title: RNAseq_SKNO1_DOX_Rep2

description: RNAseq


title: YMB1_KAT6 inhibitor_120hr_R1

status: Public on Jun 05 2023

type: SRA

city: San Diego

first: Chi-Yeh

last: Chung

state: CA

address: 10770 Science Center Drive

country: USA

institute: Pfizer Inc.

library_source: transcriptomic

data_processing:
Bulk RNA sequencing reads were mapped against the Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium (http://ftp.ensembl.org/, build 38, R100) and alignment files converted into BAM format using the R package Rsubread (ver 2.6.4) (Liao et al., 2019). Aligned reads were then counted and assigned to features of the corresponding gene annotation file (ensemble R100) using featureCounts from Rsubread. Read counts data were converted to log2 counts per million (logCPM) and were normalised using the trimmed mean of M-values (TMM) method (Robinson and Oshlack, 2010) using all genes in the panel.
Differential expression (DE) and pathway enrichment analysis were carried out using R/Bioconductor packages edgeR (v3.30.3) (McCarthy et al., 2012; Robinson et al., 2010) and limma (v3.44.3) (Ritchie et al., 2015). DE analysis was modelled using linear models and empirical Bayes moderated t-statistic which is more robust than a t-statistic from a classic t-test.
Assembly: hg38
Supplementary files format and content: Gene expression qunatification in TPM

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were maintained based on ATCC recommendations

extract_protocol: Cells were treated in triplicate with DMSO control or 30 nM PF-9363 for 2 or 5 days and resuspended in RNALater (Ambion #AM-7020) for RNA extraction. At this dose KAT6 biomarker, H3K23Ac is strongly inhibited while having minimal effects on KAT7 biomarker, H3K14Ac (Figure S12). RNA quality was ensured with >8 RIN value using Agilent 2100 Bioanalyzer. cDNA library was generated with TruSeq Stranded mRNA Library Prep kit (Illumina #20020595) and sequenced with Illumina HiSeq X Ten Platform with 150 bp paired-end reads with > 30 million clusters per sample.

treatment_protocol: Approximately Two million cells in triplicate were harvested, rinsed with PBS and stored in RNAlater RNA stabilization solution

tag: cell line

tag: cell type

value: Breast cancer cells

tag: genotype

value: WT

tag: treatment

value: KAT6 inhibitor

tag: time


title: SARS2 infected, untreated, 3

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

data_processing:
pseudoalignment with kallisto v0.44
DESeq2, in R
Assembly: mmGRCm38
Supplementary files format and content: geo_counts.tsv = flat file of raw per gene counts from kallisto, per sample

organism: Mus musculus

source_name: lung

extract_protocol:
NucleoSpin RNA Kit (Macherey-Nagel), manufacturer's protocol
Truseq stranded total mRNA (Illumina), manufacturer's protocol

tag: tissue

value: lung

tag: strain

tag: virus infection

value: untreated

tag: treatment timing

value: Untreated

tag: peptide


title: ThPOK-/- modified GMP Cell_18

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_18

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes. MultiPath-PSI workflow in AltAnalyze was used to quantify exon-exon and exon-intron junction expression from STAR aligned BAM files (mm10 genome/transcriptome reference), requiring detection of splicing in at least 20% of the single-cell libraries of each cellHarmony assigned cell populations (dPSI > 0.1, eBayes t-test p<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Mm-ThPOK-RSEM-TPM-log2.txt: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: ThPOK-WT_MultiPath-PSI.txt.zip: Alternative Splicing quantification and annotations text file from MultiPath-PSI (AltAnalyze) (archival and ThPOK Fluidigm)
Supplementary_files_format_and_content: groups.ThPOK-WT_MultiPath-PSI: Group annotations assigned by cellHarmony (text file) (archival and ThPOK Fluidigm) (text file)

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting, then cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

value: ThPOK-/-

value: Bone marrow derived GMP


title: YMB1_DMSO_120hr_R3

value: DMSO


title: RNAseq_SKNO1_DOX_Rep1

city: Miami

first: Gloria

last: Mas Martin

state: Florida

address: 1501 NW 10th Avenue

institute: University of Miami

description: RNAseq

data_processing:
Reads were aligned to the mm10 transcriptome and ERCC spike-in indexes using RSEM (v1.3.0) and STAR (v2.6.0c) with Gencode annotations. Differentially expressed genes were determined by DESeq2 (v1.18.1, Wald Test, p-adj < 0.05) after gene counts were corrected based on ERCC variances using RUVseq (v1.12.0).
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For RNAseq samples, the processed data files are in .txt format and contain the expected gene and transcript counts

source_name: SKNO1 AML cell line (DSMZ no.: ACC 690)

extract_protocol:
total RNA was obtained using the RNEasy Plus micro kit (Qiagen, 74034). Ribosomal RNA vas removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310) following manufacturer’s protocols, and RNA-Seq libraries were prepared using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies). RNA-Seq libraries were sequenced on an Illumina NextSeq 500 High-Output kit platform (paired-end, 75 bp reads) to obtain ~40 M reads/sample.
RNAseq libraries were prepared for sequencing using the Illumina’s TruSeq Total-stranded RNA-seq prep kit (NuGEN Technologies).

value: bone marrow

tag: age

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)

value: SKNO1 acute myeloid leukemia

value: 7 days with 1ug/ml Doxycycline


title: ThPOK-/- modified GMP Cell_72

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_72


title: YMB1_DMSO_120hr_R2


title: RNAseq_SKNO1_Rep4

description: RNAseq

value: vehicle


title: ThPOK-/- modified GMP Cell_17

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_17


title: uninfected, untreated, 3

value: Uninfected


title: SARS2 infected, untreated, 1


title: RNAseq_SKNO1_Rep2

description: RNAseq


title: YMB1_DMSO_120hr_R1


title: RNAseq_SKNO1_Rep3

description: RNAseq


title: ThPOK-/- modified GMP Cell_79

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_79


title: YMB1_KAT6 inhibitor_48hr_R3

value: 48 hr


title: ThPOK-/- modified GMP Cell_86

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_86


title: RNAseq_SKNO1_Rep1

description: RNAseq


title: uninfected, untreated, 2


title: ThPOK-/- modified GMP Cell_93

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_93


title: YMB1_KAT6 inhibitor_48hr_R2

value: Breast cancer cells


title: mRE_ZT 20-3

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description: expressionRE.tsv

data_processing:
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using Tuxedo pipeline tophat
Read counting for each gene and normalization to FPKM values  using Tuxedo pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (FPKM) of the standard RNAseq analysis are reported in the genes_fpkm.csv file

source_name: Gastrocnemius muscle

extract_protocol: WT, KO and skeletal muscle Bmal1 reconstituted mice ( see Koronowski et al Cell 2019 and Greco et al Science Advances 2021 for general model description) were used to collect tissues at 6 time points over the diurnal cycle - 12 hr light: 12 hr dark conditions and ad libitum feeding of normal chow; tissues harvested at ZT0, 4, 8, 12, 16, 20

value: Gastrocnemius muscle

value: mRE

tag: time point

value: ZT 20


title: uninfected, untreated, 1

value: lung

value: untreated


title: mRE_ZT 20-5

description: expressionRE.tsv


title: YMB1_KAT6 inhibitor_48hr_R1

value: WT

value: KAT6 inhibitor


title: Cut&Run_H3K4me1_Dpf2D/D_LK_Exp6

description: CUT&RUN

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Pair-end fastq files were processed with the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. and aligned to the mm10 genome using Bowtie2 v2.3.4.3. SAMtools v1.9 were used to convert the output file to BAM format. Duplicates were removed using Picard Tools v2.20.7. Peak calling was performed with MACS2 v2.2.4
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For ATACseq, ChIPseq and Cut&Run samples, the processed data files are in bigwig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

molecule: genomic DNA

source_name: bone marrow sorted LK cells

extract_protocol:
Lin- cKit+ cells were obtained from bone marrow of 28-days old Dpf2f/f and Dpf2D/D mice. Approximately 0.5 million cells/sample were crosslinked (1 min, 1% formaldehyde), quenched (125mM Glycine) and washed in buffers following the CUTANA ChIC/CUT&RUN kit according to the manufacturer’s CUT&RUN cross-linking protocol (EpiCypher, 14-1048). 0.5 million cells were used per IP with 1 ug of antibody.
Cut&Run libraries were generated using the NEBNext Ultra II DNA library Prep kit for Illumina (NEB, E7370L)

value: post natal day 28


title: ThPOK-/- modified GMP Cell_44

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_44

value: ThPOK-/-

value: Bone marrow derived GMP


title: SARS2 infected, untreated, 2

value: Untreated


title: mRE_ZT 20-1

description: expressionRE.tsv


title: Cut&Run_H3K4me1_Dpf2f/f_LK_Exp6

description: CUT&RUN

value: bone marrow


title: YMB1_DMSO_48hr_R3

value: DMSO


title: mRE_ZT 16-6

description: expressionRE.tsv

value: ZT 16


title: Cut&Run_H3K27ac_Dpf2D/D_LK_Exp6

description: CUT&RUN


title: ThPOK-/- modified GMP Cell_3

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_3


title: ThPOK-/- modified GMP Cell_10

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_10


title: YMB1_DMSO_48hr_R2


title: DU4475_KAT6 inhibitor_120hr_R3


title: Cut&Run_H3K27ac_Dpf2f/f_LK_Exp6

description: CUT&RUN


title: mRE_ZT 16-2

description: expressionRE.tsv


title: YMB1_DMSO_48hr_R1


title: Cut&Run_IgG_Dpf2f/f_LK_Exp6

description: CUT&RUN


title: Cut&Run_IgG_Dpf2D/D_LK_Exp6

description: CUT&RUN


title: ThPOK-/- modified GMP Cell_64

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_64


title: mRE_ZT 16-1

description: expressionRE.tsv


title: Cut&Run_Nrf2_Dpf2D/D_LK_Exp6

description: CUT&RUN


title: DU4475_KAT6 inhibitor_120hr_R2


title: mRE_ZT 12-3

description: expressionRE.tsv

value: ZT 12


title: ThPOK-/- modified GMP Cell_71

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_71


title: ThPOK-/- modified GMP Cell_78

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_78


title: Cut&Run_Nrf2_Dpf2f/f_LK_Exp6

description: CUT&RUN


title: mRE_ZT 12-2

description: expressionRE.tsv


title: DU4475_DMSO_120hr_R3


title: ThPOK-/- modified GMP Cell_85

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_85


title: ThPOK-/- modified GMP Cell_9

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_9


title: DU4475_DMSO_120hr_R2


title: ThPOK-/- modified GMP Cell_92

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_92


title: mRE_ZT 8-5

description: expressionRE.tsv

value: ZT 8


title: DU4475_DMSO_120hr_R1

value: Breast cancer cells


title: ThPOK-/- modified GMP Cell_43

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_43


title: Cut&Run_Dpf2_Dpf2f/f_LK_Exp6

description: CUT&RUN


title: DU4475_KAT6 inhibitor_120hr_R1


title: Cut&Run_Brg1_Dpf2D/D_LK_Exp6

description: CUT&RUN


title: DU4475_KAT6 inhibitor_48hr_R3

value: 48 hr


title: DU4475_KAT6 inhibitor_48hr_R2


title: mRE_ZT 8-1

description: expressionRE.tsv

value: Gastrocnemius muscle

value: mRE


title: SN-38.6h_Actinomycin_D.6h

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
The 96 RNA-seq samples in this submission were combined with 34 RNA-seq samples from our previous studies (GEO accession numbers GSE173221 and GSE190735). Quality filtered NGS reads from the 130 RNA-seq samples were trimmed with fastx toolkit (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/download.html) and aligned to the human genome (GRCh38/hg38) by Tophat2 (version 2.1.1). PCR duplicates were removed using Picard suite (version 2.0.1). The alignments were sorted and indexed by SAMtools (version 1.9) and used for RNA editing sites detection. REDItools, RED-ML and SPRINT were separately applied to detect RNA editing sites. REDItools (https://sourceforge.net/projects/reditools) was run with the parameters ‘-m 50 -u -T 6-0 -n 0.0’. RED-ML (https://github.com/BGIRED/RED-ML) and SPRINT (https://github.com/jumphone/SPRINT) were run using the default parameters. Putative ADAR editing sites were filtered against the common SNPs from dbSNP 151 and K562 in-house SNPs to remove sequence variants. The sites mapping to repeats as annotated by the RepeatMasker track of the UCSC Genome Browser were removed. The remaining sites were then filtered based on their mappability scores as defined by the “Mappability or Uniqueness of Reference Genome from ENCODE” track from the UCSC Genome Browser. Only the sites with a mappability score of 1 based on 100mer alignability and an average mappability score of > 0.5 calculate based on the 24mer alignability in the ± 150bp window around the sites were kept. The editing level for each site was determined as the ratio of the reads containing the A>G change out of the total number of reads mapping to the site. RNA editing candidates with the maximum editing level among the 130 samples of > 0.2 and found in at least 2 samples were kept and then further processed using in-house pipeline based on Sanger validation to generate a compendium of authentic ADAR sites.
Assembly: GRCh38/hg38
Supplementary files format and content: A tab-delimited text file that contains information on the 4,149 authentic ADAR editing sites detected in the K562 cell line. The information for each site includes: the genomic coordinates; strand; the analytical method(s) by which it was detected; location in a genomic element; the annotated or unannotated status of the site; and the editing level in each of the 130 samples (with the exception of the 46 sites detected by Sanger only). The coordinates are based on the UCSC BED files system: 0-based, half-open.

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated with TRNzol (TIANGEN, Beijing).
The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

value: human erythroleukemic cell line


title: mRE_ZT 4-4

description: expressionRE.tsv

value: ZT 4


title: ThPOK-/- modified GMP Cell_1

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_1


title: Cut&Run_Brg1_Dpf2f/f_LK_Exp6

description: CUT&RUN


title: ThPOK-/- modified GMP Cell_56

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_56


title: mRE_ZT 12-1

description: expressionRE.tsv


title: DU4475_DMSO_48hr_R3

value: WT


title: mRE_ZT 4-3

description: expressionRE.tsv


title: DU4475_KAT6 inhibitor_48hr_R1

value: KAT6 inhibitor


title: Cut&Run_Dpf2_Dpf2D/D_LK_Exp6

description: CUT&RUN

value: post natal day 28


title: RNAseq_Dpf2D/D_Tcells_Stimulated_rep3

description: RNAseq

source_name: sorted CD4+ T helper cells

value: spleen

value: 3 hours with 50ng/ml PMA and 1ug/ml Ionomycin


title: mRE_ZT 4-1

description: expressionRE.tsv


title: DU4475_DMSO_48hr_R2


title: mRE_ZT 8-4

description: expressionRE.tsv


title: RNAseq_Dpf2D/D_Tcells_Stimulated_rep2

description: RNAseq


title: ThPOK-/- modified GMP Cell_70

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_70

value: ThPOK-/-

value: Bone marrow derived GMP


title: ThPOK-/- modified GMP Cell_2

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_2


title: ThPOK-/- modified GMP Cell_77

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_77


title: MCF7_KAT6 inhibitor_120hr_R3


title: RNAseq_Dpf2D/D_Tcells_Stimulated_rep4

description: RNAseq


title: MCF7_KAT6 inhibitor_120hr_R2


title: ThPOK-/- modified GMP Cell_84

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_84


title: mRE_ZT 0-2

description: expressionRE.tsv

value: ZT 0


title: RNAseq_Dpf2f/f_Tcells_Stimulated_rep4

description: RNAseq


title: ThPOK-/- modified GMP Cell_91

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_91


title: MCF7_KAT6 inhibitor_120hr_R1


title: KO_ZT 20-5

description: expressionKO.tsv

value: KO

value: ZT 20


title: ThPOK-/- modified GMP Cell_42

description:
ThPOK-/- modified GMP
Dec12_x_x_078_Cell_42


title: mRE_ZT 0-4

description: expressionRE.tsv


title: mRE_ZT 0-1

description: expressionRE.tsv


title: KO_ZT 20-3

description: expressionKO.tsv


title: AM285_AS

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

description: Short Nascent Strand_ASO anti-GAA_Replicate 2

data_processing:
Quality control of sequenced reads was performed using FastQC (Babraham Institute) and MultiQC
Reads were aligned to the Homo sapiens genome (hg19 build) (Ensembl v75) using Bowtie2 (v.2.3.4.2)
Picard (v.2.18.17) (Broad Institute) was used to remove duplicate reads.
Peaks were called using MACS2 (v. 2.1.0.20151222) (threshold q=0.1) and EPIC2 (v. 0.0.40) (threshold FDR=0.1)
Bigwig files were generated with deepTools (v.3.2.0)
Assembly: hg19
Supplementary files format and content: bigWig files
Supplementary files format and content: peak bed files
Library strategy: SNSseq

source_name: Colorectal Cancer

growth_protocol: HCT116 cells were grown in RPMI medium at 37ºC

extract_protocol:
Phenol:chlorophorm
Based on Blecher-Gonen et al. 2013

treatment_protocol: ASO transfection with lipofectamine 2000

value: HCT116 cell line

value: ASO anti-GAA

tag: replicate

tag: molecule subtype

value: Nascent Strands (ssDNA converted to dsDNA)


title: ThPOK-/- modified GMP Cell_63

description:
ThPOK-/- modified GMP
Dec12_x_x_079_Cell_63


title: RNAseq_Dpf2f/f_Tcells_Stimulated_rep2

description: RNAseq


title: RNAseq_Dpf2f/f_Tcells_Stimulated_rep3

description: RNAseq


title: RNAseq_Dpf2D/D_Tcells_Stimulated_rep1

description: RNAseq


title: MCF7_DMSO_120hr_R3

value: Breast cancer cells

value: DMSO


title: KO_ZT 20-1

description: expressionKO.tsv

value: Gastrocnemius muscle


title: RNAseq_Dpf2f/f_Tcells_Stimulated_rep1

description: RNAseq


title: KO_ZT 16-5

description: expressionKO.tsv

value: ZT 16


title: RNAseq_Dpf2D/D_Tcells_not_stimulated_rep4

description: RNAseq

value: 3 hours with vehicle


title: AM285_C

description: Short Nascent Strand_ASO control_Replicate 2

value: ASO control


title: MCF7_DMSO_120hr_R2

value: WT


title: MCF7_DMSO_120hr_R1


title: DU4475_DMSO_48hr_R1

value: 48 hr


title: RNAseq_Dpf2D/D_Tcells_not_stimulated_rep3

description: RNAseq

value: spleen

value: post natal day 28


title: AM260_AS

description: Short Nascent Strand_ASO anti-GAA_Replicate 1


title: KO_ZT 16-3

description: expressionKO.tsv


title: KO_ZT 16-2

description: expressionKO.tsv


title: RNAseq_Dpf2D/D_Tcells_not_stimulated_rep2

description: RNAseq


title: AM260_C

description: Short Nascent Strand_ASO control_Replicate 1


title: ZR751_KAT6 inhibitor_120hr_R2

value: KAT6 inhibitor


title: ChIPseq_SKNO1_shDpf2_Input

description: Input

data_processing:
Raw reads were trimmed for adapters using Cutadapt (v1.15 –nextseq-trim=20 –m 18). Fastq files were aligned to Human GRCh38.p3 using BWA (v0.7.13) with parameters aln -q 5 -l 32 -k 2, and deduplicated using Picard Mark Duplicates (v2.10.6). Peaks were called using narrow peaks by macs2 (v2.1.1.20160309) with IgG used as background. ChIPseeker (v1.14.0) and R (v3.4.1) were used for genomic annotation.
Genome_build: mm10; hg38
Supplementary_files_format_and_content: For ATACseq, ChIPseq and Cut&Run samples, the processed data files are in bigwig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

extract_protocol:
10 million SKNO1 cells carrying shLuciferase or shDpf2#2487 were grown in the presence of doxycycline for 7 days to induce Dpf2 depletion. At day 7 of culture, cells were crosslinked with 1% formaldehyde for 15 minutes, quenched with 125mM Glycine for 5 minutes, washed in PBS and flash frozen at -80C. Crosslinked cell pellets were processed for ChIPseq following a previously described protocol (Boulay G et al., Cell 2017).
ChIPseq libraries were generated using NEBNExt Ultra II DNA library prep kit for Illumina (NEB, E7370L).

value: bone marrow

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)

value: SKNO1 acute myeloid leukemia

value: 7 days with 1ug/ml Doxycycline


title: RNAseq_Dpf2D/D_Tcells_not_stimulated_rep1

description: RNAseq


title: ZR751_KAT6 inhibitor_120hr_R1


title: RNAseq_Dpf2f/f_Tcells_not_stimulated_rep4

description: RNAseq


title: KO_ZT 12-2

description: expressionKO.tsv

value: KO

value: ZT 12


title: ZR751_DMSO_120hr_R3

value: Breast cancer cells

value: DMSO


title: RNAseq_Dpf2f/f_Tcells_not_stimulated_rep3

description: RNAseq


title: RNAseq_Dpf2f/f_Tcells_not_stimulated_rep2

description: RNAseq


title: ZR751_DMSO_120hr_R2


title: KO_ZT 8-7

description: expressionKO.tsv

value: Gastrocnemius muscle

value: ZT 8


title: KO_ZT 12-1

description: expressionKO.tsv


title: ZR751_DMSO_120hr_R1


title: KO_ZT 8-3

description: expressionKO.tsv


title: ChIPseq_SKNO1_shLuc_ARID1A

description: ChIPseq using anti-ARID1A antibody (D2A8U, Cell Signaling Technology, Cat#12354, lot#1; RRID:AB_2637010)

value: stable cell line carrying doxycycline inducible shDpf2 #2487 hairpin (puromycin-selected)


title: ChIPseq_SKNO1_shLuc_Input

description: Input


title: KO_ZT 12-3

description: expressionKO.tsv


title: RNAseq_SKNO1_shDpf2#2487_DOX_Rep4

description: RNAseq


title: RNAseq_Dpf2f/f_Tcells_not_stimulated_rep1

description: RNAseq

value: 3 hours with vehicle


title: T47D_KAT6 inhibitor_120hr_R3

value: WT


title: RNAseq_Dpf2D/D_M2_rep5

description: RNAseq

source_name: bone marrow derived macrophages (day 7)

value: 24 hours with 10ng/ml recombinant murine IL-4 (Peprotech 214-14)


title: RNAseq_SKNO1_shDpf2#2487_DOX_Rep3

description: RNAseq


title: KO_ZT 8-1

description: expressionKO.tsv


title: RNAseq_SKNO1_shDpf2#2487_DOX_Rep2

description: RNAseq


title: T47D_KAT6 inhibitor_120hr_R2


title: KO ZT 4-3

description: expressionKO.tsv

value: ZT 4


title: T47D_KAT6 inhibitor_120hr_R1

value: KAT6 inhibitor


title: RNAseq_Dpf2D/D_M2_rep3

description: RNAseq

value: bone marrow

value: post natal day 28


title: ChIPseq_SKNO1_shDpf2_ARID1A

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)


title: KO ZT 4-2

description: expressionKO.tsv


title: RNAseq_Dpf2D/D_M2_rep1

description: RNAseq


title: T47D_DMSO_120hr_R1


title: T47D_DMSO_120hr_R3


title: RNAseq_Dpf2D/D_M2_rep2

description: RNAseq


title: RNAseq_SKNO1_shDpf2#2487_Rep1

description: RNAseq

value: SKNO1 acute myeloid leukemia

value: vehicle


title: RNAseq_SKNO1_shDpf2#2487_Rep4

description: RNAseq


title: KO ZT 4-1

description: expressionKO.tsv

value: KO


title: RNAseq_Dpf2f/f_M2_rep5

description: RNAseq


title: RNAseq_Dpf2f/f_M2_rep3

description: RNAseq


title: T47D_DMSO_120hr_R2

value: Breast cancer cells


title: KO ZT 0-4

description: expressionKO.tsv

value: ZT 0


title: RNAseq_SKNO1_shDpf2#2487_Rep3

description: RNAseq


title: MCF7_KAT6 inhibitor_48hr_R3

value: 48 hr


title: RNAseq_Dpf2f/f_M2_rep4

description: RNAseq


title: MCF7_KAT6 inhibitor_48hr_R2


title: WT_ZT 20-5

description: expressionWT.tsv

value: Gastrocnemius muscle

value: ZT 20


title: KO_ZT 0-2

description: expressionKO.tsv


title: RNAseq_SKNO1_shDpf2#1357_DOX_Rep4

description: RNAseq

value: 7 days with 1ug/ml Doxycycline


title: RNAseq_Dpf2D/D_M2_rep4

description: RNAseq


title: ZR751_KAT6 inhibitor_120hr_R3

value: WT


title: WT_ZT 20-3

description: expressionWT.tsv


title: RNAseq_SKNO1_shDpf2#2487_DOX_Rep1

description: RNAseq


title: RNAseq_Dpf2f/f_M2_rep2

description: RNAseq

value: 24 hours with 10ng/ml recombinant murine IL-4 (Peprotech 214-14)


title: KO ZT 0-3

description: expressionKO.tsv


title: RNAseq_SKNO1_shDpf2#2487_Rep2

description: RNAseq


title: MCF7_DMSO_48hr_R3

value: DMSO


title: WT_ZT 16-5

description: expressionWT.tsv

value: ZT 16


title: MCF7_DMSO_48hr_R2


title: RNAseq_Dpf2D/D_M1_rep5

description: RNAseq

value: bone marrow

value: 24 hours with 100U/ml recombinant murine IFNg (Peprotech 315-05-250ug) and 100ng/ml LPS-EB Ultrapure (Invivogen tlrl-3pelps)


title: RNAseq_SKNO1_shDpf2#1357_DOX_Rep2

description: RNAseq

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse


title: RNAseq_SKNO1_shDpf2#1357_DOX_Rep1

description: RNAseq

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)


title: WT_ZT 16-2

description: expressionWT.tsv


title: Smarce1-AID_dmso_120min_aid06_rep2

city: Memphis

first: Xiaolong

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

description:
nascent RNA
Smarce1-AID_dmso_120_aid06_2425093

data_processing:
Illumina Casava1.7 software used for basecalling.
Total stranded RNA sequencing data were mapped to mouse genome assemblymm10 using an internalAutoMapperpipeline. Briefly, the raw reads were trimmed with trimgalore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a.
Then the read counts were computed usingRSEM(V1.3.0) based on GENCODE vM23.
RPM (Reads Per Million) was applied to normalize read counts in bigwig tracks
Assembly: mm10
Supplementary files format and content: read counts from RSEM

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
Click-iT® Nascent RNA Capture Kit (https://www.thermofisher.com/order/catalog/product/C10365)
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off. For mitotic release, mitotic cells were washed out three times by fresh mESC culture medium to remove residual nocodazole and then cultured in mESC medium for the indicated time.

value: mouse embryonic stem cells

value: cells were released from mitosis for 120 min


title: MCF7_KAT6 inhibitor_48hr_R1

value: KAT6 inhibitor


title: MCF7_DMSO_48hr_R1

value: Breast cancer cells


title: RNAseq_SKNO1_shDpf2#1357_Rep4

description: RNAseq

value: SKNO1 acute myeloid leukemia

value: vehicle


title: RNAseq_Dpf2D/D_M1_rep3

description: RNAseq

value: post natal day 28


title: RNAseq_SKNO1_shDpf2#1357_DOX_Rep3

description: RNAseq


title: ZR751_KAT6 inhibitor_48hr_R3

value: 48 hr


title: RNAseq_Dpf2D/D_M1_rep4

description: RNAseq


title: RNAseq_Dpf2D/D_M1_rep1

description: RNAseq


title: WT_ZT 16-1

description: expressionWT.tsv

value: Gastrocnemius muscle


title: ZR751_KAT6 inhibitor_48hr_R2

value: WT


title: WT_ZT 12-2

description: expressionWT.tsv

value: ZT 12


title: WT_ZT 12-4

description: expressionWT.tsv


title: RNAseq_SKNO1_shDpf2#1357_Rep1

description: RNAseq


title: ZR751_DMSO_48hr_R3

value: DMSO


title: RNAseq_Dpf2f/f_M2_rep1

description: RNAseq

value: 24 hours with 10ng/ml recombinant murine IL-4 (Peprotech 214-14)


title: RNAseq_SKNO1_shDpf2#1357_Rep2

description: RNAseq

value: bone marrow


title: ZR751_KAT6 inhibitor_48hr_R1


title: WT_ZT 20-1

description: expressionWT.tsv

value: ZT 20


title: RNAseq_Dpf2f/f_M1_rep5

description: RNAseq

value: 24 hours with 100U/ml recombinant murine IFNg (Peprotech 315-05-250ug) and 100ng/ml LPS-EB Ultrapure (Invivogen tlrl-3pelps)


title: RNAseq_Dpf2D/D_M1_rep2

description: RNAseq


title: RNAseq_SKNO1_shDpf2#1357_Rep3

description: RNAseq

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)


title: RNAseq_SKNO1_shLuc_DOX_Rep4

description: RNAseq

value: 7 days with 1ug/ml Doxycycline


title: RNAseq_Dpf2f/f_M1_rep4

description: RNAseq


title: WT_ZT 8-5

description: expressionWT.tsv

value: ZT 8


title: RNAseq_SKNO1_shLuc_DOX_Rep2

description: RNAseq


title: ZR751_DMSO_48hr_R1

value: Breast cancer cells


title: RNAseq_SKNO1_shLuc_DOX_Rep3

description: RNAseq

value: SKNO1 acute myeloid leukemia


title: WT_ZT 8-3

description: expressionWT.tsv


title: T47D_KAT6 inhibitor_48hr_R2

value: KAT6 inhibitor


title: T47D_KAT6 inhibitor_48hr_R3


title: ZR751_DMSO_48hr_R2


title: RNAseq_Dpf2f/f_M1_rep2

description: RNAseq

value: post natal day 28


title: RNAseq_Dpf2f/f_M1_rep3

description: RNAseq


title: RNAseq_Dpf2f/f_M1_rep1

description: RNAseq


title: WT_ZT 4-5

description: expressionWT.tsv

value: ZT 4


title: WT_ZT 8-1

description: expressionWT.tsv

value: Gastrocnemius muscle


title: WT_ZT 12-1

description: expressionWT.tsv

value: WT


title: T47D_KAT6 inhibitor_48hr_R1

value: 48 hr


title: RNAseq_SKNO1_shLuc_DOX_Rep1

description: RNAseq


title: RNAseq_Dpf2D/D_M0_rep5

description: RNAseq

value: vehicle (24 hours with PBS)


title: RNAseq_SKNO1_shLuc_Rep3

description: RNAseq

value: vehicle


title: WT_ZT 4-2

description: expressionWT.tsv


title: T47D_DMSO_48hr_R3

value: DMSO


title: WT_ZT 4-1

description: expressionWT.tsv


title: T47D_DMSO_48hr_R2


title: RNAseq_Dpf2D/D_M0_rep4

description: RNAseq

value: bone marrow


title: RNAseq_SKNO1_shLuc_Rep2

description: RNAseq


title: RNAseq_Dpf2D/D_M0_rep3

description: RNAseq


title: WT_ZT 0-5

description: expressionWT.tsv

value: ZT 0


title: RNAseq_SKNO1_shLuc_Rep1

description: RNAseq

value: established in 1990 from the bone marrow of a 22-year-old man with acute myeloid leukemia (AML M2) in second relapse


title: RNAseq_SKNO1_shLuc_Rep4

description: RNAseq

value: stable cell line carrying doxycycline inducible shRenilla luciferase hairpin (puromycin-selected)


title: WT_ZT 0-2

description: expressionWT.tsv


title: HCT116 cells, Glucose, Serum Starvation _3

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

data_processing:
Clean reads were aligned to hg38 reference genome with Hisat2 using default parameters. Gene expression levels were counted with HT-seq using default. Differential expression analysis of two groups was performed using the DESeq2 R package.
Assembly: hg38

extract_protocol:
Total RNA was extracted by phenol/chloroform.
RNA-Seq was performed using BGISEQ platform (BGI) and  Illumina HiSeq .

value: Colorectal cancer cell line

value: Glucose, Serum Starvation


title: T47D_DMSO_48hr_R1

value: Breast cancer cells


title: RNAseq_Dpf2D/D_M0_rep2

description: RNAseq


title: RNAseq_Dpf2D/D_M0_rep1

description: RNAseq


title: AM348a_WT

description:
Nascent Strands (ssDNA converted to dsDNA)
λ-exonuclease
Short Nascent Strand Replicate 3

data_processing:
Library strategy: SNS-seq
Quality control of sequenced reads was performed using FastQC (Babraham Institute) and MultiQC.
Reads were aligned to the Homo sapiens genome (hg19 build) (Ensembl v75) using Bowtie2 (v.2.3.4.2).
Picard (v.2.18.17) (Broad Institute) was used to remove duplicate reads.
Peaks were called using MACS2 (v. 2.1.0.20151222) (threshold q=0.1) and EPIC2 (v. 0.0.40) (threshold FDR=0.1).
ChiPseeker R/Bioconductor package was used for SNS-seq peak annotation, comparison and visualization.
Bigwig files were generated with deepTools (v.3.2.0).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: Peak bed files

growth_protocol: HCT116 cells were grown in RPMI medium at 37ºC.

extract_protocol:
Phenol:chloroform
Based on Blecher-Gonen et al. 2013.

value: Untreated

tag: strategy

value: lambda-exonuclease


title: HCT116 cells, Glucose, Serum Starvation _2


title: AM280_WT

description:
Nascent Strands (ssDNA converted to dsDNA)
λ-exonuclease
Short Nascent Strand Replicate 2


title: RNAseq_Dpf2f/f_M0_rep4

description: RNAseq

value: post natal day 28


title: RNAseq_SKNO1_DOX_Rep4

description: RNAseq

value: SKNO1 acute myeloid leukemia

value: 7 days with 1ug/ml Doxycycline


title: RNAseq_Dpf2f/f_M0_rep5

description: RNAseq


title: WT_ZT 0-1

description: expressionWT.tsv

value: Gastrocnemius muscle

value: WT


title: HCT116 cells, Control_3

value: Control


title: AM260_WT

description:
Nascent Strands (ssDNA converted to dsDNA)
λ-exonuclease
Short Nascent Strand Replicate 1


title: 234_Control

description: Total RNA-Seq control treatment Replicate 2

data_processing:
Sequenced reads were trimmed for adaptor sequence.
Data were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ASOknockdown.rnaseq.counts.txt: Tab-delimited text matrix including raw counts values of each gene in each sample.

extract_protocol:
Total RNA was extracted using Maxwell Simply RNA kit (Promega) following manufacturer instructions.
Tru-Seq Total RNA (Illumina).

treatment_protocol: 48 hours transfection of control or anti-GAA antisense oligonucleotides.

value: Transfected control ASOs


title: RNAseq_Dpf2f/f_M0_rep3

description: RNAseq

value: vehicle (24 hours with PBS)


title: HCT116 cells, Control_2


title: Smarce1-AID_dmso_120min_aid06_rep1

description:
nascent RNA
Smarce1-AID_dmso_120_aid06_2425077

value: mouse embryonic stem cells

value: cells were released from mitosis for 120 min


title: 234_Antisense

description: Total RNA-Seq anti-GAA treatment Replicate 2

value: Transfected anti-GAA ASOs


title: RNAseq_Dpf2f/f_M0_rep2

description: RNAseq

value: bone marrow


title: HCT116 cells, Control_1

value: Colorectal cancer cell line


title: RNAseq_Dpf2f/f_M0_rep1

description: RNAseq


title: arg1_def_cd3_46_1

type: RNA

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were analyzed in R (v4.2.2) using a standard limma (v3.54.2) pipeline. Probes were first filtered using the detectionPValues() and removed if they were not expressed in at least 2 samples; data were normalized using neqc(); differential gene expression testing was performed using lmFit() and eBayes(); pathway analysis was performed with GSEA (v4.2.3). Scripts for the analysis can be found at https://github.com/jackbibby1/E-West-2023

label: biotin

molecule: polyA RNA

source_name: cd4 t cells

label_protocol: cDNA was labelled usin NuGen Encore Biotin IL kits

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using NuGen Ovation Pico WTA System V2

tag: individual

value: patient2 with Arginase 1 deficiency

tag: disease state

value: cd4 t cells


title: HCT116 cells, Glucose, Serum Starvation _1

tag: cell line

value: Glucose, Serum Starvation


title: WT-3

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were aligned to the human genome (hg38) using default parameters of HISAT2.
Alignments were filtered using SAMtoolsv1.19 to remove duplicate reads.
Peak-calling normalized to respective inputs was performed using MACSv2.1 with default settings; the window size was set as 300 bp.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file

source_name: 293T cells

extract_protocol:
Cell pellets biological triplicates/group) were crosslinked with 1% formaldehyde and quenched with 125 mM glycine. Pelleted cells were washed thoroughly with 1XPBS containing protease inhibitors and subjected to lysis and sonication, as previously described (Lee et al. 2006). Briefly, pellets were re-suspended and rotated for 15 minutes in 1 mL LB1 buffer [50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X 100 plus protease inhibitors] at 4°C. Following pelleting, cells were then re-suspended in 1 mL LB2 buffer [10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, plus protease inhibitors] and rotated for 10 minutes at 4°C. Pelleted cells/nuclei were then re-suspended in 1 mL LB3 buffer [10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus protease inhibitors] and sonicated using a Covaris S220 (Covaris Inc., Worburn, MA, USA) for 50 minutes at 4°C, resulting in approximately 150-300 bp DNA fragments. Following sonication, 1/10 volume of 10% Triton-X 100 was added and samples were spun at 18,000 x g for 10 minutes at 4°C to crack nuclei. Supernatants were then collected and incubated with a rabbit anti-H3K9me3 ChIP-grade antibody (Abcam, ab8898, Lot GR3217595-2, 6 μg/sample) bound sheep anti-rabbit IgG M-280 Dynabeads (Invitrogen, 11204D) on a rotator at 4°C overnight. The following day, immunoprecipitates were washed 8X with 1 mL RIPA buffer [50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate, plus protease inhibitors], rinsed 1X with 1 mL TE + 50 mM NaCl buffer and then eluted at 65°C for 30 minutes (shaking at 1000 RPM) in 210 μl elution buffer [50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 1% SDS]. After centrifugation, samples, and respective inputs, were reversed crosslinked in elution buffer 65°C overnight. Next, RNA and protein were digested with RNAse (one hour at 37°C; Roche, 10109134001) and proteinase K (two hours at 55°C; Roche, 3115887001), respectively, prior to DNA fragment purification using a Qiagen PCR purification kit (Qiagen, 28106).
ChIP-seq libraries were prepared according to Illumina protocols and sequenced on an Illumina HiSeq 4000 Sequencer_High Output mode v4.

value: IP

tag: chip antibody


title: 232_Antisense

description: Total RNA-Seq anti-GAA treatment Replicate 1


title: ThPOK-/- modified GMP-gate scRNA-Seq

description: GMP mRNA

data_processing:
The 10x Genomics libraries were each sequenced to a depth of ~0.9 to 1-million reads (modGMP) or ~300 million reads for cKit. The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index quantified (UMI) gene counts obtained using the Cell Ranger workflow (v2.1.0), from the automated filtered cell barcode output. Using the default filtered cellular barcodes, the associated sparse-filtered matrix files were processed in AltAnalyze, ICGS2 and cellHarmony as previously described to obtain normalized gene counts (counts per ten thousands UMIs) and cell population identitites. SoupX was used to remove ambient RNAs with a 10% threshold to produce the resultant sparse matrix results.
The antibody derived tag (ADT)-linked library for each 10x Genomics capture was sequenced separately from the same 10x Genomics sample. To obtain ADT UMIs for each cellular barcode, each ADT barcode was supplied as input in the CITE-Seq-Counts python program with the ADT fastqs files.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq.SoupX.metadata.txt: Cell Clusters: cellHarmony assigned clusters for wild-type and mutant cells with UMAP coordinates
Supplementary_files_format_and_content: Tags-mouseADT.csv: ADT: Antibody Derived Tag names and barcodes
Supplementary_files_format_and_content: cKit.cell-types.UMAP.coordinates.txt: Cell Clusters: cellHarmony assigned clusters for cKit cells with UMAP coordinates
Supplementary_files_format_and_content: cKit-reference-centroids.txt: cellHarmony reference centroids for cell-type classification

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with TotalSeq antibodies and fluorchome-conjugated antibodies for FACS-sorting, then 15,000 cells per sample were loaded in each lane of a Chromium Controller Instrument (10x Genomics).
The 10x Genomics single cell 3’ v3 assay protocol was followed as described until the cDNA amplification step. The cDNA amplification mix was modified to include 1 mL of a 2 mM dilution of ADT PCR additive primer (5’-CCTTGGCACCCGAGAATT*C*C-3’ where * indicates a phosphorotioate bond) and 1 mL of a 2 mM dilution of HTO PCR additive primer (5’-GTGACTGGAGTTCAGACGTGTGC*T*C-3’ where * indicates a phosphorotioate bond) when applicable, replacing 1-2 mL of water. An 0.6X SPRI selection was performed, and the resulting supernatant was set aside (contains ADTs and HTOs) while the beads (mRNA-derived cDNA) were processed according to the standard 10x Genomics single cell 3’ v2 assay protocol. The ADTs and HTOs were further processed according to the CITE-Seq protocol (New York Genome Center, https://cite-seq.com/protocol/). ADT and mRNA libraries were sequenced separately.
scRNA-Seq with Illumina NovaSeq and ADT with Illumina HiSeq 4000

tag: cell type

value: Bone marrow derived Modified GMP

tag: genotype

value: ThPOK-/-

tag: cdna synthesis

value: ThPOK-/- ModGMP scRNA-Seq


title: WT_3__input

value: Input

value: none (input)


title: Wild-Type GFP modified GMP-gate scRNA-Seq

description: GMP mRNA

value: Wild-type

value: WT GFP ModGMP scRNA-Seq


title: 243_Input

description: Input of RIP Replicate 2

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic (Bolget et al., 2014).
Data were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Flag_Input.rnaseq.counts.txt: Tab-delimited text matrix including raw counts values of each gene in each sample,

extract_protocol:
Total Immunoprecipitated RNA was extracted using Maxwell Simply RNA kit (Promega) following manufacturer instructions.
Tru-Seq Total RNA (Illumina)

treatment_protocol: 48 hours transfection of pcDNA3.1-ORC1-3xFLAG.

tag: treatment

value: Transfected pcDNA3- ORC13xFLAG

tag: antibody


title: WT-2

value: WT


title: arg1_def_cd3_46

value: patient1 with Arginase 1 deficiency


title: arg1_def_cd3


title: 242_Input

description: Input of RIP Replicate 1


title: 243_Flag

description: ORC1-FLAG IP of RIP Replicate 2

value: FLAG antibody (M2, F1804, Sigma)


title: Wild-Type modified GMP-gate scRNA-Seq

description: GMP mRNA

tag: strain

value: WT ModGMP scRNA-Seq


title: WT-1


title: 242_Flag

description: ORC1-FLAG IP of RIP Replicate 1


title: OGD_PARP14_2

city: Nanjing

first: Ying

last: Tang

address: Dingjiaqiao 87

institute: southeast university

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: primary mouse microglia

growth_protocol: primary mouse microglia were obtained from brain of postnatal C57BL/6J mice (postnatal 1-2 d, purchased from Model Animal Research Center of Nanjing University, Nanjing, China). Cells were plated in poly-D-lysine-precoated cell culture flasks (25 cm2) containing Dulbecco’s modified Eagle’s medium (DMEM) supplemented with fetal bovine serum (FBS, 10% v/v) and penicillin/streptomycin (1% v/v). All cells were kept in a humidified incubator (5% CO2, 37°C)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: Cells were transfected with the PARP14 CRISPR Activation Plasmid (ACT-PARP14) or ACT-Con for 24 h and then treated with OGD for 6 h.

tag: tissue

value: brain

value: post natal day 2


title: OGD_PARP14_1


title: AM_113_ORC1_S6

description: ORC1 IP of RIP Replicate 3

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic (Bolget et al., 2014).
Data were aligned to the genome assembly hg19 using STAR (Dobin et al., 2013) with default parameters.
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters.
RIP-seq RPKM normalised track were calculated as the ORC1 immunoprecipitated versus input control log2 fold ratio and binned per 10 nucleotides.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: resdata.native.orc1.txt: Tab-delimited text matrix including raw counts values of each gene in each sample.
Supplementary_files_format_and_content: ORC1_RIP_merged_log2_hg19.bw: bigWig file.

extract_protocol:
Total Immunoprecipitated RNA was extracted using Maxwell Simply RNA kit (Promega) following manufacturer instructions.
Tru-Seq Total RNA (Illumina).

value: Untreated

value: ORC1 antibody (Bruce Stillman)


title: 232_Control

description: Total RNA-Seq control treatment Replicate 1

value: Transfected control ASOs


title: WT_1__input


title: KO3

value: IP


title: Wild-Type cKit+ gate scRNA-Seq

description: cKit mRNA

value: Bone marrow derived cKit

value: WT cKit+ scRNA-Seq


title: arg1_def_cd3_1

value: patient2 with Arginase 1 deficiency

value: cd4 t cells


title: AM_113_INP_S3

description: Input of RIP Replicate 3


title: arg1_def_none


title: healthy_cd3_1

value: control patient2

value: healthy


title: arg1_def_none_1


title: OGD_Con_2


title: KO3__input

value: Input

value: none (input)


title: AM_103_ORC1_S5

description: ORC1 IP of RIP Replicate 2


title: healthy_cd3_46

value: control patient1


title: healthy_none_1


title: del_PNPase_biol_rep_2

city: Oeiras

first: José

last: Andrade

address: Av. República

country: Portugal

institute: ITQB Nova/ Universidade Nova de Lisboa

data_processing:
RNA-Seq data quality was confirmed using fastQC program
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped against Listeria monocytogenes genome (NC_003210.1 downloaded from NCBI Genome Database) using Bowtie2 program.
The mapping files were sorted by genomic position using the Samtools and the quantification of the transcripts expression was done using FeatureCounts.
The differential expression analysis was done with the R package edgeR.
Assembly: NCBI_Assembly:GCF_000196035.1
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

organism: Listeria monocytogenes

source_name: Biofilms

growth_protocol: Bacterial biofilm cultures were grown for 48h at 37ºC in BHI medium in static conditions.

extract_protocol:
RNA was harvested using Phenol/Chloroform extraction. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared Kapa RNA Hyper Prep Library preparation kit with QIA FastSelect -5S/16S/23S rRNA depletion.

value: EGDe

value: Biofilms

value: PNPase deletion


title: WT_2__input

value: WT


title: PARP14_2

value: brain

value: post natal day 2


title: KO2


title: OGD_Con_1


title: del_PNPase_biol_rep_1


title: healthy_cd3_46_1


title: KO2__input


title: WT_biol_rep_2


title: PARP14_1


title: AM_102_ORC1_S4

description: ORC1 IP of RIP Replicate 1

value: Untreated

value: ORC1 antibody (Bruce Stillman)


title: Con_2


title: AM_102_INP_S1

description: Input of RIP Replicate 1


title: KO1

value: IP


title: WT_biol_rep_1


title: healthy_none


title: AM_103_INP_S2

description: Input of RIP Replicate 2


title: healthy_cd3


title: Con_1


title: KO1__input


title: P2-Pre-dec-H3K27me4

status: Public on Jun 04 2023

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome hg38.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: Primary human endometrial stromal cells

growth_protocol: Primary human endometrial stromal cells (HESCs) from three different donors were cultured in DMEM/F12 supplemented with 10% FBS and 1XP/S

extract_protocol: 1M cells were fixed with 1% PFA for 15min, neutralized by 2.5M glycine, washed with PBS and sent to Active motif for ChIP-Seq

treatment_protocol: no treatment

value: Primary human endometrial stromal cells


title: P1-Pre-dec-H3K27AC


title: P1-Pre-dec-TRIM28


title: P2-Pre-dec-input


title: P2-Pre-dec-TRIM28


title: P2-Dec-TRIM29

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped to genome hg38 with bowtie2.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The uniquely mapped reads in each sample were dwon to 10M.
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.
Library strategy: Cut&Run

extract_protocol:
0.5M cells were scraped from the plate for the cut and run analysis using Epicypher CUTANA kit.
The library was amplified by Accel-NGS® 2S DNA Library Kits (Swift bioscience)

tag: hormone treatment

value: EPC


title: P2-Dec-IgG


title: P1-Pre-dec-H3K27me3


title: P2-Dec-PGR


title: P1-Pre-dec-input


title: P1-Dec-IgG


title: P2-siTRIM28-Pre-dec-ATAC

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome hg38.
After removing the mitochondria and duplicated reads, only 9bp at the terminal of the fragment was saved for following analysis.
All the samples were randomly downsized to the same sequencing depth.
The peak was called by MACS with FDR cutoff at 0.0001
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

extract_protocol:
25K single cell suspension from each sample were lysis on ice and incubated with Transposase for 30min at 37°C
RNA libraries were prepared by Nextera DNA Flex kit (Illumina)

treatment_protocol: The HESCs were transfected with siNT (Non-targeting siRNA) and siTRIM28 for 48h. The the siRNA transfected HESCs were treated with vehicle or EPC (the mixture of 17beta-estradiol, medroxyprogesterone acetate, and cAMP) for 72h

tag: sirna treatment

value: vehicle


title: P1-Dec-TRIM28


title: P2-siNT-Dec-ATAC

value: siNT


title: P1-Dec-PGR


title: P2-siNT-Pre-dec-ATAC


title: P2-siTRIM28-Dec-ATAC


title: cfdna_sample_id_63

city: Ithaca

first: Conor

middle: James

last: Loy

state: NY

address: 237 Tower Road

department: BME

institute: Cornell Univeristy

data_processing:
DNA sequencing data was processed using a custom bioinformatics pipeline utilizing the Snakemake workflow management system (v7.7.0). Samples were quality filtered and trimmed using BBDUK (v38.46), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) and deduplicated using Bismark (v0.22.1) with default parameters, and quality filtered using samtools (v1.14).
For cfDNA methylation analysis, a custom bioinformatic pipeline utilizing the Snakemake workflow management system (v7.7.0) was used to process publicly available methylation references, convert to a standard data format, and normalize across samples. Metline (v0.2-7) was used to discover differentially methylated regions and a quadratic programming algorithm estimated relative contributions of the tissues represented in the methylation references. Tissue specific cfDNA concentration was calculated for each sample by multiplying the estimated fractional contribution from each tissue by the cfDNA concentration, calculated using the formula shown above. Similarly, mitochondrial cfDNA concentration was calculated for each sample by multiplying the fraction of mitochondrial aligned reads by the cfDNA concentration.
Assembly: gencode v38 primary assembly
Supplementary files format and content: tab deliminated text file contains methylation fraction of genomic loci

source_name: MIS-C acute

extract_protocol:
DNA extraction was performed according to the manufactors instructions using the Qiagen Circulating Nucleic Acid Kit (55114, Qiagen) and eluted to 45 µl.
Bisulfite treatment was peformed and sequencing libraries were constructed from 20 µl of extracted DNA as previously described (Burnham et al., 2016; Gansauge and Meyer 2013)

value: plasma

tag: diagnosis

value: MIS-C

tag: time

value: acute

value: Bisulfite


title: cfdna_sample_id_67


title: cfdna_sample_id_65


title: cfdna_sample_id_64

source_name: COVID-19 acute


title: cfdna_sample_id_66


title: cfdna_sample_id_60


title: cfdna_sample_id_62


title: cfdna_sample_id_61

source_name: COVID-19 Not-hospitalized

value: Not-hospitalized


title: cfdna_sample_id_58


title: cfdna_sample_id_57


title: cfdna_sample_id_55


title: cfdna_sample_id_56


title: cfdna_sample_id_54


title: cfdna_sample_id_53


title: cfdna_sample_id_51


title: cfdna_sample_id_52


title: cfdna_sample_id_49


title: cfdna_sample_id_50


title: NS/PC-Ci5_v1

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

description: SAMPLE 1

data_processing: The data were loaded into R for background correction, quantile normalization and log (base 2)   conversion with the limma package.

source_name: hiPSC-derived NS/PC

label_protocol: Total RNA was reverse-transcribed, labeled with biotin using the Target Amp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

extract_protocol: Total RNA was extracted with RNAeasy Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: hiPSC derived lt-NES cells

tag: batch


title: cfdna_sample_id_48


title: cfdna_sample_id_45


title: cfdna_sample_id_47


title: cfdna_sample_id_46


title: cfdna_sample_id_44


title: cfdna_sample_id_59


title: cfdna_sample_id_43


title: NS/PC-Ci5_v2

description: SAMPLE 3


title: NS/PC-Ci4_v2

description: SAMPLE 4


title: cfdna_sample_id_41


title: NS/PC-Ci4_v1

description: SAMPLE 2


title: cfdna_sample_id_40


title: Ci4_84

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: Ci4_91


title: Ci4_136


title: Ci4_60


title: Ci4_102


title: Ci4_74


title: Ci4_70


title: Ci4_88


title: cfdna_sample_id_39


title: Ci4_122


title: Ci4_123


title: Ci4_54


title: B2 NCC d10 2

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
Raw reads were mapped to reference genome hg19 using Sailfish (v0.7.6) with default settings.
The count matrix data from sailfish was loaded into R software (v4.1.1) and downstream analysis was performed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: hiPSC-derived NCCs

extract_protocol:
Total RNA was extracted with RNAeasy Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Samples for RNA-seq were prepared using the TruSeq RNA Sample Prep Kit (Illumina) according to the protocol provided by the manufacture.

value: NCCs


title: B2 NCC d10 1


title: cfdna_sample_id_42


title: cfdna_sample_id_36


title: cfdna_sample_id_35


title: Ci-4 107

source_name: hiPSC-derived NS/PCs

value: lt-NES cells


title: Ci4_83


title: Ci4_35


title: Ci4_2


title: Ci4_23


title: Ci4 38


title: Ci4_14


title: Ci-4 123


title: Ci4_57


title: cfdna_sample_id_34


title: Ci4_1


title: Ci4_3


title: cfdna_sample_id_33


title: MSC 2

source_name: human mesenchymal stem cells

value: MSC


title: cfdna_sample_id_32


title: Ci4_121


title: Ci4_116


title: cfdna_sample_id_38


title: cfdna_sample_id_31


title: Ci4 23


title: MSC 1


title: WBM 2

source_name: human whole bone marrow

value: WBM


title: cfdna_sample_id_30


title: Ci4_135


title: cfdna_sample_id_29


title: Ci4_51


title: WBM 1


title: Ci4_47


title: Ci4_66


title: Ci4_96


title: Ci4_79


title: cfdna_sample_id_28


title: Ci4_F2_H11

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using sailfish version 0.7.6 with default setting.
Low quality samples were removed from data set based on mapping rate and detected gene number.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: hiPSC-lt-NES cells

extract_protocol:
Cells were sorted into 96 well plate with a flow cytometer SH800 (SONY) and dissolved with single cell lysis buffer (0.5% NP40).
Whole-transcript amplification was performed as previously described (Sasagawa et al. 2013; Sasagawa et al. 2017). Amplified cDNA from single cell was processed for library preparation using Nextera XT Library Prep Kit (Illumina).


title: Ci4_94


title: Ci4_F2_H10


title: P2-Pre-dec-H3K27AC


title: Ci4_31


title: Ci4_86


title: Ci4_115


title: Ci4_89


title: Ci4_85


title: Ci4_75


title: cfdna_sample_id_27


title: cfdna_sample_id_26


title: Ci4_F2_H09


title: cfdna_sample_id_25


title: Ci4_F2_H08


title: Ci4_F2_H06


title: Ci4_F2_H05


title: Ci4_8


title: Ci4_61


title: Ci4_130


title: Ci4_6


title: Ci4_F2_H07


title: cfdna_sample_id_23


title: cfdna_sample_id_22


title: cfdna_sample_id_24


title: Ci4_F2_H04


title: cfdna_sample_id_21


title: Ci4_F2_H03


title: Ci4_10


title: Ci4_118


title: Ci4_69


title: cfdna_sample_id_20


title: Ci4_55


title: Ci4_73


title: Ci4_76


title: Ci4_104


title: Ci4_52


title: Ci4_22


title: Ci4_9


title: Ci4_129


title: Ci4_131


title: Ci4_F2_H02


title: cfdna_sample_id_19


title: cfdna_sample_id_18


title: Ci4_F2_G12


title: Ci4_F2_G11


title: Ci4_F2_H01


title: Ci4_95


title: cfdna_sample_id_17


title: Ci4_107


title: cfdna_sample_id_16


title: Ci4_F2_G10


title: Ci4_29


title: Ci4_15


title: cfdna_sample_id_15


title: Ci4_38


title: Ci4_80


title: cfdna_sample_id_37


title: Ci4_108


title: Ci4_124


title: Ci4_127


title: Ci4_97


title: Ci4_98


title: Ci4_72


title: Ci4_65


title: Ci4_F2_G09


title: Ci4_112


title: cfdna_sample_id_14


title: Ci4_F2_G08


title: cfdna_sample_id_12


title: Ci4_F2_G07


title: cfdna_sample_id_9


title: Ci4_F2_G06


title: cfdna_sample_id_8


title: Ci4_92


title: cfdna_sample_id_11


title: Ci4_90


title: Ci4_39


title: Ci4_F2_G05


title: Ci4_105


title: cfdna_sample_id_10


title: cfdna_sample_id_13


title: Ci4_101


title: Ci4_133


title: Ci4_41


title: Ci4_F2_F12


title: Ci4_43


title: Ci4_32


title: Ci4_119


title: Ci4_F2_G03


title: Ci4_26


title: Ci4_134


title: cfdna_sample_id_4


title: cfdna_sample_id_7


title: Ci4_F2_G04


title: cfdna_sample_id_5


title: Ci4_F2_F09


title: Ci4_F2_G02


title: Ci4_36


title: cfdna_sample_id_6


title: Ci4_F2_F08


title: Ci4_64


title: Ci4_21


title: cfdna_sample_id_3


title: Ci4_F2_F11


title: Ci4_77


title: Ci4_16


title: Ci4_7


title: Ci4_F2_F10


title: Ci4_28


title: Ci4_45


title: Ci4_F2_F07


title: Ci4_F2_F06


title: cfdna_sample_id_1


title: prevail_cu_cfrna_236

data_processing:
RNA sequencing data was processed using a custom bioinformatics pipeline utilizing the Snakemake workflow management system (v7.7.0) for the cfRNA samples and a bash script for the wbRNA samples. Samples were quality filtered and trimmed using BBDUK (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR (v2.7.0f) default parameters, and features quantified using featureCount (v2.0.0). cfRNA samples were also deduplicated using Picard MarkDuplicates prior to feature quantification (v2.19.2)
Assembly: gencode v38 primary assembly
Supplementary files format and content: tab deliminated text file contains raw gene count information

extract_protocol:
RNA was extracted using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (51000, Norgen). Extracted RNA was DNase treated with 14 µl of 10 µl DNase Turbo Buffer (AM2238, Invitrogen), 3 µl DNase Turbo (AM2238, Invitrogen), 1µl Baseline Zero DNase (DB0715K, Lucigen-Epicenter) for 30 min at 37°C and then concentrated into 12 µl using the Zymo RNA Clean and Concentrate Kit (R1015, Zymo).
Cell-free RNA: Sequencing libraries were constructed from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (634418, Takara).

tag: timepoint


title: prevail_cu_cfrna_269

source_name: MIS-C post-acute

value: post-acute


title: Ci4_F2_F05


title: Ci4_F2_F04


title: prevail_cu_cfrna_235


title: PV338

extract_protocol:
RNA was extracted from whole blood samples (400 µl) using the Quick-RNA Whole Blood kit (R1201, Zymo Research) following manufacturer’s instructions. Ribosomal depletion was not performed. RNA was eluted in 15 µl of RNase-free water and stored at -80 oC until use
Extracted RNA (7 µl or 10-200 ng) was processed using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310, NEB) and the NEBNext Ultra II Directional RNA Library Prep Kit (E7760 & E7765, NEB) following manufacturer’s specifications.

value: blood


title: PV319

source_name: COVID-19 1m


title: PV316


title: PV340

source_name: COVID-19 post-acute


title: PDX005

city: ChangSha

first: Yongwei

last: Zhu

state: Hunan

address: No.87,  Xiangya Street

institute: CSU Xiangya hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR (v2.7.5)with default parameters. BAM files of aligned reads were quantified by featureCounts (v2.0.1).
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Trapnell C et al., Nat Biotechnol, 2010.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized read counts for each Sample

source_name: glioma PDX

extract_protocol:
total RNA extraction was performed using RNeasy Plus Mini Kit (QIAGEN) according to manufacturer protocol. RNA integrity number (RIN) was determined using Agilent Bioanalyzer. All samples had RIN > 9.8.
Library preparation was performed using NEBNext Ultra II Directional polyA mRNA Library Prep Kit.
Sequencing was performed on Illumina NovaSeq 6000 with 60 million paired end reads per sample at 100 bp read length.

value: glioma PDX


title: cfdna_sample_id_2


title: Ci4_F2_F03


title: PV336


title: prevail_cu_cfrna_234

source_name: MIS-C 1m


title: PV295


title: PV296


title: PDX006


title: PV297


title: prevail_cu_cfrna_270


title: Ci4_F2_F02


title: Ci4_F2_F01


title: PV293


title: prevail_cu_cfrna_271


title: Ci4_20


title: Ci4_F2_E12


title: PV286


title: Ci4_27


title: PV287


title: Ci4_11


title: Ci4_30


title: prevail_cu_cfrna_278


title: PV298


title: Ci4_12


title: Ci4_F2_E11


title: Ci4_50


title: prevail_cu_cfrna_272


title: PV332


title: PV334


title: Ci4_F2_E10


title: PV289


title: PV335


title: PV331


title: prevail_cu_cfrna_197


title: PV285


title: PV291


title: Ci4_F2_E09


title: Ci4_F2_E08


title: prevail_cu_cfrna_196


title: Ci4_F2_E07


title: PV290


title: PV288


title: prevail_cu_cfrna_195


title: PV292


title: prevail_cu_cfrna_193


title: Ci4_F2_E06


title: PV276


title: Ci4_F2_E05


title: prevail_cu_cfrna_192


title: Ci4_F2_E04


title: PV233


title: prevail_cu_cfrna_230


title: prevail_cu_cfrna_191


title: Ci4_F2_E02


title: Ci4_F2_E03


title: PV303

source_name: MIS-C 3m+


title: PV230


title: Ci4_F2_E01


title: PV277


title: prevail_cu_cfrna_185


title: prevail_cu_cfrna_228


title: PV227


title: prevail_cu_cfrna_182


title: PV231


title: Ci4_F2_D11


title: PV226


title: PV229


title: prevail_cu_cfrna_194


title: Ci4_F2_D12


title: PV225


title: PV275


title: Ci4_F2_D10


title: PV273


title: PV304


title: PV301


title: PV223


title: PV224


title: PV41


title: PV232


title: prevail_cu_cfrna_177


title: Ci4_F2_D09


title: PV222


title: PV218


title: PV248


title: prevail_cu_cfrna_183


title: Ci4_F2_D06


title: Ci4_F2_D08


title: prevail_cu_cfrna_175


title: PV220


title: prevail_cu_cfrna_181


title: PV217


title: PV243


title: PV272


title: prevail_cu_cfrna_179


title: PV239


title: prevail_cu_cfrna_174


title: Ci4_F2_D04


title: PV271


title: Ci4_F2_D05


title: PV247


title: prevail_cu_cfrna_152


title: PV270


title: prevail_cu_cfrna_171


title: Ci4_F2_D03


title: PV216


title: PV219


title: PV269


title: PV268


title: prevail_cu_cfrna_165


title: Ci4_F2_D02


title: Ci4_F2_D01


title: prevail_cu_cfrna_164


title: PV266


title: PV265


title: PV215


title: prevail_cu_cfrna_148


title: PV214


title: Ci4_F2_C10


title: PV264


title: PV263


title: prevail_cu_cfrna_151


title: Ci4_F2_C11


title: PV262


title: prevail_cu_cfrna_149


title: PV267


title: Ci4_F2_C09


title: Ci4_F2_C08


title: PV213


title: prevail_cu_cfrna_162


title: PV261


title: prevail_cu_cfrna_170


title: PV235


title: PV260


title: Ci4_F2_C07


title: PV212


title: prevail_cu_cfrna_169


title: PV259


title: PV246


title: prevail_cu_cfrna_150


title: Ci4_F2_C05


title: Ci4_F2_C06


title: PV250


title: PV369


title: prevail_cu_cfrna_167


title: prevail_cu_cfrna_159


title: PV368


title: PV249


title: prevail_cu_cfrna_166


title: PV363


title: PV244


title: Ci4_F2_C02


title: Ci4_F2_C01


title: PV204


title: prevail_cu_cfrna_112


title: prevail_cu_cfrna_110


title: Ci4_F2_B11


title: PV144


title: PV171


title: PV139


title: Ci4_F2_B10


title: PV168


title: PV130


title: PV199


title: PV198


title: Ci4_F2_C04


title: prevail_cu_cfrna_118


title: PV306


title: prevail_cu_cfrna_142


title: Ci4_F2_B08


title: PV255


title: prevail_cu_cfrna_131


title: Ci4_F2_C03


title: PV133

source_name: COVID-19 3m+


title: PV187


title: PV195


title: PV160


title: PV194


title: Ci4_F2_B07


title: PV193


title: prevail_cu_cfrna_286


title: prevail_cu_cfrna_109


title: Ci4_F2_B04


title: prevail_cu_cfrna_140


title: PV355


title: Ci4_F2_B03


title: PV158


title: PV135


title: PV159


title: prevail_cu_cfrna_42


title: PV162


title: PV132


title: prevail_cu_cfrna_121


title: prevail_cu_cfrna_135


title: Ci4_F2_A11


title: Ci4_F2_B01


title: PV60


title: prevail_cu_cfrna_128


title: Ci4_F2_B09


title: PV157


title: PV189


title: Ci4_F2_B06


title: PV131


title: PV58


title: prevail_cu_cfrna_139


title: PV186


title: Ci4_F2_A09


title: PV177


title: prevail_cu_cfrna_132


title: prevail_cu_cfrna_147


title: prevail_cu_cfrna_299


title: Ci4_F2_A08


title: PV185


title: PV163


title: Ci4_F2_A07


title: prevail_cu_cfrna_138


title: Ci4_F2_C12


title: prevail_cu_cfrna_296


title: Ci4_F2_B02


title: PV33


title: PV367


title: Ci4_F2_A06


title: prevail_cu_cfrna_130


title: prevail_cu_cfrna_24


title: Ci4_F2_A05


title: PV166


title: PV180


title: PV56


title: Ci4_F2_A04


title: prevail_cu_cfrna_114


title: PV55


title: PV183


title: Ci4_F2_A03


title: Ci4_F2_A10


title: PV178


title: PV164


title: PV170


title: prevail_cu_cfrna_141


title: Ci4_F2_A01


title: PV54


title: Ci4_F2_A02


title: PV156


title: PV175


title: prevail_cu_cfrna_292


title: Ci4_F1_H11


title: Ci4_F1_H10


title: PV53


title: PV174


title: prevail_cu_cfrna_129


title: prevail_cu_cfrna_126


title: prevail_cu_cfrna_125


title: Ci4_F1_H09


title: PV51


title: Ci4_F1_H08


title: Ci4_F1_H07


title: PV48


title: PV362


title: PV240


title: PV49


title: prevail_cu_cfrna_285


title: Ci4_F1_H05


title: PV184


title: PV356


title: prevail_cu_cfrna_136


title: prevail_cu_cfrna_295


title: PV30


title: PV234


title: PV52


title: PV32


title: Ci4_F1_H04


title: PV27


title: prevail_cu_cfrna_120


title: PV28


title: PV31


title: prevail_cu_cfrna_12


title: Ci4_F1_H02


title: Ci4_F1_H01


title: Ci4_F1_G09


title: prevail_cu_cfrna_284


title: Ci4_F1_G12


title: PV123


title: PV126


title: PV128


title: PV26


title: PV122


title: PV29


title: PV119


title: PV25


title: PV24


title: prevail_cu_cfrna_291


title: prevail_cu_cfrna_282


title: PV23


title: Ci4_F1_G07


title: PV22


title: Ci4_F1_G06


title: prevail_cu_cfrna_146


title: PV21


title: PV127


title: prevail_cu_cfrna_124


title: PV125


title: Ci4_F1_G05


title: prevail_cu_cfrna_137


title: PV115


title: PV116


title: prevail_cu_cfrna_287


title: Ci4_F1_G04


title: PV112


title: PV114


title: PV113


title: Ci4_F1_G03


title: prevail_cu_cfrna_127


title: PV111


title: Ci4_F1_G02


title: Ci4_F1_G08


title: prevail_cu_cfrna_294


title: PV110


title: PV109


title: PV108


title: prevail_cu_cfrna_119


title: Ci4_F1_G01


title: prevail_cu_cfrna_108


title: Ci4_F1_F12


title: prevail_cu_cfrna_222


title: PV105


title: PV107


title: Ci4_F1_F09


title: prevail_cu_cfrna_290


title: PV106


title: PV20


title: prevail_cu_cfrna_201


title: PV103


title: PV102


title: PV104


title: Ci4_F1_F06


title: PV8


title: PV9


title: PV100


title: prevail_cu_cfrna_310


title: Ci4_F1_F05


title: Ci4_F1_F04


title: prevail_cu_cfrna_309


title: PV101


title: PV98


title: PV96


title: Ci4_F1_F03


title: prevail_cu_cfrna_280


title: PV97


title: Ci4_F1_F02


title: PV95


title: Ci4_F1_F08


title: Ci4_F1_F01


title: prevail_cu_cfrna_303


title: prevail_cu_cfrna_95


title: PV90


title: PV91


title: PV94


title: Ci4_F1_E12


title: Ci4_F1_E11


title: PV92


title: eWAT, AKO-3 2147_1

city: Ann Arbor

first: Liangyou

last: Rui

state: Michigan

address: 2800 plymouth road

department: Molecular and Integrative Physiology

institute: University of Michigan

data_processing:
Firstly, we removed the reads mapped to rRNAs and got raw data, then we filtered the low-quality reads (More than 20% of the qualities of the base are lower than 10), reads with adaptors, and reads with unknown bases (N bases more than 5%) to get the clean reads. And then, we assembled those clean reads into Unigenes, followed by Unigene functional annotation, and calculated the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
We use internal software SOAPnuke to filter reads, as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases (N) are more than 10%; 3) Remove low-quality reads (we define the low-quality read as the percentage of the base which quality is lesser than15 is greater than 50% in a read). After filtering, the remaining reads are called"CleanReads" and stored in FASTQ format.    SOAPnuke: version：v1.5.2 parameters: -l 15 -q 0.5 -n 0.1 website: https://github.com/BGI-flexlab/SOAPnuke
Genome Mapping We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT2, which is much faster, sensitive, and high-accuracy analysis software.    HISAT2: Version: v2.0.4 Parameters: -p 8 --phred33 --sensitive -I 1 -X1000 Website: http://www.ccb.jhu.edu/software/hisat
Gene Expression Analysis  We mapped clean reads to reference using Bowtie2, and then calculate geneexpression level with RSEM. RSEM is a software package for estimating gene and isoform expression levelsfrom RNA-Seq data.calculate pearson correlation between all samples using cor, perform hierarchicalclustering between all samples using hclust, perform PCA analysis with all samplesusing princomp, and draw the diagrams with ggplot2 with functions of R.Software information:Bowtie2 :Version: v2.2.5Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml   RSEM :Version: v1.2.12Parameters: defaultWebsite: http://deweylab.biostat.wisc.edu/ RSEM
DEG Detection We detect DEGs with DEseq2 as requested.DEseq2 is based on the negative binomial distribution
Assembly: M. musculus, UCSC mm10
Supplementary files format and content: Fpkm of each genotype

source_name: eWAT

extract_protocol:
Mettl14f/f and Mettl14Δfat male mice (8 weeks) were fed a HFD for 16 weeks and eWAT was dissected. Total RNA was extracted by RNeasy Mini Kit (Qiagen Cat#74104) and used for RNA-seq
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription:  Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random  primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair  and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA  fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification  were performed to enrich the purified cDNA template using PCR primer;5)Denature and  cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and  DNA ligase;6) Sequencing on DNBseq platform.

value: eWAT

tag: Sex

value: male

tag: diet

value: HFD

value: Mettl14 AKO

value: overnight fast


title: prevail_cu_cfrna_318

value: plasma

value: MIS-C


title: PV99


title: PV88

value: acute


title: Ci4_F1_E10

tag: cell line


title: prevail_cu_cfrna_317


title: PV89

source_name: MIS-C acute


title: eWAT, AKO-2 2146_1


title: Ci4_F1_E09


title: prevail_cu_cfrna_307


title: PV87


title: prevail_cu_cfrna_321


title: Ci4_F1_E08


title: eWAT, ff-2 2142_1

value: WT


title: PV86

source_name: COVID-19 acute


title: prevail_cu_cfrna_226


title: PV370


title: Ci4_F1_E07

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: eWAT, ff-1 1704_1


title: Ci4_F1_E06


title: prevail_cu_cfrna_258


title: prevail_cu_cfrna_83


title: prevail_cu_cfrna_313


title: prevail_cu_cfrna_260


title: PV85


title: Ci4_F1_E05


title: FR_11_WEHI

city: Nedlands

first: Rachael

middle: M

last: Zemek

address: 15 hospital Ave

department: Cancer Centre

country: Australia

institute: Telethon Kids Institute

data_processing:
read alignment with Kallisto
count quantification with tximport
Assembly: GRCm38.100
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: tumour

growth_protocol: Subcutaneous tumour growth

extract_protocol:
Frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy mini kit (Qiagen)
RNA libraries were prepared by AGRF for Illumina 150bp paired end sequencing

treatment_protocol: Samples surgically collected prior to treatment and stored in RNAlater. Poly(I:C) loaded hydrogel was applied to residual tumour and monitored for response

value: tumour

value: fibrosarcoma

value: untreated

tag: response

value: RS

value: BALB/c

value: F


title: eWAT, ff-3 2293_1


title: FR_12_WEHI

tag: cell type


title: Ci4_F1_E03


title: FR_09_WEHI

tag: genotype


title: PV84

value: blood

value: post-acute


title: prevail_cu_cfrna_82


title: Ci4_F1_E04


title: eWAT, AKO-1 1705_1

value: eWAT

value: male


title: FR_10_WEHI


title: PV81


title: FR_07_WEHI

value: NR


title: prevail_cu_cfrna_81


title: Ci4_F1_E02


title: prevail_cu_cfrna_305


title: Ci4_F1_E01


title: FR_06_WEHI


title: prevail_cu_cfrna_304


title: PV7


title: Ci4_F1_D11


title: FR_05_WEHI


title: prevail_cu_cfrna_76


title: PV42


title: PV366


title: prevail_cu_cfrna_263


title: PV365


title: FR_03_WEHI


title: Ci4_F1_D09


title: FR_02_WEHI


title: PV82


title: prevail_cu_cfrna_300


title: Ci4_F1_D10


title: PV77


title: PV80


title: prevail_cu_cfrna_308


title: FR_01_WEHI


title: Ci4_F1_D07


title: Ci4_F1_D08


title: PV78


title: prevail_cu_cfrna_301


title: prevail_cu_cfrna_319


title: PV364


title: Ci4_F1_D06


title: FR_14_CT26

data_processing:
read alignment with Kallisto
count quantification with tximport
Assembly: GRCm38.100
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Frozen tumour dissociation with Trizol followed by chloroform extraction and purification using RNeasy mini kit (Qiagen)
RNA libraries were prepared by AGRF for Illumina 150bp paired end sequencing
PolyA RNAseq, 20M reads

value: colorectal carcinoma


title: FR_15_CT26


title: Ci4_F1_D05


title: FR_12_CT26


title: prevail_cu_cfrna_298

value: plasma


title: PV74

value: MIS-C


title: Ci4_F1_D04


title: PV72

value: acute


title: prevail_cu_cfrna_293


title: FR_11_CT26

value: WT


title: Ci4_F1_D03

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: FR_10_CT26

value: tumour


title: PV70


title: prevail_cu_cfrna_289


title: prevail_cu_cfrna_315


title: prevail_cu_cfrna_320


title: FR_09_CT26


title: PV69


title: Ci4_F1_D01


title: prevail_cu_cfrna_252


title: Ci4_F1_D02


title: Ci4_F1_C11


title: FR_05_CT26


title: PV66


title: FR_04_CT26


title: Ci4_F1_C10


title: prevail_cu_cfrna_209


title: prevail_cu_cfrna_221


title: PV63


title: Ci4_F1_C08


title: FR_02_CT26


title: Ci4_F1_C09


title: FR_03_CT26


title: prevail_cu_cfrna_203


title: Ci4_F1_C06


title: PV65


title: D4_3_WEHI

source_name: fibrosarcoma tumor

growth_protocol: Subcutaneous tumor growth

extract_protocol:
Frozen tumor dissociation with Trizol followed by chloroform extraction and purification using RNeasy mini kit (Qiagen)
RNA libraries were prepared by AGRF for Illumina 100bp single end sequencing
PolyA RNAseq, 20M reads

treatment_protocol: Poly(I:C) dosed intratumorally 1ug in 25 uL daily for a total of  6 doses. Samples collected at specified timepoints and stored in RNAlater

value: fibrosarcoma tumor

value: fibrosarcoma

value: day 7


title: D4_2_WEHI

value: BALB/c


title: prevail_cu_cfrna_212


title: PV360


title: PV64


title: PV62


title: prevail_cu_cfrna_225


title: PV61


title: Ci4_F1_C04


title: D4_1_WEHI

value: F


title: D3_3_WEHI

value: day 5


title: PV358

value: blood


title: prevail_cu_cfrna_219


title: Ci4_F1_C05


title: prevail_cu_cfrna_220


title: PV359


title: Ci4_F1_C03


title: D3_1_WEHI


title: Ci4_F1_C01


title: PV357


title: PV1


title: prevail_cu_cfrna_216


title: D3_2_WEHI


title: D2_3_WEHI

value: day 3


title: D2_2_WEHI


title: PV353


title: prevail_cu_cfrna_217


title: D2_1_WEHI


title: prevail_cu_cfrna_205


title: Ci4_F1_B11


title: PV352


title: prevail_cu_cfrna_204


title: Ci4_F1_B10


title: Ci4_F1_C02


title: D1_3_WEHI

value: day 1


title: prevail_cu_cfrna_199


title: prevail_cu_cfrna_224


title: D1_2_WEHI


title: PV351


title: Ci4_F1_B09


title: PV18


title: D1_1_WEHI


title: Ci4_F1_B08


title: Ci4_F1_B12


title: Ci4_F1_B07


title: Ci4_F1_B06


title: prevail_cu_cfrna_215


title: prevail_cu_cfrna_223


title: T0_2_WEHI

value: untreated

value: day 0


title: T0_3_WEHI


title: PV354


title: Ci4_F1_B05


title: P3-siTRIM28-Dec

data_processing:
The raw reads were initially filtered by removing low quality reads (average quality scores < 20)
Reads were mapped to the human genome (hg19) using Tophat version 2.0.4
The bam files generated by the aligner were further processed, including (i) excluding reads aligned to chrM and chrUn, (ii) retaining uniquely mapped and properly paired reads only, (iii) removing duplicates via Picard MarkDuplicates,  and (iv) normalized with Picard DownsampleSam
Assembly: hg19
Supplementary files format and content: Read count was calculated for each gene in each sample by using HTSeq.

source_name: Primary human endometrial stromal cells

extract_protocol:
The total RNA was collected by QIagen Rneasy mini kit.
RNA libraries were prepared by Nextera DNA Flex kit (Illumina)

value: Primary human endometrial stromal cells

value: EPC


title: prevail_cu_cfrna_206

value: plasma

value: MIS-C

value: acute


title: prevail_cu_cfrna_211


title: P3-siTRIM28-Pre-dec

value: vehicle


title: P3-siNT-Dec

value: siNT


title: Ci4_F1_B04

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: T0_1_WEHI

value: fibrosarcoma tumor

value: fibrosarcoma

value: WT


title: D3.5dd scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: The filtered feature count matrix was generated from Cell Ranger.

source_name: uterus

growth_protocol: Pgrcre/+TRIM28f/f and TRIM28f/f female mice were mated with wildtype males, and dissected at Pregnancy day 3.5

extract_protocol:
Single cell suspension were collected by Trypsion digestion at 37 degress for 50min, then filtered through 70um and 40um cell strainer.
RNA libraries were prepared by Chromium Single Cell 3’ Library & Gel Bead Kit v3.1

treatment_protocol: No treatment

value: uterus

value: female

tag: pregnancy day

value: Pregnant day 3.5


title: Ci4_F1_B03


title: D3.5-TRIM28-ChIP-seq R2

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome mm10.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

growth_protocol: C57B6/J female mice were mated at 8 weeks old whose uterus were collected at Pregnancy day 3.5

extract_protocol: The uterus were frozen and sent to Active motif for ChIP-Seq analysis

tag: gender

value: TRIM28 antibody (ab10484, Abcam)


title: D3.5ff scRNA-seq


title: PV19

value: blood


title: P3-siNT-Pre-dec


title: prevail_cu_cfrna_202


title: Pgrcre/+-P4-4

data_processing:
Paired-end raw reads were filtered for quality score > 20.
Reads were mapped to the mouse genome (mm10) using Tophat version 2.0.4
Assembly: mm10
Supplementary files format and content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

growth_protocol: Pgrcre/+ female mice were ovariectomized at 6 weeks old

extract_protocol:
Total RNA was isolated by Trizol and purified using Qiagen Rneasy min kit
RNA libraries were prepared by Nextera DNA Flex kit (Illumina)

treatment_protocol: 2 weeks after ovariecotmy, Pgrcre/+ female mice were treated with either oil or 1mg Progesteroen (P4) for 6h

tag: treatment

value: 1mg Progesteron (P4) 6h

value: Pgrcre/+


title: Ci4_F1_B01


title: P2-siTRIM28-Dec

value: Primary human endometrial stromal cells

value: EPC


title: D3.5-PGR-ChIP-seq R2

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome mm10.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases
Assembly: mm10

tag: strain

tag: antibody

value: PGR antibody (Active Motif sc7208)


title: P2-siTRIM28-Pre-dec

tag: hormone treatment


title: D3.5-PGR-ChIP-seq

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20).
Mapped with genome mm10.
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases.
Assembly: mm10
Supplementary files format and content: bigWig file

growth_protocol: C57B6/J female mice were mated at 8 weeks old whose uterus were collected at Pregnancy day 3.5.

extract_protocol: The uterus were frozen and sent to Active Motif for ChIP-Seq analysis.

tag: tissue

tag: chip antibody

value: anti-PGR


title: Pgrcre/+-P4-3


title: Ci4_F1_B02


title: Ci4_F1_A11


title: D3.5dd-4-RNA-seq


title: D3.5dd-3-RNA-seq


title: Pgrcre/+-P4-1


title: Ci4_F1_A10


title: P2-siNT-Pre-dec

tag: sirna treatment

value: vehicle


title: D3.5dd-2-RNA-seq


title: Pgrcre/+-oil-3

value: Oil 6h


title: Ci4_F1_A08

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: Pgrcre/+-oil-4


title: P1-siTRIM28-Pre-dec


title: D3.5dd-1-RNA-seq


title: P1-siTRIM28-Dec


title: Ci4_F1_A07


title: Pgrcre/+-oil-2


title: Ci4_F1_A06


title: Pgrcre/+-oil-1


title: D3.5ff-4-RNA-seq


title: P1-siNT-Dec

value: siNT


title: Ci4_F1_A04


title: Monocytes, MCD-fed, melatonin gavaged, rep2

city: Beijing

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

institute: Beijing Friendship Hospital, Capital Medical University

description: 10x Genomics

data_processing:
We used Cell Ranger Single Cell Software Suite v.3.0.2 (http://support.10xgenomics.com/) developed by 10× Genomics to process the raw FASTQ files. We used the mm10 genome and transcriptome (refdata-cellranger-mm10-1.2.0.tar.gz) as the reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Eight-week-old weight-matched male wild-type (WT) C57BL/6 mice and Rag1-/- mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). These mice were fed either a normal control diet (NCD), a methionine/choline-deficient diet (MCD, 10401, Beijing HFK Bioscience, Beijing, China), or an MCD diet with melatonin (100g/kg per day) treatment by oral gavage for six weeks. The immune cells were harvested, and then the expression levels of various cell surface and intracellular markers were detected. All samples were examined through a FACS Aria II flow cytometer (BD Biosciences, CA, USA), and the data were analyzed using FlowJo software (Treestar, Ashland, OR, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Liver

value: 7AAD-CD45+Ly6G-CD11b int F4/80 hi monocytes

tag: age

value: 12-14 weeks old

value: methionine/choline-deficient diet (MCD) with melatonin


title: P2-siNT-Dec


title: D3.5ff-3-RNA-seq

value: uterus

value: female

value: Pregnant day 3.5


title: Ci4_F1_A05


title: Monocytes, MCD-fed, melatonin gavaged, rep1

description: 10x Genomics


title: Pgrcre/+-P4-2

value: 1mg Progesteron (P4) 6h


title: D3.5ff-2-RNA-seq


title: Ci4_F1_A09


title: Monocytes, MCD-fed, normal saline gavaged, rep2

description: 10x Genomics

value: methionine/choline-deficient diet (MCD)


title: Ci4_F1_A03


title: D3.5-TRIM28-input


title: P1-siNT-Pre-dec

value: Primary human endometrial stromal cells


title: P1-siNT-Pre-dec-ATAC

data_processing:
The raw reads were trimmed by trim_galore (v0.4.4) (quality score < 20),
mapped with genome hg38.
After removing the mitochondria and duplicated reads, only 9bp at the terminal of the fragment was saved for following analysis.
All the samples were randomly downsized to the same sequencing depth.
The peak was called by MACS with FDR cutoff at 0.0001
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

extract_protocol:
25K single cell suspension from each sample were lysis on ice and incubated with Transposase for 30min at 37°C
RNA libraries were prepared by Nextera DNA Flex kit (Illumina)


title: D3.5-TRIM28-ChIP-seq


title: TGS - MEL2

status: Public on Jun 03 2023

city: Chicago

first: Ruli

last: Gao

state: IL

address: Simpson Querrey, 7th Floor

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description:
scNanoRNAseq
NP9

data_processing:
For NGS, the reads are analyzed by cellranger-arc 4.0 to generate gene expression matrix.
For Nanopore, the reads are analyzed by scNanoGPS to generate gene expression, isoform, SNV matrices. The detailed process is described at: https://github.com/gaolabtools/scNanoGPS_v0.10/ .
deconvolution into single cells
make consensus sequencces of single molecules
calculate same cell multiomics
Assembly: GRCh38
Supplementary files format and content: NGS: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Nanopore: matrix.tsv.gz, matrix_isoform.tsv.gz, matrix_SNV.vcf.gz

source_name: Skin

extract_protocol:
Single nuclei of cell lines were prepared by following the 10X Genomics  protocol(CG000365 Rev C).   Single nucleus suspensions of frozen tumor tissues were prepared according to the method as previously described (dx.doi.org/10.17504/protocols.io.t3aeqie)
NGS libraries were prepared by following 10X genomics 3'scRNAseq protocol.   For Nanopore long-read sequencing, cDNA libraries were prepared with SQK-LSK110 ligation sequencing kit.

value: Skin

value: nuclei of tumor

value: unknown

tag: tumor stage

value: Melanoma brain metastatis


title: TGS - RCC2

description:
scNanoRNAseq
NP7

source_name: Kidney

value: Kidney

value: RCC brain metastatis


title: TGS - RCC1

description:
scNanoRNAseq
NP6

value: Primary RCC


title: TGS - H2030

description:
scNanoRNAseq
NP18

value: nuclei of cancer cell line


title: TGS - A375

description:
scNanoRNAseq
NP19


title: P1-siTRIM28-Dec-ATAC

value: EPC


title: P1-siTRIM28-Pre-dec-ATAC

value: vehicle


title: P1-siNT-Dec-ATAC

value: siNT


title: Ci4_F1_A02

source_name: hiPSC-lt-NES cells

value: human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)


title: MCT 6

city: Boston

first: Scott

middle: C

last: Fligor

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Children's Hospital

data_processing:
Data processing was performed by Novogene Inc: "Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed."
Assembly: GCF_000003025.6
Supplementary files format and content: Processed data are provided as a tab-delimited text file including read counts for all genes across all samples, including FPKM values

organism: Sus scrofa domesticus

extract_protocol:
Liver sections were flash frozen in liquid nitrogen and stored a -80C. RNA was harvested using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene, Inc.

tag: dose

value: Isovolumetric Vehicle Control (3ml/kg)

tag: breed

value: Yorkshire

value: Liver

value: MCT


title: MCT 5


title: MCT 4


title: D3.5ff-1-RNA-seq

value: uterus

tag: Sex

value: female

value: Pregnant day 3.5


title: MCT 2


title: SEFA-6179 5

value: 48 mg/kg


title: SEFA-6179 4


title: TGS - MEL1

description:
scNanoRNAseq
NP8

value: Skin

tag: cell line

value: nuclei of tumor

value: unknown

value: Primary melanoma


title: J02_054

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.

data_processing: Probe intensities were normalized with MAS5.

source_name: fresh frozen tumor

label_protocol: RNA (1 μg; RIN value >6) was used for generation of second-strand cDNA, and cRNA was amplified with the Oligo dT primer, then biotinated and fragmented with One-Cycle Target Labeling or and control reagents (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from tumor tissues obtained at the surgery with the aid of the Qiagen RNeasy® mini kit (QIAGEN Sciences, Germantown, MD).

treatment_protocol: The patients agreed to have their research specimens cryopreserved for future use after undergoing radical breast cancer surgery, and also received endocrine therapy following the surgery.

value: breast tumor

tag: menopause

value: postmenopausal

tag: ct

tag: cn

tag: er

value: Positive

tag: pgr

tag: hg

value: No


title: J02_046


title: J02_041


title: SEFA-6179 2

tag: treatment


title: SEFA-6179 1


title: J02_049

value: Yes


title: J02_051

value: premenopausal


title: J02_045


title: J02_047


title: J02_055


title: J02_044


title: J02_040


title: J02_056


title: J02_048


title: J02_043