title: M07E-IgG

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description: CUT&Tag

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.1)
Peaks were identified using MACS2 (v2.0.10)
Assembly: hg38
Supplementary files format and content: bw files for each Sample
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).


title: Male_C26-Cisplatin_5

status: Public on Aug 12 2026

type: SRA

city: Fayetteville

first: Ana

middle: Regina

last: Cabrera

state: AR

address: 155 Stadium Dr

country: USA

institute: University of Arkansas

description: Library name: 72

library_source: transcriptomic

data_processing:
Raw sequencing reads were assessed for quality using the software FastQC and summarized using MultiQC.
Adapter sequences and low-quality bases (Phred score < 25) were removed using fastp. Reads shorter than 20 bp after trimming were discarded.
Transcript abundances were quantified using the mapping-based mode of Salmon.
Transcript-level estimates were imported into R using the tximport package to summarize expression at the gene level.
Raw counts were processed using edgeR. Counts per million (CPM) were calculated and lowly expressed genes were filtered based on CPM thresholds. Data were normalized using trimmed mean of M-values (TMM) and differential gene expression analysis was performed using limma with the voom transformation. Genes with an adjusted p-value (FDR) < 0.05 were considered significantly differentially expressed.
Assembly: Mus musculus genome assembly mm39 (GRCm39).
Supplementary files format and content: Processed data files include normalized gene expression per sample

molecule: total RNA

organism: Mus musculus

source_name: Gastrocnemius

extract_protocol:
TRI-zol and PureLink RNA Mini Kit
Total RNA was extracted from gastrocnemius muscle and RNA libraries were prepared by the Clinical Genomics Center at the Oklahoma Medical Research Foundation (OMRF, USA). Libraries were constructed for Illumina sequencing and sequenced using 150-bp paired-end reads to a depth of approximately 20 million reads per sample on an Illumina platform.

tag: tissue

value: Gastrocnemius

tag: Sex

value: Male

tag: cancer

tag: chemotherapy

value: Cisplatin

tag: batch


title: M07E-BRD4

city: Suzhou

country: China

description: CUT&Tag

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: genotype

value: WT

tag: treatment


title: Male_C26-Cisplatin_4

description: Library name: 71


title: MSC3-berberine

city: guangzhou

first: Wu

middle: Meng

last: ye

state: Guangdong

address: Guangzhou Yuexiu

department: The Biotherapy Center,

institute: the Third Affiliated Hospital, Sun Yat-Sen University

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  and 2 ng/mL basic fibroblast growth factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmentedninto short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: mesenchymal cells were treated with 5μM berberine for 24h

value: umbilical cord

value: mesenchymal stem cells

tag: cell type

value: 5uM berberine 24h


title: Wild type neurons-22

city: New York

first: Michelle E.

last: Ehrlich

state: NY

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired-end RNA sequencing FASTQ files for all samples were aligned to Homo sapiens Reference genome (Grch38) using STAR read aligner and mapped reads were summarized to gene counts using subread function of FeatureCounts. Genes with expression (< 1 FPKM) across all samples were filtered from all subsequent analysis. Hierarchical clustering and Principal component analysis (PCA) were preformed as part of quality control to visualize biological variance between replicates, which were further exhibited by Volcano plots and Venn diagrams. We then performed differential gene expression analysis to compare all cell types with each other on normalized counts with EdgeR. Multiple biological replicates were used for all comparative analysis. Differentially expressed genes (DEGs) were identified at a false discovery rate (FDR) of 0.05. To identify biological pathways that may be differentially dysregulated by MIR155KO or MIR155 overexpression, we performed gene set enrichment analysis (GSEA) on the identified DEGs by using Enrichr, GSEA-MSIGDB and IPA (Ingenuity Pathways Analysis), where we identified enriched biological pathways, gene ontology sets, and mRNA targets of miRNA at an adjusted p-value < 0.05.
Assembly: Homo sapiens Reference genome (Grch38)

source_name: Differentiated human Induced pluripotent stem cells

growth_protocol: hiPSCs were maintained in 6-well plates (Corning) in feeder-free conditions using Geltrex in complete mTeSR1 medium in a humidified incubator (5% CO2, 37°C).

extract_protocol:
RNA isolation was performed on the lysates of WT, MIR155KO Clone 5 and MIR155KO Clone 25 hiPSC-derived cells, and MIR155-overexpressing NSCs and cortical neurons, according to the manufacturer’s protocol (miRNeasy mini-kit, Qiagen). Isolated RNA samples were submitted to Novogene Corporation Inc. for analysis of RNA quality and integrity.
All samples passed quality control, and RNA-seq libraries were prepared for sequencing using NovaSeq

treatment_protocol:
For neural differentiation to generate NSCs, hiPSCs were dissociated with Accutase and replated on 12-well tissue culture plates coated with Geltrex in complete mTeSR1 medium with 10 µM ROCK inhibitor. When cells were 100% confluent, the medium was replaced with Neural Induction medium (NIM, 50% DMEM/F12 medium, 50% Neurobasal medium, 2% B27 minus Vitamin A, 1% N2 supplement, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) (day in vitro 0 (DIV0)) and maintained for 15 days. Inhibitors used in dual-SMAD inhibition protocol (LDN/SB/XAV, DIV0-10; XAV, DIV11-15;) included LDN193189 (100 nM), SB431542 (10 µM) and XAV939 (1.0 µM). On DIV15 hiPSC-derived NSCs were dissociated using Accutase and can be stocked in Synth-a-Freeze™ Cryopreservation Medium (Thermo Fisher Scientific) in liquid Nitrogen tank.
For terminal differentiation to generate functional cortical neurons, hiPSC-derived NSCs (DIV15) were replated at 200,000-300,000 cells/cm2 in NIM medium with 10 µM ROCK inhibitor on dried poly-l-ornithine (Sigma-Aldrich) and laminin-coated 6-well plates or 8-well slide chambers. Cells were left to adhere overnight and on DIV16 NIM medium with ROCK inhibitor was replaced with Neuron Maturation media (BrainPhys™ Neuronal Medium, 2% B27 with Vitamin A, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) supplemented with PD0325901 (10 µM), SU5402 (10 µM), DAPT (10 µM), BDNF (40 ng/mL), GDNF (40 ng/mL), Laminin (1.0 µg/mL), dBcAMP (250 µM) and L-Ascorbic acid (200 µM). During DIV16-23 Neuron Maturation media were half-changed every other day. After DIV24, the medium was replaced with Neuronal Maintenance media (BrainPhys™ Neuronal Medium, 2% B27 with Vitamin A, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) supplemented with BDNF (40 ng/mL), GDNF (40 ng/mL), Laminin (1.0 µg/mL), dBcAMP (250 µM) and L-Ascorbic acid (200 µM). After DIV32, hiPSC-derived cortical neurons were active at this stage which can be confirmed with Ca2+ imaging. Between DIV50 and DIV60 hiPSC-derived cortical neurons were used for electrophysiological recordings.

value: Wild type neurons

value: hiPSC differentiation


title: APACT13

type: RNA

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

hyb_protocol: 15 µg of fragmented biotin-labeled cRNA was hybridized to Affymetrix Human Genome U13 Plus 2.0 Array

scan_protocol: standard Affymetrix protocol

data_processing: Raw data was normalized by the MAS5.0 algorithm and log2-transformed (log2(x+1))

label: biotin

source_name: tumor tissue

label_protocol: total RNA was used to prepare biotin-labeled cRNA using the Affymetrix GeneChip Kit according to the manufacturer’s protocol

extract_protocol: RNA was isolated from the tumor tissue with the DNA/RNA AllPrep Mini Kit (Qiagen) according to the manufactors instruction

tag: dna methylation-based risk group

value: Low Risk 2

value: pediatric adrencocortical tumor


title: Male_C26-Cisplatin_3

description: Library name: 70


title: APACT26


title: MSC3

value: no treatment


title: Wild type neurons-14

value: Differentiated human Induced pluripotent stem cells


title: Wild type neurons-13


title: Male_C26-Cisplatin_2

description: Library name: 69


title: Male_C26-Cisplatin_1

description: Library name: 68


title: MSC2-berberine


title: MSC2


title: Wild type neurons-12


title: APACT27

value: Low Risk 3


title: Male_C26-PTX_6

description: Library name: 67

value: Paclitaxel


title: Wild type neurons-11


title: APACT14


title: Male_C26-PTX_5

description: Library name: 66


title: MSC1-berberine


title: co-culture with U251_replicate6

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

description:
Library name: CoCul_U251_n6
data2_raw_counts.csv

data_processing:
Demultiplexing of pooled libraries by Illumina BaseSpace with BCL Convert (3.10.4)
Quality-, adapter- and polyA-trimming with Cutadapt (version 1.18)
Alignment to the human genome (GRCh38) using STAR (version 2.7.10a) with the following parameters: --alignEndsType EndToEnd --outSAMattributesNH HI AS nM NM MD jM jI --outFilterMultimapNmax 10
transcript counts were determined using htseq-count (2.0.2)
Assembly: GRCh38
Supplementary files format and content: csv files include raw counts for each sample

molecule: polyA RNA

source_name: primary human monocytes

growth_protocol: Human CD14-positive monocytes were isolated from PBMCs with MACS and cultured in RPMI with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin, and 50 ng/mL recombinant human M-CSF.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kits (Qiagen) or TRIzol (Thermo Fisher Scientific).
Sequencing libraries were prepared with the QuantSeq 3‘mRNA-Seq V2 Library Prep Kit FWD with UDI (12 nt).

treatment_protocol: Co-culture was introduced by adding transwell inserts (0.4 µm) with pre-seeded LN229 or U251 cells to primary human monocytes and incubation for 24 hours. Cells were treated with 50 pg/mL human recombinant GM-CSF or 0.5 µg/mL Human GM-CSF Antibody (biotechne, catalog: AF-215-NA) or Normal Goat IgG Control (biotechne, catalog: AB-108-C) for 24 hours.

value: primary human monocytes

tag: culture-condition

value: co-culture with U251


title: APACT11


title: APACT38

value: Low Risk 1


title: MSC1


title: APACT16

value: High Risk


title: co-culture with LN229_replicate6

description:
Library name: CoCul_LN229_n6
data2_raw_counts.csv

value: co-culture with LN229


title: ATO shADAR1

city: LA JOLLA

first: QINGFEI

last: JIANG

state: CA

address: 2880 TORREY PINES SCENIC DR

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

description: scRNA-seq of cord blood CD34 HSPC transduced with shADAR1 and cultured in ATO for 2 weeks

library_source: transcriptomic single cell

data_processing:
Low-quality cells were removed using these quality control criteria ( <20% genomic reads and/or < 1000 genes were detected per barcode). Cell type specific t-distribution stochastic neighbor embedding (tSNE) cluster was analysis based on specified marker genes that define each cell type. Statistical analysis of scRNA-seq data was carried out using core functions of R programming language and the library Seurat (Satija et al., 2015). After reading the raw 10X data, filtering cells for fraction of mitochondrially-encoded genes (< 20%) and for number of genes detected per cell (>1500 in shCTRL cells and >500 in shADAR1 cells), we obtained 4890 shCTRL cells and 1049 shADAR1 cells for further analysis. Cells from these two samples were integrated using SCTransform (Hafemeister and Satija, 2019). We detected 3788 genes and 16,273 total reads per each cell on average. The two-dimensional UMAP and clustering was done using Seurat’s functions. Differential expression (DE) analysis between clusters and/or genotypes was done using the bootstrap algorithm of Pollard and van der Laan (Laan, 2005) using SCTransform-ed expression levels. Significance of each gene in each comparison was expressed as local false discovery rate lfdr using Efron’s Empirical Bayes approach. Genes in a DE comparison were subject to Gene Set Enrichment Analysis using a fast implementation fgsea 102. UMAP plots, violin plots and heatmaps are standard functions of Seurat.
Assembly: GRCh38.p12
Supplementary files format and content: Raw 10X count matrix

source_name: cord blood

extract_protocol:
Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3
Single cell will be barcoded using a 10X Chromium Controller (10x Genomics) and sequencing libraries were prepared with reagents from a Chromium Single Cell 3’ kit. All sequencing will be performed on Illumina NovaSeq. Library will be sequenced at a typical depth of 20-50x103 reads per cell on average for scRNA-seq.

value: cord blood

value: Lymphoid progenitors

value: WT


title: Male_C26-PTX_3

description: Library name: 64

value: Gastrocnemius

value: Male


title: mono-culture, GMCSF_replicate6

description:
Library name: MoCul_GMCSF_n6
data2_raw_counts.csv

value: mono-culture

value: GMCSF (50 pg/mL)


title: ATO shCTRL

description: scRNA-seq of cord blood CD34 HSPC transduced with control shRNA and cultured in ATO for 2 weeks

value: shCTRL


title: APACT21

value: Low Risk 2

value: pediatric adrencocortical tumor


title: mono-culture_replicate6

description:
Library name: MoCul_n6
data2_raw_counts.csv

value: no treatment


title: APACT99

type: genomic

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium HumanMethylation BeadChip (EPIC / EPIC v2) according to the manufacturer’s instructions (Illumina).

scan_protocol: Arrays were scanned using the Illumina iScan System, and raw image data were processed with Illumina GenomeStudio (Methylation Module).

data_processing:
Raw IDAT files were processed, normalized, filtered and batch effect corrected as described in Capper et. al. 2018 by using the Bioconductor package minfi
Processed values represent Beta values (β-values), i.e. the ratio of methylated probe intensity to overall intensity (M / [M+U+100]), ranging from 0 (unmethylated) to 1 (fully methylated). Values were derived from IDAT files after background correction and normalization using the minfi.

label: Cy3 and Cy5

source_name: tumor

label_protocol: llumina Infinium HD Methylation Assay; single-base extension with biotin- and DNP-labeled nucleotides according to the manufacturer’s protocol.

extract_protocol: DNA was isolated from the tumor tissue with the DNA/RNA AllPrep Mini Kit (Qiagen) according to the manufactors instruction

value: tumor

tag: clinical presentation

tag: age at diagnosis (years)

tag: overall survival (years)

tag: tumor stage

value: IV

value: Female

tag: dna methylation based subgroup

value: Low Risk 3


title: APACT22

value: Low Risk 1


title: APACT1

value: High Risk


title: Male_C26-PTX_1

description: Library name: 62

value: Paclitaxel


title: APACT98

value: I


title: co-culture with U251_replicate5

description:
Library name: CoCul_U251_n5
data2_raw_counts.csv

value: primary human monocytes

value: co-culture with U251


title: Male_C26-5FU_8

description: Library name: 61

value: Gastrocnemius

value: Male

value: 5 fluorouracil


title: co-culture with LN229_replicate5

description:
Library name: CoCul_LN229_n5
data2_raw_counts.csv

value: co-culture with LN229


title: APACT23


title: APACT97


title: Male_C26-5FU_7

description: Library name: 60


title: mono-culture, GMCSF_replicate5

description:
Library name: MoCul_GMCSF_n5
data2_raw_counts.csv

value: mono-culture

value: GMCSF (50 pg/mL)


title: APACT4

value: pediatric adrencocortical tumor


title: APACT96

value: tumor

value: Virilization


title: APACT8


title: APACT9


title: Male_C26-5FU_6

description: Library name: 59


title: mono-culture_replicate5

description:
Library name: MoCul_n5
data2_raw_counts.csv

value: no treatment


title: APACT95

value: Cushings

value: Female

value: Low Risk 3


title: APACT5

value: Low Risk 1


title: Male_C26-5FU_5

description: Library name: 58


title: co-culture with U251_replicate4

description:
Library name: CoCul_U251_n4
data2_raw_counts.csv


title: APACT2


title: APACT94

value: I


title: co-culture with LN229_replicate4

description:
Library name: CoCul_LN229_n4
data2_raw_counts.csv

value: primary human monocytes


title: Male_C26-5FU_4

description: Library name: 57


title: APACT93

value: Hypertension/Conn


title: Male_C26-5FU_3

description: Library name: 56

value: Gastrocnemius


title: APACT92

value: II

value: Male

value: Low Risk 2


title: APACT10


title: mono-culture, GMCSF_replicate4

description:
Library name: MoCul_GMCSF_n4
data2_raw_counts.csv

value: mono-culture


title: APACT6


title: APACT12


title: Male_C26-5FU_2

description: Library name: 55

value: 5 fluorouracil


title: APACT91


title: mono-culture_replicate4

description:
Library name: MoCul_n4
data2_raw_counts.csv


title: Male_C26-5FU_1

description: Library name: 54


title: co-culture with U251_replicate3

description:
Library name: CoCul_U251_n3
data2_raw_counts.csv

value: co-culture with U251


title: APACT36

value: pediatric adrencocortical tumor


title: APACT90

value: tumor


title: Wild type neurons-21

value: Differentiated human Induced pluripotent stem cells

value: Wild type neurons

value: hiPSC differentiation


title: Male_C26-Saline_8

description: Library name: 53

value: Saline


title: co-culture with LN229_replicate3

description:
Library name: CoCul_LN229_n3
data2_raw_counts.csv

value: co-culture with LN229

value: no treatment


title: APACT9

value: Low Risk 1


title: APACT17

value: High Risk


city: Ithaca

first: Yicheng

last: Luo

address: 215 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: Library name: Luciferase_Panx_tethering_4yrs_Maternal_no_Panx_rep2

library_source: other

data_processing:
smRNA-seq reads were trimmed by Cutadapt to rRNA and filter out those shorter than 15 bp after trimming
Select reads size 21-22bp (siRNA) and 23-29bp (piRNA) and 21-30bp (small RNA)
mapped to dm6 genome, mapped to luciferase reporter. (parameters: -v 0 -a -m 1 -t --best --strata), and plus, minus strand of genome regions and vectors were separate. The luciferase reporter was inserted at Chr3L:19204358.
smRNA profilings were generated by Matlab after mapping
Assembly: dm3 and dm6
Supplementary files format and content: xlsx
Supplementary files format and content: bw

molecule: other

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Fly stocks were maintained at 25ºC on standard diet

extract_protocol:
Total smRNA from ovary was isolated with Ribozol reagent and do size selection from 19nt to 30nt. For ChIP, ovaries were fixed using Paraformaldehyde (PFA) at a final concentration of 1.8% in PBS  for 10min at RT. Samples were quenched by 125mM glycine for 5 min at RT and washed 3 times in PBS. Ovaries were afterwards slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM NaCl; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.35% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Lysates were sonicated using Bioruptor (Diagenode, 30 cycles of 30sec ON, 30sec OFF) then add IP diluted buffer (20mM Tris pH7.4; 150mM NaCl; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM). Supernatants were pre-cleared for 2h at 4°C using Dynabeads Protein G (Invitrogen) beads. 5% of samples were saved for inputs. The rest of the lysates were incubated with antibodies for 2h to overnight at 4°C, then added BSA and DNA blocked Dynabeads Protein G beads and incubated for 3h at 4°C beads The beads were washed 5 times at 4°C with LiCl IP wash buffer (10mM  Tris pH 7.4;  500mM  LiCL;  1%NP40/Igepal;  1%  Sodium  Deoxycholate) and once with TE. Protein was digested with proteinase K for 3hrs at 55°C and reverse-crosslinked by incubation at 65°C overnight. DNA was extracted by phenol:chloroform standard protocol.
ChIPseq libraries were made by NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, smRNAseq libraries were made by using NEBNext® Small RNA Library Prep Set for Illumina®. Libraries were sequenced on the Illumina HiSeq 2000 platform.

treatment_protocol: Flies were fed with yeast for 2-3 days prior to dissection

value: Ovary

value: pNanos-Luc-BoxB;+


title: Male_C26-Saline_7

description: Library name: 52

value: Gastrocnemius

value: Male


title: mono-culture, GMCSF_replicate3

description:
Library name: MoCul_GMCSF_n3
data2_raw_counts.csv

value: primary human monocytes

value: mono-culture

value: GMCSF (50 pg/mL)


title: APACT89

value: II

value: Female

value: Low Risk 2


title: mono-culture_replicate3

description:
Library name: MoCul_n3
data2_raw_counts.csv


title: APACT88

value: tumor

value: I


title: Male_C26-Saline_5

description: Library name: 50

value: Saline


description: Library name: Luciferase_Panx_tethering_4yrs_Maternal_rep2

value: pNanos-Luc-BoxB;lambdaN-Panx


description: Library name: Luciferase_Panx_tethering_4yrs_Maternal_no_Panx_rep1


title: co-culture with U251_replicate2

description:
Library name: CoCul_U251_n2
data2_raw_counts.csv

value: co-culture with U251

value: no treatment


title: APACT87


title: co-culture with LN229_replicate2

description:
Library name: CoCul_LN229_n2
data2_raw_counts.csv

value: co-culture with LN229


title: Male_C26-Saline_4

description: Library name: 49


description: Library name: Luciferase_Panx_tethering_4yrs_Maternal_rep1

value: Ovary


title: GFP_HP1a_ChIP_IP_rep2

description: Library name: GFP_HP1a_ChIP_IP_rep2


title: APACT85


title: Male_C26-PTX_4

description: Library name: 65

value: Paclitaxel


title: GFP_HP1a_ChIP_Input_rep2

description: Library name: GFP_HP1a_ChIP_Input_rep2


title: Male_C26-Saline_3

description: Library name: 48

value: Gastrocnemius


title: mono-culture, GMCSF_replicate2

description:
Library name: MoCul_GMCSF_n2
data2_raw_counts.csv


title: Male_C26-Saline_2

description: Library name: 47

value: Male


title: mono-culture_replicate2

description:
Library name: MoCul_n2
data2_raw_counts.csv

value: primary human monocytes


title: APACT84


title: APACT86


title: Male_C26-Saline_1

description: Library name: 46


title: APACT83

value: Virilization


title: Male_C26-PTX_2

description: Library name: 63


title: co-culture with U251_replicate1

description:
Library name: CoCul_U251_n1
data2_raw_counts.csv


title: Male_PBS-Saline_8

description: Library name: 45

value: PBS


title: GFP_HP1a_ChIP_IP_rep1

description: Library name: GFP_HP1a_ChIP_IP_rep1


title: GFP_HP1a_ChIP_Input_rep1

description: Library name: GFP_HP1a_ChIP_Input_rep1


title: APACT82

value: Cushings

value: II


title: Male_PBS-Saline_7

description: Library name: 44


title: GFP_Rhi_ChIP_IP_rep2

description: Library name: GFP_Rhi_ChIP_IP_rep2


title: APACT81

value: Low Risk 2


title: GFP_Rhi_ChIP_Input_rep2

description: Library name: GFP_Rhi_ChIP_Input_rep2


title: co-culture with LN229_replicate1

description:
Library name: CoCul_LN229_n1
data2_raw_counts.csv


title: mono-culture, GMCSF_replicate1

description:
Library name: MoCul_GMCSF_n1
data2_raw_counts.csv

value: mono-culture

value: GMCSF (50 pg/mL)


title: Male_PBS-Saline_6

description: Library name: 43

value: Saline


title: mono-culture_replicate1

description:
Library name: MoCul_n1
data2_raw_counts.csv


title: APACT80

value: tumor


title: GFP_Rhi_ChIP_IP_rep1

description: Library name: GFP_Rhi_ChIP_IP_rep1


title: Male_PBS-Saline_5

description: Library name: 42


title: co-culture, anti-GMCSF_replicate6

description:
Library name: CoCul_aGMCSF_n6
data1_raw_counts.csv

value: anti-GMCSF


title: APACT8

value: I

value: Female

value: Low Risk 1


title: GFP_Rhi_ChIP_Input_rep1

description: Library name: GFP_Rhi_ChIP_Input_rep1

value: Ovary


title: mono-culture, anti-GMCSF_replicate6

description:
Library name: MoCul_aGMCSF_n6
data1_raw_counts.csv


title: APACT79


title: Male_PBS-Saline_4

description: Library name: 41

value: Gastrocnemius


title: Rhi_ChIP_IP_rep2

description: Library name: Rhi_ChIP_IP_rep2


title: Male_PBS-Saline_3

description: Library name: 40

value: Male


title: Rhi_ChIP_Input_rep2

description: Library name: Rhi_ChIP_Input_rep2


title: co-culture, IgG_replicate6

description:
Library name: CoCul_IgG_n6
data1_raw_counts.csv

value: primary human monocytes

value: co-culture with LN229

value: IgG


title: APACT77


title: Male_PBS-Saline_2

description: Library name: 39

value: PBS


title: Rhi_ChIP_IP_rep1

description: Library name: Rhi_ChIP_IP_rep1


title: APACT78

value: II


title: co-culture, anti-GMCSF_replicate5

description:
Library name: CoCul_aGMCSF_n5
data1_raw_counts.csv


title: APACT76

value: Low Risk 2


title: mono-culture, IgG_replicate6

description:
Library name: MoCul_IgG_n6
data1_raw_counts.csv

value: mono-culture


title: Male_PBS-Saline_1

description: Library name: 38


title: APACT75

value: Virilization


title: Luciferase_Panx_tethering_4yrs_pat_rep2

description: Library name: Luciferase_Panx_tethering_4yrs_pat_rep2


title: Female_C26-Cisplatin_6

description: Library name: 37

value: Cisplatin


title: mono-culture, anti-GMCSF_replicate5

description:
Library name: MoCul_aGMCSF_n5
data1_raw_counts.csv


title: Female_C26-Cisplatin_5

description: Library name: 36


title: APACT74

value: tumor


title: Rhi_ChIP_Input_rep1

description: Library name: Rhi_ChIP_Input_rep1


title: co-culture, IgG_replicate5

description:
Library name: CoCul_IgG_n5
data1_raw_counts.csv


title: mono-culture, IgG_replicate5

description:
Library name: MoCul_IgG_n5
data1_raw_counts.csv


title: Female_C26-Cisplatin_4

description: Library name: 35


title: Luciferase_Panx_tethering_4yrs_pat_rep1

description: Library name: Luciferase_Panx_tethering_4yrs_pat_rep1


title: APACT73


title: Female_C26-Cisplatin_3

description: Library name: 34


title: Luciferase_Panx_tethering_4yrs_mat_rep2

description: Library name: Luciferase_Panx_tethering_4yrs_mat_rep2

value: pNanos-Luc-BoxB;lambdaN-Panx


title: APACT72


title: co-culture, anti-GMCSF_replicate4

description:
Library name: CoCul_aGMCSF_n4
data1_raw_counts.csv

value: anti-GMCSF


title: Female_C26-Cisplatin_2

description: Library name: 33

value: Female


title: Luciferase_Panx_tethering_4yrs_mat_rep1

description: Library name: Luciferase_Panx_tethering_4yrs_mat_rep1


title: mono-culture, anti-GMCSF_replicate4

description:
Library name: MoCul_aGMCSF_n4
data1_raw_counts.csv


description: Library name: Luciferase_mkate2_tethering_4yrs_oxidized_rep2

value: Oxidization


title: APACT71

value: IV

value: Low Risk 1


title: co-culture, IgG_replicate4

description:
Library name: CoCul_IgG_n4
data1_raw_counts.csv


title: APACT70

value: I

value: Male


title: Female_C26-Cisplatin_1

description: Library name: 32

value: Gastrocnemius


title: Female_C26-PTX_7

description: Library name: 31

value: Paclitaxel


title: APACT7


title: mono-culture, IgG_replicate4

description:
Library name: MoCul_IgG_n4
data1_raw_counts.csv

value: primary human monocytes

value: IgG


description: Library name: Luciferase_mkate2_tethering_4yrs_oxidized_rep1

value: Ovary


title: Female_C26-PTX_6

description: Library name: 30


description: Library name: Luciferase_Panx_tethering_4yrs_oxidized_rep2


title: co-culture, anti-GMCSF_replicate3

description:
Library name: CoCul_aGMCSF_n3
data1_raw_counts.csv

value: co-culture with LN229


title: APACT69

value: Virilization

value: II


title: APACT68

value: tumor


title: mono-culture, anti-GMCSF_replicate3

description:
Library name: MoCul_aGMCSF_n3
data1_raw_counts.csv

value: mono-culture


title: Luciferase_mkate2_tethering_4yrs_rep2

description: Library name: Luciferase_mkate2_tethering_4yrs_rep2


title: Female_C26-PTX_5

description: Library name: 29


description: Library name: Luciferase_Panx_tethering_4yrs_oxidized_rep1

value: pNanos-Luc-BoxB;lambdaN-Panx


title: Female_C26-PTX_4

description: Library name: 28

value: Female


title: co-culture, IgG_replicate3

description:
Library name: CoCul_IgG_n3
data1_raw_counts.csv


title: APACT67


title: mono-culture, IgG_replicate3

description:
Library name: MoCul_IgG_n3
data1_raw_counts.csv


title: Luciferase_mkate2_tethering_4yrs_rep1

description: Library name: Luciferase_mkate2_tethering_4yrs_rep1


title: Luciferase_Panx_tethering_4yrs_rep2

description: Library name: Luciferase_Panx_tethering_4yrs_rep2


title: APACT66


title: Female_C26-PTX_2

description: Library name: 26


title: Female_C26-PTX_3

description: Library name: 27


title: Female_C26-PTX_1

description: Library name: 25


title: APACT65


title: co-culture, anti-GMCSF_replicate2

description:
Library name: CoCul_aGMCSF_n2
data1_raw_counts.csv

value: anti-GMCSF


title: Luciferase_Panx_tethering_4yrs_rep1

description: Library name: Luciferase_Panx_tethering_4yrs_rep1


title: mono-culture, anti-GMCSF_replicate2

description:
Library name: MoCul_aGMCSF_n2
data1_raw_counts.csv


title: APACT64


title: Luciferase_mkate2_tethering_rep2

description: Library name: Luciferase_mkate2_tethering_rep2


title: Female_C26-FU_8

description: Library name: 24

value: 5 fluorouracil


title: APACT63

value: Low Risk 1


title: co-culture, IgG_replicate2

description:
Library name: CoCul_IgG_n2
data1_raw_counts.csv


title: Luciferase_mkate2_tethering_rep1

description: Library name: Luciferase_mkate2_tethering_rep1


title: Female_C26-FU_7

description: Library name: 23


title: APACT62


title: mono-culture, IgG_replicate2

description:
Library name: MoCul_IgG_n2
data1_raw_counts.csv


title: APACT61


title: co-culture, anti-GMCSF_replicate1

description:
Library name: CoCul_aGMCSF_n1
data1_raw_counts.csv


title: Female_C26-FU_6

description: Library name: 22


title: Luciferase_Panx_tethering_rep2

description: Library name: Luciferase_Panx_tethering_rep2


title: Luciferase_Panx_tethering_rep1

description: Library name: Luciferase_Panx_tethering_rep1


title: APACT60

value: III


title: Female_C26-FU_5

description: Library name: 21


title: mono-culture, anti-GMCSF_replicate1

description:
Library name: MoCul_aGMCSF_n1
data1_raw_counts.csv


title: Female_C26-FU_4

description: Library name: 20


title: H3KK9me3_White_GLKD_ChIP_IP_rep2

description: Library name: White_GLKD_H3K9_ChIP_IP_2nd


title: co-culture, IgG_replicate1

description:
Library name: CoCul_IgG_n1
data1_raw_counts.csv


title: APACT6


title: Rhi_White_GLKD_ChIP_IP_rep2

description: Library name: White_GLKD_Rhi_ChIP_IP_2nd


title: Female_C26-FU_3

description: Library name: 19


title: mono-culture, IgG_replicate1

description:
Library name: MoCul_IgG_n1
data1_raw_counts.csv


title: APACT59

value: I


title: Female_C26-FU_2

description: Library name: 18

value: Gastrocnemius


title: White_GLKD_ChIP_Input_rep2

description: Library name: White_GLKD_ChIP_input_2nd


title: U251, rep3

description: Library name: U251_n3

data_processing:
Demultiplexing of pooled libraries by Illumina BaseSpace with BCL Convert (4.2.7)
Quality-, adapter- and polyA-trimming with Cutadapt (version 1.18)
Alignment to the human genome (GRCh38) using STAR (version 2.7.10a) with the following parameters: --alignEndsType EndToEnd --outSAMattributesNH HI AS nM NM MD jM jI --outFilterMultimapNmax 10
transcript counts were determined using htseq-count (2.0.2)
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: Human glioblastoma cell lines were cultured in RPMI with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin for 48 hours.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kits (Qiagen).
Sequencing libraries were prepared with the QuantSeq 3‘mRNA-Seq V2 Library Prep Kit FWD with UDI (12 nt).

value: glioblastoma cells

value: no treatment


title: H3KK9me3_White_GLKD_ChIP_IP_rep1

description: Library name: White_GLKD_H3K9_ChIP_IP_1st


title: APACT58

value: Male


title: Female_C26-FU_1

description: Library name: 17


title: APACT57


title: U87, rep3

description: Library name: U87_n3


title: Female_C26-Saline_8

description: Library name: 16


title: T98G, rep3

description: Library name: T98G_n3


title: Rhi_White_GLKD_ChIP_IP_rep1

description: Library name: White_GLKD_Rhi_ChIP_IP_1st

value: Ovary


title: APACT56


title: Female_C26-Saline_7

description: Library name: 15

value: Saline


title: White_GLKD_ChIP_Input_rep1

description: Library name: White_GLKD_ChIP_input_1st


title: LN229, rep3

description: Library name: LN229_n3


title: APACT55

value: High Risk


title: H3KK9me3_Panx_GLKD_ChIP_IP_rep2

description: Library name: Panx_GLKD_H3K9_ChIP_IP_2nd


title: Female_C26-Saline_6

description: Library name: 14


title: U251, rep2

description: Library name: U251_n2


title: APACT54

value: II


title: Rhi_Panx_GLKD_ChIP_IP_rep2

description: Library name: Panx_GLKD_Rhi_ChIP_IP_2nd


title: Female_C26-Saline_5

description: Library name: 13


title: APACT53

value: tumor

value: IV


title: U87, rep2

description: Library name: U87_n2


title: T98G, rep2

description: Library name: T98G_n2


title: Female_C26-Saline_4

description: Library name: 12


title: Panx_GLKD_ChIP_Input_rep2

description: Library name: Panx_GLKD_ChIP_input_2nd


title: APACT52


title: Female_C26-Saline_3

description: Library name: 11


title: H3KK9me3_Panx_GLKD_ChIP_IP_rep1

description: Library name: Panx_GLKD_H3K9_ChIP_IP_1st


title: LN229, rep2

description: Library name: LN229_n2


title: Rhi_Panx_GLKD_ChIP_IP_rep1

description: Library name: Panx_GLKD_Rhi_ChIP_IP_1st


title: APACT51

value: Cushings


title: Female_C26-Saline_2

description: Library name: 10

value: Female


title: U251, rep1

description: Library name: U251_n1


title: APACT50


title: Panx_GLKD_ChIP_Input_rep1

description: Library name: Panx_GLKD_ChIP_input_1st


title: Female_C26-Saline_1

description: Library name: 9


title: APACT5


title: U87, rep1

description: Library name: U87_n1


title: MI08850_Ubi-GFP_White_GLKD_rep2

description: Library name: MI08850_Ubi-GFP_White_GLKD_rep2


title: Female_PBS-Saline_8

description: Library name: 8

value: PBS


title: MI08850_Ubi-GFP_White_GLKD_rep1

description: Library name: MI08850_Ubi-GFP_White_GLKD_rep1


title: Female_PBS-Saline_7

description: Library name: 7


title: APACT49


title: T98G, rep1

description: Library name: T98G_n1


title: APACT48


title: LN229, rep1

description: Library name: LN229_n1


title: MI07308_Ubi-GFP_White_GLKD_rep2

description: Library name: MI07308_Ubi-GFP_White_GLKD_rep2


title: Female_PBS-Saline_6

description: Library name: 6


title: IFN, rep3

description: Library name: CoCul_n3

data_processing:
Demultiplexing of pooled libraries by Illumina BaseSpace with BCL Convert (3.10.4)
Quality-, adapter- and polyA-trimming with Cutadapt (version 1.18)
Alignment to the human genome (GRCh38) using STAR (version 2.7.10a) with the following parameters: --alignEndsType EndToEnd --outSAMattributesNH HI AS nM NM MD jM jI --outFilterMultimapNmax 10
transcript counts were determined using htseq-count (2.0.2)
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using RNeasy Mini or Micro Kits (Qiagen).
Sequencing libraries were prepared with the QuantSeq 3‘mRNA-Seq V2 Library Prep Kit FWD with UDI (12 nt).

treatment_protocol: Co-culture was introduced by adding primary human monocytes to pre-seeded LN229 cells and incubation for 48 hours. Cells were treated with 1 ng/mL IFN-β for 6 h.

value: primary human monocytes

value: mono-culture, 1 ng/mL IFN-β for 6h


title: APACT47


title: MI07308_Ubi-GFP_White_GLKD_rep1

description: Library name: MI07308_Ubi-GFP_White_GLKD_rep1


title: Female_PBS-Saline_5

description: Library name: 5


title: co-culture, rep3

description: Library name: MoCul_IFN_n3

value: co-culture with LN229, no treatment


title: APACT46


title: MI08850_Ubi-GFP_Panx_GLKD_rep2

description: Library name: MI08850_Ubi-GFP_Panx_GLKD_rep2


title: Female_PBS-Saline_4

description: Library name: 4


title: APACT45

value: Low Risk 3


title: mono-culture, rep3

description: Library name: MoCul_n3

value: mono-culture, no treatment


title: APACT44

value: Virilization


title: MI08850_Ubi-GFP_Panx_GLKD_rep1

description: Library name: MI08850_Ubi-GFP_Panx_GLKD_rep1


title: Female_PBS-Saline_3

description: Library name: 3

value: Gastrocnemius


title: co-culture, rep2

description: Library name: MoCul_IFN_n2


title: Female_PBS-Saline_2

description: Library name: 2


title: APACT43

value: Male

value: Low Risk 2


title: IFN, rep2

description: Library name: CoCul_n2


title: MI07308_Ubi-GFP_Panx_GLKD_rep2

description: Library name: MI07308_Ubi-GFP_Panx_GLKD_rep2

value: Ovary


title: MI07308_Ubi-GFP_Panx_GLKD_rep1

description: Library name: MI07308_Ubi-GFP_Panx_GLKD_rep1


title: mono-culture, rep2

description: Library name: MoCul_n2


title: APACT42

value: Low Risk 1


title: Female_PBS-Saline_1

description: Library name: 1

value: Saline


title: meningeal CD45-CD31+PDPN+ cells, 4T1-DM, ZOL+Ang2

city: Shanghai

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

description: Library name: Sample 3

data_processing:
Raw reads of fastq format were processed through fastp software. Use HISAT2 (2.2.1) to map reads to the reference genome. FeatureCounts (2.0.6) was used to count the reads numbers.
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes FPKM values for each sample

source_name: dura mater

extract_protocol:
For total RNA extraction: the GeneJET RNA Purification Micro Kit (Thermo Fisher Scientific) was used following the manufacturer' s instructions.
Using the isolated total RNA as the template, cDNA synthesis and amplification were performed with the Single Cell Full Length mRNA-Amplification Kit (Cat. No. N712-03, Vazyme), followed by purification with VAHTS DNA Clean Beads (Cat. No. N411-02, Vazyme). The purified cDNA was subjected to quality assessment via gel electrophoresis (Agilent 4200 Bioanalyzer) and Qubit 4.0 Fluorometer (Invitrogen). Library preparation for sequencing was conducted referring to the instructions of the TruePrep® DNA Library Prep Kit V2 (Cat. No. TD503-02, Vazyme).

value: dura mater

value: meningeal CD45-CD31+PDPN+ cells


title: H3K9me3_ChIP_IP_rep2

description: Library name: H3K9me3_ChIP_IP_rep2


title: APACT41

value: tumor

value: IV


title: IFN, rep1

description: Library name: CoCul_n1


title: Male_C26-Saline_6

description: Library name: 51


title: meningeal CD45-CD31+PDPN+ cells, 4T1-DM, ZOL

description: Library name: Sample 2

value: ZOL


title: co-culture, rep1

description: Library name: MoCul_IFN_n1

value: primary human monocytes


title: mono-culture, rep1

description: Library name: MoCul_n1


title: APACT4


title: H3K9me3_ChIP_Input_rep1

description: Library name: H3K9me3_ChIP_Input_rep1


title: H3K9me3_ChIP_IP_rep1

description: Library name: H3K9me3_ChIP_IP_rep1


title: APACT40

value: II

value: Female


title: H3K9me3_ChIP_Input_rep2

description: Library name: H3K9me3_ChIP_Input_rep2


title: 20 uM methionine culture for 14 days_22

city: Philadelphia

first: Erick

last: Mitchell-Velasquez

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed using atria v4.0.0 (default parameters)
Sequence reads were aligned to a synthetic hg38.dm6 genome using bowtie2 v2.5.1 (parameters - local, no-mixed, no-discordant)
Sam files were converted to sorted bam files using samtools v1.18 (parameters - sort, write-index, -o BAM)
The bam files were split into respective alignments (hg38 and dm6) using split_bam.py from spiker v1.0.5
Bigwigs and bed files with appropriate controls were generated after applying calculated spikeins using spiker.py v1.0.5 (parameters - spikeIn, -bw )
Assembly: hg38
Supplementary files format and content: BigWig files for each sample

source_name: VCaP

growth_protocol: VCaP parental and NNMT cells were maintained in methionine free DMEM supplemented with 10% dialyzed FBS and 20 uM methionine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ChIP was done following the Diagenode for histones
ChIP-seq libraries were made using NEBNext Ultra II FS DNA Library Prep

treatment_protocol: 20 uM methionine for 14 days for in vitro studies  and 0.12% methionine  diet for  in vivo studies

value: VCaP

value: epithelial

value: WT

value: physiological methionine levels

value: 14 Days


title: meningeal CD45-CD31+PDPN+ cells, 4T1-DM, PBS

description: Library name: Sample 1

value: PBS


title: WT to WT (anti-CD40L dataset)

city: Stony Brook

first: Kehan

last: Ren

address: 101 Nicolls Road

department: Medicine

institute: Stony Brook University

description: Library name: Sample 10

data_processing:
Demultiplexing, barcode processing, gene counting, and sample aggregation were performed using Cell Ranger v9.0.0 (10x Genomics) according to the manufacturer’s recommended pipeline.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values and matrix files

source_name: Bone marrow

extract_protocol:
Femurs were collected from euthanized mice and cleaned of surrounding soft tissue under sterile conditions. Bone marrow was flushed from each femur using sterile PBS containing 2% FBS and gently triturated to generate a single-cell suspension. The suspension was filtered through a 40-µm cell strainer to remove aggregates and debris. After centrifugation, the cell pellet was incubated in RBC lysis buffer to deplete red blood cells. Lysis was stopped by addition of excess PBS containing 2% FBS, followed by centrifugation and washing. The resulting nucleated bone marrow cells were resuspended in PBS containing 0.04% bovine serum albumin for downstream single-cell RNA-sequencing workflow. Cell concentration and viability were determined prior to loading onto the single-cell capture platform.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v4 platform with polyA-based mRNA capture, following the manufacturer’s protocol. Briefly, single cells were encapsulated, barcoded, reverse transcribed, and processed for 3′ gene expression library generation prior to Illumina sequencing.

value: Bone marrow

tag: dataset

value: anti-CD40L dataset

value: WT to WT


title: monolayer_P_3

city: Wuhan

first: Ying

last: Liu

address: Luojia Hill, Wuchang District

institute: Wuhan university

description: Library name: Sample6

data_processing:
Raw reads were processed with SOAPnuke software to obtain clean reads, which were then aligned to the mouse reference genome (GRCm38.p6) using HISAT.
Assembly: Raw sequencing reads were aligned to the Mus musculus reference genome GRCm38.p6 (RefSeq assembly accession: GCF_000001635.26) obtained from NCBI.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: jawbone

extract_protocol:
After 48h of culture, cell spheroids (3D) and monolayer culture (2D) were harvested, and total RNA was extracted using the EZNA HP Total RNA Kit (Omega Bio-Tek, Georgia, USA).
Library preparation and sequencing were performed by the Beijing Genomics Institute (BGI, Beijing, China), where single-stranded circular DNA libraries were constructed and sequenced on the DNBSEQ platform.

tag: tissue

value: jawbone

value: primary cells


title: Tet2-/- to Gsdmd-/- (anti-CD40L dataset)

description: Library name: Sample 9

value: Tet2-/- to Gsdmd-/-


title: APACT38

value: tumor

value: Cushings

value: IV

tag: Sex

value: Low Risk 1


title: 20 uM methionine culture for 14 days_21


title: monolayer_P_2

description: Library name: Sample5


title: Tet2-/- to WT with CD40L Blocking Antibody (anti-CD40L dataset)

description: Library name: Sample 8


title: APACT37

value: Virilization

value: II

value: Female


title: 20 uM methionine culture for 14 days_20

source_name: VCaP NNMT

value: VCaP NNMT

value: epithelial

value: NNMT overexpression


title: monolayer_P_1

description: Library name: Sample4


title: Tet2-/- to WT with IgG Control (anti-CD40L dataset)

description: Library name: Sample 7

value: Tet2-/- to WT with IgG Control


title: APACT36


title: 20 uM methionine culture for 14 days_19

value: physiological methionine levels

value: 14 Days


title: aggregate_P_3

description: Library name: Sample3


title: aggregate_P_2

description: Library name: Sample2


title: Arf-C cells, at Day 8 rep3

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

description:
Library name: Sample18
Column name in FPKMs_all_samples.txt: Arf-C_D8

data_processing:
Reads alignment: HiSat2
Reads count: featureCounts
Differentially expressed genes analysis: DESeq2
Assembly: mm10
Supplementary files format and content: Tabular files of normalized counts contain: ensembl gene id, sample name, gene name, chromosome, strand, gene length, biotype, description and tf family

growth_protocol: mESCs were cultured on 0,1 % gelatine in complete GMEM medium, supplemented with 15% fetal bovine serum, 1,000 U/mL leukaemia inhibitory factor, 1.0 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2.0 mM L-glutamine, 0.1 mM β-mercaptoethanol, 500 U/mL penicillin/streptomycin  at 37°C in 5% CO2. Cell culture medium was changed daily, and cells were routinely splitted every 2–3 days.

extract_protocol:
RNA was extracted using Trizol reagent
Novogene NGS RNA Library Prep Set. Library quality

treatment_protocol: In order to induce pancreatic differentiation, mESCs were treated at Day 0 with Activin A (20 ng/mL) in the presence of Matrigel, and at Day 4 with Retinoic Acid (RA 5μM/ml) and Fibroblast Growth Factor (FGF10, 10 ng/ml) until Day 8.

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: Arf-C cells, at Day 8 rep2

description:
Library name: Sample17
Column name in FPKMs_all_samples.txt: Arf-C_D8


title: 20 uM methionine culture for 14 days_18

value: VCaP

value: WT


title: 20 uM methionine culture for 14 days_17


title: aggregate_P_1

description: Library name: Sample1

value: jawbone

value: primary cells


title: Arf-C cells, at Day 8 rep1

description:
Library name: Sample16
Column name in FPKMs_all_samples.txt: Arf-C_D8


title: APACT34

value: tumor

value: IV

value: Male

value: Low Risk 1


title: 20 uM methionine culture for 14 days_16

value: VCaP NNMT


title: APACT33

value: Female


title: Arf-C cells, at Day 0 rep3

description:
Library name: Sample15
Column name in FPKMs_all_samples.txt: Arf-C_D0


title: A549_CEBPG_rep2

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression in A549 cells overexpressing CEBPG gene.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: A549, CEBPG overexpression, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS

extract_protocol: Total RNA was extracted with RNAiso Plus (TAKARA Bio, Japan) according to the manufacturer's instructions.

value: Cancer cell line


title: 20 uM methionine culture for 14 days_15

value: epithelial

value: NNMT overexpression


title: A549_CEBPG_rep1

source_name: A549, CEBPG overexpression, replicate 1


title: 20 uM methionine culture for 14 days_14

value: physiological methionine levels

value: 14 Days


title: APACT31

value: High Risk


title: APACT30


title: 20 uM methionine culture for 14 days_13


title: A549_CTL_rep2

description: Gene expression in A549 control cells.

source_name: A549, control cell, replicate 2


title: 20 uM methionine culture for 14 days_12


title: A549_CTL_rep1

description: Gene expression in A549 control cells.

source_name: A549, control cell, replicate 1


title: APACT3

value: II


title: Arf-B cells, at Day 8 rep3

description:
Library name: Sample12
Column name in FPKMs_all_samples.txt: Arf-B_D8

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: Ex17-2_iPS_Thal_high_H3K27ac

city: Bunkyo-ku

first: Satoshi

last: Otsuka

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the hg19 genome assembly.
Data were filtered using the following specifications. Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg19
Supplementary files format and content: wig files

source_name: HPS0063 (Riken BRC, 201B7)

growth_protocol: The ESCs and iPSCs were maintained under feeder-free condition using mTeSR1 (STEMCELL Technologies, Vancouver, Canada) on Matrigel-coated dishes (BD Biosciences, San Jose, CA).

extract_protocol:
After the fixation with 1% paraformaldehyde, they were collected and sonicated. Then, histone-DNA complexes were isolated with histone modification specific antibodies.
The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: ESCs or iPSCs were exposed to 0.1% DMSO, 10 (low) or 30 (high) nM bisphenol A, or 0.1 (low)or 1 (high) µM thalidomide for 48 hours.

value: HPS0063 (Riken BRC, 201B7)

value: pluripotent stem cell

tag: chip antibody

value: 1 μM thalidomide


title: Arf-B cells, at Day 8 rep2

description:
Library name: Sample11
Column name in FPKMs_all_samples.txt: Arf-B_D8


title: APACT29

value: tumor


title: 20 uM methionine culture for 14 days_11


title: Arf-B cells, at Day 8 rep1

description:
Library name: Sample10
Column name in FPKMs_all_samples.txt: Arf-B_D8


title: Ex17-2_iPS_Thal_low_H3K27ac

value: 0.1 μM thalidomide


title: 20 uM methionine culture for 14 days_10

value: VCaP NNMT


title: APACT28

value: Female


title: Arf-B cells, at Day 0 rep3

description:
Library name: Sample9
Column name in FPKMs_all_samples.txt: Arf-B_D0


title: APACT27

value: IV

value: Low Risk 3


title: Arf-B cells, at Day 0 rep2

description:
Library name: Sample8
Column name in FPKMs_all_samples.txt: Arf-B_D0


title: Ex17-2_iPS_BPA_low_H3K27ac

value: 10 nM bisphenol A


title: APACT26

value: Virilization

value: I

value: Male

value: Low Risk 2


title: Ex17-2_iPS_control_H3K27ac

value: 0.1% DMSO


title: APACT25

value: Low Risk 1


title: Ex17-1_ES_Thal_high_H3K27ac

source_name: HES0003 (Riken BRC, KhES-3)

value: HES0003 (Riken BRC, KhES-3)


title: 20 uM methionine culture for 14 days_6

value: VCaP

value: epithelial

value: WT

value: physiological methionine levels

value: 14 Days


title: APACT24

value: tumor

value: III

value: High Risk


title: Ex17-1_ES_Thal_low_H3K27ac

value: pluripotent stem cell

value: 0.1 μM thalidomide


title: 20 uM methionine culture for 14 days_5


title: Ctrlv2 cells, at Day 8 rep2

description:
Library name: Sample5
Column name in FPKMs_all_samples.txt: Ctrlv2_D8

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: APACT23

value: Female


title: Ex17-1_ES_BPA_high_H3K27ac

value: 30 nM bisphenol A


title: Ctrlv2 cells, at Day 8 rep1

description:
Library name: Sample4
Column name in FPKMs_all_samples.txt: Ctrlv2_D8


title: APACT22

value: Virilization

value: II

value: Low Risk 1


title: 20 uM methionine culture for 14 days_4

value: VCaP

value: epithelial


title: Ex17-1_ES_BPA_low_H3K27ac

value: HES0003 (Riken BRC, KhES-3)

value: 10 nM bisphenol A


title: Ctrlv2 cells, at Day 0 rep3

description:
Library name: Sample3
Column name in FPKMs_all_samples.txt: Ctrlv2_D0


title: 20 uM methionine culture for 14 days_3

value: WT

value: physiological methionine levels

value: 14 Days


title: APACT21

value: tumor

value: I

value: Low Risk 2


title: Ex17-1_ES_control_H3K27ac

value: pluripotent stem cell

value: 0.1% DMSO


title: Ctrlv2 cells, at Day 0 rep2

description:
Library name: Sample2
Column name in FPKMs_all_samples.txt: Ctrlv2_D0

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: 20 uM methionine culture for 14 days_2


title: Ex17-2_iPS_Thal_high

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 2.1.0 with parameters  -p 12 -q --dta-cufflinks.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuffdiff from the Cufflinks package using -p 12 --no-diff as parameters.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw FPKM values for each Sample.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA kit (MACHEREY-NAGEL) from human ESCs or iPSCs treated with various chemical substances.
RNA libraries were prepared using TruSeq V2 RNA-Seq kit (Illumina) using standard Illumina protocols.

value: HPS0063 (Riken BRC, 201B7)

value: 1 μM thalidomide


title: APACT20

value: Male


title: Ctrlv2 cells, at Day 0 rep1

description:
Library name: Sample1
Column name in FPKMs_all_samples.txt: Ctrlv2_D0


title: Ex17-2_iPS_Thal_low

value: 0.1 μM thalidomide


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep3

city: Tokyo

first: Yosuke

last: Isota

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, JAPAN

department: Graduate school of science

description: Library name: Morc1dIDR_3

data_processing:
RNA-seq data were first adapter-trimmed using TrimGalore.
Trimmed reads were mapped to mouse genome (mm10) using STAR with following parameters --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 -outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000.
Read counts for transposons were summarized at the subfamily level using featureCounts with the options -p -M.
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file

growth_protocol: NIH3T3 cells were cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and Penicillin-Streptomycin-Glutamine (Gibco).

extract_protocol:
Total RNA was extracted from NIH3T3 cells using ISOGEN II (FUJIFILM Wako Pure Chemical)  according to the manufacturer’s instructions. Purified RNA was treated with Turbo DNase (Thermo Fisher Scientific) at 37 °C for 30 min and subsequently cleaned up by phenol–chloroform extraction and ethanol precipitation. The resulting RNA was resuspended in nuclease-free water.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with doxycycline (100 ng/mL) for 48 h prior to harvest.

value: fibroblast

value: TRE-3xFlag-MORC1 dIDR-bpNLS; rtTA

value: Doxycycline addition 100 ng/mL 48 h prior


title: APACT19

value: III

value: Female

value: High Risk


title: Ex17-2_iPS_BPA_high

value: WT

value: 30 nM bisphenol A


title: HU-input-rep2

first: Santosh

middle: Kumar

last: Gothwal

address: Kakumamachi

data_processing:
FastQC
Trim galore
STAR
Edge
Assembly: Grch38
Supplementary files format and content: comma-delimited texxt files include cpm values for combined sample

source_name: Blood

extract_protocol:
Raji cellls treated with DMSO, HU were processed for ChIP using histone H3K4me3 ab (CST) and library was prepared as per instruction (Thruplex DNA-seq kit, Takara  Japan).
Library construction was performed by Santosh Kumar Gothwal using the instruction from manufacturer  (Thruplex DNA-seq kit, Takara  Japan)

value: Blood

value: Raji

value: B-lymphoma

value: HU

tag: antibody


title: APACT18

value: tumor

value: Virilization

value: IV

value: Low Risk 1


title: HU-input-rep1


title: Ex17-2_iPS_BPA_low

value: HPS0063 (Riken BRC, 201B7)

value: pluripotent stem cell

value: 10 nM bisphenol A


title: HU-IgG-rep2

value: IgG


title: APACT17

value: Cushings


title: Ex17-2_iPS_control

value: 0.1% DMSO


title: HU-IgG-rep1


title: APACT16

value: II

value: Female

value: High Risk


title: Ex17-1_ES_Thal_high

value: HES0003 (Riken BRC, KhES-3)

value: WT

value: 1 μM thalidomide


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep2

description: Library name: Morc1WT_2

value: fibroblast

value: TRE-3xFlag-MORC1 WT; rtTA

value: Doxycycline addition 100 ng/mL 48 h prior


title: HU-rep2

value: Blood

value: Raji

value: B-lymphoma

value: HU


title: APACT15

value: tumor

value: IV


title: HU-rep1


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep3

description: Library name: Morc1WT_3


title: APACT39

value: Low Risk 1


title: Ex17-1_ES_BPA_high

value: pluripotent stem cell

value: 30 nM bisphenol A


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep3

description: Library name: mCherry_3

value: TRE-3xFlag-mCherry; rtTA


title: APACT35

value: III

value: Male


title: Cont-input-rep2

value: DMSO


title: APACT32

value: Female


title: Ex17-1_ES_Thal_low

value: HES0003 (Riken BRC, KhES-3)

value: WT

value: 0.1 μM thalidomide


title: Arf-C cells, at Day 0 rep2

description:
Library name: Sample14
Column name in FPKMs_all_samples.txt: Arf-C_D0

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: Arf-C cells, at Day 0 rep1

description:
Library name: Sample13
Column name in FPKMs_all_samples.txt: Arf-C_D0


title: APACT13

value: I

value: Low Risk 2


title: Ex17-1_ES_BPA_low

value: 10 nM bisphenol A


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep2

description: Library name: mCherry_2

value: fibroblast

value: Doxycycline addition 100 ng/mL 48 h prior


title: Cont-input-rep1

value: Blood

value: Raji

value: B-lymphoma


title: APACT12

value: tumor

value: II

value: Male


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep1

description: Library name: Morc1WT_1

value: TRE-3xFlag-MORC1 WT; rtTA


title: Ex17-1_ES_control

value: HES0003 (Riken BRC, KhES-3)

value: pluripotent stem cell

value: WT

value: 0.1% DMSO


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep1

description: Library name: mCherry_1

value: TRE-3xFlag-mCherry; rtTA


title: Cont-IgG-rep2

value: DMSO

value: IgG


title: Ex17-2_iPS_BPA_high_H3K27ac

value: HPS0063 (Riken BRC, 201B7)

value: 30 nM bisphenol A


title: 20 uM methionine culture for 14 days_9

value: VCaP NNMT

value: epithelial

value: NNMT overexpression

value: physiological methionine levels

value: 14 Days


title: APACT11

value: tumor

value: II

value: Female

value: Low Risk 2


title: APACT14

value: IV

value: Male

value: Low Risk 3


title: Cont-IgG-rep1

value: Blood

value: Raji

value: B-lymphoma


title: HMDHip3

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

data_processing:
RNA was extracted according to the manufacturer's instructions, and RNA integrity was checked using an Agilent 2100 Bioanalyzer.
Libraries were constructed using an Illumina NovaSeq X Plus, and 150 bp paired-end reads were generated on the platform.
Fastp (version 0.19.7) was used for quality control. Clean reads for subsequent analysis were obtained after raw data filtering, sequencing error rate check, and GC content distribution check. Clean reads were aligned with the reference genome using HISAT2 (v2.1.0) under default parameters to obtain the positioning information of reads on the reference genome.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: C57BL/6 male mice (6-8 weeks old) were purchased from the Experimental Animal Center of Shanxi Medical University and fed with a high-methionine diet or a standard diet for more than 8 weeks.

extract_protocol:
The mice were fed with high-methionine or standard diet for 8 weeks, and the hippocampus of the two groups were isolated after being euthanized by cervical dislocation.
RNA libraries for RNA-seq were prepared using Agilent 2100 RNA Nano 6000 Assay Kit following manufacturer's protocols and the NanoPhotometer® spectrophotometer following  the purity of the samples.

treatment_protocol: Two mice per cage were housed at a stable temperature (24±2℃), with 12h/12h light/dark time alternation, and constant humidity. Free food and drinks available at all times.

value: hippocampus

value: high methionine feeding


title: 20 uM methionine culture for 14 days_8

value: VCaP

value: WT


title: Arf-B cells, at Day 0 rep1

description:
Library name: Sample7
Column name in FPKMs_all_samples.txt: Arf-B_D0

value: blastocyst-derived embryonic stem cell line

value: wild type

value: pancreatic differentiation


title: Thy-Noc-rep3

data_processing:
FastQC
Trim galore
STAR
Deseq2
Edge
Assembly: Grch38
Supplementary files format and content: comma-delimited texxt files include cpm values for combined sample

extract_protocol:
Raji cellls treated with DMSO, HU or Thy-Noc  were used for RNA-isolation kit (Takara Bio Japan).
Library construction was performed by Macrogen Japan (TruSeq stranded mRNA kit)

value: Thymidine-Nocodazole


title: Thy-Noc-rep2


title: HMDHip2


title: APACT109

value: tumor

value: Virilization

value: II


title: Cont-rep2

value: DMSO


title: Ctrlv2 cells, at Day 8 rep3

description:
Library name: Sample6
Column name in FPKMs_all_samples.txt: Ctrlv2_D8


title: 20 uM methionine culture for 14 days_7

value: epithelial

value: physiological methionine levels

value: 14 Days


title: Thy-Noc-rep1

value: Blood

value: Raji


title: HMDHip1

value: hippocampus


title: APACT108

value: Cushings

value: IV

value: Female

value: Low Risk 3


title: Cont-rep1

value: B-lymphoma


title: APACT107


title: HU-rep3

value: Hydroxyurea


title: MhcUBA1RNAi2_BL25957_3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: MhcUBA1RNAi2_BL25957_3
UBA1 RNAi treatment 2 replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to BDGP Release 6 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for all 9 samples

source_name: skeletal muscles

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase.
RNA sequencing libraries for each sample were prepared with 1 ug total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: skeletal muscles

value: UBA1 RNAi treatment 2


title: ConHip3

value: WT


title: APACT106

data_processing:
Raw IDAT files were processed, normalized, filtered and batch effect corrected as described in Capper et. al. 2018 by using the Bioconductor package minfi
Processed values represent Beta values (β-values), i.e. the ratio of methylated probe intensity to overall intensity (M / [M+U+100]), ranging from 0 (unmethylated) to 1 (fully methylated). Values were derived from IDAT files after background correction and normalization using the minfi.

extract_protocol: DNA was isolated from the tumor tissue with the DNA/RNA AllPrep Mini Kit (Qiagen) according to the manufactors instruction

value: tumor

value: III


title: ConHip2


title: MhcUBA1RNAi2_BL25957_2

description:
Library name: MhcUBA1RNAi2_BL25957_2
UBA1 RNAi treatment 2 replicate 2


title: APACT105

value: I

value: Male


title: HU-rep1


title: MhcUBA1RNAi2_BL25957_1

description:
Library name: MhcUBA1RNAi2_BL25957_1
UBA1 RNAi treatment 2 replicate 1


title: APACT104

value: II


title: ConHip1


title: Cont-rep3

value: Blood

value: DMSO


title: HMDCor3

source_name: cortex

growth_protocol: C57BL/6 male mice (6-8 weeks old) were purchased from the Experimental Animal Center of Shanxi Medical University and fed with a high-methionine diet or a standard diet  for more than 8 weeks.

extract_protocol:
The mice were fed with high-methionine or standard diet for 8 weeks, and the cortex of the two groups were isolated after being euthanized by cervical dislocation.
RNA libraries for RNA-seq were prepared using Agilent 2100 RNA Nano 6000 Assay Kit following manufacturer's protocols and the NanoPhotometer® spectrophotometer following  the purity of the samples.

value: cortex

value: high methionine feeding


title: APACT103

source_name: tumor


title: MhcUBA1RNAi1_BL76066_3

description:
Library name: MhcUBA1RNAi1_BL76066_3
UBA1 RNAi treatment 1 replicate 3

value: UBA1 RNAi treatment 1


title: Cont-rep2

value: Raji


title: HMDCor2


title: APACT102

value: Virilization

value: Female

value: Low Risk 3


title: MhcUBA1RNAi1_BL76066_2

description:
Library name: MhcUBA1RNAi1_BL76066_2
UBA1 RNAi treatment 1 replicate 2

value: skeletal muscles


title: Cont-rep1

value: B-lymphoma


title: HMDCor1


title: APACT101


title: TWT to WT

description: Library name: Sample 3

value: Bone marrow

value: loss of Gsdmd dataset

value: TWT to WT


title: ConCor3

value: WT


title: APACT100

value: tumor

value: I


title: 20 uM methionine culture for 14 days_1

value: VCaP

value: epithelial

value: physiological methionine levels

value: 14 Days


title: MhcCherryRNAi_3

description:
Library name: MhcCherryRNAi_3
control RNAi replicate 3

value: control RNAi (mcherry RNAi)


title: ConCor2

value: cortex


title: TKO to WT

description: Library name: Sample 2

value: TKO to WT


title: MhcCherryRNAi_2

description:
Library name: MhcCherryRNAi_2
control RNAi replicate 2


title: APACT2

value: II

value: Female

value: Low Risk 1


title: APACT10

value: Male

value: Low Risk 2


title: DKO to WT

description: Library name: Sample 1

value: Bone marrow

value: loss of Gsdmd dataset

value: DKO to WT


title: ConCor1

value: WT


title: MhcCherryRNAi_1

description:
Library name: MhcCherryRNAi_1
control RNAi replicate 1

value: skeletal muscles


title: 1T strain, planktonic, 90 min, rep 3

status: Public on Aug 11 2026

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

description: Library name: 1T_3_planktonic_90min

data_processing:
The paired-end reads were assessed for quality using FastQC (v0.11.9).
The reference genome was indexed using the subread-buildindex function in subread (v2.0.6). We then mapped the paired-end reads to the reference genome using the subread-align function in subread (v2.0.6), including multi-mapped reads, mapping to the best 10 genomic loci (parameters: –multiMapping, -B 10)
Transcript abundance for each gene was computed using the featureCounts function in subread (v2.0.6), counting only read-pairs where both ends map to the same chromosome (parameters: -B, -C, –countReadPairs). The transcript abundance table was generated by consolidating all serial isolates, biological replicates, time point (90 minutes, 8 hours and 24 hours) and growth condition (biofilm and planktonic growth condition) using a custom Python script (v3.8.18) and were used for subsequent differential expression analyses.
Differential expression analysis was performed using DESeq2 (v1.44.0).
Assembly: ASM18276v2
Supplementary files format and content: tab-delimited txt file contains transcript abundance counts for all samples.

organism: Lodderomyces parapsilosis

source_name: planktonic

growth_protocol: Biofilms were harvested by gently pipetting up and down along the bottoms of the 12-well plates and combining the biofilm slurry of the same strain from each well of one 12-well plate into a 50 mL conical tube. Planktonic cultures of a given biological replicate were combined in a 50 mL conical tube.

extract_protocol:
The conical tubes were centrifuged at 4,000 x g for 5 minutes and the supernatant was aspirated. Pellets were snap-frozen and stored at -80°C until RNA extraction. Total RNA was extracted using the Ribopure RNA Purification Kit for Yeast (AM1926). mRNA was separated from total RNA using the NEBNext Poly(A) mRNA Isolation Module (E7490L).
500 ng of purified mRNA were made into cDNA libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775L).

value: planktonic

tag: time

value: 90 min


title: APACT1

value: tumor

value: Virilization

value: I

value: High Risk


title: 1T strain, planktonic, 24 hr, rep 2

description: Library name: 1T_2_planktonic_24hr

value: 24 hr


title: 1T strain, planktonic, 8 hr, rep 1

description: Library name: 1T_1_planktonic_8hr

value: 8 hr


title: 1T strain, planktonic, 24 hr, rep 1

description: Library name: 1T_1_planktonic_24hr


title: 1T strain, planktonic, 24 hr, rep 3

description: Library name: 1T_3_planktonic_24hr


title: 1T strain, planktonic, 8 hr, rep 3

description: Library name: 1T_3_planktonic_8hr


title: 49B strain, planktonic, 8 hr, rep 3

description: Library name: 49B_3_planktonic_8hr


title: 49B strain, planktonic, 24 hr, rep 3

description: Library name: 49B_3_planktonic_24hr


title: 1T strain, planktonic, 90 min, rep 1

description: Library name: 1T_1_planktonic_90min


title: 1T strain, planktonic, 90 min, rep 2

description: Library name: 1T_2_planktonic_90min


title: 49B strain, planktonic, 24 hr, rep 2

description: Library name: 49B_2_planktonic_24hr


title: 49B strain, planktonic, 8 hr, rep 2

description: Library name: 49B_2_planktonic_8hr


title: 49B strain, planktonic, 24 hr, rep 1

description: Library name: 49B_1_planktonic_24hr


title: 49B strain, planktonic, 8 hr, rep 1

description: Library name: 49B_1_planktonic_8hr


title: 49B strain, planktonic, 90 min, rep 1

description: Library name: 49B_1_planktonic_90min


title: 35B strain, planktonic, 24 hr, rep 3

description: Library name: 35B_3_planktonic_24hr


title: 49B strain, planktonic, 90 min, rep 2

description: Library name: 49B_2_planktonic_90min


title: 35B strain, planktonic, 8 hr, rep 3

description: Library name: 35B_3_planktonic_8hr


title: 35B strain, planktonic, 90 min, rep 3

description: Library name: 35B_3_planktonic_90min


title: 1T strain, planktonic, 8 hr, rep 2

description: Library name: 1T_2_planktonic_8hr


title: 35B strain, planktonic, 90 min, rep 2

description: Library name: 35B_2_planktonic_90min


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep2

description: Library name: Morc1dIDR_2

tag: cell line

value: fibroblast

value: TRE-3xFlag-MORC1 dIDR-bpNLS; rtTA

value: Doxycycline addition 100 ng/mL 48 h prior


title: 35B strain, planktonic, 24 hr, rep 2

description: Library name: 35B_2_planktonic_24hr

tag: genotype


title: 35B strain, planktonic, 8 hr, rep 1

description: Library name: 35B_1_planktonic_8hr


title: 29T strain, planktonic, 24 hr, rep 3

description: Library name: 29T_3_planktonic_24hr


title: 35B strain, planktonic, 90 min, rep 1

description: Library name: 35B_1_planktonic_90min


title: 35B strain, planktonic, 24 hr, rep 1

description: Library name: 35B_1_planktonic_24hr


title: 29T strain, planktonic, 8 hr, rep 3

description: Library name: 29T_3_planktonic_8hr


title: MhcUBA1RNAi1_BL76066_1

description:
Library name: MhcUBA1RNAi1_BL76066_1
UBA1 RNAi treatment 1 replicate 1

tag: treatment

value: UBA1 RNAi treatment 1


title: 35B strain, planktonic, 8 hr, rep 2

description: Library name: 35B_2_planktonic_8hr

tag: cell type


title: 29T strain, planktonic, 90 min, rep 3

description: Library name: 29T_3_planktonic_90min


title: 29T strain, planktonic, 24 hr, rep 2

description: Library name: 29T_2_planktonic_24hr


title: 29T strain, planktonic, 8 hr, rep 2

description: Library name: 29T_2_planktonic_8hr


title: 29T strain, planktonic, 90 min, rep 2

description: Library name: 29T_2_planktonic_90min


title: 29T strain, planktonic, 8 hr, rep 1

description: Library name: 29T_1_planktonic_8hr


title: 29T strain, planktonic, 24 hr, rep 1

description: Library name: 29T_1_planktonic_24hr


title: RNA-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep1

description: Library name: Morc1dIDR_1


title: 49B strain, biofilm, 90 min, rep 3

description: Library name: 49B_3_biofilm_90min

source_name: biofilm

value: biofilm


title: 49B strain, biofilm, 24 hr, rep 3

description: Library name: 49B_3_biofilm_24hr


title: 49B strain, biofilm, 8 hr, rep 1

description: Library name: 49B_1_biofilm_8hr


title: 49B strain, biofilm, 8 hr, rep 2

description: Library name: 49B_2_biofilm_8hr


title: 49B strain, biofilm, 24 hr, rep 1

description: Library name: 49B_1_biofilm_24hr


title: 49B strain, biofilm, 90 min, rep 2

description: Library name: 49B_2_biofilm_90min


title: 49B strain, biofilm, 24 hr, rep 2

description: Library name: 49B_2_biofilm_24hr


title: 49B strain, biofilm, 8 hr, rep 3

description: Library name: 49B_3_biofilm_8hr


title: 49B strain, biofilm, 90 min, rep 1

description: Library name: 49B_1_biofilm_90min


title: 35B strain, biofilm, 8 hr, rep 3

description: Library name: 35B_3_biofilm_8hr


title: 35B strain, biofilm, 90 min, rep 3

description: Library name: 35B_3_biofilm_90min


title: 35B strain, biofilm, 24 hr, rep 2

description: Library name: 35B_2_biofilm_24hr


title: 35B strain, biofilm, 90 min, rep 2

description: Library name: 35B_2_biofilm_90min


title: 35B strain, biofilm, 8 hr, rep 2

description: Library name: 35B_2_biofilm_8hr


title: 35B strain, biofilm, 24 hr, rep 1

description: Library name: 35B_1_biofilm_24hr


title: 35B strain, biofilm, 8 hr, rep 1

description: Library name: 35B_1_biofilm_8hr


title: 35B strain, biofilm, 90 min, rep 1

description: Library name: 35B_1_biofilm_90min


title: 29T strain, biofilm, 24 hr, rep 3

description: Library name: 29T_3_biofilm_24hr


title: 35B strain, biofilm, 24 hr, rep 3

description: Library name: 35B_3_biofilm_24hr


title: 29T strain, biofilm, 8 hr, rep 3

description: Library name: 29T_3_biofilm_8hr


title: 29T strain, biofilm, 90 min, rep 3

description: Library name: 29T_3_biofilm_90min


title: 29T strain, biofilm, 8 hr, rep 2

description: Library name: 29T_2_biofilm_8hr


title: 29T strain, biofilm, 24 hr, rep 1

description: Library name: 29T_1_biofilm_24hr


title: 29T strain, biofilm, 24 hr, rep 2

description: Library name: 29T_2_biofilm_24hr


title: 1T strain, biofilm, 24 hr, rep 3

description: Library name: 1T_3_biofilm_24hr


title: 29T strain, biofilm, 90 min, rep 2

description: Library name: 29T_2_biofilm_90min


title: 29T strain, biofilm, 8 hr, rep 1

description: Library name: 29T_1_biofilm_8hr


title: 1T strain, biofilm, 8 hr, rep 3

description: Library name: 1T_3_biofilm_8hr


title: 1T strain, biofilm, 24 hr, rep 2

description: Library name: 1T_2_biofilm_24hr


title: 1T strain, biofilm, 8 hr, rep 2

description: Library name: 1T_2_biofilm_8hr


title: 1T strain, biofilm, 90 min, rep 2

description: Library name: 1T_2_biofilm_90min


title: 1T strain, biofilm, 90 min, rep 3

description: Library name: 1T_3_biofilm_90min


title: 1T strain, biofilm, 8 hr, rep 1

description: Library name: 1T_1_biofilm_8hr


title: 1T strain, biofilm, 24 hr, rep 1

description: Library name: 1T_1_biofilm_24hr


title: MOC1, FIR, rep3

city: Zhengzhou

first: Yuantong

state: Henan

address: kexue road

institute: Zhengzhou University

description:
Library name: Sample6
MOC1, FIR, rep3

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality bases.
Clean reads were aligned to the Mus musculus reference genome/transcriptome GRCm38.p6 using FANSe3.
Gene expression was quantified using uniquely mapped reads, and TPM values were calculated.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

extract_protocol:
Total RNA was extracted from the cells using Trizol (Invitrogen) according to manual instruction.
RNA-sequencing libraries were prepared from total RNA by Chi Biotech Co., Ltd. RNA was fragmented and reverse-transcribed into cDNA. Sequencing adapters were ligated, and the libraries were amplified and circularized to generate single-stranded circular DNA libraries. The circular libraries were amplified by phi29-mediated rolling-circle amplification to generate DNA nanoballs (DNBs). DNBs were loaded onto patterned arrays and sequenced in paired-end mode on a DNBSEQ-T7 platform (MGI Tech).

treatment_protocol: MOC1 cells were subjected to repeated fractionated irradiation. Control cells were cultured under the same conditions without irradiation.

value: murine oral squamous cell carcinoma cell

value: Fractionated irradiation group, biological replicate 3


title: MOC1, FIR, rep1

description:
Library name: Sample4
MOC1, FIR, rep1

value: Fractionated irradiation group, biological replicate 1


title: MOC1, CON, rep2

description:
Library name: Sample2
MOC1, CON, rep2

value: Control group, biological replicate 2


title: MOC1, FIR, rep2

description:
Library name: Sample5
MOC1, FIR, rep2

value: Fractionated irradiation group, biological replicate 2


title: 1T strain, biofilm, 90 min, rep 1

description: Library name: 1T_1_biofilm_90min

value: 90 min


title: MOC1R, COF, rep3

description:
Library name: Sample6
MOC1R, COF, rep3

treatment_protocol: MOC1-R cells were treated with COF-Tpy-Se-Cu followed by X-ray irradiation. RNA was collected 24 h after treatment.

value: COF-Tpy-Se-Cu in combination with irradiation, biological replicate 3


title: MOC1R, COF, rep2

description:
Library name: Sample5
MOC1R, COF, rep2

value: COF-Tpy-Se-Cu in combination with irradiation, biological replicate 2


title: MOC1R, COF, rep1

description:
Library name: Sample4
MOC1R, COF, rep1

value: COF-Tpy-Se-Cu in combination with irradiation, biological replicate 1


title: MOC1R, CON, rep3

description:
Library name: Sample3
MOC1R, CON, rep3

value: Control group, biological replicate 3


title: MOC1R, CON, rep2

description:
Library name: Sample2
MOC1R, CON, rep2


title: MOC1R, CON, rep1

description:
Library name: Sample1
MOC1R, CON, rep1

value: Control group, biological replicate 1


title: Skin; Vegfr2ecko; P3 (postnatal day 3); ecko3

city: Suzhou

first: Yulong

last: He

address: 199 Ren-Ai Road

institute: Soochow University

description: Library name: sample6

data_processing:
Sequencing was performed on the BGISEQ /DNBSEQ platform with a read length of PE150 (BGI-Shenzhen, China)
Raw data filtered using SOAPnuke (v 2.3.2)
RNA-seq reads aligned to a reference genome using hisat2 (v 2.2.1)
The clean data was aligned to the reference gene set using Bowtie2 (v2.4.5) . Gene expression quantification was performed using RSEM (v1.3.1) software
Assembly: Mus_musculus：NCBI, GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: Skin

extract_protocol:
Total RNA was isolated from the ear skin tissues using Trizol (Invitrogen) according to the manufacturer's instructions
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

treatment_protocol: Ear skin tissues from the endothelial specific knockout and control mice were collected, and then snap‑frozen in liquid nitrogen.

value: Skin

value: ecko

value: tamoxifen treatment


title: MOC1, CON, rep1

description:
Library name: Sample1
MOC1, CON, rep1


title: Skin; Vegfr2ecko; P3 (postnatal day 3); ecko2

description: Library name: sample5


title: Skin; Vegfr2ecko; P3 (postnatal day 3); ecko1

description: Library name: sample4


title: MOC1, CON, rep3

description:
Library name: Sample3
MOC1, CON, rep3


title: Skin; Control; P3 (postnatal day 3); control2

description: Library name: sample2

value: Control


title: Skin; Control; P3 (postnatal day 3); control1

description: Library name: sample1


title: Skin; Control; P3 (postnatal day 3); control3

description: Library name: sample3


title: mLEC; Vegfr2 siRNA; 48h; siRNA5

description: Library name: sample10

source_name: LEC

extract_protocol:
Total RNA was isolated from the treated and control mLECs using Trizol (Invitrogen) according to the manufacturer's instructions
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

treatment_protocol: Mouse primary lymphatic endothelial cells were tranfected with siRNA to knockdown Kdr.

value: LEC

value: siRNA

value: siRNA knockdown


title: mLEC; Vegfr2 siRNA; 48h; siRNA4

description: Library name: sample9


title: mLEC; Vegfr2 siRNA; 48h; siRNA2

description: Library name: sample7


title: mLEC; Vegfr2 siRNA; 48h; siRNA1

description: Library name: sample6


title: mLEC; Control; 48h; control5

description: Library name: sample5


title: mLEC; Vegfr2 siRNA; 48h; siRNA3

description: Library name: sample8


title: mLEC; Control; 48h; control4

description: Library name: sample4


title: mLEC; Control; 48h; control3

description: Library name: sample3


title: Skin; Vegfr2lecko; P21 (postnatal day 21); lecko2

description: Library name: sample5

treatment_protocol: Ear skin tissues from the lymphatic specific knockout and control mice were collected, and then snap‑frozen in liquid nitrogen.

value: lecko


title: Skin; Vegfr2lecko; P21 (postnatal day 21); lecko1

description: Library name: sample4


title: mLEC; Control; 48h; control1

description: Library name: sample1


title: Skin; Vegfr2lecko; P21 (postnatal day 21); lecko3

description: Library name: sample6


title: mLEC; Control; 48h; control2

description: Library name: sample2


title: IL15_5

city: changchun

first: Qi

last: Li

address: No. 5333 Xi'an Avenue, Changchun City, Jilin Province

institute: Institute of Zoonosis, and College of Veterinary Medicine, Jilin University

description: Library name: Sample 6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: tumor

value: melanoma cell line


title: Skin; Control; P21 (postnatal day 21); control2

description: Library name: sample2


title: Skin; Control; P21 (postnatal day 21); control3

description: Library name: sample3


title: IL15_3

description: Library name: Sample 5


title: IL15_2

description: Library name: Sample 4


title: Skin; Vegfr2ecko; P21 (postnatal day 21); ecko3

description: Library name: sample6


title: Skin; Control;P21 (postnatal day 21); control1

description: Library name: sample1


title: Skin; Vegfr2ecko; P21 (postnatal day 21); ecko2

description: Library name: sample5


title: Skin; Vegfr2ecko; P21 (postnatal day 21); ecko1

description: Library name: sample4


title: PBS_2

description: Library name: Sample 1

value: PBS


title: PBS_3

description: Library name: Sample 2


title: PBS_4

description: Library name: Sample 3


description: Library name: sample3


title: Old 3

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

description: vc13, N1

hyb_protocol: Labeled RNA was hybridized at 48 °C for 42 h at 60 rpm on an Affymetrix GeneChip™ human miRNA 4.0 array

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner G3000 7G with standard setting to capture signal intensities for the miRNAs.

data_processing: The raw intensity of miRNA microarray data was imported into Affymetrix Expression Console software (v1.4.1.46) for signal pre-processing including background correction utilizing the robust multi-array average (RMA) algorithm, median polish summarization from probe to probe set level of signal values, and the quantile method to normalize across multiple arrays and then calculate the log2 scale expression signals of miRNAs. Removal of unwanted variations correction of microarray data was performed by following the manual of the RUV package. The RUV III function was used to globally adjust the microarray data matrix using both negative controls and replicates. And the negative controls were the spike-in controls found on many microarray platforms. The significantly differentially expressed miRNAs between young and old samples in basal ganglia regions were identified by limma method with the adjusted p value < 0.05.

source_name: cortex, non-diseased

label_protocol: Flashtag™ Biotin HSR RNA labeling kit

extract_protocol: Qiagen FFPE Rneasy extraction kit

treatment_protocol: FFPE human brain sections

tag: age

value: 91 yr

tag: gender

value: female


title: Old 1

description: vc6,  N1

value: 83 yr

value: male


title: Old 2

description: vc15,  N1

value: 84 yr


title: Skin; Control;P21 (postnatal day 21); control2

description: Library name: sample2