title: 20_425_3

description: N007028_Cell1_20211006_1058_1Color_IntegratedResult.txt


title: 20_425_2

status: Public on Jan 22 2025

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

description: N007004_Cell1_20211001_1009_1Color_IntegratedResult.txt

hyb_protocol: Hybridization was carried out in accordance with the supplier's (3D-Gene®, Toray Industries, Inc ) instructions.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using "Extraction"(Toray Industries, Inc.) .

data_processing:
A positive call of microRNA was a microarray signal of greater than the [mean + 2×standard deviation] of the negative control signals of which the highest and least intense signals were removed. A positive call signal was subtracted from a mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed and was log-transformed on a base-2 logarithm scale.
Normalization of serum microRNA signals across the different microarrays was performed with the internal control correction coefficient (Int-con). Int-con was a mean of three internal control miRNA signals (miR-149-3p, miR-2861, and miR-4463) (1). Each data was normalized based on the value obtained by subtracting Int-Con from 12.6 (average Int-con value, house data). Each data was then multiplied with the microRNA-specific adjustment coefficient that had been previously obtained from the microRNA–specific calibration curve. As a result, each serum microRNA signal was normalized with the ratio to adjusted Int-con.
In 100 probes, 19 miRNAs which will be analyzed (shown in Matrix sheets.)
Other 81 probes are not utilized for this study.
Our data process steps are simply as follows,
1 Background subtraction
2 Average of triplicated spots
3 Normalize the averaged data

molecule: total RNA

organism: Homo sapiens

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit (Toray Industries, Inc.) in accordance with the manufacturer's instructions.

growth_protocol: Human serum

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: tissue

value: serum

tag: age

tag: gender

value: female

tag: disease

value: Healthy control

tag: Stage

tag: block in array


title: 20_426_2

description: N006998_Cell1_20210929_1006_1Color_IntegratedResult.txt


title: 20_426_1

description: N006981_Cell1_20210928_1109_1Color_IntegratedResult.txt


title: 20_425_1

description: N006982_Cell1_20210929_1113_1Color_IntegratedResult.txt


title: 20_430_2

description: N007038_Cell1_20211006_0927_1Color_IntegratedResult.txt


title: 20_424_2

description: N007010_Cell1_20211001_1104_1Color_IntegratedResult.txt


title: 20_423_1

description: N006996_Cell1_20210928_1010_1Color_IntegratedResult.txt


title: 20_424_3

description: N007034_Cell1_20211008_1053_1Color_IntegratedResult.txt


title: 20_423_3

description: N007031_Cell1_20211008_1051_1Color_IntegratedResult.txt


title: 20_422_1

description: N006992_Cell1_20210928_1007_1Color_IntegratedResult.txt


title: 20_423_2


title: 20_421_1

value: male


title: 20_421_3

description: N007022_Cell1_20211006_1056_1Color_IntegratedResult.txt


title: 20_429_1

description: N006993_Cell1_20210928_1008_1Color_IntegratedResult.txt


title: 20_422_2

description: N007016_Cell1_20211001_1107_1Color_IntegratedResult.txt


title: 20_422_3


title: 20_421_2

description: N007005_Cell1_20211001_1010_1Color_IntegratedResult.txt


title: 20_420_2

description: N007003_Cell1_20210929_1009_1Color_IntegratedResult.txt


title: 20_428_3


title: 20_428_2


title: 20_419_3

description: N007017_Cell1_20211005_1106_1Color_IntegratedResult.txt


title: 20_419_1

description: N006980_Cell1_20210928_1108_1Color_IntegratedResult.txt


title: 20_418_3

description: N007023_Cell1_20211006_1057_1Color_IntegratedResult.txt


title: 20_418_2

description: N007006_Cell1_20211001_1011_1Color_IntegratedResult.txt


title: 20_418_1

description: N006987_Cell1_20210929_1115_1Color_IntegratedResult.txt


title: 20_424_1

description: N006995_Cell1_20210928_1009_1Color_IntegratedResult.txt


title: 20_417_2

description: N007012_Cell1_20211001_1105_1Color_IntegratedResult.txt

value: Pancreatic cancer


title: 20_416_3

description: N007039_Cell1_20211008_0928_1Color_IntegratedResult.txt

value: Biliary cancer


title: 20_417_1


title: 20_416_2

description: N007038_Cell1_20211006_0927_1Color_IntegratedResult.txt


title: 20_415_3

description: N007033_Cell1_20211008_1052_1Color_IntegratedResult.txt


title: 20_416_1

description: N007037_Cell1_20211005_0928_1Color_IntegratedResult.txt


title: 20_420_3

description: N007019_Cell1_20211005_1108_1Color_IntegratedResult.txt


title: 20_415_2


title: 20_415_1

description: N006992_Cell1_20210928_1007_1Color_IntegratedResult.txt


title: 20_413_3


title: 20_420_1


title: 20_413_2


title: 20_413_1

description: N006983_Cell1_20210929_1114_1Color_IntegratedResult.txt


title: 20_412_3

description: N007031_Cell1_20211008_1051_1Color_IntegratedResult.txt


title: 20_412_2


title: 20_411_2

description: N007014_Cell1_20211001_1106_1Color_IntegratedResult.txt


title: 20_411_3

description: N007035_Cell1_20211008_1054_1Color_IntegratedResult.txt


title: 20_411_1


title: 20_412_1

description: N006993_Cell1_20210928_1008_1Color_IntegratedResult.txt


title: 20_410_3


title: 20_410_2


title: 20_410_1


title: 20_419_2

description: N007001_Cell1_20210929_1008_1Color_IntegratedResult.txt


title: 20_417_3


title: 20_409_3

description: N007029_Cell1_20211006_1059_1Color_IntegratedResult.txt


title: 20_409_1


title: 20_409_2

description: N007006_Cell1_20211001_1011_1Color_IntegratedResult.txt


title: 20_408_2

description: N007003_Cell1_20210929_1009_1Color_IntegratedResult.txt


title: 20_408_3

description: N007018_Cell1_20211005_1107_1Color_IntegratedResult.txt


title: 20_408_1

description: N006977_Cell1_20210928_1107_1Color_IntegratedResult.txt


title: 20_407_3


title: 20_407_2


title: 20_407_1


title: 20_406_1

description: N006981_Cell1_20210928_1109_1Color_IntegratedResult.txt


title: 20_405_1

description: N006987_Cell1_20210929_1115_1Color_IntegratedResult.txt


title: 20_404_2

description: N007033_Cell1_20211008_1052_1Color_IntegratedResult.txt


title: 20_405_3

description: N007023_Cell1_20211006_1057_1Color_IntegratedResult.txt


title: 20_403_3


title: 20_406_2


title: 20_404_1

description: N007016_Cell1_20211001_1107_1Color_IntegratedResult.txt


title: 20_403_2

description: N007010_Cell1_20211001_1104_1Color_IntegratedResult.txt


title: 20_402_2

description: N007008_Cell1_20211001_1012_1Color_IntegratedResult.txt


title: 20_401_3

description: N007021_Cell1_20211005_1109_1Color_IntegratedResult.txt


title: 20_402_3


title: 20_403_1

description: N006992_Cell1_20210928_1007_1Color_IntegratedResult.txt


title: 20_401_2


title: 20_402_1

description: N006982_Cell1_20210929_1113_1Color_IntegratedResult.txt


title: 20_401_1

description: N006980_Cell1_20210928_1108_1Color_IntegratedResult.txt


title: 20_400_3

description: N007017_Cell1_20211005_1106_1Color_IntegratedResult.txt


title: 20_400_2

description: N006998_Cell1_20210929_1006_1Color_IntegratedResult.txt


title: 20_400_1


title: 20_399_3


title: 20_399_1


title: 20_399_2

description: N007000_Cell1_20210929_1007_1Color_IntegratedResult.txt


title: 20_396_2

description: N007004_Cell1_20211001_1009_1Color_IntegratedResult.txt


title: 20_396_3

description: N007022_Cell1_20211006_1056_1Color_IntegratedResult.txt


title: 20_396_1


title: 20_395_3

description: N007035_Cell1_20211008_1054_1Color_IntegratedResult.txt


title: 20_406_3


title: 20_405_2


title: 20_395_1


title: 20_394_3

description: N007039_Cell1_20211008_0928_1Color_IntegratedResult.txt


title: 20_394_2

description: N007038_Cell1_20211006_0927_1Color_IntegratedResult.txt


title: 20_394_1

description: N007037_Cell1_20211005_0928_1Color_IntegratedResult.txt


title: 20_393_2


title: 20_392_3

description: N007028_Cell1_20211006_1058_1Color_IntegratedResult.txt


title: 20_393_1

description: N006993_Cell1_20210928_1008_1Color_IntegratedResult.txt


title: 20_392_2


title: 20_391_3

description: N007019_Cell1_20211005_1108_1Color_IntegratedResult.txt


title: 20_391_1

description: N006977_Cell1_20210928_1107_1Color_IntegratedResult.txt


title: 20_392_1

description: N006983_Cell1_20210929_1114_1Color_IntegratedResult.txt


title: 20_390_3


title: Entorhinal CERAD_B Braak_II rep4

type: SRA

city: Boston

first: Jean-Pierre

last: Roussarie

state: MA

address: 72 E Concord Street

department: Anatomy & Neurobiology

country: USA

institute: Boston University School of Medicine

description: Library name: AD4

library_source: transcriptomic single cell

data_processing:
raw reads were processed using Cell Ranger v5.0.0 for alignment and generation of gene expression matrices. Seurat v4.0.3 was used for downstream analysis. Doublets were removed using Scrublet. In addition, nuclei with more than 2.5% mitochondrial RNA content, with less than 200 or more than 7,500 genes, or with UMI counts in the top 1% of all nuclei, were excluded. Remaining nuclei were integrated using SCT within Seurat.
Assembly: hg38
Supplementary files format and content: General_clusters.RDS, count matrix and metadata for the initial general clustering
Supplementary files format and content: Astro.rds, count matrix and metadata for the subclustering of astrocytes
Supplementary files format and content: Exc_neu_integrated_with_Leng.rds, count matrix and metadata for the integration of this dataset's excitatory neurons along with the Leng et al, Nature Neuro, 2021 excitatory neurons
Supplementary files format and content: Inh_neu.rds, count matrix and metadata for the subclustering of inhibitory neurons
Supplementary files format and content: Micro.rds, count matrix and metadata for the subclustering of microglia
Supplementary files format and content: Oligo.rds, count matrix and metadata for the subclustering of oligodendrocytes
Supplementary files format and content: OPC.rds, count matrix and metadata for the subclustering of oligodendrocyte progenitor cells

molecule: nuclear RNA

source_name: entorhinal cortex

growth_protocol: fresh frozen postmortem human tissue

extract_protocol:
We extracted nuclei in the following way for C1-C5, AD1, AD4, AD5 : we homogenized the tissue with a motorized teflon-glass homogenizer, pelleted nuclei and removed myelin by centrifuging the nuclei in iodixanol 29% solution. For C1-C3 and AD1. we then sorted nucleus singlets using DyeCycle Ruby. C4-C5 and AD4-AD5 were not sorted before loading of the Chromium X. Lastly nuclei from AD2b and AD3b were extracted using the 10x nucleus extraction protocol: lysates were strained through a MACS cell strainer, myelin was removed using myelin removal beads, and nuclei were then further cleaned up on a sucrose cushion prior to Chromium X loading.
All libraries were constructed using the 10X 3’ single cell RNA-seq v3 kit

treatment_protocol: no treatment - all samples from individuals who died with no AD symptoms

value: entorhinal cortex

tag: cell type

value: all cells

tag: treatment

value: no AD symptoms at death


title: 20_390_2


title: 20_391_2

description: N007001_Cell1_20210929_1008_1Color_IntegratedResult.txt


title: Entorhinal CERAD_B Braak_II rep5

description: Library name: AD5


title: Entorhinal CERAD_B Braak_II rep3

description: Library name: AD3b


title: Entorhinal CERAD_B Braak_II rep2

description: Library name: AD2b


title: Entorhinal CERAD_0 Braak_0 rep4

description: Library name: C4


title: NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II rep3

description: Library name: NeuN_AD4

library_source: transcriptomic

data_processing:
reads were trimmed with fastp, aligned with STAR 2.7.1a and differential expression tested with DESeq2
Assembly: hg38
Supplementary files format and content: rpkm_NeuN_RBFOX1.csv, rpkm obtained with EdgeR
Supplementary files format and content: rpkm_NeuN.csv, rpkm obtained with EdgeR

extract_protocol:
We extracted nuclei in the following way for all samples : we homogenized the tissue with a motorized teflon-glass homogenizer, pelleted nuclei and removed myelin by centrifuging the nuclei in iodixanol 29% solution. Nuclei were then stained for NeuN, Rbfox1 and singlets were identified with DyeCycle Ruby. Singlets either positive for Rbfox1 and NeuN or only for NeuN were sorted, and bulk RNA-sequenced using Trio RNA-seq
Trio RNA-seq (Nugen) on bulk RNA from Rbfox1+/NeuN+ or Rbfox1-/NeuN+ neuron populations

value: NeuN+/RBFOX1- nuclei


title: Entorhinal CERAD_0 Braak_II

description: Library name: AD1


title: Entorhinal CERAD_0 Braak_0 rep3

description: Library name: C3


title: NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II rep2

description: Library name: NeuN_AD3


title: 20_393_3


title: NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 rep3

description: Library name: NeuN_C3


title: 20_395_2

description: N007010_Cell1_20211001_1104_1Color_IntegratedResult.txt


title: Entorhinal CERAD_0 Braak_0 rep1

description: Library name: C1


title: Entorhinal CERAD_0 Braak_0 rep2

description: Library name: C2


title: NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II rep1

description: Library name: NeuN_AD2


title: Entorhinal CERAD_B Braak_0

description: Library name: C5


title: NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II rep2

description: Library name: NeuN_RBFOX1_AD3

value: NeuN+/RBFOX1+ nuclei


title: NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II rep4

description: Library name: NeuN_RBFOX1_AD5


title: NeuN+/RBFOX1+ Entorhinal CERAD_0 Braak_0 rep4

description: Library name: NeuN_RBFOX1_C4


title: NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II rep1

description: Library name: NeuN_RBFOX1_AD2


title: NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 rep1

description: Library name: NeuN_C1


title: The specificity of gene activation by RNA-seq transfected with the dhpAsCas12f1-VPR targeting IL1RN, repeat 1.

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: Library name: dhpAsCas12f1_Rep1

data_processing:
The raw paired-end reads were preprocessed to remove the adapters with cutadapt
Subsequently, the reads were mapped to the human genome (hg38) using HISAT2 aligner
The uniquely mapped reads that passed the "markdup –r" filter by sambamba
The generation of gene counts (reads aligned to each gene of each sample) was performed using gencode.v43.primary_assembly.basic.annotation GTF file (available at https://www.gencodegenes.org/human/) and FeatureCounts
Assembly: hg38
Supplementary files format and content: Gene counts for each library

source_name: HEK293T cell line

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested.
RNA was isolated using Trizol Reagent according to the manufacturer’s protocol. The constructed sequencing libraries were sequenced on the Illumina HiSeq Platform with 150 bp paired-end reads.

treatment_protocol: In 24-well plates, HEK293T cells were transfected with 490ng gRNA plasmids and 10ng dCasMINI or dhpCasMINI plasmids.

tag: cell line

value: HEK293T cell line

value: Human embryonic Kidney


title: The specificity of gene activation by RNA-seq transfected with the dAsCas12f1-VPR targeting IL1RN, repeat 2.

description: Library name: dAsCas12f1_Rep2


title: NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 rep2

description: Library name: NeuN_C2


title: The specificity of gene activation by RNA-seq transfected with the dhpAsCas12f1-VPR targeting IL1RN, repeat 2.

description: Library name: dhpAsCas12f1_Rep2


title: NeuN+/RBFOX1+ Entorhinal CERAD_0 Braak_0 rep1

description: Library name: NeuN_RBFOX1_C1


title: The specificity of gene activation by RNA-seq transfected with the dAsCas12f1-VPR targeting IL1RN, repeat 1.

description: Library name: dAsCas12f1_Rep1


title: The specificity of gene activation by RNA-seq transfected without dAsCas12f1-VPR or dhpAsCas12f1-VPR, repeat 3.

description: Library name: Ctrl_AsCas12f1_Rep3


title: NeuN+/RBFOX1- Entorhinal CERAD_B Braak_II rep4

description: Library name: NeuN_AD5


title: NeuN+/RBFOX1- Entorhinal CERAD_0 Braak_0 rep4

description: Library name: NeuN_C4


title: The specificity of gene activation by RNA-seq transfected without dAsCas12f1-VPR or dhpAsCas12f1-VPR, repeat 1.

description: Library name: Ctrl_AsCas12f1_Rep1


title: LN229 cell, Ischemic culture MK25, Rep2

city: Hershey

first: Wei

last: Li

state: PA

address: 500 University Drive

institute: Penn State College of Medicine

data_processing:
Sequencing data were analyzed using Galaxy (https://usegalaxy.org/). Briefly, reads were trimmed and aligned to reference human genome and annotation files (GRCh38, build 38) using HISAT2. Difference of gene expression were detected by edgeR.
Assembly: human genome and annotation files (GRCh38, build 38)
Supplementary files format and content: tsv, normalized counts

growth_protocol: Human GBM cell lines LN229 were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Corning, 10-013-CV) supplemented with 10% fetal bovine serum (FBS; Gibco, 10437028) and 1% Antibiotic-Antimycotic Solution (Corning, 30-004-CI) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were lysed in TRIzol reagent (Invitrogen) and total RNA was extracted by following the protocol from the manufacture.
RNA-seq libraries were prepared using the SMART-Seq mRNA HT kit (Takara Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions.

treatment_protocol: To mimic ischemic conditions in vitro, a combination of low nutrients and hypoxia was used as described in the published manuscript.

value: glioblastoma cell line

tag: culture condition

value: Ischemic culture


title: The specificity of gene activation by RNA-seq transfected without dAsCas12f1-VPR or dhpAsCas12f1-VPR, repeat 2.

description: Library name: Ctrl_AsCas12f1_Rep2


title: LN229 cell, Ischemic culture MK25, Rep1


title: LN229 cell, Ischemic culture VX745, Rep2


title: LN229 cell, Ischemic culture VX745, Rep1


title: LN229 cell, Regular culture MK25, Rep2

value: Regular culture


title: LN229 cell, Ischemic culture DMSO, Rep1

value: DMSO


title: NeuN+/RBFOX1+ Entorhinal CERAD_B Braak_II rep3

description: Library name: NeuN_RBFOX1_AD4


title: LN229 cell, Regular culture MK25, Rep1


title: LN229 cell, Regular culture DMSO, Rep2


title: NeuN+/RBFOX1+ Entorhinal CERAD_0 Braak_0 rep3

description: Library name: NeuN_RBFOX1_C3


title: The specificity of gene activation by RNA-seq transfected with the dAsCas12f1-VPR targeting IL1RN, repeat 3.

description: Library name: dAsCas12f1_Rep3


title: LN229 cell, Regular culture VX745, Rep2


title: LN229 cell, Regular culture DMSO, Rep1


title: The specificity of gene activation by RNA-seq transfected with the dhpAsCas12f1-VPR targeting IL1RN, repeat 3.

description: Library name: dhpAsCas12f1_Rep3


title: LN229 cell, Regular culture VX745, Rep1


title: LN229 cell, Ischemic culture, Rep1


title: LN229 cell, Ischemic culture, Rep2


title: TRM_233_TIL, scTCRseq

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

country: South Korea

institute: SungKyunKwan University

description: 10x Genomics v7.0.0

data_processing:
The scTCR-seq data were assembled using the Cell Ranger VDJ pipeline (10x Genomics).
For demultiplexing for HCC_M1_LIL sample, we used Demuxlet software in scRNA-seq data.
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: Comma-separated matrix files
Library strategy: TCR-Seq

source_name: liver tumor

extract_protocol:
The library preparation was performed using either the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction.
The libraries were processed according to manufacturer’s recommendation (10x Genomics), and sequenced on a HiSeq 2500, MGI seq, and Novaseq systems.

treatment_protocol: Tissues were minced and mechanically dissociated using gentleMACS (Miltenyi biotec), and then enzymatically dissociated using a tumor dissociation kit (Miltenyi biotec, 130-095-929) at 37°C for 20 minutes.

value: liver tumor

value: T cell receptors


title: LN229 cell, Regular culture, Rep1


title: 0762_onT

city: Uppsala

first: Veronica

last: Rendo

address: Dag Hammarskjölds väg 20, Rudbeck Laboratory, C11:3

country: Sweden

institute: Uppsala University

data_processing:
Quality control, alignment and initial analyses were performed with VIPER
Assembly: hg38
Supplementary files format and content: csv file contains normalized counts for each Sample

source_name: GBM

extract_protocol:
RNA was isolated using the RNeasy Mini Kit with an on-column DNase digestion (79254, Qiagen). Resulting RNA concentrations were quantified with a Nanodrop 2000 Spectrophotometer (ND-2000, Thermo Scientific), and up to 500 ng were submitted for total RNA sequencing.
Samples were subjected to rRNA depletion using the QIAseq FastSelect -rRNA HMR kit (334385, Qiagen) and sequencing was performed to generate 50M 150 bp read pairs (100M reads) per sample.

value: GBM

value: on-treatment


title: 0762_pre

value: pre-treatment


title: LN229 cell, Regular culture, Rep2


title: 0121a_pre


title: 0059_onT


title: 0059_pre


title: LN229 cell, Ischemic culture DMSO, Rep2


title: 0120a_pre


title: 0121_onT


title: 0120_onT


title: 8420_onT


title: 8420_pre


title: TRM_261_TIL, scTCRseq

description: 10x Genomics v7.0.0


title: 7259_onT


title: 7059_pre


title: 7059_onT


title: 6714_pre


title: 6714_onT


title: BT286 DMSO 3


title: TRM_184_TIL, scTCRseq

description: 10x Genomics v7.0.0


title: BT286 DMSO 2


title: BT286 DMSO 1


title: BT286 AMG 3

value: AMG


title: BT286 AMG 1


title: BT286 AMG 2


title: BT145 DMSO 2


title: BT145 DMSO 3


title: BT145 DMSO 1


title: BT145 AMG 3


title: BT145 AMG 1


title: BT145 AMG 2


title: Patient dervied xenograft 2

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Raw RNA-Seq reads were first trimmed for quality and adapter removal using Trim Galore. The cleaned reads were then aligned to the reference genome using HISAT2. Subsequently, read counts were quantified using featureCounts with the Gencode v43 GTF annotation file.
Assembly: hg38
Supplementary files format and content: tab-delimeted raw count matrix

source_name: rectal tissue sample

extract_protocol:
RNA from fresh patient tissue samples was extracted using Trizol reagent, and total RNA quality and quantity were assessed using Agilent 4150 Tape Station system and Qubit 4 Fluorometer. The rRNA was depleted using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), cat. No. #E6310X by following the manufacturer's protocol.
RNA-Seq libraries were prepared with rRNA depleted sample using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770L), according to manufacturer's protocols, and quality and quantity were assessed using Agilent 4150 TapeStation system, and Qubit 4 Fluorometer.

value: rectal tissue sample


title: Patient derived xenograft 1

source_name: colon tissue sample

value: colon tissue sample


title: Tumor 2


title: Tumor 1


title: Adjacent normal 2


title: Adjacent normal 1


title: 7259_pre


title: Oci-Ly8_H3K27me3_rep3

city: Amsterdam

first: Rachele

last: Niccolai

address: Plesmanlaan 121

department: Tumor Biology and Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

library_source: genomic

data_processing:
Preprocessing of raw paired-end FASTA files was performed using the nf-core ATAC pipeline (version 2.0, https://nf-co.re/atacseq/2.0/) default settings.
Trim Galore! (version 0.6.7) was performed for adapter trimming before alignment.
Reads were aligned against reference genome GRCh38 (Ensembl v109) with BWA (version 0.7.17).
Broad/narrow peaks were called with MACS2 (version 2.2.7.1).
Quality controls include FastQC (version 0.11.9), Samtools (version 1.15.1), Picard (version 2.27.4), and DeepTools (version 3.5.1).
For downstream analysis, we used the merged BigWig file of filtered alignments across three biological replicates and normalized by scaling to 1 million mapped reads.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: IMDM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and cell lysis, chromatin was sonicated using Bioruptor Pico sonication device.
ChIP-Seq libraries were prepared using the KAPA LTP Library preparation kit using the manufacturer’s protocol with slight modifications. Briefly, after end‐repair and A‐tailing adaptor were ligated followed by Solid Phase Reversible Immobilization (SPRI) clean‐up. Libraries were amplified by PCR and fragments between 250 and 450 bp were selected using AMPure XP beads (Beckman Coulter, catalog number A63881). The libraries were analyzed for size and quantity of DNAs on a 2100 Bioanalyzer using a High Sensitivity DNA kit (Agilent), diluted and pooled in multiplex sequencing pools.

value: GCB-DLBCL

tag: chip antibody

value: H3K27me3, Active Motif, catalog number 39055


title: Oci-Ly7_H3K27me3_rep3

value: H3K79me2, Cell Signaling, catalog number #5427


title: Oci-Ly7_H3K27me3_rep2


title: Oci-Ly7_H3K27me3_rep1


title: Oci-Ly18, Combo, Rep3

data_processing:
FASTQ files were produced by BCL Convert using demultiplexing.
Sample distribution was based on indexing using IDT UDI indexes.
Seqpurge was used for adapter trimming.
RNA-seq data were aligned with STAR against reference genome GRCh38, and reads were counted and annotated per gene using GenSum (https://www.github.com/NKI-GCF/gensum) against Ensembl GRCh38.107.
DESeq2 package was used to normalize read counts and to obtain the differential gene expression of RNA-seq samples.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files includes raw counts for each sample

growth_protocol: Oci-Ly8, SUDHL6, Oci-Ly8 and Oci-Ly18 were maintained in IMDM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen).
RNA-seq libraries were prepared using the xGen polyA+ stranded RNA library kit, according to manufacturer’s protocol.

treatment_protocol: Cells were treated with EPZ-5676 (DOT1Li) and GSK343 (EZH2i) for 6 days. At day 3, 5x10^4 cells/ml were reseeded with fresh medium and inhibitors.


title: Oci-Ly8_H3K27me3_rep1


title: Oci-Ly18, Combo, Rep2


title: Oci-Ly18, EZH2i_Rep3


title: Oci-Ly18, EZH2i_Rep2


title: Oci-Ly18, DOT1Li_Rep2


title: Oci-Ly18, DOT1Li_Rep3


title: Oci-Ly18, DOT1Li_Rep1


title: Oci-Ly18, Combo, Rep1


title: Oci-Ly18, EZH2i_Rep1


title: Oci-Ly18, DMSO_Rep3


title: Oci-Ly18, DMSO_Rep2


title: SUDHL6, Combo_Rep3


title: Oci-Ly18, DMSO_Rep1


title: SUDHL6, Combo_Rep2


title: SUDHL6, Combo_Rep1


title: SUDHL6, EZH2i_Rep2


title: SUDHL6, EZH2i_Rep3


title: SUDHL6, DMSO_Rep3


title: SUDHL6, DOT1Li_Rep1


title: SUDHL6, DOT1Li_Rep3


title: SUDHL6, DOT1Li_Rep2


title: Oci-Ly8, Combo, Rep3


title: Oci-Ly8, Combo, Rep1


title: SUDHL6, EZH2i_Rep1


title: SUDHL6, DMSO_Rep1


title: Oci-Ly8, EZH2i_Rep3


title: Oci-Ly8, EZH2i_Rep2


title: Oci-Ly8, Combo, Rep2


title: Oci-Ly8_H3K27me3_rep2


title: Oci-Ly8, EZH2i_Rep1


title: SUDHL6, DMSO_Rep2


title: Oci-Ly8, DMSO_Rep1


title: Oci-Ly8, DMSO_Rep2


title: Oci-Ly8, DOT1Li_Rep3


title: Oci-Ly8, DOT1Li_Rep1


title: Oci-Ly7, Combo, Rep1


title: Oci-Ly7, EZH2i_Rep3


title: Oci-Ly8, DOT1Li_Rep2


title: Oci-Ly8, DMSO_Rep3


title: Oci-Ly7, DOT1Li_Rep3


title: Oci-Ly7, EZH2i_Rep2


title: Oci-Ly7, Combo, Rep2


title: Oci-Ly7, Combo, Rep3


title: Oci-Ly7, DOT1Li_Rep2


title: Oci-Ly7, DOT1Li_Rep1


title: Oci-Ly7, DMSO_Rep3


title: Oci-Ly7, DMSO_Rep1


title: Oci-Ly7, DMSO_Rep2


title: SplitCsy4_Grazoprevir_Replicate 3

city: Hangzhou

first: Lihang

last: Zhang

state: Zhejiang

address: Shilongshan street 18

department: Department of Life science

institute: Westlake University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1).
Trimed sequence reads were mapped to hg38 reference genome using Hisat (v2.2.1)
Read count extraction was performed using HTSeq (v0.6.1)
Statistical analysis was performed with Deseq2 (v.1.44.0) package
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
Total RNA of cells was isolated using the Trizol RNA Extraction method. In brief, 400,000 cells were mixed with 1ml TRIzol™ Reagent (ThermoFisher Scientific, cat. no. 15596018),1 ug of total RNA was used for the construction of sequencing libraries
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: 70000 Cells were transfected with split Csy4 and treated with 0.5 uM Grazoprevir at 6 hours post transfection


title: SplitCsy4_Grazoprevir_Replicate 1


title: SplitCsy4_Grazoprevir_Replicate 2


title: SplitCsy4_DMSO_Replicate 3

value: 70000 Cells were transfected with split Csy4 and treated with 0.5 uM DMSO at 6 hours post transfection


title: SplitCsy4_DMSO_Replicate 1


title: wtCsy4_Replicate 3

value: 70000 cells were transfected with full-length Csy4 and treated with 0.5 uM DMSO at 6 hours post-transfection.


title: SplitCsy4_DMSO_Replicate 2


title: wtCsy4_Replicate 2


title: wtCsy4_Replicate 1


title: Rapamycin_Replicate 1

value: 70000 cells were treated with 0.1 uM Rapamycin


title: Grazoprevir_Replicate 3

value: 70000 cells were treated with 0.5 uM Grazoprevir


title: Grazoprevir_Replicate 2


title: DMSO_Replicate 2

value: 70000 Cells were treated with 0.5 uM DMSO


title: Grazoprevir_Replicate 1


title: DMSO_Replicate 1


title: RS-Pem-POST-48-3

city: Houston

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

institute: The University of Texas MD Anderson Cancer Center

data_processing:
RNA-seq FASTQ files were processed through FastQC (v0.11.5). Using this program, the files were processed for the purpose of evaluating the quality of sequencing reads at both the base and read levels. As well, RNA-SeQC (v1.1.8) was used to generate a series of RNA-seq related quality control metrics. STAR 2-pass alignment (v2.7.0f) was performed with default parameters to generate RNA-seq BAM files. RNA-Seq gene expression raw read counts were generated from HTSeq-count (v0.9.1)
Assembly: GRCh37.p13
Supplementary files format and content: gene expression count matrix

source_name: Peri-T

extract_protocol:
In brief, total RNA was extracted from patients’ frozen tissues using a Qiagen RNeasy Mini Kit (Qiagen Inc.) following the manufacturer’s instruction. Quantification of total RNA was performed using the Quant-iTTM RiboGreenTM RNA Assay Kit (Thermo Fisher Sci.), and quality assessment was carried out using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies).
The cDNA was synthesized from the extracted total RNA using SureSelect cDNA Module (Agilent) and subsequently purified suing AMPure XP beads. The purified cDNA was chemically fragmented with 2X Priming Buffer (Agilent, Inc). Library preparation was carried out using the SureSelect XT Low Input Reagent Kit with indexes 1-96 (Cat: G9703A, Agilent Technologies) and automated on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.).

value: Peri-T

value: post


title: Rapamycin_Replicate 2


title: DMSO_Replicate 3


title: Rapamycin_Replicate 3


title: Oci-Ly7, EZH2i_Rep1


title: RS-Pem-POST-42-3

source_name: OM-T

value: OM-T


title: RS-Pem-POST-44-1

source_name: Mesentery-T

value: Mesentery-T


title: RS-Pem-POST-42-2


title: RS-Pem-POST-48-2


title: RS-Pem-POST-42-1


title: RS-Pem-POST-44-2


title: RS-Pem-POST-48-1


title: RS-Pem-POST-41-1


title: RS-Pem-POST-41-2


title: RS-Pem-POST-40-3


title: RS-Pem-POST-40-5


title: RS-Pem-POST-40-6


title: RS-Pem-POST-40-4


title: RS-Pem-POST-35-2


title: RS-Pem-POST-40-2


title: RS-Pem-POST-40-1

source_name: Abdominal-T

value: Abdominal-T


title: RS-Pem-POST-33-1


title: RS-Pem-POST-32-2


title: RS-Pem-POST-33-2


title: RS-Pem-POST-23-1

source_name: ROV-T

value: ROV-T


title: RS-Pem-POST-32-1


title: RS-Pem-POST-22-3


title: RS-Pem-POST-31-1


title: RS-Pem-POST-21-2


title: RS-Pem-POST-21-3


title: RS-Pem-POST-21-1


title: RS-Pem-POST-17-6


title: RS-Pem-POST-17-7


title: RS-Pem-POST-17-4


title: RS-Pem-POST-17-1


title: RS-Pem-POST-17-2


title: RS-Pem-POST-12-3

source_name: Colon-T

value: Colon-T


title: RS-Pem-POST-17-5


title: RS-Pem-POST-12-1


title: RS-Pem-POST-9-4

source_name: Cecum-T

value: Cecum-T


title: RS-Pem-POST-9-1


title: RS-Pem-POST-9-3


title: RS-Pem-POST-9-2


title: RS-Pem-POST-35-1

source_name: OV-T

value: OV-T


title: RS-Pem-POST-12-2


title: RS-Pem-POST-23-2


title: RS-Pem-POST-7-3


title: RS-Pem-POST-7-2


title: RS-Pem-POST-3-1


title: RS-Pem-POST-2-1


title: RS-Pem-POST-1-2


title: RS-Pem-POST-2-2


title: RS-Pem-POST-22-2


title: RS-Pem-POST-3-3


title: RS-Pem-POST-7-1


title: RS-Pem-POST-17-3


title: RS-Pem-POST-1-1

source_name: LOV-T

value: LOV-T


title: RS-Pem-PRE-48-1

value: pre


title: RS-Pem-PRE-42-1


title: RS-Pem-PRE-44-1


title: RS-Pem-PRE-40-1


title: RS-Pem-POST-7-4


title: RS-Pem-PRE-33-1


title: RS-Pem-PRE-31-2


title: RS-Pem-PRE-31-3


title: RS-Pem-PRE-22-4


title: RS-Pem-PRE-31-1


title: RS-Pem-PRE-22-2


title: RS-Pem-PRE-21-2


title: RS-Pem-PRE-21-1


title: RS-Pem-PRE-17-4


title: RS-Pem-PRE-17-3


title: RS-Pem-PRE-17-2


title: RS-Pem-PRE-12-2


title: RS-Pem-PRE-12-4


title: RS-Pem-PRE-12-3


title: RS-Pem-PRE-12-1


title: RS-Pem-PRE-17-1


title: RS-Pem-PRE-9-1


title: RS-Pem-PRE-41-1


title: RS-Pem-PRE-35-1


title: RS-Pem-PRE-9-3


title: RS-Pem-PRE-7-4


title: RS-Pem-PRE-7-3


title: RS-Pem-PRE-7-2


title: RS-Pem-PRE-23-1


title: RS-Pem-PRE-31-4


title: RS-Pem-PRE-22-3


title: RS-Pem-PRE-22-1


title: RS-Pem-PRE-7-1


title: RS-Pem-PRE-2-3


title: RS-Pem-PRE-3-1


title: RS-Pem-PRE-3-2


title: RS-Pem-PRE-3-3

source_name: Diaphragm-T

value: Diaphragm-T


title: RS-Pem-PRE-2-2


title: RS-Pem-PRE-2-1


title: RS-Pem-PRE-1-2


title: RS-Pem-PRE-9-2


title: hm_liver_ald_rep1_TCR

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

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

data_processing:
Cellranger 7.1.0 (multi) 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 500-25,000 UMIs, 200-6000 features, and <10% UMIs from genes encoded by mitocondrial genes
Cells were noramlized, corrected for batch, and integrated using Seurat(4.3.0)
Assembly: GRCh38
Supplementary files format and content: human_metadata.tsv.gz; sample assignments and related metadata, including TCR clonotype, for all filtered cell barcodes
Supplementary files format and content: human_cell_barcodes.tsv.gz, human_normalized_rna_matrix.mtx, human_normalized_rna_features.tsv.gz; Normalized RNA counts matrix and column/row labels
Library strategy: TCR-seq

source_name: liver

extract_protocol:
Portions of diseased livers were harvested, put into a single-cell suspesion, then 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 Human TCR Amplification Kit (TCR). cDNA libraries were sequenced on an Illumina NovaSeq 6000 at a depth of 50,000 reads / cell for RNA and 4,000 / cell for TCRs.

value: liver

value: disease - ALD


title: hm_liver_mash_rep1_TCR

value: disease - MASH


title: hm_liver_ald_rep3_TCR


title: RS-Pem-PRE-1-1


title: hm_liver_mash_rep2a_TCR


title: hm_liver_nd_rep1_TCR

value: no treatment


title: hm_liver_mash_rep2b_gex

description:
mRNA sequencing
human_metadata.tsv.gz
human_cell_barcodes.tsv.gz
human_normalized_rna_matrix.mtx
human_normalized_rna_features.tsv.gz

data_processing:
Cellranger 7.1.0 (multi) 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 500-25,000 UMIs, 200-6000 features, and <10% UMIs from genes encoded by mitocondrial genes
Cells were noramlized, corrected for batch, and integrated using Seurat(4.3.0)
Assembly: GRCh38
Supplementary files format and content: human_metadata.tsv.gz; sample assignments and related metadata, including TCR clonotype, for all filtered cell barcodes
Supplementary files format and content: human_cell_barcodes.tsv.gz, human_normalized_rna_matrix.mtx, human_normalized_rna_features.tsv.gz; Normalized RNA counts matrix and column/row labels


title: hm_liver_ald_rep2_TCR


title: hm_pbmc_nd_1_TCR

source_name: pbmc

value: pbmc


title: hm_liver_mash_rep1_gex


title: RS-Pem-PRE-3-4

value: Peri-T


title: hm_liver_ald_rep2_gex


title: hm_liver_mash_rep2a_gex


title: hm_liver_nd_rep2_gex


title: hm_pbmc_nd_1_gex


title: hm_liver_nd_rep1_gex


title: hm_liver_ald_rep1_gex


title: hm_liver_ald_rep3_gex


title: 886 iPS_692D2 input

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: cell lines

data_processing:
Sequencing reads were aligned to the hg19 reference genome using bowtie2 following adapter trimming using Cutadapt. Duplicates and reads falling within blacklisted regions (ENCODE) were removed using Picards and bedtools, respectively. For visualization, bigwig files were created using the bamCoverage tool from deepTools, with the options of normalization using Bins Per Million, smoothLength 60, and binSize 20. Peak calling was performed using Homer. All figures were displayed using IGV.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: cell lines

extract_protocol:
ChIP-seq experiments were conducted using feeder-free iPSCs, CD45+CD34+ HPCs, and K562 cells. A Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) was used to eliminate dead cells from feeder-free iPSCs and HPCs. Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) with gentle mixing for 10 minutes at room temperature. The reaction was stopped by adding a glycine solution (10x; Cell Signaling Technology) and incubating for 5 minutes at room temperature, followed by two rounds of cold PBS washing. The cells were processed using the SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. The chromatin was sonicated with Covaris E220 (Covaris) using a microTUBE AFA Fiber Pre-Slit Crimp-Cap (130 µL). Immunoprecipitation of the cross-linked chromatin was performed using antibodies directed against histone H3 lysine 27 acetylation (H3K27ac) (Cell Signaling Technology).
ChIP-seq libraries were constructed using a ThruPLEX DNA-Seq Kit (Takara) according to the manufacturer’s protocol and sequenced using NextSeq 500 or NovaSeq 6000 (Illumina)

value: cell lines

tag: genotype

value: Leukemia


title: 1143 iPS_25G1_EB input

description: HPCs

source_name: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)

value: MDS


title: 888 K562 input

description: iPSC

source_name: iPSC

value: iPSC

value: Control


title: 1142 iPS_25G1_EB H3K27ac

description: HPCs

value: human iPSC derived CD45+CD34+ hematopoietic progenitor cells (HPCs)


title: 889 K562 H3K27ac

description: iPSC


title: hm_liver_nd_rep2_TCR


title: 1140 iPS_25G1_iPS H3K27ac

description: iPSC


title: 887 iPS_692D2 H3K27ac

description: cell lines


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 7003

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-647

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

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: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 3837

description:
cell-free DNA 5hmC
PLCO-649


title: hm_liver_mash_rep2b_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 9080

description:
cell-free DNA 5hmC
PLCO-643


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 7080

description:
cell-free DNA 5hmC
PLCO-651


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 6658

description:
cell-free DNA 5hmC
PLCO-642


title: 1141 iPS_25G1_iPS input

description: iPSC


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 6062

description:
cell-free DNA 5hmC
PLCO-635


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

description:
cell-free DNA 5hmC
PLCO-638


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 9403

description:
cell-free DNA 5hmC
PLCO-645


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0547

description:
cell-free DNA 5hmC
PLCO-641


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LR 1208

description:
cell-free DNA 5hmC
PLCO-639


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3861

description:
cell-free DNA 5hmC
PLCO-648


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 5139

description:
cell-free DNA 5hmC
PLCO-644


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 4602

description:
cell-free DNA 5hmC
PLCO-636


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 0487

description:
cell-free DNA 5hmC
PLCO-630


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 3248

description:
cell-free DNA 5hmC
PLCO-634


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5335

description:
cell-free DNA 5hmC
PLCO-646


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 3317

description:
cell-free DNA 5hmC
PLCO-633


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 7880

description:
cell-free DNA 5hmC
PLCO-627


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 9717

description:
cell-free DNA 5hmC
PLCO-631


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 8430

description:
cell-free DNA 5hmC
PLCO-628


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 8933

description:
cell-free DNA 5hmC
PLCO-637


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 7444

description:
cell-free DNA 5hmC
PLCO-625


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IZ 0327

description:
cell-free DNA 5hmC
PLCO-624


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 0079

description:
cell-free DNA 5hmC
PLCO-622


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 5416

description:
cell-free DNA 5hmC
PLCO-623


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3449

description:
cell-free DNA 5hmC
PLCO-619


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7738

description:
cell-free DNA 5hmC
PLCO-620


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 9486

description:
cell-free DNA 5hmC
PLCO-615


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 9949

description:
cell-free DNA 5hmC
PLCO-617


title: Smad4-KD MEF TNF ChIP-seq (replicate 2)

city: La Jolla

first: Shandy

last: Shahabi

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

description:
Library name: Smad4-KD_TNF_2_ChIP
Smad4-KD MEF TNF ChIP-seq (replicate 2)

data_processing:
Sequencing quality was first assessed by FastQC and libraries with high quality reads were trimmed with Trimmomatic (v0.39). Trimmed FASTQ files were mapped to the mm10 mouse reference genome using Bowtie2. Peaks were then identified using HOMER (findPeaks) with the parameters “-style factor -L 0 -C 0 -fdr 0.9 -minDist 200 -size 200 -o auto”. Raw tag counts were quantified with HOMER (annotatepeaks.pl) and tag counts were averaged between experimental replicates.
Assembly: mm10
Supplementary files format and content: XLSX file with genomic coordinates and normalized ChIP-seq intensity values across all data sets.

organism: Mus musculus

source_name: Mouse embryonic fibroblast (MEF)

growth_protocol: MEF were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. All cells were incubated at 37C in 5% CO2 and grown to 80-90% confluence for passaging.

extract_protocol:
After stimulating cells, cells were washed with PBS and double-crosslinked with 100 mM disuccinimidyl glutarate/PBS solution (DSG, ProteoChem) for 30-min at room temperature followed by 1% methanol-free formaldehyde/PBS solution (Fisher). Crosslinking was quenched with addition of 125 mM glycine for 5-min at room temperature. Cells were washed once with PBS and harvested by scraping. Cell nuclei was isolated and resuspended in 1 mL RIPA buffer with protease inhibitors, then DNA was sonicated using a Model 120 sonic dismembrator (Fisher) to obtain DNA fragments in a general range of 200-1000 bp. DNA fragments were incubated with 1uL anti-RelA antibody (Diagenode) bound to 30uL protein G magnetic beads (NEB). Beads were washed and immunoprecipitated DNA was eluted and decrosslinked with incubation at 65C overnight.
Eluted DNA was PCR amplified (Roche) using ready mix primers (Roche). Amplified DNA was then purified with Ampure XP beads and quantified by dsDNA Qubit (ThermoFisher). Libraries were pooled and size selected with PippinHT (Sage Science) before 50 bp paired-end sequencing.

treatment_protocol: ~80% confluent MEF cells were treated with 10 ng/mL TNF or DMSO control in growth media for 30 min.

value: Mouse embryonic fibroblast (MEF)

tag: plasmid vector

tag: knockdown

value: TNF


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 5425

description:
cell-free DNA 5hmC
PLCO-614


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 0201

description:
cell-free DNA 5hmC
PLCO-621


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 6600

description:
cell-free DNA 5hmC
PLCO-618


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0500

description:
cell-free DNA 5hmC
PLCO-616


title: Cux1-KD MEF TNF ChIP-seq (replicate 2)

description:
Library name: Cux1-KD_TNF_2_ChIP
Cux1-KD MEF TNF ChIP-seq (replicate 2)


title: Cux1-KD MEF TNF ChIP-seq (replicate 1)

description:
Library name: Cux1-KD_TNF_1_ChIP
Cux1-KD MEF TNF ChIP-seq (replicate 1)


title: Smad4-KD MEF TNF ChIP-seq (replicate 1)

description:
Library name: Smad4-KD_TNF_1_ChIP
Smad4-KD MEF TNF ChIP-seq (replicate 1)


title: Tead3-KD MEF TNF ChIP-seq (replicate 2)

description:
Library name: Tead3-KD_TNF_2_ChIP
Tead3-KD MEF TNF ChIP-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2269

description:
cell-free DNA 5hmC
PLCO-611


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 2376

description:
cell-free DNA 5hmC
PLCO-613


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 7870

description:
cell-free DNA 5hmC
PLCO-610


title: Tead3-KD MEF TNF ChIP-seq (replicate 1)

description:
Library name: Tead3-KD_TNF_1_ChIP
Tead3-KD MEF TNF ChIP-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 6438

description:
cell-free DNA 5hmC
PLCO-608


title: Nfat5-KD MEF TNF ChIP-seq (replicate 2)

description:
Library name: Nfat5-KD_TNF_2_ChIP
Nfat5-KD MEF TNF ChIP-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 6991

description:
cell-free DNA 5hmC
PLCO-605


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 4932

description:
cell-free DNA 5hmC
PLCO-606


description:
Library name: Nfatc1-KD_TNF_1_ChIP
Nfatc1-KD MEF TNF ChIP-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 1310

description:
cell-free DNA 5hmC
PLCO-626


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 4573

description:
cell-free DNA 5hmC
PLCO-604


description:
Library name: Scramble-KD_TNF_2_ChIP
Scramble-KD MEF TNF ChIP-seq (replicate 2)

value: Scramble-KD


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 0266

description:
cell-free DNA 5hmC
PLCO-603


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 4862

description:
cell-free DNA 5hmC
PLCO-612


description:
Library name: Scramble-KD_unstim_2_ChIP
Scramble-KD MEF unstim ChIP-seq (replicate 2)

value: unstimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 6975

description:
cell-free DNA 5hmC
PLCO-601


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 6275

description:
cell-free DNA 5hmC
PLCO-602


description:
Library name: Scramble-KD_unstim_1_ChIP
Scramble-KD MEF unstim ChIP-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 2378

description:
cell-free DNA 5hmC
PLCO-600


title: Endoderm_Donor_rep4_A485_H3K27ac

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: 24L011525
2x 50 bp

data_processing:
Sequencing reads were aligned to the Xenopus laevis genome (XENLA_10.1) and a spike-in genome (Escherichia coli, GCA_001606525) using Bowtie2 (v2.4). The alignment process excluded discordant and mixed reads, with paired-end reads mapped to the reference genome. Aligned reads were converted to BAM format and filtered to retain only properly paired alignments.
Normalization scaling factors were computed using deepTools (v3.5.3) based on the read distribution across genomic regions.
Assembly: Xenopus laevis (XENLA_10.1)
Supplementary files format and content: .bigwig - H3K27ac and IgG coverage files, normalized using E. coli spike-in
Library strategy: CUT&Run

organism: Xenopus laevis

extract_protocol:
CUT&RUN was performed according to Phelps W et al. eLife (2023) with some modifications. Endoderm was collected from 25 neurula-stage embryos (NF stage 18) per sample. For nuclear isolation, the endoderm tissues were incubated in Newport 2.0 buffe (Briggs et al. 2016) to facilitate tissue dissociation, by gently agitating the supernatant but not disturbing the tissue. The nuclei were extracted by resuspending in 1 ml ice-cold nuclear extraction buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 500 μM spermidine, 0.1% Triton X-100, 20% glycerol), and subsequently resuspended in 600 µl nuclear extraction buffer. 150 µl concanavalin A beads (Epicypher, 21-1401) were resuspended in 850 µl binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1mM CaCl2, 1mM MnCl2) per sample and activated by washing twice with 1 ml binding buffer. The nuclei were added to 300 µl bead suspension under gentle vortexing and incubated for 10 min at RT while rotating to allow binding of the nuclei to the beads. The supernatant was discarded and the nuclei were incubated in 1 ml blocking buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 2 mM EDTA,1x protease inhibitor)  for 5 min at RT, then incubated in 1:100 primary antibody solution overnight at 4°C and washed twice using 1 ml wash buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 1x protease inhibitor). To facilitate pAG-MNase (Epicypher, 15-1116) binding to the primary antibody, samples were incubated under rotation at 4°C for 1 h, washed twice using wash buffer, and resuspended in 150 µl wash buffer. To activate the MNase digestion reaction, 3 µl 100 mM CaCl2 was added to each sample and incubated at 0°C for 30 min, then quenched using 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 40 μg/mL glycogen), containing 1 ng exogenous spike-in DNA (E. coli, Epicypher 18-1401). To release chromatin fragments, the samples were incubated at 37°C for 20 min, following centrifugation at 16.000 g for 5 min at 4°C. The supernatant containing soluble chromatin fragments was mixed with SDS and proteinase K (Sigma-Aldrich) at 70°C for 10 min and subjected to on-column DNA purification (QIAGEN, MiniElute PCR Purification Kit).
CUT&RUN sequencing libraries were prepared using NEB Ultra II DNA library prep kit (NEB, #E7645), following the manufacturer’s instructions, using 12 PCR amplification cycles with CUT&RUN-specific cycling parameters (45 s 98°C for polymerase activation, 14 cycles of 15 s 98°C DNA melting and 10 s 60°C primer annealing and short extension, 1 min 72°C final extension), without size selection. The libraries were sequenced on a NovaSeq X+ sequencing platform.

treatment_protocol: IVF-derived gastrulae (NF stage 12) were treated with 40 µM SGC-CBP30 (Sigma, SML1133), 30 µM A-485 (Tocris, #6387) or DMSO in 0.1x MMR at 23°C until they reached neurula stage (NF stage 18). 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 further experiments.

value: endoderm

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 1526

description:
cell-free DNA 5hmC
PLCO-596


title: Endoderm_Donor_rep4_CBP30_H3K27ac

description:
Library name: 24L011524
2x 50 bp


title: Endoderm_Donor_rep4_IgG

description:
Library name: 24L011512
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 4596

description:
cell-free DNA 5hmC
PLCO-595


title: Nfat5-KD MEF TNF ChIP-seq (replicate 1)

description:
Library name: Nfat5-KD_TNF_1_ChIP
Nfat5-KD MEF TNF ChIP-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 7711

description:
cell-free DNA 5hmC
PLCO-593


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 8538

description:
cell-free DNA 5hmC
PLCO-599


title: Endoderm_Donor_rep3_CBP30_H3K27ac

description:
Library name: 24L011493
2x 50 bp


description:
Library name: Nfatc1-KD_TNF_2_ChIP
Nfatc1-KD MEF TNF ChIP-seq (replicate 2)


title: Endoderm_Donor_rep3_DMSO_H3K27ac

description:
Library name: 24L011492
2x 50 bp

value: DMSO


title: Endoderm_Donor_rep2_IgG

description:
Library name: 24L011491
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 7016

description:
cell-free DNA 5hmC
PLCO-594


title: RS-Pem-POST-22-1

value: LOV-T

value: post


title: Endoderm_Donor_rep3_IgG

description:
Library name: 24L011495
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 4925

description:
cell-free DNA 5hmC
PLCO-590


title: Endoderm_Donor_rep3_A485_H3K27ac

description:
Library name: 24L011494
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 1089

description:
cell-free DNA 5hmC
PLCO-591


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1470

description:
cell-free DNA 5hmC
PLCO-592


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 4440

description:
cell-free DNA 5hmC
PLCO-587


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7754

description:
cell-free DNA 5hmC
PLCO-586


title: Endoderm_Donor_rep2_A485_H3K27ac

description:
Library name: 24L011490
2x 50 bp


title: Endoderm_Donor_rep2_CBP30_H3K27ac

description:
Library name: 24L011489
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 4073

description:
cell-free DNA 5hmC
PLCO-589


description:
Library name: Scramble-KD_TNF_1_ChIP
Scramble-KD MEF TNF ChIP-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 8650

description:
cell-free DNA 5hmC
PLCO-597


title: Endoderm_Donor_rep2_DMSO_H3K27ac

description:
Library name: 24L011488
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 0211

description:
cell-free DNA 5hmC
PLCO-581


title: Endoderm_Donor_rep1_IgG

description:
Library name: 24L011487
2x 50 bp


title: Endoderm_Donor_rep4_DMSO_H3K27ac

description:
Library name: 24L011523
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 7860

description:
cell-free DNA 5hmC
PLCO-585


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 8378

description:
cell-free DNA 5hmC
PLCO-579


title: Endoderm_Donor_rep1_A485_H3K27ac

description:
Library name: 24L011486
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 7958

description:
cell-free DNA 5hmC
PLCO-577


description:
Library name: Smad4-KD_unstim_3_RNA
Smad4-KD MEF unstim RNA-seq (replicate 3)

data_processing:
Sequencing quality was assessed by FastQC and high-quality reads of libraries were trimmed using Trimmomatic (v0.39) prior to being mapped onto the mm10 mouse reference genome using STAR (v2.7.10b). Transcripts were quantified using StringTie (v1.3.6) and counts were imported to R using prep.de.py3 for normalization and differential expression analysis with DESeq2 (v1.42.0).
Assembly: mm10
Supplementary files format and content: XLSX file with DESeq2 normalized gene counts for all data sets.

molecule: polyA RNA

extract_protocol:
Cells were washed once with PBS and total RNA was isolated with TriZol following manufacturer's recommendations. RNA concentration was quantified by ND-1000 spectrophotometer (Nanodrop).
DNA libraries were prepared from 1 ug of total RNA using KAPA mRNA Hyperprep Kit (Roche). PolyA+ mRNA was enriched and reverse transcribed to double stranded cDNA. The cDNA was end repaired, adenylated, and ligated with KAPA Unique Dual-Indexed adapters (Roche). Libraries were amplified by PCR for 8 cyclces and quantified by dsDNA Qubit (Thermo) before pooling and sequencing.

treatment_protocol: ~80% confluent MEF cells were treated with 10 ng/mL TNF or DMSO control in growth media for 60 min.


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 6554

description:
cell-free DNA 5hmC
PLCO-583


title: Endoderm_Donor_rep1_DMSO_H3K27ac

description:
Library name: 24L011484
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 4846

description:
cell-free DNA 5hmC
PLCO-582


title: C3H/HeSn-Paf/J, time 2, scRNA-seq

city: Bar Harbor

first: Selcan

last: Aydin

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
Library name: Pooled-C3H-timepoint2
10X Genomics

data_processing:
FASTQ files for all samples were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics 10x Genomics mm10 2020-A reference build (GRCm38.93) using 10X Genomics CellRanger count version 6.1.2 for all samples.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
Assembly: GRCm38.93 with GENCODE vM23 annotations
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format. Rows correspond to genes in the order provided in genes.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.
Supplementary files format and content: Each timepoint contains three XX, three XY, and three XO cell lines that were later deconvoluted by gene expression as described in the paper.

source_name: Embryonic stem cells

growth_protocol: Cells were cultured on plates coated in gelatin and irradiated MEF feeders and maintained on ESM (DMEM, 15% FBS, 1% Penicillin/Streptomycin, 1% GlutaMAX-1, 1% MEM NEAA, 100mM Sodium Pyruvate, 55 mM BME, 107 units LIF). Cells were passaged every 2-3 days using 0.25% Typsin-EDTA except when collected for flow cytometry or single-cell sequencing, where they were collected using 1X Accutase.

extract_protocol: Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform (Zheng et al, 2017) version 3.1 NEXTGEM chemistry and according to the manufacturer’s protocol (#CG00315) with modifications for generating the LMO libraries. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and libraries were pooled using a ratio of 95% gene expression library and 5% LMO library before sequencing; each gene expression-LMO library pair was sequenced at 91% of an Illumina NovaSeq 6000 S4 flow cell lane, targeting 20,000 barcoded cells with an average sequencing depth of 100,000 read pairs per cell. LMO libraries were not using in the analysis due to low efficiency of tagging and are not uploaded to the repository.

value: Embryonic stem cells

value: Passaged 10 times since time 1

tag: Sex

value: pooled male and female


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 8132

description:
cell-free DNA 5hmC
PLCO-588


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9192

description:
cell-free DNA 5hmC
PLCO-576


title: C3H/HeSn-Paf/J, time 1, scRNA-seq

description:
Library name: Pooled-C3H-timepoint1
10X Genomics

value: Initial timepoint


description:
Library name: Smad4-KD_unstim_2_RNA
Smad4-KD MEF unstim RNA-seq (replicate 2)


title: Pooled DO mESC scRNAseq

description:
Library name: Pooled-DO-mESC
Chromium Single Cell 3’ v2

data_processing:
Data was processed using cellranger version v1.3.1.
Demultiplexing was done using custom scripts and the cell barcodes per DO strain background can be found in the csv files shared in the supplementary file strain_barcodes.tar.gz
Assembly: mm10
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format. Rows correspond to genes in the order provided in genes.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

growth_protocol: Male and female Diversity Outbred mice (JR #009376) were obtained at approximately four weeks of age and maintained at Predictive Biology, Inc. for several rounds of breeding. At 24-26 days of age females were superovulated and subsequently mated to males aged 7-15 weeks. mESC lines were derived from random blastocysts using previously described protocols. Blastocysts were transferred to 2i medium in 96 well round-bottom ultra-low attachment plates for 5-7 days. Those that had some inner cell mass outgrowth were dispersed and transferred onto MEF feeders in 96 well flat-bottom tissue culture plates in ES medium (ESM, 1i+LIF: Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum, 100 U/mL Penicillin-Streptomycin, 2mM GlutaMAX, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, approximately 2000U/ml LIF, and 3uM CHIR99021). Recombinant LIF protein was produced using a Chinese Hamster Ovary cell line. As the ES cells expanded, they were transferred into 24 well plates, followed by 6 well plates, and finally 10cM dishes, all without feeder cells but in the same media. Thus, as the cells expanded they were weaned off feeder cells by dilution.

extract_protocol:
RNA was not extracted.
The single cell procedure was the Chromium 3’ end gene expression assay, version 2. In that procedure, single cell suspension is added to the Chromium chip (labware) and all of the cell dissociation and library construction are conducted in the droplet in the Chromium instrument.

value: Diversity Outbred


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2259

description:
cell-free DNA 5hmC
PLCO-573


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IY 7214

description:
cell-free DNA 5hmC
PLCO-580


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 8693

description:
cell-free DNA 5hmC
PLCO-572


title: Smad4-KD MEF TNF RNA-seq (replicate 3)

description:
Library name: Smad4-KD_TNF_3_RNA
Smad4-KD MEF TNF RNA-seq (replicate 3)


title: Smad4-KD MEF TNF RNA-seq (replicate 2)

description:
Library name: Smad4-KD_TNF_2_RNA
Smad4-KD MEF TNF RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 6196

description:
cell-free DNA 5hmC
PLCO-578


title: Smad4-KD MEF TNF RNA-seq (replicate 1)

description:
Library name: Smad4-KD_TNF_1_RNA
Smad4-KD MEF TNF RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 4000

description:
cell-free DNA 5hmC
PLCO-570


description:
Library name: Cux1-KD_unstim_2_RNA
Cux1-KD MEF unstim RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0519

description:
cell-free DNA 5hmC
PLCO-568


description:
Library name: Cux1-KD_unstim_1_RNA
Cux1-KD MEF unstim RNA-seq (replicate 1)


title: Endoderm_Donor_rep1_CBP30_H3K27ac

description:
Library name: 24L011485
2x 50 bp


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0281

description:
cell-free DNA 5hmC
PLCO-566


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IY 7201

description:
cell-free DNA 5hmC
PLCO-584


description:
Library name: Tead3-KD_unstim_3_RNA
Tead3-KD MEF unstim RNA-seq (replicate 3)


description:
Library name: Smad4-KD_unstim_1_RNA
Smad4-KD MEF unstim RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 4652

description:
cell-free DNA 5hmC
PLCO-563


title: Cux1-KD MEF TNF RNA-seq (replicate 3)

description:
Library name: Cux1-KD_TNF_3_RNA
Cux1-KD MEF TNF RNA-seq (replicate 3)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7291

description:
cell-free DNA 5hmC
PLCO-574


title: Cux1-KD MEF TNF RNA-seq (replicate 2)

description:
Library name: Cux1-KD_TNF_2_RNA
Cux1-KD MEF TNF RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 0891

description:
cell-free DNA 5hmC
PLCO-560


title: Cux1-KD MEF TNF RNA-seq (replicate 1)

description:
Library name: Cux1-KD_TNF_1_RNA
Cux1-KD MEF TNF RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9110

description:
cell-free DNA 5hmC
PLCO-571


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0815

description:
cell-free DNA 5hmC
PLCO-559


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 6668

description:
cell-free DNA 5hmC
PLCO-558


description:
Library name: Cux1-KD_unstim_3_RNA
Cux1-KD MEF unstim RNA-seq (replicate 3)


title: Tead3-KD MEF TNF RNA-seq (replicate 3)

description:
Library name: Tead3-KD_TNF_3_RNA
Tead3-KD MEF TNF RNA-seq (replicate 3)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 4011

description:
cell-free DNA 5hmC
PLCO-569


description:
Library name: Nfat5-KD_unstim_3_RNA
Nfat5-KD MEF unstim RNA-seq (replicate 3)


description:
Library name: Nfat5-KD_unstim_2_RNA
Nfat5-KD MEF unstim RNA-seq (replicate 2)


title: Tead3-KD MEF TNF RNA-seq (replicate 2)

description:
Library name: Tead3-KD_TNF_2_RNA
Tead3-KD MEF TNF RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 9313

description:
cell-free DNA 5hmC
PLCO-575


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 6882

description:
cell-free DNA 5hmC
PLCO-555


title: Nfatc1-KD MEF TNF RNA-seq (replicate 3)

description:
Library name: Nfatc1-KD_TNF_3_RNA
Nfatc1-KD MEF TNF RNA-seq (replicate 3)


title: Nfatc1-KD MEF TNF RNA-seq (replicate 2)

description:
Library name: Nfatc1-KD_TNF_2_RNA
Nfatc1-KD MEF TNF RNA-seq (replicate 2)


description:
Library name: Nfat5-KD_unstim_1_RNA
Nfat5-KD MEF unstim RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3752

description:
cell-free DNA 5hmC
PLCO-564


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 3576

description:
cell-free DNA 5hmC
PLCO-565


description:
Library name: Tead3-KD_unstim_2_RNA
Tead3-KD MEF unstim RNA-seq (replicate 2)


description:
Library name: Tead3-KD_unstim_1_RNA
Tead3-KD MEF unstim RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9767

description:
cell-free DNA 5hmC
PLCO-562


title: Nfat5-KD MEF TNF RNA-seq (replicate 3)

description:
Library name: Nfat5-KD_TNF_3_RNA
Nfat5-KD MEF TNF RNA-seq (replicate 3)


description:
Library name: Nfatc1-KD_unstim_2_RNA
Nfatc1-KD MEF unstim RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 6868

description:
cell-free DNA 5hmC
PLCO-550


title: Nfat5-KD MEF TNF RNA-seq (replicate 2)

description:
Library name: Nfat5-KD_TNF_2_RNA
Nfat5-KD MEF TNF RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 7011

description:
cell-free DNA 5hmC
PLCO-549


title: Nfat5-KD MEF TNF RNA-seq (replicate 1)

description:
Library name: Nfat5-KD_TNF_1_RNA
Nfat5-KD MEF TNF RNA-seq (replicate 1)


description:
Library name: Scramble-KD_TNF_3_RNA
Scramble-KD MEF TNF RNA-seq (replicate 3)


title: Tead3-KD MEF TNF RNA-seq (replicate 1)

description:
Library name: Tead3-KD_TNF_1_RNA
Tead3-KD MEF TNF RNA-seq (replicate 1)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0204

description:
cell-free DNA 5hmC
PLCO-548


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7829

description:
cell-free DNA 5hmC
PLCO-556


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2236

description:
cell-free DNA 5hmC
PLCO-557


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 0331

description:
cell-free DNA 5hmC
PLCO-546


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0134

description:
cell-free DNA 5hmC
PLCO-544


description:
Library name: Scramble-KD_unstim_2_RNA
Scramble-KD MEF unstim RNA-seq (replicate 2)


title: B_IR_SPX

city: shanghai

first: qiang

last: long

address: OE

institute: OE

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: heart

value: immune cells

value: wild type

tag: strain

value: Male


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 5618

description:
cell-free DNA 5hmC
PLCO-554

tag: tissue

value: peripheral plasma

value: cell-free DNA


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3781

description:
cell-free DNA 5hmC
PLCO-553


title: A_IR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 5739

description:
cell-free DNA 5hmC
PLCO-540


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 8934

description:
cell-free DNA 5hmC
PLCO-552


title: EMT6-LEN-4

city: Tsukuba

first: Megumi

last: Kuronishi

state: Ibaraki

address: Tokodai 5-1-3

institute: Eisai Co., Ltd.

data_processing:
Illumina bcl2fastq was used to de-multiplex and convert reads to FASTQ.
Sequencing data were processed by using Trimmomatic (version 0.36) to remove all Illumina adaptor sequences and bases with low quality scores.
Filtered reads were mapped to the mouse genome (Mm10 and Ensembl 88) by using STAR software (version 2.5.2b) .
Gene expression levels, in transcripts per million, were estimated for all samples by using RSEM software (version 1.2.31).
Assembly: GRCm38
Supplementary files format and content: TSV file containing TPM values for each sample

source_name: tumor tissue

extract_protocol:
RNA was purified using Maxwell RSC simplyRNA Tissue Kit (Promega) following manufacturer’s instructions.
RNA libraries were prepared for sequencing with rRNA depletion and sequenced at GeneWiz.

treatment_protocol: Tumors were collected Day8 after treatment with lenvatinib at 10 mg/kg.

value: tumor tissue

value: BALB/cAnNCrlCrlj

value: LEN

tag: time


title: Nfatc1-KD MEF TNF RNA-seq (replicate 1)

description:
Library name: Nfatc1-KD_TNF_1_RNA
Nfatc1-KD MEF TNF RNA-seq (replicate 1)

value: Mouse embryonic fibroblast (MEF)

value: TNF


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 8676

description:
cell-free DNA 5hmC
PLCO-539


title: EMT6-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6481

description:
cell-free DNA 5hmC
PLCO-551


description:
Library name: Nfatc1-KD_unstim_3_RNA
Nfatc1-KD MEF unstim RNA-seq (replicate 3)

value: unstimulated


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 5707

description:
cell-free DNA 5hmC
PLCO-538


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 8177

description:
cell-free DNA 5hmC
PLCO-536


title: EMT6-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 0715

description:
cell-free DNA 5hmC
PLCO-535


title: EMT6-NT-4

value: NT


description:
Library name: Nfatc1-KD_unstim_1_RNA
Nfatc1-KD MEF unstim RNA-seq (replicate 1)


title: EMT6-NT-2


title: EMT6-NT-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3877

description:
cell-free DNA 5hmC
PLCO-547


title: B16F10-LEN-5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 9336

description:
cell-free DNA 5hmC
PLCO-532


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9317

description:
cell-free DNA 5hmC
PLCO-545


description:
Library name: Scramble-KD_TNF_1_RNA
Scramble-KD MEF TNF RNA-seq (replicate 1)

value: Scramble-KD


description:
Library name: Scramble-KD_unstim_3_RNA
Scramble-KD MEF unstim RNA-seq (replicate 3)


description:
Library name: Scramble-KD_TNF_2_RNA
Scramble-KD MEF TNF RNA-seq (replicate 2)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2956

description:
cell-free DNA 5hmC
PLCO-543


title: B16F10-NT-5


description:
Library name: Scramble-KD_unstim_1_RNA
Scramble-KD MEF unstim RNA-seq (replicate 1)


title: B16F10-NT-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0177

description:
cell-free DNA 5hmC
PLCO-542


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7013

description:
cell-free DNA 5hmC
PLCO-524


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2972

description:
cell-free DNA 5hmC
PLCO-523


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 2973

description:
cell-free DNA 5hmC
PLCO-541


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 7176

description:
cell-free DNA 5hmC
PLCO-522


title: B16F10-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 8386

description:
cell-free DNA 5hmC
PLCO-530


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2934

description:
cell-free DNA 5hmC
PLCO-534


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 7386

description:
cell-free DNA 5hmC
PLCO-533


title: LL2-NT-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7078

description:
cell-free DNA 5hmC
PLCO-520


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9424

description:
cell-free DNA 5hmC
PLCO-518


title: Renca-LEN-5

value: Renca


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 2008

description:
cell-free DNA 5hmC
PLCO-529


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 1650

description:
cell-free DNA 5hmC
PLCO-531


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 7047

description:
cell-free DNA 5hmC
PLCO-528


title: B16F10-NT-4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 4835

description:
cell-free DNA 5hmC
PLCO-516


title: Renca-NT-5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 6355

description:
cell-free DNA 5hmC
PLCO-515


title: B16F10-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 1082

description:
cell-free DNA 5hmC
PLCO-526


title: LL2-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 5832

description:
cell-free DNA 5hmC
PLCO-525


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 4340

description:
cell-free DNA 5hmC
PLCO-514


title: LL2-LEN-2


title: LL2-NT-1


title: LL2-NT-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7607

description:
cell-free DNA 5hmC
PLCO-521


title: Renca-LEN-4


title: BNL-LEN-4

value: BNL 1ME A.7R.1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 4844

description:
cell-free DNA 5hmC
PLCO-510


title: LL2-LEN-4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 6252

description:
cell-free DNA 5hmC
PLCO-517


title: Renca-NT-3


title: Renca-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 7753

description:
cell-free DNA 5hmC
PLCO-513


title: Renca-NT-2


title: BNL-NT-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 5851

description:
cell-free DNA 5hmC
PLCO-512


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9448

description:
cell-free DNA 5hmC
PLCO-508


title: BNL-LEN-5


title: KLN205-LEN-3


title: BNL-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 6741

description:
cell-free DNA 5hmC
PLCO-511


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 3867

description:
cell-free DNA 5hmC
PLCO-505


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 6920

description:
cell-free DNA 5hmC
PLCO-509


title: BNL-NT-4


title: KLN205-NT-4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 6610

description:
cell-free DNA 5hmC
PLCO-507


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 1820

description:
cell-free DNA 5hmC
PLCO-506


title: KLN205-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2777

description:
cell-free DNA 5hmC
PLCO-503


title: KLN205-LEN-1


title: KLN205-NT-3


title: KLN205-NT-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2008

description:
cell-free DNA 5hmC
PLCO-501


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1535

description:
cell-free DNA 5hmC
PLCO-504


title: MC38-LEN-5


title: BNL-NT-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7451

description:
cell-free DNA 5hmC
PLCO-498


title: MC38-LEN-2


title: MC38-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1270

description:
cell-free DNA 5hmC
PLCO-497


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 4056

description:
cell-free DNA 5hmC
PLCO-500


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 1428

description:
cell-free DNA 5hmC
PLCO-499


title: MC38-NT-3


title: MC38-NT-4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9726

description:
cell-free DNA 5hmC
PLCO-495


title: MBT2-LEN-4


title: MBT2-NT-5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9100

description:
cell-free DNA 5hmC
PLCO-494


title: MBT2-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3028

description:
cell-free DNA 5hmC
PLCO-493


title: MBT2-NT-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 6136

description:
cell-free DNA 5hmC
PLCO-491


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

description:
cell-free DNA 5hmC
PLCO-502


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2598

description:
cell-free DNA 5hmC
PLCO-488


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 5995

description:
cell-free DNA 5hmC
PLCO-490


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 7156

description:
cell-free DNA 5hmC
PLCO-489


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 8725

description:
cell-free DNA 5hmC
PLCO-486


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

description:
cell-free DNA 5hmC
PLCO-487


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 3176

description:
cell-free DNA 5hmC
PLCO-496


title: MC38-NT-2


title: 4T1-LEN-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 2773

description:
cell-free DNA 5hmC
PLCO-485


title: 4T1-NT-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 0274

description:
cell-free DNA 5hmC
PLCO-484


title: 4T1-NT-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 4433

description:
cell-free DNA 5hmC
PLCO-483


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 0100

description:
cell-free DNA 5hmC
PLCO-481


title: MBT2-LEN-1


title: Hepa-LEN-4

value: Hepa 1-6


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3244

description:
cell-free DNA 5hmC
PLCO-480


title: MBT2-NT-1


title: Hepa-NT-3


title: Hepa-NT-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2792

description:
cell-free DNA 5hmC
PLCO-474


title: 4T1-LEN-4


title: Hepa-NT-4


title: 4T1-LEN-5


title: RAG-LEN-4

value: RAG


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 3802

description:
cell-free DNA 5hmC
PLCO-475


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 6954

description:
cell-free DNA 5hmC
PLCO-477


title: RAG-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9425

description:
cell-free DNA 5hmC
PLCO-472


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 9757

description:
cell-free DNA 5hmC
PLCO-471


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 0119

description:
cell-free DNA 5hmC
PLCO-482


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2611

description:
cell-free DNA 5hmC
PLCO-469


title: RAG-LEN-2


title: 4T1-NT-1


title: RAG-NT-5


title: Hepa-LEN-5


title: RAG-NT-2


title: RAG-NT-1


title: Hepa-LEN-1


title: CT26-LEN-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 5321

description:
cell-free DNA 5hmC
PLCO-466


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IZ 1445

description:
cell-free DNA 5hmC
PLCO-467


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 9096

description:
cell-free DNA 5hmC
PLCO-476


title: CT26-LEN-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 1834

description:
cell-free DNA 5hmC
PLCO-473


title: CT26-NT-5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 4855

description:
cell-free DNA 5hmC
PLCO-463


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IZ 1541

description:
cell-free DNA 5hmC
PLCO-465


title: CT26-NT-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 4074

description:
cell-free DNA 5hmC
PLCO-462


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 2020

description:
cell-free DNA 5hmC
PLCO-461


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2141

description:
cell-free DNA 5hmC
PLCO-460


title: CT26-NT-3


title: Hepa-Base-2

value: Baseline


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 3457

description:
cell-free DNA 5hmC
PLCO-459


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1970

description:
cell-free DNA 5hmC
PLCO-458


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 5877

description:
cell-free DNA 5hmC
PLCO-468


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 2882

description:
cell-free DNA 5hmC
PLCO-457


title: Hepa-Base-1


title: KLN205-Base-3


title: KLN205-Base-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9018

description:
cell-free DNA 5hmC
PLCO-456


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9260

description:
cell-free DNA 5hmC
PLCO-455


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 3095

description:
cell-free DNA 5hmC
PLCO-454


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 9750

description:
cell-free DNA 5hmC
PLCO-453


title: MBT2-Base-2


title: KLN205-Base-1


title: MBT2-Base-1


title: LL2-Base-3


title: Hepa-Base-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0725

description:
cell-free DNA 5hmC
PLCO-452


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UM 1017

description:
cell-free DNA 5hmC
PLCO-449


title: LL2-Base-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2011

description:
cell-free DNA 5hmC
PLCO-448


title: B16F10-Base-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 1269

description:
cell-free DNA 5hmC
PLCO-447


title: B16F10-Base-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 0102

description:
cell-free DNA 5hmC
PLCO-446


title: CT26-LEN-2


title: B16F10-Base-1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 1997

description:
cell-free DNA 5hmC
PLCO-445


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 6905

description:
cell-free DNA 5hmC
PLCO-444


title: MBT2-Base-3


title: hepatopancreas, Pearl-scale goldfish, Repeat 2

city: YangZhou

first: Jianqiao

last: Wang

address: 48 Wenhui East Road

institute: Yangzhou University

data_processing:
Index of the reference genome was built using STAR and paired-endclean reads were aligned to the reference genome using STAR (v 2.5.1b)
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed using theDESeq2 R package (1.10.1).
Geneswith an adjusted P-value <0.05 found by DESeq2 were assigned as differentiallyexpressed.
Assembly: GCF_003368295.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Carassius auratus

source_name: hepatopancreas

extract_protocol:
Total RNA was extracted from the hepatopancreas of goldfish using TRIzol reagent. 3 μg of total RNA was used for construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations.

value: hepatopancreas

tag: breed

value: Pearl-scale goldfish (PS)


title: hepatopancreas, Pearl-scale goldfish, Repeat 3


title: MC38-Base-3


title: MC38-Base-2


title: hepatopancreas, Pearl-scale goldfish, Repeat 1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 5427

description:
cell-free DNA 5hmC
PLCO-443

value: peripheral plasma


title: hepatopancreas, Crane-top red goldfish, Repeat 2

value: Crane-top red goldfish (HDH)


title: hepatopancreas, Crane-top red goldfish, Repeat 1


title: Renca-Base-2

value: tumor tissue


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 2626

description:
cell-free DNA 5hmC
PLCO-442

value: cell-free DNA


title: LL2-Base-2


title: S.pombe, WT total RNA no poly(A) selection, replicte1

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: WT total RNA
total RNA isolated from WT S. pombe cells, no poly(A) selection or ribosomal RNA depletion

data_processing:
sequence reads were filtered for low quality reads with PRINSEQ++ 1.2 (-min-len 36, -trim_qual_left 15, trim_qual_right 15) and trimmed with Trimmomatic-0.39 for adapter sequences
Paired-end RNA-seq reads were aligned to the S. pombe reference genome (ASM294v2) using HISAT2.2.1 allowing a maximum intron length of 2,000 bps
Alignment files were sorted and indexed using SAMtools1.21101. Un-normalized bigwig files were generated with bamCoverage from deepTools3.5.5102 with 1 bp resolution.
To avoid any bias from rRNAs transcribed on chromosome III, raw signals were normalized by the coverage of chromosome I (CovNChrI4E8 bw files) with in-house scripts
For Extended Fig 7j we normlised bigwigfiles for the geometric mean of median exon coverage of all annotated ORFs in S. pombe with in-house scripts (MedGmean50 bw files)
Assembly: Schizosaccharomyces pombe (fission yeast) genome assembly ASM294v2
Supplementary files format and content: xxx.CovNChrI4e8.f.bw and xxx.CovNChrI4e8.r.bw files are Chromosome I coverage normlaised bigwig files with forward(f) or reverse(r) signal
Supplementary files format and content: xxx.MedGmean50.f.bw and xxx.MedGmean50.r.bw files are bigwig files normliased for the geometric mean of median exon coverage of all annotated ORFs in S. pombe with forward (f) or reverse (r) signal

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: cultured at 30C in YAE medium

extract_protocol:
RNP complex was harvested from ~10-12 L YEA cultures of the yeast strain grown to OD600 of 1.8-2.2. Cell pellets were snap-frozen in liquid nitrogen and subsequently mechanically lysed by a cryogenic cell mill (Retsch MM400). The cell lysate was resuspended in lysis buffer containing 20 mM HEPES pH 7.5, 100 mM NaCl, 1.5 mM MgCl2 supplemented with 0.05 % NP-40 (Sigma-Aldrich), 1 mM DTT, 1 mM phenylmethylsulfonyl fluoride, protease inhibitor cocktail (EDTA-free, Roche) and RiboLock RNase inhibitor (Thermo Fischer Scientific). The cell lysate was cleared by centrifugation and the supernatant was loaded onto IgG Sepharose 6 Fast Flow beads (Cytiva) for overnight (ON) incubation at 4 °C. Non-specifically bound proteins were removed by washing with lysis buffer supplemented with 0.01 % NP-40, followed by TEV cleavage for 5 h at 4 °C. For the second affinity purification, the eluate from IgG beads was loaded onto Flag beads (Anti-Flag M2 Affinity Gel, Sigma-Aldrich) for ON incubation at 4 °C. The beads were washed and eluted with buffer containing 3X Flag peptide at a final concentration of 0.4 mg/mL. RNA was isolated from the Flag-eluate, using RNA Clean and Concentrator Kit (Zymo Research), treated with 20 U Turbo DNase (Thermo Fischer) at 37C for 30 minutes. RNA Clean and Concentration Kit was used once again to remove DNase and full amount of RNA was used to prepare sequencing libraries. For total RNA sequencing, RNA was isolated by TRI reagent (ThermoFIscher AM9738) following the manufacturer's instructions), treated with 20 U Turbo DNase (Thermo Fischer) at 37C for 30 minutes and RNA Clean and Concentration Kit was used  again to remove DNase. 100ng total RNA was used to library preparation.
RNA sequencing libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB) Section 4: Protocol for use with Purified mRNA or rRNA Depleted RNA, following the manufacturer’s instructions.

treatment_protocol: no treatment

value: yeast cells

value: MatMsmt0 leu1-32 ura4 DS/E ade6-210 his2 Otr1R::Ura4 (SphI)


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3358

description:
cell-free DNA 5hmC
PLCO-441


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9454

description:
cell-free DNA 5hmC
PLCO-470


title: S.pombe, RNA-IP of no-tag control strain (negative control), replicate1

description:
Library name: RNA-IP NoTag
total RNA isolated from the RNA-IP

value: h+ HIS leu1-32 ade6-210 ura4-D18


title: Renca-Base-1

value: BALB/cAnNCrlCrlj


title: S.pombe, RNA-IP of Nrl1-MTP_Prp43-6xFlag, replicate1

description:
Library name: RNA-IP Nrl1-MTP_Prp43-6xFlag Rep1
total RNA isolated from the RNA-IP

value: h+ HIS leu1-32 ade6-216 ura4-D18 Nrl1-13*Myc-Tev-ProA::NatNt2 prp43-6flag::kanMX6


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 0643

description:
cell-free DNA 5hmC
PLCO-451