals latently infected with the CMV virus


title: WT_Ven_Rep3

value: cultured cells

value: inducible immortalized DC


title: CNS-tumor_pediatric-LGG_91744

value: Female

value: hemispheric, cortical

value: low grade glioma


title: CNS-tumor_pediatric-LGG_39732


title: WT_Ven_Rep2

value: WT

value: Venetoclax


title: WT_Ven_Rep1


title: ASO 2 SAM24380920

value: ASO 2

value: Brain


title: BCL6_cl.7 (Tn)

value: CD8 T cells

value: Tn


title: BCL4_cl.1 (Tn)

value: high avidity


title: SAM24380942


title: WT_untreated_Rep4

value: DMSO


title: WT_untreated_Rep3


title: BCL4_cl.3 (Tn)

value: low avidity


title: CNS-tumor_pediatric-LGG_76101

value: infratentorial

value: CNS tumor


title: SAM24380901


title: CNS-tumor_pediatric-LGG_60737


title: BCL4_cl.4 (Tn)

value: HLA-A2-positive healthy individuals latently infected with the CMV virus


title: CNS-tumor_pediatric-LGG_51886


title: ASO 3 SAM24380909

value: ASO 3


title: BCL1_cl.9 (Tn+15y)


title: ASO 2 SAM24380919


title: ASO 4 SAM24380926

value: ASO 4


title: WT_untreated_Rep2

value: cultured cells

value: inducible immortalized DC


title: CNS-tumor_pediatric-LGG_69046

value: Female

value: supratentorial, midline

value: low grade glioma


title: BCL1_cl.8 (Tn+15y)


title: biventricular heart, CON, ZT04, biol rep 3

city: Birmingham

first: Lamario

last: Williams

address: 1825 University Boulevard, Room 121

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using bcl2fastq v2.18.12 for NextSeq output.
Raw FASTQ files were uploaded to Qiagen's GeneGlobe website for their default microRNA analysis and differential expression analysis.
Assembly: mm10
Supplementary files format and content: raw UMIs values for each microRNA in each sample

source_name: biventricular heart

extract_protocol:
RNA was harvested using miRNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Small RNA sequencing libraries were prepared using the QIAseq miRNA library kit.

tag: strain

value: male

value: biventricular heart

value: CON


title: SAM24380931

value: Brain


title: CNS-tumor_pediatric-LGG_30709

value: Male


title: Mix tumor [1946T1-Mix]

city: Jerusalem

first: nofar

last: rosenberg

address: Hadassah University Hospital

country: Israel

institute: Hebrew university

data_processing:
The demultiplexing, alignment, gene counting and aggregation were made using the cellranger software v3.0.2 or v3.1.0.
The datasets were further filtered to retain only high-quality cells with more than 200 expressed genes, and less than 5% for HCC and 10% for Non tumor and HCC-CCA of mitochondrial RNA transcripts. Genes expressed in less than 3 cells were removed. Finally, 11485 HCC, 11164 Non tumor and 1553 HCC-CCA cells were retained for analysis using the R package Seurat, v3.0.2 or v4.0.4. From each sample, 2000 highly variable genes were selected for the downstream analysis. The 3 datasets were then subjected to scaling, centering, dimension reduction, generating nearest neighbor graphs using PCA1 to PCA20, clustering at 0.6 and visualization by Uniform Manifold Approximation and Projection (UMAP) for the HCC and Non tumor samples, and PCA1 to PCA30 at resolution 1.0 for the HCC-CCA sample.
Assembly: GRCm38
Supplementary files format and content: Results of cellranger count are given as is in the HDF5 format (see 10X support for details). In addition, for each sample the assignment of cluster and cell type to each cell is given in a tab-delimited text file, with a single header row, followed by data for each cell.

source_name: liver

extract_protocol:
Liver tissue were cut to small pieces and digested in three subsequent steps. At the first step, liver fragments were incubated in PBS with Trypsin C (1:1) at 37oC, 5 min; the reaction was stopped with 2 volumes of complete DMEM. The mix was span down at 4oC, 188 g, 5 min, and the pellet was re-suspended with 0.5 ml of HBSS buffer. At the second step, the mix was digested with collagenase P (2.5 mg/ml) in the presence of trypsin inhibitor (0.1 mg/ml) at 37oC, 15 min. Then, equal volume of HBSS was added, the mix was pipetted and span down, as described in step one. At the third step, the pellet was re-suspended in PBS with Trypsin C (1:1) and incubated at 37oC, 5 min. Following intensive pipetting and verification that most of the cells are single, the reaction was stopped with 2 volumes of complete DMEM. Cells were spanned down and washed again with complete DMEM, as described above, and re-suspended in the FACS buffer (Dulbecco’s PBS with 1% BSA, 1mM EDTA, 0.01% sodium azide) for FACS analysis. Cells were stained with Trypan blue and propidium iodide to determine the percentage of alive cells (95% in our case).
cDNA library construction using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics, 6230 Stoneridge Mall Road Pleasanton, CA 94588 USA)

value: liver

value: HCC-CCA tumor

tag: genotype

value: 18 month-old


title: WT_untreated_Rep1

value: WT

value: DMSO


title: BCL1_cl.8 (Tn)

value: HLA-A2-positive healthy individuals latently infected with the CMV virus

value: CD8 T cells

value: high avidity

value: Tn


title: ASO 2 SAM24380903

value: ASO 2


title: ST2-U3C,interferon alpha,2h,STAT2,rep3

value: Human fibrosarcoma

value: STAT2 (SantaCruz, #sc-839)


title: CNS-tumor_pediatric-LGG_92564

value: infratentorial

value: low grade glioma

value: CNS tumor


title: HCC tumor [958T1-HCC]

value: HCC tumor


title: Ctrl10

city: Baoding

first: Hanbin

last: Wang

state: Hebei province

address: 212 Yuhua East Road

institute: Affiliated Hospital of Hebei University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles
Supplementary files format and content: (normalized_counts)

source_name: plasma

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: plasma

value: healthy


title: Non tumor tissue [1507-NT]

value: liver

value: normal tissue


title: SAM24380916

value: Brain


title: CNS-tumor_pediatric-LGG_3659

value: Male


title: Ctrl8


title: ASO 4 SAM24380945

value: ASO 4


title: Ctrl9


title: ASO 3 SAM24380910

value: ASO 3


title: Input2

description: PCR DNA amplicon from plasmid library

value: single cell eukaryotic microorganism

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: protein expression


title: CNS-tumor_pediatric-LGG_888

value: hemispheric, cortical


title: BCL1_cl.9 (Tn)

value: HLA-A2-positive healthy individuals latently infected with the CMV virus

value: CD8 T cells

value: low avidity

value: Tn


title: CNS-tumor_pediatric-LGG_87984

value: Female

value: low grade glioma

value: CNS tumor


title: E10.5 limb mesenchymal cells (lib5_E10.5)

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

description:
mouse.rds
combined.rds
E10.5 limb mesenchymal cells

data_processing:
All four human samples were multiplexed with mouse and chick samples. The chick data was not presented in this manuscript. Thus, for species demultiplexing, Ensembl release 99 hg38 transcriptome, Ensembl release 98 Gallus gallus-6.0 transcriptome and the filtered Ensembl release 98 mm10 transcriptome was merged using the cellranger mkgtf command to generate human-mouse-chick transcriptome for initial mapping for demultiplexing.
For InDrop preprocessing, sequencing results were demultiplexed by dropTag from dropEst package (Petukhov et al. 2018) and demultiplexed reads were aligned with STAR aligner (Dobin et al. 2013). The aligned reads were split into forward and reverse alignment, since InDrop is directional. The resulting forward and reverse alignment files were quantified using dropEst package including directional UMI correction option (Petukhov et al. 2018) with transcriptome annotation split into forward and reverse direction to avoid mapping of antisense reads.
Sequencing results were demultiplexed by cellranger and aligned using cellranger count (internally by STAR aligner (Dobin et al. 2013)). For the four libraries that needed species demultiplexing, cellular barcodes that had less than 5% of UMI counts from other species were selected for subsequent mapping with the corresponding species transcriptome.
Cellular barcodes with high mitochondrial content (>15%), high hemoglobin gene count (>10%) and low gene counts (<1,200) were filered out. All libraries were subject to doublet detection via Scrublet (Wolock et al. 2019). Batch effect was assessed by simply merging the individual UMI count matrices for clustering and Seurat v3 integration procedure was applied (Stuart, Butler et al. 2019) with 30 dimensions for the individual batches. Further, cell cycle effect, fraction of mitochondrial genes were regressed out. Principal component analysis (PCA) was performed on the integrated, scaled features for dimensional reduction and Uniform Manifold Appxoimation and Projection (UMAP) (McInnes et al. 2018) was used primarily for the cellular embedding coordinates. Leiden algorithm was applied on the shared neighborhood graph with 10 iterations (Seurat default) to derive cluster boundaries (Traag et al. 2019).
Genome_build: For all mouse samples, Ensembl release 98 mm10 transcriptome was used as base transcriptome annotation, with pseudogenes filtered from the GTF file using cellranger mkgtf command . For retroviral infected hyaluronan samples, transgenes for human Lin28a, EGFP (for Prx1GFP transgene) was added to generate custom transcriptome annotation for quantification for reprogrammed cells (mm10.98.hlin28a.gtf.gz). For lentiviral infected Matrigel samples, transgenes for EGFP (for Prx1GFP transgene), rtTA, and human Lin41 as well as PLZF, and 3’UTR sequences of WPRE were added to generate custom transcriptome annotation for quantification for reprogrammed cells (mm10.98.4factor.tdtomato.gtf.gz). The limb progenitor cells were subject to the same transcriptome annotation (yielding zero counts for the transgenes). For human-specific mapping, the filtered hg38 transcriptome with transgenes for EGFP, rtTA, and mouse Prdm16 and mouse Lin28a were added (hg38.4factor.gtf.gz).
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes) as well as meta information in tab-delimited format are included. The whole data is split into mouse-only data (prefix mouse.), human-only data (prefix human.), and for convenience, combined data (prefix combined.) which only contains the matching features and MNN coordinates are provided.

source_name: E10.5 embryonic limb

growth_protocol: Non-limb fibroblasts cultured in 2D, Lentivirally-expressed non-limb fibroblasts (reprogrammed cells) in 3D hyaluronan or matrigel growth culture condition, directly harvested embryonic primary mesenchyme

extract_protocol:
For sorting reprogrammed Prx1-GFP or Prx1-tdTomato cells from embryos, a FACS sorter Astrios (Beckman Coulter) or On-chip Sort HSG (On-chip Biotechnologies) was used. After washing with PBS, the cells cultured in the HA-gels or on Matrigel were incubated in TryPLE Express (gibco) for 30 min at 37℃. The cell suspension was pipetted with cut P1000 pipette tips every 10 min, to completely dissociate the cell clusters. The suspension was filtrated by 100 μm Cell strainers (Falcon) and 40 μm Cell strainers (VWR), and cells were pelleted by centrifugation (400 x g for 5 min). The pellets were dissociated by DRAQ5/DAPI in 0.1% BSA/PBS and incubated for 5 min before the sorting. DRAQ5-positive, DAPI-negative cells were sorted for cells on reprogramming at day 2, 4, 8. For HA-gel reprogrammed cells at day 14, additional gating on GFP channel derived GFP-positive and GFP-negative samples. For Matrigel-derived day 14 reprogrammed cells for PZL- as well as PZLL- factors, only GFP-positive cells were collected. DRAQ5-positive, DAPI-negative, Matrigel-derived day 8 cultured E9.5 and E10.5 limb progenitors were collected. The E9.5 cultured limb progenitors were subject to 4-OHT, such that large fraction were tdtomato-positive, but the cells were collected regardless of tdTomato-positivity. DRAQ5-positive, DAPI-negative, tdTomato-positive cells were sorted for the limb mesenchyme cells for E10.5, E11.5 as well as E12.5 cells. For E9.5 limb progenitors, samples were collected without tdTomato gating to maximize yield. InDrop cell capture was processed in Harvard Medical School Single Cell Core. All libraries included about 10-15% of Non-limb fibroblasts to mitigate batch effect. Cells were captured by the Chromium Controller (10X genomics, Biopolymer facility at Harvard Medical School).
single cell RNA libraries were prepared for sequencing using 10X Genomics Chromium V3 protocols and inDrops libraries were prepared by the Harvard Single Cell Core according to the published protocol
scRNA-seq

value: mesenchymal cells

tag: treatment/condition

value: Directly from embryo

value: inDrop scRNA-seq


title: Hyaluronan 3D cultured rLPCs for 14 d (lib4_Neg)

description:
mouse.rds
combined.rds
Hyaluronan 3D cultured rLPCs for 14 days

source_name: Non limb fibroblasts cultured in hyaluronan 3D culture for 14 days with 3-factor expression, Prx1EGFP-negative

value: Haluronan hydorgel 3D culture, DMEM 10% FBS, Chir99021 (3uM), Fgf8 (150ng/ml), Retinoic acid (25nM), SB431542 (5uM), Y-27632 (10uM)


title: Ctrl7

value: plasma

value: healthy


title: ASO 1 SAM24380933

value: ASO 1

value: Brain


title: Ctrl6


title: CNS-tumor_pediatric-LGG_76280

value: Male


title: CNS-tumor_pediatric-LGG_82322

value: supratentorial, midline


title: Non-limb fibroblasts cultured in normal 2D condition (lib2_MEF)

description:
mouse.rds
combined.rds
Non-limb fibroblasts cultured in normal 2D condition

source_name: Non limb fibroblasts cultured in normal 2D plate condition

value: DMEM/10% FBS petridish culture


title: Saline SAM24380924

value: saline

value: Saline


title: SAM24380922


title: CNS-tumor_pediatric-LGG_812


title: E9.5 limb mesenchymal cells (lib1_LPr)

description:
mouse.rds
combined.rds
E9.5 limb mesenchymal cells

source_name: E9.5 embryonic limb


title: Ctrl4


title: SAM24380917


title: Hyaluronan 3D cultured Non-limb fibroblasts (lib07_MEF)

description:
mouse.rds
combined.rds
Hyaluronan 3D cultured Non-limb fibroblasts

source_name: Non limb fibroblasts cultured in hyaluronan 3D culture for 14 days with empty vector control


title: Hyaluronan 3D cultured rLPCs for 14 d (lib03_Neg)


title: ASO 2 SAM24380904

value: ASO 2


title: CNS-tumor_pediatric-LGG_23038

value: Female

value: infratentorial


title: Hyaluronan 3D cultured rLPCs for 14 d (lib3_Rep)

source_name: Non limb fibroblasts cultured in hyaluronan 3D culture for 14 days with 3-factor expression, Prx1EGFP-positive


title: Ctrl3


title: Ctrl2


title: CNS-tumor_pediatric-LGG_80204

source_name: CNS tumor

value: low grade glioma

value: CNS tumor


title: ASO 4 SAM24380928

value: ASO 4


title: Ctrl1


title: SAM24380943


title: E10 limb mesenchymal cells (lib01_E10)

description:
mouse.rds
combined.rds
E10 limb mesenchymal cells

source_name: E10 embryonic limb

value: mesenchymal cells

value: Directly from embryo

value: inDrop scRNA-seq


title: Hyaluronan 3D cultured rLPCs for 14 d (lib02_Rep)

value: Haluronan hydorgel 3D culture, DMEM 10% FBS, Chir99021 (3uM), Fgf8 (150ng/ml), Retinoic acid (25nM), SB431542 (5uM), Y-27632 (10uM)


title: Ctrl5

value: plasma

value: healthy


title: Saline SAM24380925

value: Brain


title: 2fTGH,interferon alpha,72h,phospho-STAT1

value: Human fibrosarcoma

tag: chip antibody


title: CNS-tumor_pediatric-LGG_85857

value: hemispheric, cortical


title: NS_IA9

value: non-smoking IA patient


title: CNS-tumor_pediatric-LGG_97501


title: CNS-tumor_pediatric-LGG_70127

value: Male


title: SAM24380937

tag: group


title: CNS-tumor_pediatric-LGG_4783

value: supratentorial, midline


title: SAM24380936


title: 2fTGH,interferon alpha,2h,phospho-STAT1


title: SAM24380907


title: NS_IA7


title: CNS-tumor_pediatric-LGG_69722

value: Female


title: CNS-tumor_pediatric-LGG_26060

value: infratentorial


title: 2fTGH,untreated,phospho-STAT1


title: NS_IA6


title: Saline SAM24380923

value: saline

value: Saline


title: CNS-tumor_pediatric-LGG_57677

value: low grade glioma

value: CNS tumor


title: NS_IA10


title: TG05b

first: Kirsi

middle: J.

last: Rautajoki

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: patient TG05

data_processing:
Base-calling Illumina HiSeq 2000
Alignment Bowtie 2 (version 2.2.9) against UCSC genome browser hg38 human genome assembly
Duplicate reads were masked using Samblaster (version 0.1.22)
Somatic mutations with at least three unique supporting reads and a allele fraction of 10% or higher were called
Technical artifacts (variants with similar allele fractions between cohort samples) were filtered out using chi-square goodness of fit test (null hypothesis: samples have identical allele fractions for mutations)
Mutations reported in the gnomAD v3.0 database of human germline variants were filtered out
Assembly: hg38
Supplementary files format and content: Somatic protein-altering mutation calls in tab-delimited text file. Case-specific columns include the following fields separated by ":" Number of alternate allele reads : Number of total reads: * means the alteration is filling criteria to be identified as mutation

source_name: brain

extract_protocol:
QIAamp DNA Mini kit (QIAGEN) with RNase treatment
TruSeq DNA kit (Illumina)

value: brain

tag: malignancy

value: IDHmut astrocytoma

value: male

tag: age group_at_primary_diagnosis

tag: tumor stage

value: grade 4

value: radiation and chemotherapy (CCNU)


title: ASO 4 SAM24380927

tag: treatment

value: ASO 4

value: Brain


title: TG05a

description: patient TG05

value: grade 2

value: radiation


title: CNS-tumor_pediatric-LGG_32814

value: Male


title: 2fTGH,interferon alpha,24h,phospho-STAT1

source_name: Human fibrosarcoma

value: Human fibrosarcoma


title: NS_IA4

value: plasma

value: non-smoking IA patient


title: BEAS-2B cells,serum-free medium,28h,rep1 [MOCK1]

source_name: lung

value: lung

tag: cell type

value: bronchial epithelium

value: serum-free medium,28h


title: TG04b

description: patient TG04

tag: Sex


title: NS_IA8


title: CNS-tumor_pediatric-LGG_30200

value: Female

tag: age

value: infratentorial

value: low grade glioma

value: CNS tumor


title: NS_IA3


title: CNS-tumor_pediatric-LGG_73960

tag: location

value: hemispheric, cortical


title: TG04a

description: patient TG04

value: brain

value: IDHmut astrocytoma

value: male

value: grade 3

value: treatment naive


title: SAM24380908

source_name: Brain

value: Brain


title: TG03b

description: patient TG03

value: grade 4

value: radiation and chemotherapy (PCV)


title: NS_IA2

value: plasma

value: non-smoking IA patient


title: ASO 3 SAM24380915

value: ASO 3


title: CNS-tumor_pediatric-LGG_88625

value: Male

tag: tumor subgroup


title: TG03a

description: patient TG03

tag: tissue


title: NS_IA1

tag: cell line


title: CNS-tumor_pediatric-LGG_32196


title: NS_IA5


title: S_IA10

value: smoking IA patient


title: ASO 3 SAM24380913


title: CNS-tumor_pediatric-LGG_83701

value: Female

value: infratentorial


title: TG02b

description: patient TG02

value: female

value: radiation and chemotherapy (CCNU)


title: CNS-tumor_pediatric-LGG_83675

value: hemispheric, cortical

value: low grade glioma

value: CNS tumor


title: S_IA9


title: ASO 4 SAM24380944

value: ASO 4


title: CNS-tumor_pediatric-LGG_95301


title: ASO 1 SAM24380940

value: ASO 1


title: TG01b

description: patient TG01

value: brain

value: IDHmut astrocytoma

value: male


title: CNS-tumor_pediatric-LGG_37486


title: TG02a

description: patient TG02

value: IDHmut oligoastrocytoma

value: grade 3

value: treatment naive


title: S_IA7

value: plasma


title: e15.5 mouse MGE, WT_3

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

data_processing:
The Illumina NovaSeq's paired-end run produced two compressed fastq.gz files for each replicate.
Adaptor sequences were trimmed in individual fastq files using cutadapt.
The trimmed read files were then aligned to the reference genome using bowtie2, resulting in output .sam files. The .sam files were converted into .bam files using samtools view -Sb and samtools sort.
Multimappers were removed from each .bam file using samtools view with a parameter -q 20. Subsequently, Picard MarkDuplicates was used to remove PCR duplicates from the .bam files.
BigWig files from the deduplicated .bam files were created using bamCoverage. Peaks were called using epic2.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig for CUT&Tag reads
Supplementary files format and content: bed for CUT&Tag peaks
Library strategy: CUT&Tag

source_name: MGE

extract_protocol:
E12.5 and E15.5 embryos were removed and placed in ice-cold carbogenated ACSF. Tails were clipped for PCR genotyping. During genotyping, embryonic brains were harvested and MGEs were dissected from each embryo and stored in ice-cold carbogenated ACSF. For E12.5, the entire MGE was removed as previously described92. For E15.5, the MGE was dissected under a fluorescent dissecting microscope to ensure collection of only Tom+ MGE cells and minimize collection of postmitotic MGE-derived cells in the striatum anlage and other ventral forebrain structures. Upon obtaining genotyping results (~90 minutes), MGEs from embryos of the same genotype were combined (when applicable) to generate single nuclei dissociations. MGEs were transferred to a 1 mL Dounce homogenizer containing DNA Lysis Buffer (10 mM Tris-HCl (Ph.7.4), 10 mM NaCl, 3 mM CaCl2, 0.1% Tween-20, 1.5% BSA and 0.1% IGEPAL CA-630 in nuclease-free water, 1 mL per sample). Lyse cells by douncing with pestle A and pestle B, ~10-15 times each. Place a 40 μm filter onto a pre-chilled 50 mL conical tube on ice and wet with 1 mL of DNA Nuclei Wash Buffer (in mM: 10 Tris-HCl (Ph.7.4), 10 NaCl, 3 CaCl2, with 0.1% Tween-20 and 1.5% BSA in nuclease-free water, 5 mL per sample). Transfer lysed nuclei suspension through pre-wetted filter, then rinse dounce with 1 mL Nuclei Wash Buffer and transfer through filter. Divide nuclei suspension into 2 pre-chilled 2 mL tubes and spin at 500 g for 5 minutes at 4oC. After removing supernatant, wash nuclei pellet once with 1 mL Nuclei Wash Buffer and then once with 1 mL of 1X CUT&Tag Wash Buffer (from Active Motif CUT&Tag IT Assay kit). Remove CUT&Tag Wash Buffer, leaving ~30-50 μL in each, triturate and combine nuclei suspensions from both tubes. Nuclei concentration was determined on Countess II FL Automated Cell Counter. 100,000-125,000 nuclei were used for each CUT&Tag reaction. Proceed with CUT&Tag IT Assay Kit (Active Motif, #53610) per manufacturer’s instructions. Primary antibody was H3K27me3 (Cell Signaling, 9733T, 1:50) or H3K27ac (Cell Signaling, and secondary antibody was guinea pig anti-rabbit (Active Motif, 105465 from CUT&TagIT kit, 1:100).
DNA quantity was determined with a Thermo Qubit and library quality characterized with an Agilent Tapestation. Libraries were balanced for DNA content and pooled before performing a final SPRIselect bead 1x left size selection and paired-end sequenced (50 x 50 bp) on an Illumina NovaSeq.

value: MGE

value: WT

tag: developmental stage

tag: biological replicate


title: e15.5 mouse MGE, WT_2

tag: genotype


title: S_IA8

value: smoking IA patient


title: CNS-tumor_pediatric-LGG_14581

value: Female

value: infratentorial


title: e15.5 mouse MGE, WT_1


title: TG06b

description: patient TG06

data_processing:
Base-calling Illumina HiSeq 2000
Aligment STAR 2.7.0 against human genome assembly GRCh38 using GENCODE v.30 annotations
Gene counts using featureCounts Rsubread package v. 1.34.6
Differential expression and normalization using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including normalized gene expression values for each sample

extract_protocol:
mirVana™ miRNA Isolation Kit (Life Technologies), large RNA (>200 nucleotides) molecules were divided into a separate fraction
Illumina, strand-specific 140-160 bp short insert library protocol

value: grade 4

value: radiation and chemotherapy (PCV)


title: CNS-tumor_pediatric-LGG_11409

value: Male

value: low grade glioma

value: CNS tumor


title: TG06a

description: patient TG06

value: brain

value: grade 2


title: TG01a

description: patient TG01

value: IDHmut astrocytoma

value: male


title: S_IA5


title: ASO 2 SAM24380905

data_processing:
GSNAP was used to align reads to GRCm38.
The HTSeqGenie Bioconductor package was used to count genes.
Gene models were obtained from an internal database.
Assembly: GRCm38
Supplementary files format and content: Tab-delimeted text files with raw counts, width, and rpkm normalized values for each gene.

value: ASO 2

value: Brain


title: CNS-tumor_pediatric-LGG_64407

value: hemispheric, cortical


title: e15.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_3

value: MGE

value: KO


title: S_IA4

value: plasma

value: smoking IA patient


title: WT, rep1

first: Yabing

last: Song

address: Chaoyang District

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). CGD Gene Ontology Term Finder (http://www.candidagenome.org/cgi-bin/GO/goTermFinder).
Assembly: C. auris B8441 (GCA_002759435.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: WT

extract_protocol:
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)

tag: strain

value: WT

value: Untreated


title: TG05b

description: patient TG05

value: grade 4

value: radiation and chemotherapy (CCNU)


title: e15.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_2


title: Flank and Neck (HH19)

data_processing:
After bclfastq processing to demultiplex paired-end library, Tophat (version 1.4.0) was used for alignment.
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text file with read counts and fold change, p-value comparison

organism: Gallus gallus

source_name: Flank and Neck mesenchyme (HH19)

growth_protocol: Directly dissected from chick embryos from all stages

extract_protocol:
polyadenylated RNA was extracted by mRNA purification kit by Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mesenchyme cells

value: Flank&Neck


title: S_IA3


title: e15.5 mouse MGE, Nkx2.1-CreC/+;Ezh2;Ai9F/+_1


title: TG05a

description: patient TG05

value: brain

value: radiation


title: Flank_9

source_name: Flank mesenchyme (HH19)

value: Flank


title: S_IA2

source_name: plasma


title: TG04b

description: patient TG04

value: IDHmut astrocytoma

value: male


title: CNS-tumor_pediatric-LGG_74701

value: Male

value: supratentorial, midline

value: low grade glioma

value: CNS tumor


title: S_IA6

value: plasma


title: e15_Het_3

data_processing:
Paired-end run Illumina NovaSeq produced 2 compressed fastq.gz files for each replicate. For each age (E12.5 and E15.5) and each genotype, a total of 3 different biological reps from 3 different experiments were combined. Duplicate reads from sequencing were removed and fastq_processing was executed to produce .bam and .bam.bai files for each replicate. For each genotype, ‘samtools merge -o’ was used to merge 3 sorted alignment biological replicates .bam files into one output file. The biological replicates were used to create bigwig files and for MACS peak calling. The biological bio.bam files also underwent bam_processing and had duplicates removed. The resulting biological nodup.bam files were merged using samtools to produce the final WT, Het, and KO replicates.
Assembly: GRCm38/mm10
Supplementary files format and content: bw for CUT&Tag signal
Library strategy: CUT&Tag

value: MGE

value: Het


title: TG04a

description: patient TG04

value: grade 3

value: treatment naive


title: Hindlimb_18

source_name: Hindlimb mesenchyme (HH18)

value: Hindlimb


title: Neck_19

source_name: Neck mesenchyme (HH19)

value: Mesenchyme cells

value: Neck


title: S_IA1

value: smoking IA patient


title: TG03b

description: patient TG03

value: brain

value: grade 4

value: radiation and chemotherapy (PCV)


title: e15_Het_1


title: TG03a

description: patient TG03

value: IDHmut astrocytoma

value: male


title: Forelimb_19

source_name: Forelimb mesenchyme (HH19)

value: Forelimb


title: Human male MIX tumor, rep3

data_processing:
Assembly: GRCh38
The first 12 nucleotides of each read were trimmed with the FASTX package (v0.0.14), then adapter sequences were removed with Cutadapt (v1.12). Low quality reads were filtered out with the FASTX package, v0.0.14, using parameters -q 20 and -p 90.
Reads were aligned with Tophat (v2.1.1), using parameters -G genes.gtf (from Ensembl release 89), -N 2, --read-gap-length 5, --read-edit-dist 7, --segment-length 18, --read-realign-edit-dist 3, --no-coverage-search and --library-type fr-secondstrand.
Raw counts were obtained with htseq-count (v0.6.0), then normalization and differential expression were calculated with the R package DESeq2 (v1.12.4), using default parameters, except setting independentFiltering=F.
Supplementary files format and content: DESeq2_final_M.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing HCC to DR samples; BA-BE, results comparing MIX to DR samples; BF-BJ, results comparing MIX to HCC samples.
Supplementary files format and content: DESeq2_final_H.xlsx: columns A-J, general gene details; K-AB, raw counts; AC-AT, normalized counts; AU, baseMean (average expression); AV-AZ, result comparing ICC to HCC samples; BA-BE, results comparing MIX to HCC samples; BF-BJ, results comparing MIX to ICC samples.

source_name: liver

extract_protocol:
Snap-frozen liver tissue samples were obtained, and 10 µm-thick sections were obtained by cryostat microtomy.  Tumor areas were localized by hematoxylin and eosin staining. Laser capture microdissection was performed using the Leica LMD6500 system. Total mRNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Libraries were prepared using the Lexogen QuantSeq 3′mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna, Austria) which was followed by an amplification step according to the manufacturer’s instructions.

value: liver

value: HCC-CCA tumor

tag: gender


title: e12.5 mouse MGE, WT_3

value: WT


title: Human male MIX tumor, rep2


title: TG02b

description: patient TG02

value: female

value: radiation and chemotherapy (CCNU)


title: e12.5 mouse MGE, WT_2

value: MGE


title: Forelimb_15

source_name: Presumptive forelimb mesenchyme (HH15)

value: Presumptive forelimb


title: Human female MIX tumor, rep3


title: EPXDz_DL1

city: Hamilton

first: Monsur

last: Ali

state: ON

address: ETB 303, Biointerface Institute, 1280 Main St West

department: Biointerfaces Institute

country: Canada

institute: McMaster University

data_processing:
Sequence data processing was performed on a Windows 10 computer running Ubuntu 20.04 under WSL2.
Raw paired-end reads were trimmed of sequencing and library primers using cutadapt 3.4.
Trimmed paired-end reads were then: 1) merged into a consensus sense read; 2) dereplicated; and, 3) clustered at 90% identity using USEARCH v11.0.667_i86linux32.
Sequence frequencies and ranking lists were generated using custom Python scripts. Multiple sequence alignments were performed using MUSCLE v3.8.1551 and converted to sequence logos using WebLogo 3.7.8.
Analysis of sequence copy number, frequency, cluster linkage and data plots were performed using the database and Microsoft Excel
Assembly: NA
Supplementary files format and content: tab-delimited text files include sequence frequency and ranking

organism: synthetic construct

extract_protocol:
It was a synthetic DNA pool. Therefore, no extraction was necessary
The random DNA library conatining approximately 10^14 individual sequences were prepared by chemical synthesis.
The DNA pool obtained from 15 rounds of in vitro selection was amplified by PCR using Illumina seqencing primers tagged with unique barcodes.

tag: time


title: e12.5 mouse MGE, WT_1