title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 8324

description:
cell-free DNA 5hmC
PLCO-254


title: Endoderm_H3K9me3_ChIP_Xencode_Group3_1

status: Public on Jan 22 2025

type: SRA

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

description: Library name: Endoderm_H3K9me3_ChIP_Xencode_Group3_1

library_source: genomic

data_processing:
Raw ChIP-seq data were aligned to the Xenopus laevis genome (v10.1) using BWA (v0.7.17-foss-2018b).
Low-quality mapped reads (MAPQ < 10) were discarded using samtools (v1.16.1), and PCR duplicates were removed with sambamba (v0.8.2). Coverage track files (.bigwig) were generated using deepTools (v3.5.1), with normalization to Counts Per Million (CPM).
Assembly: Xenopus laevis 10.1
Supplementary files format and content: bigwig coverage tracks, merged replicates with input subtracted

molecule: genomic DNA

organism: Xenopus laevis

source_name: endoderm

extract_protocol:
As described in Hörmanseder et al 2017.
ChIP-seq library preparation with the TruSeq DNA kit (Illumina, FC-121-2001).

treatment_protocol: No treatment

tag: tissue

value: endoderm

tag: cell type

tag: genotype

value: WT

tag: batch


title: ms_liver_hfhc_25weeks_rep1_TCR

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

country: USA

institute: University of Colorado - Anschutz Medical Campus

description:
T cell receptor sequencing (TCR)
mouse_metadata.tsv.gz

library_source: transcriptomic

data_processing:
Cellranger 6.0.1 for demultiplexing, barcode processing, and gene counting.
Ambient RNA was removed using DecontX(1.14.2). Cells containing >50% ambient RNA were also removed.
Multiplets were identified and removed with DoubletFinder(2.0.3)
Cells were filtered and retained if they had 500-20,000 UMIs and <5% UMIs from genes encoded by mitocondrial genes
Cells were noramlized, corrected for batch, and projected into latent space using Suerat(4.3.0)
Assembly: mm10
Supplementary files format and content: mouse_metadata.tsv.gz; sample assignments and related metadata, including TCR clonotype, for all filtered cell barcodes
Supplementary files format and content: mouse_cell_barcodes.tsv.gz, mouse_normalized_rna_matrix.mtx, mouse_normalized_rna_features.tsv.gz; Normalized RNA counts matrix and column/row labels
Library strategy: TCR-seq

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Livers were perfused, extracted, digested, then put into a single cell suspension and enriched for T cells and live cells using cell isolation kits.
Library construction was preformed per manufacturers instructions with the Chromium Next GEM Single Cell 5' Kit V2 (GEX) or the Chromium Single Cell Mouse TCR Amplification Kit (TCR).  cDNA libraries were sequenced on a NovaSeq6000 at a depth of 50,000 reads / cell for RNA and 4,000 reads / cell for TCRs.

value: liver

tag: treatment

value: HFHC diet


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 8482

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

description:
cell-free DNA 5hmC
PLCO-253

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

organism: Homo sapiens

source_name: peripheral plasma

growth_protocol: Not applicable

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).

treatment_protocol: Not applicable

value: peripheral plasma

tag: dna source

value: cell-free DNA


title: Endoderm_H3K4me2_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K4me2_ChIP_Xencode_Group3_1


title: ms_liver_chow_25weeks_rep4_TCR

value: Chow diet


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 3788

description:
cell-free DNA 5hmC
PLCO-252


title: ms_liver_chow_25weeks_rep3_TCR


title: Endoderm_Input_Xencode_Group3_1

description: Library name: Endoderm_Input_Xencode_Group3_1


title: Ectoderm_H3K79me3_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K79me3_ChIP_Xencode_Group3_1

source_name: ectoderm

value: ectoderm


title: Ectoderm_H3K36me3_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K36me3_ChIP_Xencode_Group3_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 6603

description:
cell-free DNA 5hmC
PLCO-251


title: Ectoderm_H3K27me3_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K27me3_ChIP_Xencode_Group3_1


title: ms_liver_chow_25weeks_rep2_TCR


title: ms_liver_hfhc_25weeks_rep3_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 4782

description:
cell-free DNA 5hmC
PLCO-250


title: Ectoderm_H3K27ac_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K27ac_ChIP_Xencode_Group3_1


title: ms_liver_chow_25weeks_rep1_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0541

description:
cell-free DNA 5hmC
PLCO-256


title: Ectoderm_H3K4me3_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group3_1


title: ms_liver_reversal_31weeks_rep4_TCR

value: Reversal diet


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 6598

description:
cell-free DNA 5hmC
PLCO-248


title: Ectoderm_H3K4me2_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K4me2_ChIP_Xencode_Group3_1


title: Ectoderm_H3K9me3_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K9me3_ChIP_Xencode_Group3_1


title: Ectoderm_H3K4me1_ChIP_Xencode_Group3_1

description: Library name: Ectoderm_H3K4me1_ChIP_Xencode_Group3_1


title: Endoderm_H3K4me1_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K4me1_ChIP_Xencode_Group3_1


title: ms_liver_reversal_31weeks_rep3_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9308

description:
cell-free DNA 5hmC
PLCO-247


title: Ectoderm_Input_Xencode_Group3_2

description: Library name: Ectoderm_Input_Xencode_Group3_2


title: Endoderm_H3K4me3_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H3K4me3_ChIP_Xencode_Group2_2


title: Ectoderm_Input_Xencode_Group3_1

description: Library name: Ectoderm_Input_Xencode_Group3_1


title: Endoderm_H2A.ub_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H2A.ub_ChIP_Xencode_Group2_2


title: Endoderm_H2A.x.3_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H2A.x.3_ChIP_Xencode_Group2_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2050

description:
cell-free DNA 5hmC
PLCO-246


title: ms_liver_reversal_31weeks_rep1_TCR

description:
T cell receptor sequencing (TCR)
mouse_metadata.tsv.gz


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5856

description:
cell-free DNA 5hmC
PLCO-245


description: Library name: Endoderm_H2AH4Ser1P_ChIP_Xencode_Group2_2


title: ms_liver_hfhc_31weeks_rep4_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7266

description:
cell-free DNA 5hmC
PLCO-244


title: Endoderm_H3K27ac_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H3K27ac_ChIP_Xencode_Group2_2


title: Endoderm_H3K27me3_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group2_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 0636

description:
cell-free DNA 5hmC
PLCO-243


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 9930

description:
cell-free DNA 5hmC
PLCO-249


title: ms_liver_hfhc_31weeks_rep3_TCR


title: Endoderm_Input_Xencode_Group2_2

description: Library name: Endoderm_Input_Xencode_Group2_2


title: ms_liver_hfhc_31weeks_rep2_TCR


title: Endoderm_H3K36me3_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group2_2


title: Endoderm_H3K4me3_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H3K4me3_ChIP_Xencode_Group2_1


title: ms_liver_hfhc_31weeks_rep1_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 0675

description:
cell-free DNA 5hmC
PLCO-241


title: Endoderm_H3K9me3_ChIP_Xencode_Group2_2

description: Library name: Endoderm_H3K9me3_ChIP_Xencode_Group2_2


title: Endoderm_H2A.ub_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H2A.ub_ChIP_Xencode_Group2_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 0791

description:
cell-free DNA 5hmC
PLCO-240


title: Endoderm_H2A.x.3_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H2A.x.3_ChIP_Xencode_Group2_1


description: Library name: Endoderm_H2AH4Ser1P_ChIP_Xencode_Group2_1


title: ms_liver_chow_31weeks_rep4_TCR


title: ms_liver_reversal_31weeks_rep2_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2695

description:
cell-free DNA 5hmC
PLCO-239


title: Endoderm_H3K36me3_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group2_1


title: ms_liver_chow_31weeks_rep2_TCR


title: Endoderm_H3K9me3_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H3K9me3_ChIP_Xencode_Group2_1


title: Endoderm_H3K27me3_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group2_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3415

description:
cell-free DNA 5hmC
PLCO-238


title: Endoderm_H3K27ac_ChIP_Xencode_Group2_1

description: Library name: Endoderm_H3K27ac_ChIP_Xencode_Group2_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 1359

description:
cell-free DNA 5hmC
PLCO-237


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 9565

description:
cell-free DNA 5hmC
PLCO-236


title: Ectoderm_H3K4me3_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group2_2


title: ms_liver_chow_31weeks_rep1_TCR


title: Ectoderm_H2A.x.3_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H2A.x.3_ChIP_Xencode_Group2_2


title: ms_liver_hfhc_25weeks_rep4_gex

description:
mRNA sequencing
mouse_metadata.tsv.gz
mouse_cell_barcodes.tsv.gz
mouse_normalized_rna_features.tsv.gz
mouse_normalized_rna_matrix.mtx

library_source: transcriptomic single cell

data_processing:
Cellranger 6.0.1 for demultiplexing, barcode processing, and gene counting.
Ambient RNA was removed using DecontX(1.14.2). Cells containing >50% ambient RNA were also removed.
Multiplets were identified and removed with DoubletFinder(2.0.3)
Cells were filtered and retained if they had 500-20,000 UMIs and <5% UMIs from genes encoded by mitocondrial genes
Cells were noramlized, corrected for batch, and projected into latent space using Suerat(4.3.0)
Assembly: mm10
Supplementary files format and content: mouse_metadata.tsv.gz; sample assignments and related metadata, including TCR clonotype, for all filtered cell barcodes
Supplementary files format and content: mouse_cell_barcodes.tsv.gz, mouse_normalized_rna_matrix.mtx, mouse_normalized_rna_features.tsv.gz; Normalized RNA counts matrix and column/row labels


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 7720

description:
cell-free DNA 5hmC
PLCO-235


title: Ectoderm_H2Aub_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H2Aub_ChIP_Xencode_Group2_2


title: Ectoderm_H3K27ac_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H3K27ac_ChIP_Xencode_Group2_2


title: Ectoderm_H3K36me3_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H3K36me3_ChIP_Xencode_Group2_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 8242

description:
cell-free DNA 5hmC
PLCO-234


title: ms_liver_hfhc_25weeks_rep2_gex


title: Ectoderm_H3K27me3_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H3K27me3_ChIP_Xencode_Group2_2


title: ms_liver_hfhc_25weeks_rep3_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 4566

description:
cell-free DNA 5hmC
PLCO-233


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 3948

description:
cell-free DNA 5hmC
PLCO-232


description: Library name: Ectoderm_H2AH4Ser1P_ChIP_Xencode_Group2_2


title: ms_liver_hfhc_25weeks_rep1_gex


title: ms_liver_chow_31weeks_rep3_TCR

description:
T cell receptor sequencing (TCR)
mouse_metadata.tsv.gz


title: Ectoderm_Input_Xencode_Group2_2

description: Library name: Ectoderm_Input_Xencode_Group2_2


title: Ectoderm_H2Aub_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H2Aub_ChIP_Xencode_Group2_1


title: ms_liver_chow_25weeks_rep4_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UR 0830

description:
cell-free DNA 5hmC
PLCO-231


title: Ectoderm_H3K9me3_ChIP_Xencode_Group2_2

description: Library name: Ectoderm_H3K9me3_ChIP_Xencode_Group2_2


title: Ectoderm_H3K4me3_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group2_1


title: ms_liver_chow_25weeks_rep2_gex


title: Ectoderm_H2A.x.3_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H2A.x.3_ChIP_Xencode_Group2_1


title: ms_liver_chow_25weeks_rep3_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6836

description:
cell-free DNA 5hmC
PLCO-230


description: Library name: Ectoderm_H2AH4Ser1P_ChIP_Xencode_Group2_1


title: Ectoderm_H3K27ac_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H3K27ac_ChIP_Xencode_Group2_1


title: Endoderm_Input_Xencode_Group2_1

description: Library name: Endoderm_Input_Xencode_Group2_1


title: Ectoderm_H3K27me3_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H3K27me3_ChIP_Xencode_Group2_1


title: ms_liver_chow_25weeks_rep1_gex


title: Ectoderm_H3K36me3_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H3K36me3_ChIP_Xencode_Group2_1


title: Ectoderm_H3K9me3_ChIP_Xencode_Group2_1

description: Library name: Ectoderm_H3K9me3_ChIP_Xencode_Group2_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 6582

description:
cell-free DNA 5hmC
PLCO-228


title: Ectoderm_Input_Xencode_Group2_1

description: Library name: Ectoderm_Input_Xencode_Group2_1


title: Endoderm_H2A.ub_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H2A.ub_ChIP_Xencode_Group1_2


description: Library name: Endoderm_H2AH4Ser1P_ChIP_Xencode_Group1_2


title: Endoderm_H3K4me3_ChIP__Xencode_Group1_2

description: Library name: Endoderm_H3K4me3_ChIP__Xencode_Group1_2


title: ms_liver_reversal_31weeks_rep4_gex

description:
mRNA sequencing
mouse_metadata.tsv.gz
mouse_cell_barcodes.tsv.gz
mouse_normalized_rna_features.tsv.gz
mouse_normalized_rna_matrix.mtx


title: ms_liver_reversal_31weeks_rep3_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9953

description:
cell-free DNA 5hmC
PLCO-226


title: Endoderm_H2A.x.3_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H2A.x.3_ChIP_Xencode_Group1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1844

description:
cell-free DNA 5hmC
PLCO-227


title: Endoderm_H3K27me3_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group1_2


title: Endoderm_H3K27ac_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H3K27ac_ChIP_Xencode_Group1_2


title: Endoderm_H3K9me3_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H3K9me3_ChIP_Xencode_Group1_2


title: Endoderm_H3K36me3_ChIP_Xencode_Group1_2

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group1_2


title: ms_liver_hfhc_31weeks_rep4_gex


title: ms_liver_reversal_31weeks_rep2_gex


title: ms_liver_reversal_31weeks_rep1_gex


title: ms_liver_hfhc_31weeks_rep3_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 5099

description:
cell-free DNA 5hmC
PLCO-224


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 1513

description:
cell-free DNA 5hmC
PLCO-220


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IY 7287

description:
cell-free DNA 5hmC
PLCO-221


title: Ectoderm_H2A.XF3_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H2A.XF3_ChIP_Xencode_Group1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 1689

description:
cell-free DNA 5hmC
PLCO-229


title: Ectoderm_H3K4me3_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 1884

description:
cell-free DNA 5hmC
PLCO-219


title: ms_liver_hfhc_31weeks_rep2_gex


title: Ectoderm_H3K27me3_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H3K27me3_ChIP_Xencode_Group1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 8634

description:
cell-free DNA 5hmC
PLCO-223


title: Ectoderm_H3K36me3_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H3K36me3_ChIP_Xencode_Group1_2


title: ms_liver_hfhc_31weeks_rep1_gex


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 3302

description:
cell-free DNA 5hmC
PLCO-218


title: ms_liver_chow_31weeks_rep4_gex


description: Library name: Ectoderm_H2AH4Ser1P_ChIP_Xencode_Group1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6146

description:
cell-free DNA 5hmC
PLCO-217


title: Ectoderm_H2Aub_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H2Aub_ChIP_Xencode_Group1_2


title: Endoderm_Input_Xencode_Group1_2

description: Library name: Endoderm_Input_Xencode_Group1_2


title: Ectoderm_H3K9me3_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H3K9me3_ChIP_Xencode_Group1_2


title: Ectoderm_Input_Xencode_Group1_2

description: Library name: Ectoderm_Input_Xencode_Group1_2


title: Ectoderm_H3K27ac_ChIP_Xencode_Group1_2

description: Library name: Ectoderm_H3K27ac_ChIP_Xencode_Group1_2


title: Endoderm_H2A.ub_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H2A.ub_ChIP_Xencode_Group1_1


title: ms_liver_chow_31weeks_rep2_gex

description:
mRNA sequencing
mouse_metadata.tsv.gz
mouse_cell_barcodes.tsv.gz
mouse_normalized_rna_features.tsv.gz
mouse_normalized_rna_matrix.mtx


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 8766

description:
cell-free DNA 5hmC
PLCO-215


title: ms_liver_chow_31weeks_rep3_gex


title: Endoderm_H2A.x.3_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H2A.x.3_ChIP_Xencode_Group1_1


title: Endoderm_H3K36me3_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group1_1


title: Endoderm_H3K27me3_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2768

description:
cell-free DNA 5hmC
PLCO-213


title: Endoderm_H3K27ac_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H3K27ac_ChIP_Xencode_Group1_1


title: DC2 cell, control siRNA treated, sample 4

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

description:
Control-4
abundance_gene_ift88.csv

data_processing:
Reads were trimmed using fastp v0.20.0. Quality control was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.8 and MultiQC v1.8. The quantification was performed with Kallisto v0.46.2 against the Mus musculus transcriptome (downloaded from Ensembl release 101).
Assembly: Mus musculus transcriptome (downloaded from Ensembl release 101)
Supplementary files format and content: abundances at the gene levels (from Kallisto)

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit from DC2 cells exposed to shear stress of 1 dyn/cm2 for 3 hours and DC2 cells kept in static conditions .
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare total RNA sequencing libraries according to manufacturer’s instruction using 1 ug of total RNA

tag: cell line

value: Distal Caput Principal cells

value: control siRNA treated


title: Endoderm_H3K9me3_ChIP_Xencode_Group1_1

description: Library name: Endoderm_H3K9me3_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 9172

description:
cell-free DNA 5hmC
PLCO-212


title: Endoderm_Input_Xencode_Group1_1

description: Library name: Endoderm_Input_Xencode_Group1_1


title: DC2 cell, control siRNA treated, sample 3

description:
Control-3
abundance_gene_ift88.csv


title: Ectoderm_H3K4me3_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H3K4me3_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2665

description:
cell-free DNA 5hmC
PLCO-211


title: DC2 cell, control siRNA treated, sample 2

description:
Control-2
abundance_gene_ift88.csv


title: Endoderm_H3K4me3_ChIP__Xencode_Group1_1

description: Library name: Endoderm_H3K4me3_ChIP__Xencode_Group1_1


title: DC2 cell, control siRNA treated, sample 1

description:
Control-1
abundance_gene_ift88.csv


title: Ectoderm_H3K36me3_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H3K36me3_ChIP_Xencode_Group1_1


title: Ectoderm_H2Aub_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H2Aub_ChIP_Xencode_Group1_1


description: Library name: Ectoderm_H2AH4Ser1P_ChIP_Xencode_Group1_1


title: Ectoderm_H2A.XF3_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H2A.XF3_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 0951

description:
cell-free DNA 5hmC
PLCO-209


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9371

description:
cell-free DNA 5hmC
PLCO-210


title: Ectoderm_H3K27me3_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H3K27me3_ChIP_Xencode_Group1_1


title: Ectoderm_Input_Xencode_Group1_1

description: Library name: Ectoderm_Input_Xencode_Group1_1


title: Ectoderm_H3K9me3_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H3K9me3_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3414

description:
cell-free DNA 5hmC
PLCO-207


title: DC2 cell, ift88 siRNA treated, sample 4

description:
IFT88-4
abundance_gene_ift88.csv

value: ift88 siRNA treated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1467

description:
cell-free DNA 5hmC
PLCO-206


title: Endoderm_IVF_12_Group8

description:
Library name: Endoderm_IVF_12_Group8
50

data_processing:
Paired sequencing reads were processed using Kallisto (v0.48) for pseudoalignment and quantification of transcript abundance.
Transcript and annotation files were downloaded from Xenbase (v10.1) for Xenopus laevis (transcripts and annotation).
After quantification, transcript-level abundances were imported using 'tximport' and converted to a 'SummarizedExperiment' object in R (v4.3.1).
Datasets of two independent batches were merged and subjected to differential expression analysis performed with DESeq2 (v1.40.2).
Assembly: Xenopus laevis 10.1
Supplementary files format and content: Kallisto output containing transcript abundance as transcript per million.

source_name: in vitro fertilized embryo stage 11

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s instructions. To lyse the embryonic tissue, samples were vortexed on high speed for 10 min at 4°C. DNase digestion was performed according to the manufacturer’s instructions, using RNase-free DNase (QIAGEN, 79254).
Per sample, 400 ng total RNA of animal cap (ectoderm) tissue and 300 ng of endoderm donor tissue were used to isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).  Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760), following the manufacturer’s instructions, using 12-13 PCR amplification cycles. Libraries were multiplexed and sequenced on a NextSeq 6000 platform.

treatment_protocol: IVF-derived gastrulae (NF stage 12) were treated with 40 µM SGC-CBP30 (Sigma, SML1133), 30 µM A-485 (Tcris, #6387) or DMSO in 0.1x MMR at 23°C until they reached neurula stage (NF stage 18)59. The embryos were collected at synchronized stages to eliminate influences from different cell numbers or developmental stages. The embryos were either used as donors for nuclear transfer as described above, or frozen for RNA-extraction.Endoderm was dissected from neurula-stage embryos (NF stage 18) and allowed to dissociate into single cells in calcium- and magnesium-free 1x modified Barth saline (MBS, 88 mM NaCl, 1mM KCl, 10mM HEPES, 2.5 mM NaHCO3, pH 7.4) with 1 mM EDTA and 0.1% BSA in a Petri dish coated with 0.1% agarose in H2O. Donor cells were immediately used for NT.

value: in vitro fertilized embryo stage 11


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9558

description:
cell-free DNA 5hmC
PLCO-216


title: Endoderm_IVF_13_Group8

description:
Library name: Endoderm_IVF_13_Group8
50


title: DC2 cell, ift88 siRNA treated, sample 2

description:
IFT88-2
abundance_gene_ift88.csv


title: DC2 cell, ift88 siRNA treated, sample 3

description:
IFT88-3
abundance_gene_ift88.csv


title: Endoderm_IVF_10_Group8

description:
Library name: Endoderm_IVF_10_Group8
50


title: Ectoderm_H3K27ac_ChIP_Xencode_Group1_1

description: Library name: Ectoderm_H3K27ac_ChIP_Xencode_Group1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 1091

description:
cell-free DNA 5hmC
PLCO-208


title: Endoderm_IVF_11_Group8

description:
Library name: Endoderm_IVF_11_Group8
50


title: ms_liver_chow_31weeks_rep1_gex

description:
mRNA sequencing
mouse_metadata.tsv.gz
mouse_cell_barcodes.tsv.gz
mouse_normalized_rna_features.tsv.gz
mouse_normalized_rna_matrix.mtx


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1303

description:
cell-free DNA 5hmC
PLCO-205


title: DC2 cell, Static condition, sample 6

description:
E12_ST
abundance_gene_ST_vs_FL.csv

value: Static condition


title: DC2 cell, ift88 siRNA treated, sample 1

description:
IFT88-1
abundance_gene_ift88.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5755

description:
cell-free DNA 5hmC
PLCO-204


title: Endoderm_NT_7_Group8

description:
Library name: Endoderm_NT_7_Group8
50

source_name: mesoderm derived nuclear transfer embryo stage 11


title: DC2 cell, Static condition, sample 5

description:
E10_ST
abundance_gene_ST_vs_FL.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1415

description:
cell-free DNA 5hmC
PLCO-203


title: Endoderm_NT_5_Group8_Group8

description:
Library name: Endoderm_NT_5_Group8_Group8
50

value: mesoderm derived nuclear transfer embryo stage 11


title: DC2 cell, Static condition, sample 4

description:
E8_ST
abundance_gene_ST_vs_FL.csv


title: Endoderm_NT_6_Group8

description:
Library name: Endoderm_NT_6_Group8
50


title: Endoderm_NT_4_Group8

description:
Library name: Endoderm_NT_4_Group8
50


title: Ectoderm_IVF_12_Group8

description:
Library name: Ectoderm_IVF_12_Group8
50


title: Ectoderm_IVF_10_Group8

description:
Library name: Ectoderm_IVF_10_Group8
50


title: Ectoderm_IVF_11_Group8

description:
Library name: Ectoderm_IVF_11_Group8
50


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6133

description:
cell-free DNA 5hmC
PLCO-200


title: DC2 cell, Static condition, sample 1

description:
E2_ST
abundance_gene_ST_vs_FL.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6738

description:
cell-free DNA 5hmC
PLCO-201


title: Endoderm_IVF_9_Group8

description:
Library name: Endoderm_IVF_9_Group8
50


title: Endoderm_NT_8_Group8

description:
Library name: Endoderm_NT_8_Group8
50


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9988

description:
cell-free DNA 5hmC
PLCO-198


title: Ectoderm_NT_8_Group8

description:
Library name: Ectoderm_NT_8_Group8
50


title: Ectoderm_NT_5_Group8

description:
Library name: Ectoderm_NT_5_Group8
50


title: DC2 cell, Flow condition, sample 6

description:
E11_FL
abundance_gene_ST_vs_FL.csv


title: Ectoderm_NT_6_Group8

description:
Library name: Ectoderm_NT_6_Group8
50


title: DC2 cell, Flow condition, sample 5

description:
E9_FL
abundance_gene_ST_vs_FL.csv

value: Flow condition


title: Ectoderm_NT_4_Group8

description:
Library name: Ectoderm_NT_4_Group8
50


title: DC2 cell, Flow condition, sample 4

description:
E7_FL
abundance_gene_ST_vs_FL.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 3242

description:
cell-free DNA 5hmC
PLCO-202


title: Ectoderm_IVF_13_Group8

description:
Library name: Ectoderm_IVF_13_Group8
50


title: DC2 cell, Static condition, sample 3

description:
E6_ST
abundance_gene_ST_vs_FL.csv


title: Somite_Donor_1_Group8

description:
Library name: Somite_Donor_1_Group8
50

source_name: mesoderm

value: mesoderm


title: DC2 cell, Flow condition, sample 3

description:
E5_FL
abundance_gene_ST_vs_FL.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 8031

description:
cell-free DNA 5hmC
PLCO-196


title: 25 gRNAs (gSZRD1 + 24 gRNAs)

city: Kansas City

first: Gabriel

last: da Silva Pescador

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were generated manually, using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) at 1/8th reaction volumes (1/4th reaction volumes for RfxCas13d_R1 and RfxCas13d_R2 samples) paired with IDT for Illumina DNA/RNA UD Indexes Set A (Illumina, 20027213), and purified using the Ampure XP bead-based reagent (Beckman Coulter, Cat. No. A63882).

value: whole embryo

value: 4 hpf

value: RfxCas13d knockdown


title: 10 gRNAs (gSZRD1 + 9 gRNAs)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IW 8388

description:
cell-free DNA 5hmC
PLCO-195


title: Ectoderm_IVF_9_Group8

description:
Library name: Ectoderm_IVF_9_Group8
50

value: WT


title: DC2 cell, Static condition, sample 2

description:
E4_ST
abundance_gene_ST_vs_FL.csv


title: Ectoderm_NT_7_Group8

description:
Library name: Ectoderm_NT_7_Group8
50


title: RfxCas13d control, rep3

value: RfxCas13d control


title: RfxCas13d control, rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 7373

description:
cell-free DNA 5hmC
PLCO-194

value: peripheral plasma

value: cell-free DNA


title: RfxCas13d control, rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9156

description:
cell-free DNA 5hmC
PLCO-199


title: DC2 cell, Flow condition, sample 1

description:
E1_FL
abundance_gene_ST_vs_FL.csv


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 8572

description:
cell-free DNA 5hmC
PLCO-197


title: DC2 cell, Flow condition, sample 2

description:
E3_FL
abundance_gene_ST_vs_FL.csv


title: RfxCas13d control, rep2

data_processing:
Following sequencing, Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were generated with the Mosquito HV Genomics (SPT Labtech) nanoliter liquid-handling instrument, using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) at 1/8th reaction volumes paired with IDT for Illumina DNA/RNA UD Indexes Set A (Illumina, 20027213), and purified using the Ampure XP bead-based reagent (Beckman Coulter, Cat. No. A63882).


title: Somite_Donor_2_Group8

description:
Library name: Somite_Donor_2_Group8
50


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 5548

description:
cell-free DNA 5hmC
PLCO-193


title: Exp3_WT_PE_Rep4

first: Neelanjan

last: Mukherjee

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode M25 transcriptome assembly (parameters -l A --allowDovetail --validateMappings). All other analysis was performed in R. Briefly, Salmon data were imported using the tximport library (Soneson et al. 2015). Differential gene expression was performed using DESeq2 library (Love et al. 2014) with likelihood ratio test (padj < 0.05).
Assembly: GRCm38
Supplementary files format and content: CSV table of salmon counts for all samples

molecule: polyA RNA

source_name: ovary

extract_protocol:
Total RNA from mouse ovaries was obtained using RNeasy micro-columns (Qiagen), quantified by NanoDrop (ND1000) and DNase-I treated as described. RNASeq on ovary samples obtained from Fshb +/+, Fshb -/- and Fshb -/- HFSHB + was performed at the University of Nebraska Medical Center Genomics Core and the methods were described before. For estrus stage study, after additional quantification by Qubit RNA assay, poly-A RNA was selected from 1000 ng total RNA input using the New England Biolabs NEBNext Poly(A) mRNA magnetic isolation module.
The isolated mRNA was further used as input for library preparation with the KAPA RNA Hyper prep kit following the manufacturer’s instructions. Final libraries were quantified and quality checked using the Qubit dsDNA HS assay and Tapestation HS D1000 screentape before submitting for sequencing on the NovaSeq 6000 for 20 million 2x150bp paired-end reads per library (Novogene Corp. Inc.).

value: ovary

tag: estrus stage

value: PE


title: Cocktail 8, 25 gRNAs, rep2


title: Exp3_WT_PE_Rep3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 0160

description:
cell-free DNA 5hmC
PLCO-192


title: Cocktail 7, 25 gRNAs, rep2


title: Cocktail 7, 25 gRNAs, rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KF 9456

description:
cell-free DNA 5hmC
PLCO-191


title: Exp3_WT_PE_Rep2


title: Cocktail 6, 25 gRNAs, rep2


title: Exp3_WT_PE_Rep1


title: Cocktail 5, 25 gRNAs, rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 0689

description:
cell-free DNA 5hmC
PLCO-190


title: Exp3_WT_KO_Rep4

value: KO (anestrus)


title: Cocktail 5, 25 gRNAs, rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 3713

description:
cell-free DNA 5hmC
PLCO-188


title: Cocktail 4, 25 gRNAs, rep2


title: Exp3_WT_KO_Rep3


title: Cocktail 3, 25 gRNAs, rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 8776

description:
cell-free DNA 5hmC
PLCO-187


title: Cocktail 3, 25 gRNAs, rep1


title: Cocktail 8, 25 gRNAs, rep1


title: Cocktail 2, 25 gRNAs, rep2


title: RfxCas13d control, rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3792

description:
cell-free DNA 5hmC
PLCO-186


title: Exp3_WT_KO_Rep2


title: Cocktail 4, 25 gRNAs, rep1


title: Cocktail 2, 25 gRNAs, rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 6626

description:
cell-free DNA 5hmC
PLCO-185


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9377

description:
cell-free DNA 5hmC
PLCO-184


title: Exp3_WT_DE_Rep3

value: DE


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 8183

description:
cell-free DNA 5hmC
PLCO-189


title: Cocktail 1, 25 gRNAs, rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 6282

description:
cell-free DNA 5hmC
PLCO-183


title: gastric cancer cells, Mock_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description:
Library name: Sample 3
Gene expression after stable transfection of empty vector

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: gastric cancer

growth_protocol: Human gastric cancer cell line MKN-45 was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The SNORA37 expression or empty vector was transfected into cancer cells, and stable cell lines were screened by administration of puromycin.

value: gastric cancer

value: gastric cancer cells

value: stable transfection of empty vector


title: gastric cancer cells, SNORA37_3

description:
Library name: Sample 6
Gene expression after stable transfection of SNORA37

value: stable transfection of SNORA37


title: Exp3_WT_KO_Rep1


title: gastric cancer cells, SNORA37_2

description:
Library name: Sample 5
Gene expression after stable transfection of SNORA37


title: Cocktail 1, 25 gRNAs, rep1


title: gastric cancer cells, Mock_2

description:
Library name: Sample 2
Gene expression after stable transfection of empty vector


title: Exp3_WT_DE_Rep4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 6335

description:
cell-free DNA 5hmC
PLCO-182


title: Exp3_WT_DE_Rep2


title: gastric cancer cells, SNORA37_1

description:
Library name: Sample 4
Gene expression after stable transfection of SNORA37


title: tissues, GCa_1

description:
Library name: Sample 4
Gene expression in gastric cancer tissue

source_name: Gastric cancer tissue

extract_protocol:
Tissues were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gastric cancer tissue


title: Exp3_WT_E_Rep3

value: E


title: gastric cancer cells, Mock_1

description:
Library name: Sample 1
Gene expression after stable transfection of empty vector


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 9604

description:
cell-free DNA 5hmC
PLCO-181


title: tissues, GCa_2

description:
Library name: Sample 5
Gene expression in gastric cancer tissue


title: tissues, GCa_3

description:
Library name: Sample 6
Gene expression in gastric cancer tissue


title: Exp3_WT_E_Rep4


title: tissues, Normal_2

description:
Library name: Sample 2
Gene expression in normal gastric epithelial tissue

source_name: Normal gastric epithelial tissue

value: Normal gastric epithelial tissue


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 1221

description:
cell-free DNA 5hmC
PLCO-178


title: tissues, Normal_3

description:
Library name: Sample 3
Gene expression in normal gastric epithelial tissue


title: tissues, Normal_1

description:
Library name: Sample 1
Gene expression in normal gastric epithelial tissue


title: Exp3_WT_E_Rep2


title: Cocktail 6, 25 gRNAs, rep1

value: whole embryo

value: 4 hpf


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- RRV, Replicate 3

first: Deborah

middle: R

last: Winter

address: 240 E. Huron Street, M300

description:
Library name: RRV_DN_3
M01_Liver_RRV_neg_03

data_processing:
The resulting BCL files were demultiplexed into fastq files which were then trimmed for low quality bases and adaptors using Trimmomatic.
Trimmed reads were aligned to the mm10 reference using Tophat (21, 22) and mapped to gene exons in the Mus_musculus.GRCm38 reference with Htseq.
Gene expression counts were normalized to read depth using counts per million reads mapped (CPM).
Assembly: mm10
Supplementary files format and content: tab-delimited table of RNA counts across all samples
Supplementary files format and content: tab-delimited table of CPM values across all samples

extract_protocol:
RNA was extracted from sorted cells using the PicoPure RNA Isolation kit as per manufacturer's instructions
Fulllength cDNA libraries were synthesized using the NEBNext Ultra RNA Library Prep Kit (New England BioLabs) followed by TruSeq DNA HT Sample Prep Kit (Illumina) and sequenced by Illumina NextSeq500 to an average depth of ~15x106 reads per sample.

treatment_protocol: Newborn mice received an intra-peritoneal injection within 24 hours of life of either 50 ml RRV (1.8x10^6 pfu) to establish murine BA or 50 ml phosphate buffered saline (PBS) for controls

tag: age

value: DOL 14

value: liver

value: macrophage

tag: strain

value: BALB/c

value: RRV


title: Exp3_WT_DE_Rep1

value: ovary

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 6412

description:
cell-free DNA 5hmC
PLCO-177

value: peripheral plasma

value: cell-free DNA


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- RRV, Replicate 1

description:
Library name: RRV_DN_1
M01_Liver_RRV_neg_01


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ RRV, Replicate 2

description:
Library name: RRV_MHCII_2
M01_Liver_RRV_MHCII_02


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ RRV, Replicate 3

description:
Library name: RRV_MHCII_3
M01_Liver_RRV_MHCII_03


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UR 0992

description:
cell-free DNA 5hmC
PLCO-180


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 3474

description:
cell-free DNA 5hmC
PLCO-176


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ RRV, Replicate 1

description:
Library name: RRV_MHCII_1
M01_Liver_RRV_MHCII_01


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- RRV, Replicate 4

description:
Library name: RRV_DN_4
M01_Liver_RRV_neg_04


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ RRV, Replicate 4

description:
Library name: RRV_MHCII_4
M01_Liver_RRV_MHCII_04


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9567

description:
cell-free DNA 5hmC
PLCO-175


title: Exp2_R_NS_Rep4

value: Fshb(-/-) HFSHB


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0521

description:
cell-free DNA 5hmC
PLCO-174


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- RRV, Replicate 3

description:
Library name: RRV_Ly6c_3
M01_Liver_RRV_Ly6c_03


title: Exp2_R_NS_Rep1


title: Exp2_R_NS_Rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7470

description:
cell-free DNA 5hmC
PLCO-170


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 6414

description:
cell-free DNA 5hmC
PLCO-172


title: Exp3_WT_E_Rep1


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ RRV, Replicate 4

description:
Library name: RRV_DP_4
M01_Liver_RRV_Ly6cMHCIII_04


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ RRV, Replicate 2

description:
Library name: RRV_DP_2
M01_Liver_RRV_Ly6cMHCIII_02


title: Exp2_KO_NS_Rep4


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ RRV, Replicate 3

description:
Library name: RRV_DP_3
M01_Liver_RRV_Ly6cMHCIII_03


title: Exp2_KO_NS_Rep3


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- RRV, Replicate 4

description:
Library name: RRV_Ly6c_4
M01_Liver_RRV_Ly6c_04


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 2878

description:
cell-free DNA 5hmC
PLCO-167


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ RRV, Replicate 1

description:
Library name: RRV_DP_1
M01_Liver_RRV_Ly6cMHCIII_01


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- Controls, Replicate 1

description:
Library name: Saline_DN_1
M01_Liver_Saline_neg_01

value: Saline


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 7005

description:
cell-free DNA 5hmC
PLCO-166


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- Controls, Replicate 3

description:
Library name: Saline_DN_3
M01_Liver_Saline_neg_03


title: Exp2_KO_NS_Rep1


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII- Controls, Replicate 4

description:
Library name: Saline_DN_4
M01_Liver_Saline_neg_04


title: Exp2_R_NS_Rep3


title: Exp1_WT_NS_Rep3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9582

description:
cell-free DNA 5hmC
PLCO-165


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1907

description:
cell-free DNA 5hmC
PLCO-164


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ Controls, Replicate 2

description:
Library name: Saline_MHCII_2
M01_Liver_Saline_MHCII_02


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ Controls, Replicate 1

description:
Library name: Saline_MHCII_1
M01_Liver_Saline_MHCII_01


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- RRV, Replicate 2

description:
Library name: RRV_Ly6c_2
M01_Liver_RRV_Ly6c_02


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- RRV, Replicate 1

description:
Library name: RRV_Ly6c_1
M01_Liver_RRV_Ly6c_01


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ Controls, Replicate 4

description:
Library name: Saline_MHCII_4
M01_Liver_Saline_MHCII_04


title: Exp1_WT_NS_Rep2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3624

description:
cell-free DNA 5hmC
PLCO-168


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- Controls, Replicate 4

description:
Library name: Saline_Ly6c_4
M01_Liver_Saline_Ly6c_04


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0389

description:
cell-free DNA 5hmC
PLCO-163


title: Hi-C Ra3

city: Delhi

first: Rupesh

last: Chaturvedi

state: Delhi

address: School of biotechnology, JNU, Chattarpur

department: School of Biotechnology

country: India

institute: Jawaharlal nehru university

data_processing:
Hi-C data was processed using Hi-C explorer.
Supplementary files format and content: contact matrix file .h5

organism: Mycobacterium tuberculosis H37Ra

source_name: bacterial cell

growth_protocol: M. tuberculosis strains were cultured in 7H9 medium supplemented with ADC enrichment (5% Albumin, 2% dextrose, 0.003% catalase and 0.85% sodium chloride) and 0.05% Tween 80. All the cultures were grown at 37°C with constant shaking at 200 rpm in a biosafety level 3 facilities. OD at 600 nm was measured to monitor growth.

extract_protocol:
Hi-C experiment were conducted in biological replicates using BglII, according to the protocol published by Umbarger. Et al. Molecular cell 2011. Final DNA libraries were purified using pheonopl chloroform method.
NEBNext® UltraTM II DNA Library Prep Kit for Illumina

value: bacterial cell

value: No treatment


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- Controls, Replicate 3

description:
Library name: Saline_Ly6c_3
M01_Liver_Saline_Ly6c_03


title: Exp2_KO_NS_Rep2


title: Hi-C Ra2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 0242

description:
cell-free DNA 5hmC
PLCO-161


title: Exp1_KO_NS_Rep3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 3159

description:
cell-free DNA 5hmC
PLCO-160


title: Mapt-hTau-DLB- brain-derived Tau oligomers

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
7_S7

data_processing:
Libraries were sequenced on an Illumina Novaseq instrument and counted with CellRanger v7.2.0 using mm10 reference genome.
Assembly: mm10
Supplementary files format and content: gene expression matrix and metadata in compressed format

source_name: Brain

extract_protocol: 10X Genomics single cell 3' gene expression

value: Brain

value: Primary cortical neurons

value: Excitatory

value: Mapt-hTau

value: DLB- brain-derived Tau oligomers


title: Mapt-hTau-AD- brain-derived Tau oligomers

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
6_S6

value: AD- brain-derived Tau oligomers


title: Exp1_WT_NS_Rep1


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ Controls, Replicate 4

description:
Library name: Saline_DP_4
M01_Liver_Saline_Ly6cMHCIII_04

value: DOL 14

value: liver

value: macrophage


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ Controls, Replicate 2

description:
Library name: Saline_DP_2
M01_Liver_Saline_Ly6cMHCIII_02

value: BALB/c


title: Mapt-hTau-PSP- brain-derived Tau oligomers

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
8_S8

value: PSP- brain-derived Tau oligomers


title: Exp1_Het_NS_Rep2

value: ovary


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 3139

description:
cell-free DNA 5hmC
PLCO-158

value: peripheral plasma

value: cell-free DNA


title: Exp1_KO_NS_Rep1


title: Hi-C Ra1

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 5670

description:
cell-free DNA 5hmC
PLCO-162


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 5918

description:
cell-free DNA 5hmC
PLCO-159


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- Controls, Replicate 1

description:
Library name: Saline_Ly6c_1
M01_Liver_Saline_Ly6c_01

value: Saline


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ Controls, Replicate 3

description:
Library name: Saline_DP_3
M01_Liver_Saline_Ly6cMHCIII_03


title: Exp1_Het_NS_Rep3


title: Mapt-hTau-untreated

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
5_S5

value: untreated


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII- Controls, Replicate 2

description:
Library name: Saline_Ly6c_2
M01_Liver_Saline_Ly6c_02


title: Exp1_KO_NS_Rep2


title: Exp1_Het_NS_Rep1


title: BALB/c Murine Hepatic Macrophages Ly6c+MHCII+ Controls, Replicate 1

description:
Library name: Saline_DP_1
M01_Liver_Saline_Ly6cMHCIII_01


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1827

description:
cell-free DNA 5hmC
PLCO-157


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2134

description:
cell-free DNA 5hmC
PLCO-156


title: C57BL/9-PSP- brain-derived Tau oligomers

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
4_S4

value: Brain


title: HOXC4_Input

city: Beijing

first: Ting

last: Yang

state: Beijing

address: 10 Xitoutiao, Youanmen Wai, Fengtai District, Beijing, China

institute: Capital Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling.
The Homer（version 4.10）was used for motifs analysis and KOBAS software (version: 2.1.1) was used for GO and KEGG analysis .
Assembly: GRCm39
Supplementary files format and content: Supplementary_format_and_content_prossessed data.bw

source_name: Brown Adipocytes

extract_protocol:
Primary brown adipocytes overexpressing HOXC4 were fixed with 1% formaldehyde for 10 min at room temperature to cross-link DNA-protein complexes. Glycine was added to a final concentration of 125 mM for 5 min to terminate the crosslinking reaction. Cells were washed with PBS, harvested, and centrifuged at 900 × g for 3 min. The pellet was lysed to extract nucleus by centrifuging at 2000g for 5min. Genomic DNA was sonicated to 200 bp to 500 bp fragments. Of the sonicated chromatin, 10% was saved as the input sample, 80% underwent immunoprecipitation using anti-HA beads (MCE), and the remaining 10% was treated with rabbit IgG (Cell Signaling Technology) as the negative control.
The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: Brown Adipocytes


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9077

description:
cell-free DNA 5hmC
PLCO-154


title: C57BL/7-AD- brain-derived Tau oligomers

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
2_S2

value: Primary cortical neurons

value: Excitatory


title: MPP4-WT-1

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Analysis was done using ENCODE ATACseq pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline
Assembly: mm10
Supplementary files format and content: scaled bigwig files generated with deeptools (https://deeptools.readthedocs.io/en/develop/index.html) from bam files filtered out for duplicates and chrM.

source_name: Bone Marrow

extract_protocol: ATACseq libraries generated using standard protocol from Buenrostro et al Nat Methods. 2013 Dec;10(12):1213-8. doi: 10.1038/nmeth.2688

value: Bone Marrow


title: MPP4-WT-2


title: MPP4-2026-2


title: C57BL/6-untreated

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
1_S1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 1581

description:
cell-free DNA 5hmC
PLCO-150


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 3691

description:
cell-free DNA 5hmC
PLCO-155


title: MPP4-1013-2


title: MPP4-1013-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 9704

description:
cell-free DNA 5hmC
PLCO-153


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 8502

description:
cell-free DNA 5hmC
PLCO-149


title: C57BL/8-DLB- brain-derived Tau oligomers

description:
counts.csv
metadata.csv
combined_filtered_feature_bc_matrix.zip
3_S3

value: DLB- brain-derived Tau oligomers


title: L3b

city: Herts

first: Esther

last: Palomino Lago

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

country: United Kingdom

institute: Royal Veterinary College

data_processing:
FastQC (v0.11.9) (Babraham Bioinformatics, Cambridge, UK) and MultiQC (v1.11) were used to establish raw sequencing quality.
Raw RNA-seq reads were aligned to equine transcriptome obtained from NCBI EquCab 3.0 (GCF_002863925.1_EquCab3.0) annotation release 103 using the pseudoaligner Salmon (v1.5.2) in Quasi-mapping-based mode with GC-bias correction
Transcript level mappings were imported into RStudio (v.4.2.1) using Tximport (v1.20)
Read counts were normalized and analysed for differential expression using DESeq2 v.1.22.2
Genes with a Log2Fold Change (Log2FC) of ±1 and an adjusted p-value (p-adj) of ≤0.05 were considered as differentially expressed.
Assembly: NCBI EquCab 3.0 (GCF_002863925.1_EquCab3.0)
Supplementary files format and content: SpreadsheetML (.xlsx) includes normalised counts of sequencing reads for each sample in a matrix table and DESeq2_lowrisk vs Highrisk results

organism: Equus caballus

source_name: skin fibroblast

extract_protocol:
RNA was collected using Tri-reagent (Sigma-Aldrich) and extracted using the RNeasy Mini Kit (Qiagen, UK) following the manufacturer’s instructions. Purified RNA was treated with the DNA-free™ DNA removal kit (Invitrogen, Thermo Fisher) to remove genomic DNA contamination according to the manufacturer’s instructions. RNA concentration was determined using a Qubit (Thermo Fisher Scientific) and the purity was determined using a DS-11 spectrophotometer to ensure 260/280 ratios >1.8. RNA integrity was measured using a Tapestation (2100 Bioanalyzer (Agilent, UK) and for all samples was confirmed to be >9.0.
mRNA library preparation and transcriptome sequencing were conducted by Novogene (Cambridge, UK) using an Illumina NovaSeq 6000 to generate 26.1X-57.2X million 150 bp paired end reads per sample.

tag: breed

value: Thoroughbred

tag: polygenetic risk_score

tag: Sex

value: Male

value: skin fibroblast

value: iPSC

value: iPSC-derived osteoblast

tag: cell passage


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7023

description:
cell-free DNA 5hmC
PLCO-151


title: L2c


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 5887

description:
cell-free DNA 5hmC
PLCO-148


title: tpn-2,scRNAseq

city: Hangzhou

first: Jian

last: Zhang

address: Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province

institute: Zhejiang University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software  (http://support.10xgenomics.com/single-cell/software/overview/welcome) with STAR (https://github.com/alexdobin/STAR).
cells were filtered to include at least 200 genes present in each cell, a minimum of three cells, and cells with more than 35% of genes from the mitochondrial genome were discarded (min.cells = 3, min.features = 200, and percent.mt < 35). Doublet cells were removed using DoubletFinder v2.0.3  with parameters (PCs = 1:10, pN = 0.25, pK = 0.09).
Subsequently, the "sham," "TPN," and "starvation" groups were combined.
The gene expression measurements for each cell were normalized using Seurat's "LogNormalize" method with a scale factor of 10000. High variable genes were identified using the variance stabilizing transformation (VST) method (selection.method = "vst", nfeatures = 2000).
Principal Component Analysis (PCA) was performed (npcs = 30), followed by Uniform Manifold Approximation and Projection (UMAP) analysis (reduction = "pca", dims = 1:30).
Assembly: mm10
Supplementary files format and content: Tab-separated values files including barcodes, features and matrix

source_name: jejunum

extract_protocol:
Freshly 5 cm of mouse jejunum tissue was excised and longitudinally opened and Peyer's pathes removed, and resuspended in RPMI 1640 solution (10% FBS added) into gentleMACS C tubes. To digest the tissues, DNase I (DN25, Sigma-Aldrich) at 1:2000 dilution, Protease Inhibitor Cocktail (HY-K0010, MedChemExpress), Dispase II (40104ES80, Yeasen) and Liberase (5401054001, Roche) at 1:37.5 dilution were added. The tissue was then digested using a gentleMACS Dissociator (Miltenyi Biotec).
The obtained single cell suspensions were counted and quality checked, and the gel beads with barcodes and primers were encapsulated with individual cells in oil droplets to form a GEM (Gel bead in emulsion) through the Chromium™ Single Cell 3' Solution microfluidic platform. The cDNA with barcode was obtained by reverse transcription, amplified and purified for quality check, and the cDNA that passed the quality test was used for library construction.

value: jejunum

value: tpn


title: L2a


title: HOXC4_IP


title: MPP4-2026-1


title: BALB/c Murine Hepatic Macrophages Ly6c-MHCII+ Controls, Replicate 3

description:
Library name: Saline_MHCII_3
M01_Liver_Saline_MHCII_03

source_name: liver

value: DOL 14

value: liver

value: macrophage

value: BALB/c


title: L3a


title: MPP1-WT

value: WT


title: starvation-2,scRNAseq

description: 10x Genomics

value: starvation


title: MPP1-2026


title: L2b


title: sham-2,scRNAseq

description: 10x Genomics

value: sham


title: H3b


title: sham-1,scRNAseq

description: 10x Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9679

description:
cell-free DNA 5hmC
PLCO-147

source_name: peripheral plasma

value: peripheral plasma

value: cell-free DNA


title: L1a


title: MPP1-1013

value: Bone Marrow


title: tpn-1,scRNAseq

description: 10x Genomics


title: heart, HET group

first: Sarala Raj

last: Murthi

address: Lazarettstr. 36

institute: German Heart Center

data_processing:
Libraries were sequenced on the Illumina NextSeq500 platform. 100 bp paired-end reads were aligned to the mouse reference genome mm10 using Spliced Transcripts Alignment to a Reference (STAR). Fastq files were trimmed using skewer v0.2.2. Raw reads were normalized to the total number of reads per kilobase of transcript per million (RPKM).
Assembly: mm10
Supplementary files format and content: text file includes raw counts and RPKM values for each sample. RAWDATA_2012_pooled.mm10.rpkm

source_name: heart

growth_protocol: In the third week of life, genotyping was conducted on the subjects. By the fifth week of life, assessments were made on weight, general condition, and echocardiography. From the sixth to the twelfth week of life, the subjects received subcutaneous cyclosporine administration at a dosage of 15 mg/kg body weight in PBS twice daily, as outlined in the study by Fatkin et al. (JCI 2000). It is important to note that only male animals were utilized for this study. The control groups included wild type (WT), αMHC719/+ HCM mice (HET), and cardiomyocyte-specific Hif-1α knock out mice (cHif1aKO), while the experimental group consisted of α-MHC719/+/cHIF1aKO (HET + cHIF1aKO) mice.

extract_protocol:
Total RNA was isolated with PeqGOLD total RNA isolation kit (Peqlab) according to manufacturers recommendations yielding a RIN of 9.5-10.
Two rounds of mRNA purification were performed on total RNA (1 ug) using Dynabeads mRNA DIRECT Kit (Invitrogen). The Superscript III First-Strand Synthesis System (Invitrogen) was used to generate double-stranded cDNA. cDNA libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: Hypertrophic remodeling was accelerated in α-MHC719/+ and α-MHC719/+/cHif1aKO mice (age 6–12 weeks) by subcutaneous injection of cyclosporine (CsA) (15 mg/kg body weight in PBS, twice daily) for 6 weeks. For all CsA studies, control mice were age-matched, male CsA treated WT and age-matched, male CsA treated WT/cHif1aKO mice.

value: heart

value: cyclosporine treated for accelerated genotype


title: L1b

value: Thoroughbred

value: Male

value: skin fibroblast


title: starvation-1,scRNAseq

description: 10x Genomics

value: jejunum


title: LSF,biol rep2,RNAseq

data_processing:
The quality control for RNA sequencing raw reads was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The first 10 base pairs of both paired-end reads were trimmed using cutadapt v2.9
The processed reads were aligned to the GRCm38.97 Mus musculus reference genome using STAR v2.7.2e
Differentially expressed genes (DEGs) were determined using DESeq2 v1.32.0 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html), with a cutoff of a fold change greater than 2 and a false discovery rate (FDR) less than 0.05.
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

extract_protocol:
5 cm of mouse jejunum tissue was excised and longitudinally opened, and resuspended in RPMI 1640 solution (10% FBS added) into gentleMACS C tubes. To digest the tissues, DNase I (DN25, Sigma-Aldrich) at 1:2000 dilution, Protease Inhibitor Cocktail (HY-K0010, MedChemExpress), Dispase II (40104ES80, Yeasen) and Liberase (5401054001, Roche) at 1:37.5 dilution were added. The tissue was then digested using a gentleMACS Dissociator (Miltenyi Biotec).Epithelial cells (CD45−CD11b−CD3−B220−EpCAM+) were collected using BD FACS Aria II SORP (BD Biosciences).
After the RNA samples were tested, eukaryotic mRNA was enriched with magnetic beads with Oligo(dT) . Subsequently, mRNA was interrupted into short fragments by adding fragmentation buffer. One-stranded cDNA was synthesized by using six-base random primers (random hexamers) with mRNA as template, and then two-stranded cDNA was synthesized by adding buffer, dNTPs, and DNA polymerase I and RNase H. The purified double-stranded cDNA was first subjected to end repair, addition of A-tail and ligation of sequencing junctions, followed by fragment size selection with AMPure XP beads. Finally, PCR amplification was performed and the PCR products were purified by AMPure XP beads to obtain the final library. After the library was constructed, Qubit 2.0 was used to perform preliminary quantification and dilution of the library, followed by Agilent 2100 to detect the insert size of the library, and after the inserts met the expectation, Q-PCR was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

value: epithelial cell

value: Lunch skipping feeding pattern


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6998

description:
cell-free DNA 5hmC
PLCO-146

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).


title: heart, HET+cHIF1KO

value: alpha-MHC719/+ CMC-Hif1a-Knock-out


title: sgNT/T_IgG

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
merged-sgB2-E-sgNT-T_1_IgG.bw
merged-sgB2-E-sgNT-T_1_IgG_peaks.bed

data_processing:
Since two of the four IgG samples had insufficient reads (fewer than 3 million read pairs), the FASTQ files for the remaining two IgG controls (sgB2/E_IgG, sgNT/T_IgG) were concatenated to enable all samples to use the same IgG negative control signal for downstream peak-calling.
Adapters were trimmed from FASTQ files containing raw, paired-end reads using Fastp 0.20 with “--detect_adapter_for_pe” option.
Adapter-trimmed reads were aligned to the Mus musculus mm10 genome assembly using Bowtie2 version 2.4.1 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Duplicates were marked in BAM files using the “sambamba markdup” subcommand from Sambamba.
Peaks were called on BAM files using GoPeaks version 1.0 with default parameters and IgG samples as negative controls.
Counts-per-milion (CPM) normalized bigWig coverage tracks were generated from BAM files using bamCoverage from Deeptools version 3.5 with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: peaks files
Library strategy: CUT&Tag

growth_protocol: These cells are maintained in RPMI (11875119, Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, HyClone), 2mM GlutaMAX (35050061, Gibco), 100units/mL Penicillin and 100 ug/mL Streptomycin (15140122, Gibco), 2% SCF from CHO,  conditioned media, and 0.6µM of Estrogen (E-2758, Sigma), cultured at 5% CO2 and 37°C.

extract_protocol: CUTANA Cut&Tag kit (14-1102, EpiCypher)

treatment_protocol: Estrogen removal for 48h

value: Bone marrow immortelized

value: sgRNA non targetting/pMICH-CSF3R-T618I


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 2208

description:
cell-free DNA 5hmC
PLCO-145


title: heart, cHIF1KO


title: heart, WT group

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 8969

description:
cell-free DNA 5hmC
PLCO-140


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9246

description:
cell-free DNA 5hmC
PLCO-143


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0655

description:
cell-free DNA 5hmC
PLCO-144


title: LSF,biol rep3,RNAseq


title: H3a

value: iPSC

value: iPSC-derived osteoblast


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UM 0478

description:
cell-free DNA 5hmC
PLCO-142

value: peripheral plasma


title: H2b


title: LSF,biol rep1,RNAseq


title: sgB2/E_IgG

value: sgRNA Asxl1 B2/pMICH-Empty


title: H2a


title: sgB2/T_H2AK119ub_2

value: sgRNA Asxl1 B2/pMICH-CSF3R-T618I


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9151

description:
cell-free DNA 5hmC
PLCO-138

value: cell-free DNA


title: DSF,biol rep1,RNAseq

value: Dinner skipping feeding pattern


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0041

description:
cell-free DNA 5hmC
PLCO-137


title: DSF,biol rep2,RNAseq


title: H1c

value: Thoroughbred


title: BSF_C,biol rep3,RNAseq

value: Breakfast skipping feeding pattern combined with control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 1973

description:
cell-free DNA 5hmC
PLCO-139


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 3054

description:
cell-free DNA 5hmC
PLCO-136


title: H1b

value: Male

value: skin fibroblast


title: H1a


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 1643

description:
cell-free DNA 5hmC
PLCO-134


title: sgNT/T_H2AK119ub_1


title: sgNT/T_H2AK119ub_3


title: Sham_m6A_1

city: Tianjing

first: Ping

last: Lei

address: No. 154, Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

description: Library name: sample 2

data_processing:
RNA-seq data analysis tools (such as STAR and DESeq2) were employed for alignment and differential expression analysis of the sequencing data to identify genes associated with traumatic brain injury.
Assembly: The GRCm39 mouse genome was used as the reference genome for data alignment.
Supplementary files format and content: Processed data files were formatted as CSV, containing information such as gene expression levels, p-values, and fold changes.
Supplementary files format and content: CSV files include FPKM values for each samples
Library strategy: MeRIP-seq

source_name: cortex

extract_protocol:
Total RNA was extracted from the cerebral cortex of mice using TRIzol reagent. After cell lysis, chloroform was added and centrifuged to separate the layers. The upper aqueous phase was collected, and isopropanol was added to precipitate RNA, followed by a wash with 70% ethanol.
RNA libraries were constructed using an Illumina library preparation kit, synthesizing cDNA from m6A-modified RNA in the samples, followed by adapter ligation and PCR amplification to obtain the library.

value: cortex

tag: rip antibody

value: anti-m6A (Synaptic Systems, catalog number 202 003)

value: sham


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 7269

description:
cell-free DNA 5hmC
PLCO-133


title: con,biol rep 2,RNAseq

value: jejunum

value: epithelial cell

value: Control


title: sgB2/E_H2AK119ub_3

value: Bone marrow immortelized


title: con,biol rep 1,RNAseq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UM 0103

description:
cell-free DNA 5hmC
PLCO-131


title: Rat, Trained 3

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
The stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing a Solexa CHASTITY quality filter, the clean reads were aligned to the rat genome (UCSC RN5) using BOWTIE software (V0.12.8).
To quantify the DNA methylation level of any specific region, we extended each uniquely aligned read to 250 bp in length. A methylation score (MeDIP-score) for any region in the genome was defined as the number of extended reads per kb.
The DNA methylation status of a specific region was defined as unmethylated if the MeDIP-score was less than 9.48 reads·kb-1, as partially methylated if the MeDIP-score was between 9.48 – 50.62 reads·kb-1, and completely methylated if the MeDIP-score was greater than 50.62 reads·kb-1.
Assembly: rn5
Supplementary files format and content: wig.gz
Library strategy: MeDIP-seq

organism: Rattus norvegicus

source_name: Skeletal muscle

extract_protocol:
Genomic DNA was extracted using DNAeasy Blood and Tissue Kit (Qiagen).
Sonicated genomic DNA (300 ng) was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol.

treatment_protocol: Endurance training consisted of two 3-hour swim bouts, separated by a 30-minute rest, for five consecutive days. Rats were anesthetized with an intraperitoneal injection of pentobarbital sodium (5 mg/100 g body weight) 16 hours after the last exercise bout. Tissues were collected and frozen in liquid nitrogen and gastrocnemius muscle was used for subsequent analysis.

value: Skeletal muscle

value: Wild type

value: Trained

tag: antibody

value: anti-5-methylcytosine antibody


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1876

description:
cell-free DNA 5hmC
PLCO-135

value: peripheral plasma

value: cell-free DNA


title: sgNT/T_H2AK119ub_2

value: sgRNA non targetting/pMICH-CSF3R-T618I


title: TBI_m6A_0

description: Library name: sample 3

value: TBI


title: BSF_C,biol rep1,RNAseq

value: Breakfast skipping feeding pattern combined with control


title: sgB2/T_H2AK119ub_1

value: sgRNA Asxl1 B2/pMICH-CSF3R-T618I


title: Sham_m6A_0

description: Library name: sample 1

value: cortex


title: sgNT/E_H2AK119ub_2

value: sgRNA non targetting/pMICH-Empty


title: BSF, biol rep 2,RNAseq

value: Breakfast skipping feeding pattern


title: sgB2/E_H2AK119ub_2

value: sgRNA Asxl1 B2/pMICH-Empty


title: sgB2/E_H2AK119ub_1


title: BSF_C,biol rep2,RNAseq

value: jejunum

value: epithelial cell


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 2268

description:
cell-free DNA 5hmC
PLCO-130


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7545

description:
cell-free DNA 5hmC
PLCO-127


title: Rat, Sedentary 3

value: Sedentary


title: con,biol rep 3,RNAseq

value: Control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2534

description:
cell-free DNA 5hmC
PLCO-128


title: star,biol rep 3,bulk_RNA_seq

data_processing:
The quality control for RNA sequencing raw reads was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The first 10 base pairs of both paired-end reads were trimmed using cutadapt v2.9
The processed reads were aligned to the GRCm38.97 Mus musculus reference genome using STAR v2.7.2e
A provided set of known transcripts in GTF format (RefSeq GRCm38.97; Mus musculus, Ensembl) was used for alignment, with a maximum of 1000 multiple mapped sites allowed and no more than 3 mismatches retained. Only the best hit was kept using parameters (–outFilterMultimapNmax 1000, –outFilterMismatchNmax 3, –outSAMmultNmax 1). Gene quantification was calculated using FeatureCounts v2.0.0
Differentially expressed genes (DEGs) were determined using DESeq2 v1.32.0 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html), with a cutoff of a fold change greater than 2 and a false discovery rate (FDR) less than 0.05.
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

source_name: Jejunum

extract_protocol:
Mice were treated with sham, TPN, or starvation for 24 h, and then 5 cm of jejunal tissue was harvested and longitudinally opened.
After the RNA samples were tested, eukaryotic mRNA was enriched with magnetic beads with Oligo(dT) . Subsequently, mRNA was interrupted into short fragments by adding fragmentation buffer. One-stranded cDNA was synthesized by using six-base random primers (random hexamers) with mRNA as template, and then two-stranded cDNA was synthesized by adding buffer, dNTPs, and DNA polymerase I and RNase H. The purified double-stranded cDNA was first subjected to end repair, addition of A-tail and ligation of sequencing junctions, followed by fragment size selection with AMPure XP beads. Finally, PCR amplification was performed and the PCR products were purified by AMPure XP beads to obtain the final library. After the library was constructed, Qubit 2.0 was used to perform preliminary quantification and dilution of the library, followed by Agilent 2100 to detect the insert size of the library, and after the inserts met the expectation, Q-PCR was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

value: Jejunum

value: starvation


title: sgB2/T_H3K4me1_2

value: Bone marrow immortelized


title: BSF, biol rep 1,RNAseq


title: sgB2/T_H3K4me1_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0242

description:
cell-free DNA 5hmC
PLCO-129

value: peripheral plasma


title: sgNT/T_H3K4me1_3


title: Rat, Trained 1

value: Skeletal muscle

value: Wild type

value: Trained

value: anti-5-methylcytosine antibody


title: Rat, Sedentary 1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0947

description:
cell-free DNA 5hmC
PLCO-126

value: cell-free DNA


title: Rat, Trained 2


title: tpn,biol rep 3,bulk_RNA_seq

value: tpn


title: sgNT/E_H2AK119ub_1

value: sgRNA non targetting/pMICH-Empty


title: Healthy donor 3, 28gamma CAR, stimulated with target cells

city: Xi'an

first: Pengju

state: Shaanxi

address: Changle West Road

department: Immunology

institute: Fourth Military Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: T cell

growth_protocol: Primary T cells were stimulated with CD3/CD28 dynabeads (Gibco) at a T cell to bead ratio of 1:3, and cultured in X-VIVO15 medium (Lonza, Bend, OR, USA) supplemented with 10% FBS and 100 IU/ml recombinant IL-2 (PeproTech, Rocky Hill, NJ, USA). Twenty-four hours after stimulation, T cells were infected with lentiviruses for 24 h. At day 5 after stimulation, CD3/CD28 dynabeads were removed, T cells were cultured continuously, and medium and IL-2 was changed every second day.

extract_protocol:
RNA was isolated using the QIAGEN Rneasy following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 days of transduction, 3 x 106 CAR T cells were stimulated 36 h with targrt cells at a ratio of 1:1 while 3 x 106 CAR T cells were maintained without stimulation.

value: T cell

value: Primary human T cells

value: T cells expressing 28gamma CAR

value: stimulated with target cells


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 9831

first: Xiaolong

description:
cell-free DNA 5hmC
PLCO-124


title: Rat, Sedentary 2

value: Sedentary


title: star,biol rep 1,bulk_RNA_seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3112

description:
cell-free DNA 5hmC
PLCO-125


title: star,biol rep 2,bulk_RNA_seq


title: Healthy donor 3, 28delta CAR, stimulated with target cells

value: T cells expressing 28delta CAR


title: Healthy donor 3, 28epsilon CAR, stimulated with target cells

value: T cells expressing 28epsilon CAR


title: tpn,biol rep 2,bulk_RNA_seq

value: Jejunum


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6461

description:
cell-free DNA 5hmC
PLCO-122


title: sgNT/T_H3K4me1_1

value: Bone marrow immortelized

value: sgRNA non targetting/pMICH-CSF3R-T618I


title: sgB2/E_H3K4me1_3

value: sgRNA Asxl1 B2/pMICH-Empty


title: sgB2/E_H3K4me1_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2255

description:
cell-free DNA 5hmC
PLCO-123

value: peripheral plasma


title: Healthy donor 3, 28gamma CAR, un-stimulated

value: un-stimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 4478

description:
cell-free DNA 5hmC
PLCO-119


title: tpn,biol rep 1,bulk_RNA_seq


title: MEFs, WT18_P8

city: Dallas

first: Marek

last: Napierala

state: TX

address: Marek Napierala

institute: University of Texas Southwestern Medical Center

data_processing:
Novogene bioinformatics analysis pipeline
Raw reads of fastq format were firtly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on thecleandata with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Normalization and Differential expression analysis was performed using DESeq.
Assembly: mm39
Supplementary files format and content: Microsoft excel spreadsheet includes raw counts for each sample

source_name: Embryo

growth_protocol: MEFs were cultured in Dulbecco's modified Eagle's medium (DMEM) high-glucose medium with pyruvate (Life Technologies, 11995) supplemented with 10% fetal bovine serum (HyClone, SH30396.03).

extract_protocol:
RNA was isolated from MEF using the RNeasy Plus Mini Kit (Qiagen, #74134). Genomic DNA contamination was removed with the TURBO DNA-free™ Kit (Invitrogen, #AM1907).
Sequencing libraries were generated at Novogene Co., Ltd using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Embryo

value: Mouse Embryonic fibroblast

value: WT

tag: passage


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 8047

last: Cui

address: 680 N Lake Shore Drive

institute: Northwestern University

description:
cell-free DNA 5hmC
PLCO-118

tag: tissue

value: cell-free DNA


title: sham,biol rep 2,bulk_RNA_seq

value: sham


title: Healthy donor 3, 28zeta CAR, stimulated with target cells

value: T cell

tag: cell type

value: Primary human T cells

value: T cells expressing 28zeta CAR


title: sham,biol rep 3,bulk_RNA_seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 0633

description:
cell-free DNA 5hmC
PLCO-120


title: sgB2/E_H3K4me1_1

tag: genotype


title: sham,biol rep 1,bulk_RNA_seq


title: Healthy donor 3, 28delta CAR, un-stimulated


title: sgNT/T_H3K4me1_2


title: sgNT/E_H3K4me1_2

value: sgRNA non targetting/pMICH-Empty


title: sgNT/E_H3K4me1_1


title: MEFs, Mut4Z_P6

value: Mut G127V


title: sgB2/T_H3K27me3_2

value: sgRNA Asxl1 B2/pMICH-CSF3R-T618I


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1411

description:
cell-free DNA 5hmC
PLCO-115


title: sgNT/T_H3K27me3_2


title: Healthy donor 2, 28epsilon CAR, stimulated with target cells

value: T cells expressing 28epsilon CAR

value: stimulated with target cells


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 6761

description:
cell-free DNA 5hmC
PLCO-121


title: Healthy donor 3, 28epsilon CAR, un-stimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 3091

description:
cell-free DNA 5hmC
PLCO-112


title: sgNT/T_H3K27me3_1

value: Bone marrow immortelized

value: sgRNA non targetting/pMICH-CSF3R-T618I


title: MEFs, Mut3J_P9


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 1257

description:
cell-free DNA 5hmC
PLCO-117

value: peripheral plasma


title: Healthy donor 2, 28gamma CAR, un-stimulated

value: T cells expressing 28gamma CAR

value: un-stimulated


title: Healthy donor 2, 28delta CAR, stimulated with target cells

value: T cells expressing 28delta CAR


title: Healthy donor 3, 28zeta CAR, un-stimulated


title: MEFs, WT17_P8

value: Embryo

value: Mouse Embryonic fibroblast

value: WT


title: TBI_m6A_1

description: Library name: sample 4

value: cortex

value: anti-m6A (Synaptic Systems, catalog number 202 003)

value: TBI


title: MEFs, Mut4Z_P19


title: sgB2/T_H3K27me3_1


title: sgNT/T_H3K27me3_3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1560

description:
cell-free DNA 5hmC
PLCO-111

value: cell-free DNA


title: MEFs, Mut3J_P26

value: Mut G127V


title: Healthy donor 2, 28gamma CAR, stimulated with target cells

value: T cell

value: Primary human T cells


title: Healthy donor 2, 28epsilon CAR, un-stimulated

value: T cells expressing 28epsilon CAR


title: Healthy donor 2, 28delta CAR, un-stimulated


title: sgB2/E_H3K27me3_2

value: Bone marrow immortelized

value: sgRNA Asxl1 B2/pMICH-Empty


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7391

description:
cell-free DNA 5hmC
PLCO-110

value: peripheral plasma


title: RNA-seq of wildtype mouse CD150 neg cells  #3

city: Memphis

first: Michael

last: Walsh

address: 262 Danny Thomas

institute: St Jude Children's Research Hospital

data_processing:
RNA-Seq reads were mapped to GRChm38/mm10 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38 and
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.

source_name: HSC

extract_protocol:
RNA was extracted from CD150 negative cells in trizol using Zymo Direct-zol RNA Microprep Kit (Zymo Research, CA).
Libraries were prepared from total RNA with the Ovation® RNA-Seq System V2 according to the manufacturer’s instructions (Tecan, PN 7102-08).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

value: HSC


title: Healthy donor 2, 28zeta CAR, un-stimulated

value: T cells expressing 28zeta CAR

value: un-stimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0678

description:
cell-free DNA 5hmC
PLCO-116


title: RNA-seq of mouse CD150 neg cells with a deletion at chromosmal band 5G2 #2


title: sgNT/E_H3K27me3_1

value: sgRNA non targetting/pMICH-Empty


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 7325

description:
cell-free DNA 5hmC
PLCO-113


title: Healthy donor 1, 28epsilon CAR, stimulated with target cells

value: stimulated with target cells


title: RNA-seq of wildtype mouse CD150 neg cells  #4

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 9608

description:
cell-free DNA 5hmC
PLCO-106


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 4357

description:
cell-free DNA 5hmC
PLCO-109


title: sgB2/E_H3K27me3_3


title: sgNT/E_H3K27me3_2


title: Healthy donor 1, 28gamma CAR, stimulated with target cells

value: T cells expressing 28gamma CAR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 3125

description:
cell-free DNA 5hmC
PLCO-107


title: RNA-seq of wildtype mouse CD150 neg cells  #2


title: sgB2/T618I_3

data_processing:
Adapters were trimmed from FASTQ files containing raw, paired-end reads using Fastp 0.20 with “--detect_adapter_for_pe” option.
Adapter-trimmed reads were aligned to the Mus musculus mm10 genome assembly using BWA-MEM 0.7.17 with 8 threads and default parameters.
Reads that did not map, had an unmapped mate, were not a primary alignment, failed platform quality control checks, and/or were PCR or optical duplicates were filtered from BAM files using the “samtools view” subcommand with  “-F 1804” option from Samtools 1.9.
Reads aligning to mitochondrial genes were also removed. Duplicate reads were removed from BAM files using the “sambamba markdup” subcommand with “-r” option from Sambamba 0.6.8. Reads intersecting ENCODE blacklist regions were removed using the “bedtools intersect” subcommand with “-v” option from Bedtools 2.30.
Peaks were called on filtered BAM files using the “macs2 callpeak” subcommand with “--broad --format BAMPE --gsize mm” options from MACS2 2.2.7.1.
Counts-per-milion (CPM) normalized bigWig coverage tracks were generated from filtered BAM files using bamCoverage from Deeptools version 3.5 with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

extract_protocol:
Clean and Concentrator-5 Kit (D4003, Zymo)
As described in Buenrostro et al., 2015, Curr Protoc Mol Bio

value: sgRNA Asxl1 B2/pMICH-CSF3R-T618I


title: RNA-seq of mouse CD150 neg cells with a deletion at chromosmal band 5G2 #3


title: sgB2/E_H3K27me3_1


title: RNA-seq of mouse CD150 neg cells with a deletion at chromosmal band 5G2 #1


title: RNA-seq of wildtype mouse CD150 neg cells  #1


title: Healthy donor 1, 28gamma CAR, un-stimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5248

description:
cell-free DNA 5hmC
PLCO-105


title: Healthy donor 1, 28epsilon CAR, un-stimulated


title: Healthy donor 1, 28delta CAR, stimulated with target cells

value: T cells expressing 28delta CAR


title: WT_11-week-old_3

city: Suzhou

first: Changshun

last: Shao

state: Jiangsu

address: No.199 Renai Road

department: Institute for Translational Medicine

institute: Soochow University

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: GRCm38
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: liver


title: sgNT/T618I_1

value: sgRNA non targetting/pMICH-CSF3R-T618I


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IZ 1617

city: Chicago

description:
cell-free DNA 5hmC
PLCO-102

value: cell-free DNA


title: CKO_11-week-old_3


title: sgB2/T618I_2


title: Healthy donor 1, 28zeta CAR, stimulated with target cells

value: T cell

value: Primary human T cells


title: sgNT/T618I_2

value: Bone marrow immortelized


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 5175

description:
cell-free DNA 5hmC
PLCO-100


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5465

description:
cell-free DNA 5hmC
PLCO-103


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6046

description:
cell-free DNA 5hmC
PLCO-101