title: Wildtype infected sample

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 900 S. Ashland Ave

department: Research Resources Center

institute: University of Illinois at Chicago

description: Library name: WT_HSV1

data_processing:
Raw reads were demultiplexed and single-cell gene expression quantified using CellRanger (10X Genomics) to mouse reference genome mm10. The quality of the run was assessed through the percent of mappable reads to the genome, the percent of reads with valid barcodes, and the median UMI counts per cell, as well as the number of cells identified.
Assembly: Mouse mm10
Supplementary files format and content: Matrix, features, and barcodes files

source_name: cervical lymph nodes

extract_protocol:
Cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. Sixteen thousand cells were loaded into the Chromium iX Controller (10X Genomics, PN-1000328) on a Chromium GEM-X Single cell 3’ Chip Kit v4 (10x Genomics, PN-1000215), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol.
The cDNA and library were generated using the GEM-X Single cell 3’ Kit v4 (10x Genomics, PN-1000691) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina Novaseq X Plus sequencer with 100 cycle kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

value: cervical lymph nodes

value: Optn +/+


title: E6.5 Visceral endoderm,Ser2p,ChIP,rep1

status: Public on Mar 19 2026

type: SRA

city: chongqing,china

first: xipeng

last: shen

address: yixueyuan road NO.1

department: basic medicine

country: China

institute: CQMU

library_source: genomic

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9 or hg19
Supplementary files format and content: All attached processed data were in .bed format.

molecule: genomic DNA

organism: Mus musculus

source_name: E6.5 Visceral endoderm

growth_protocol: PWK&PhJ male mouses (6-8weeks) were mated with C57BL/6N female mouses (6-8weeks) and the time when the vaginal plug was observed the next day was considered E0.5. The embyos were disserted at E6.5 and E7.5, respectively. Germ layers were seperated using enzyme digestion coupled with mechanical separation.

extract_protocol:
ChIP-seq was performed with minor adjustments to the STAR ChIP-seq protocol. Samples were lysed in a buffer containing 0.5% Tween-20, 0.5% NP-40, and 0.1% SDS, and gently pipetted to release genomic DNA. The mixture was then digested with MNase (Sigma) at 37°C for 5 minutes. Primary antibodies-anti-Pol II RBP1 (BioLegend), anti-Phospho-POLR2A CTD-S2 (Abclonal), anti-SP1(Proteintech), anti-H3K4me3 (Millipore) or anti-H3K27me3 (Abclonal)-were added, followed by incubation at 4°C overnight. Protein A Dynabeads (Thermo Fisher Scientific) were added to the solution and incubated for 3-4 hours. Beads were washed five times with RIPA buffer containing 0.1% protease inhibitor and once with LiCl wash buffer. Elution of DNA fragments was achieved with proteinase K treatment.
The library was constructed using NEB Next® UltraTM II DNA Library Prep Kit according to the operation instruction.

treatment_protocol: C57BL/6N female mouses(5 weeks) were superovulated with PMSG following hCG 48h later. After mating with PWK mouses, PN3 zygotes were colleted in M2 medium the next day. The CRISPR-ZEN methods were used to deliver Cas9-sgRNA complex into zygotes for gene editing. Zygotes were cultured to 2-cell stage in vitro and transferred to E0.5 pseudopregnancy foster mice. Germ layers were seperated as described above. The ExVE of embryos was collected for genotyping.

tag: tissue

value: E6.5 Visceral endoderm

tag: antibody


title: E7.5 Extra-embryonic ectoderm,Pol2,ChIP,rep2

source_name: E7.5 Extra-embryonic ectoderm

value: E7.5 Extra-embryonic ectoderm


title: E6.5 Epiblast,Ser2p,ChIP,rep1

source_name: E6.5 Epiblast

value: E6.5 Epiblast


title: Tumor DNA from FFPE tissue of  206467010176_R07C01

type: genomic

city: Rotterdam

first: Bo

last: Deng

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing: RnBeads package in R environment (v4.4.2).

label: Cy3 and Cy5

organism: Homo sapiens

source_name: FFPE glioblastoma DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Tumor DNA was extracted from FFPE tissue using the QIAamp DNA FFPE Tissue Kit (Qiagen), and the quantity of isolated DNA was assessed with a Qubit 3.0 fluorometer (Invitrogen).

value: FFPE glioblastoma DNA

value: BAY

value: primary

tag: gender

value: Male

tag: age

tag: treated with tmz

value: Yes

tag: treated with rt

tag: overall survival

tag: status

value: Deceased


title: Tumor DNA from FFPE tissue of  206467110176_R03C01

value: CAD


title: E6.5 Extra-embryonic ectoderm,Ser2p,ChIP,rep1

source_name: E6.5 Extra-embryonic ectoderm

value: E6.5 Extra-embryonic ectoderm


title: Tumor DNA from FFPE tissue of  206467010176_R08C01

value: AZH

value: recurrence

value: Female


title: Tumor DNA from FFPE tissue of  206467110175_R05C01

value: AZE

value: Censored


title: E7.5 Ectoderm,Ser2p,ChIP,rep2

source_name: E7.5 Ectoderm

value: E7.5 Ectoderm


title: Tumor DNA from FFPE tissue of  206467010176_R06C01


title: E7.5 Ectoderm,Pol2,ChIP,rep1


title: WT2

city: Shanghai

first: Jinkun

last: Zhong

address: No. 130, Dong'an Road, Xuhui District, Shanghai

institute: Fudan University

description:
Library name: sample12
WT2_fpkm

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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.
(For DESeq2 with biological replicates) 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.
(For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a predefined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
Assembly: not provided
Supplementary files format and content: counts, FPKM

molecule: total RNA

source_name: liver

extract_protocol:
RNA is extracted from tissues using standard extraction methods.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: liver

tag: genotype

value: WT


title: E6.5 Visceral endoderm,Pol2,ChIP,rep2

value: E6.5 Visceral endoderm


title: E7.5 Extra-embryonic ectoderm,Pol2,ChIP,rep1

value: E7.5 Extra-embryonic ectoderm


title: Optineurin knockout infected sample

country: USA

description: Library name: OKO_HSV1

library_source: transcriptomic single cell

molecule: polyA RNA

value: cervical lymph nodes

value: Optn -/-


title: E6.5 Extra-embryonic ectoderm,Pol2,ChIP,rep3


title: Wildtype non-infected sample

description: Library name: WT_NI

value: Optn +/+


title: E7.5 Ectoderm,Pol2,ChIP,rep2


title: E6.5 Extra-embryonic ectoderm,Pol2,ChIP,rep2


title: WT3

description:
Library name: sample13
WT3_fpkm


title: Tumor DNA from FFPE tissue of  206467010178_R03C01

value: FFPE glioblastoma DNA

value: AAP

value: primary

value: Yes


title: E6.5 Epiblast,Ser2p,ChIP,rep2

value: E6.5 Epiblast


title: E6.5 Epiblast,Pol2,ChIP,rep1


title: WT4

description:
Library name: sample14
WT4_fpkm


title: KO4

description:
Library name: sample10
KO4_fpkm

value: LKO


title: KO3

description:
Library name: sample9
KO3_fpkm


title: Tumor DNA from FFPE tissue of  206467110175_R02C01

value: AZA

value: recurrence

value: Female

value: Deceased


title: E7.5 Mesoderm,Pol2,ChIP,rep1

source_name: E7.5 Mesoderm

value: E7.5 Mesoderm


title: E6.5 Visceral endoderm,Pol2,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010178_R02C01


title: Optineurin knockout non-infected sample

description: Library name: OKO_NI


title: E6.5 Extra-embryonic ectoderm,Pol2,ChIP,rep1

value: E6.5 Extra-embryonic ectoderm


title: WT1

description:
Library name: sample11
WT1_fpkm

value: liver

value: WT


title: Tumor DNA from FFPE tissue of  206467110175_R01C01

value: AZH


title: E6.5 Epiblast,Pol2,ChIP,rep2


title: E7.5 Mesoderm,Pol2,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467110175_R03C01


title: Tumor DNA from FFPE tissue of  206467110175_R04C01

value: AZE

value: Male

value: Censored


title: E6.5 Extra-embrynic ectoderm,Jarid2 ko,Pol2,ChIP,rep1

value: Jarid2 ko


title: Tumor DNA from FFPE tissue of  206467010143_R01C01

value: FFPE glioblastoma DNA

value: AAA

value: primary

value: No


title: E6.5 Extra-embrynic ectoderm,Kmt2b ko,Pol2,ChIP,rep1

value: Kmt2b ko


title: E6.5 Extra-embrynic ectoderm,Kmt2b ko,Pol2,ChIP,rep2

source_name: E6.6 Extra-embryonic ectoderm

value: E6.6 Extra-embryonic ectoderm


title: E6.5 Epiblast,Pol2,ChIP,rep3

value: E6.5 Epiblast


title: PM_POA_2

description:
Library name: sample5
PM_POA_2_fpkm

source_name: peritoneal macrophage

extract_protocol:
RNA is extracted from cells using standard extraction methods.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

tag: cell type

value: peritoneal macrophage

tag: treatment

value: POA


title: KO2

description:
Library name: sample8
KO2_fpkm

value: LKO


title: Tumor DNA from FFPE tissue of  206467110175_R08C01

value: AAJ

value: recurrence

value: Female

value: Yes

value: Deceased


title: PM_POA_1

description:
Library name: sample4
PM_POA_1_fpkm

value: WT


title: KO1

description:
Library name: sample7
KO1_fpkm

value: liver


title: E6.5 Epiblast,Jarid2 Ctr,Pol2,ChIP,rep2

value: Jarid2 Ctr


title: EXP60 plasma (exposed)

type: RNA

city: Botucatu

first: Tony

middle: Fernando

last: Grassi

state: São Paulo/SP

address: Av. Professor Mário Rubens G. Montenegro, s/nº

country: Brazil

institute: 1São Paulo State University (UNESP), Medical School

description: Plasma sample from a veterinarian occupationally exposed to waste anesthetic gases (isoflurane and sevoflurane) in veterinary operating rooms.

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions using the NanoString nCounter Human v3 miRNA Expression Assay. Total RNA was incubated with reporter and capture probes at 65 °C for 16–18 hours to allow hybridization of molecular barcodes to target miRNAs.

scan_protocol: After hybridization, samples were processed on the NanoString nCounter Prep Station for purification and immobilization of probe–target complexes on the cartridge surface. Data acquisition was performed using the NanoString nCounter Digital Analyzer at maximum resolution (555 fields of view per sample), generating RCC files with raw counts for each probe

data_processing:
Raw RCC files generated by the NanoString nCounter Digital Analyzer were processed using nSolver software for quality control and normalization based on positive controls, housekeeping miRNAs, and CodeSet content content correction. Differential expression was assessed by fold change (FC ≥ 1.5) and p-values, and ROC/AUC analyses were performed to evaluate biomarker potential. Functional analysis included target prediction (mirDIP) and PPI network construction (STRING, score ≥ 0.700).
Raw counts represent the number of barcoded probes hybridized to each target miRNA, as measured by the NanoString nCounter Digital Analyzer.

label: not applicable (NanoString barcoded probes)

source_name: Human plasma

label_protocol: Not applicable. NanoString technology employs reporter and capture probes with molecular barcodes provided by the manufacturer; no additional labeling was performed by the user.

growth_protocol: not applicable – human plasma samples

extract_protocol: Total RNA was extracted from human plasma samples using the Qiagen miRNeasy Serum/Plasma Kit, according to the manufacturer’s instructions. After initial centrifugation to remove cellular debris, plasma was mixed with QIAzol lysis reagent, followed by chloroform separation and purification on silica-membrane spin columns. RNA was eluted in 18 µL of RNase-free water and quantified using a NanoDrop spectrophotometer.

treatment_protocol: Not applicable – samples obtained directly from human plasma; groups defined by occupational exposure to waste anesthetic gases (isoflurane and sevoflurane)

tag: group

value: Exposed

tag: Sex


title: EXP59 plasma (exposed)


title: E6.5 Extra-embrynic ectoderm,Jarid2 Ctr,Pol2,ChIP,rep1

source_name: E6.7 Extra-embryonic ectoderm

value: E6.7 Extra-embryonic ectoderm


title: E6.5 Epiblast,Kmt2b ko,Pol2,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010123_R08C01

value: FFPE glioblastoma DNA

value: AAA

value: Male

value: No

value: Censored


title: E6.5Extra-embrynic ectoderm,Jarid2 Ctr,Pol2,ChIP,rep2

source_name: E6.8 Extra-embryonic ectoderm

value: E6.8 Extra-embryonic ectoderm


title: PM_POA_3

description:
Library name: sample6
PM_POA_3_fpkm

value: peritoneal macrophage

value: POA


title: E6.5 Extra-embrynic ectoderm,Jarid2 ko,Pol2,ChIP,rep2

value: E6.6 Extra-embryonic ectoderm

value: Jarid2 ko


title: EXP58 plasma (exposed)

value: Female


title: Tumor DNA from FFPE tissue of  206467110163_R01C01

value: AAJ

value: primary

value: Yes

value: Deceased


title: E6.5 Epiblast,Jarid2 Ctr,Pol2,ChIP,rep1

value: E6.5 Epiblast

value: Jarid2 Ctr


title: E6.5 Extra-embrynic ectoderm,Eed Ctr,Pol2,ChIP,rep1

value: E6.7 Extra-embryonic ectoderm

value: Eed Ctr


title: E6.5 Epiblast,Kmt2b ko,Pol2,ChIP,rep1

value: Kmt2b ko


title: EXP56 plasma (exposed)

value: Exposed


title: E6.5 Extra-embrynic ectoderm,Eed ko,Pol2,ChIP,rep2

value: Eed ko


title: E6.5 Epiblast,Jarid2 ko,Pol2,ChIP,rep1


title: E6.5 Epiblast,Jarid2 ko,Pol2,ChIP,rep2


title: PM_PA_3

description:
Library name: sample3
PM_PA_3_fpkm

value: WT

value: PA


title: E6.5Extra-embrynic ectoderm,Eed Ctr,Pol2,ChIP,rep2

value: E6.8 Extra-embryonic ectoderm


title: E7.5 Extra-embryonic ectoderm,rep2

description: Post_implantation_embryo_RNA_FPKM.txt.gz

data_processing:
The sequencing reads were processed for quality trimming using the Trim Galore (version 0.6.7), and subsequently aligned to the mouse mm9 reference genome using HISAT2 (version 2.2.1). Gene expression was calculated by StringTie (version 2.2.1) according to the refFlat database.
Assembly: mm9
Supplementary files format and content: All attached processed data were listed with gene name and RPKM.

extract_protocol:
The RNA-seq library was generated following the Smart-seq2 protocol. Samples were permeabilized in 5 µl lysis buffer containing 0.2% Triton X-100 for 30 minutes on ice. After centrifugation, 2 µl of the supernatant was transferred to a pre-cooled tube, and reverse transcribed into cDNA.
The library construction was then performed using the One-step DNA Lib Prep Kit for Illumina V2 (Abclonal) according to the manufacturer's instructions.

value: E7.5 Extra-embryonic ectoderm


title: BG38_1

city: Krakow

first: Tomasz

last: Gromowski

address: Gronostajowa 7 Str.

country: Poland

institute: Jagiellonian University in Krakow

description: Library name: Sample 22

data_processing:
Galaxy Europe server version 24.2
HISAT2 2.21
featureCounts 2.0.8
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv file include TPM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated and purified from murine livers using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s procedure. 10 ng/ul of total RNA was used  for the construction of sequencing librares.
RNA librares for RNA-seq were prepared using  Illumina Stranded mRNA Prep following manufacturer's protocols.

value: Liver

value: Hom:BRAF +/+, TRP53 flx/flx, ICMT flx/flx

tag: strain

value: B6[ICMT tm1MbrgB6.129P2-(Trp53tm1Brn)(Mmcm)(Braftm1WT)J X(Zc3h12atm1c WT)(Speer6-ps1Tg(Albcre)21Mgn]/J X B6[129P2-(Trp53tm1Brn)(Braftm1Mmcm)/J Icmt tm1Mbrg]


title: E6.5 Extra-embrynic ectoderm,Eed ko,Pol2,ChIP,rep1

value: E6.5 Extra-embryonic ectoderm


title: EXP54 plasma (exposed)

value: Female


title: E6.5 Epiblast,Eed ko,Pol2,ChIP,rep2


title: E7.5 Mesoderm,rep1

value: E7.5 Mesoderm


title: EXP57 plasma (exposed)


title: PM_PA_2

description:
Library name: sample2
PM_PA_2_fpkm

value: peritoneal macrophage


title: BG90_1

description: Library name: Sample 20


title: EXP52 plasma (exposed)


title: BG183_2

description: Library name: Sample 19


title: E6.5 Epiblast,Eed Ctr,Pol2,ChIP,rep2

value: E6.5 Epiblast


title: E6.5 Extra-embryonic ectoderm,rep1


title: PM_PA_1

description:
Library name: sample1
PM_PA_1_fpkm


title: BG38_2

description: Library name: Sample 23


title: E6.5 Epiblast,Eed Ctr,Pol2,ChIP,rep1


title: BG90_2

description: Library name: Sample 21


title: E6.5 Extra-embryonic ectoderm,rep2


title: E7.5 Mesoderm,rep2


title: E7.5 Endoderm,rep1

source_name: E7.5 Endoderm

value: E7.5 Endoderm


title: E6.5 Epiblast,Eed ko,Pol2,ChIP,rep1


title: E7.5 Ectoderm,rep1

value: E7.5 Ectoderm


title: MMTV-PyMT spontaneous tumor

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Library name: PyMT_spontaneous
3’ mRNA (v2 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence; samples were loaded on  Illumina NextSeq500 with NextSeq 500/550 Mid Output v2 kit

data_processing:
10X datasets: Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
BD Rhapsody platform: the raw FASTQ files were mapped  to the mouse genome using the BD Rhapsody Sequence Analysis Pipeline
Assembly: mm10/GRCm38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT counts in Cellranger output format, seurat R .rds objects contatining cell annotations and dimensionality reduction embeddings and text .csv files, containing the VDJ contig annotations of the BCR-seq datasets

source_name: tumor

extract_protocol: All methods listed in Caro et al. Pan-cancer single-cell atlas of mouse and human tumor-associated dendritic cells.

value: tumor

value: CD45+Viobility 488/520-

value: MMTV-PyMT in FVB background


title: E6.5 Epiblast,rep2

source_name: E6.5 epiblast

value: E6.5 epiblast


title: P2

city: Southampton

first: Rubén

last: de Dios

state: Hampshire

address: University Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts (cpm) for every sample.

organism: Acinetobacter baumannii AB5075

source_name: Acinetobacter baumannii AB5075 (VIR-O colony morphology)

growth_protocol: 3 independent replicates of A. baumannii AB5075 (VIR-O) bearing either rocR  or  pleD* were inoculated from stocks and incubated overnight (approx. 16 h) in LB (37 C, 180 rpm). Then, cultures were diluted in fresh LB supplemented with IPTG 1 mM to OD600 0.05 and incubated at 37 C, 180 rpm until reaching mid-exponential phase (OD600 0.6 approx.).

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices. Sequencing was done on a NovaSeq 6000 giving 2x51bp reads.

treatment_protocol: The treatment consisted in inducing the expression of either rocR or pleD* with IPTG 1 mM from the beginning of the growth.

value: Overexpressing pleD* (high cdGMP)

tag: culture conditions

value: 37 C, 180 rpm, grown to mid- exponential phase (OD600 0.6 approx.), IPTG 1 mM


title: EXP48 plasma (exposed)

value: Exposed


title: E6.5 Visceral endoderm,rep2

source_name: E6.5 Visceral endoderm

value: E6.5 Visceral endoderm


title: EXP53 plasma (exposed)

value: Male


title: E7.5 Extra-embryonic ectoderm,rep1

source_name: E7.5 Extra-embryonic ectoderm

value: E7.5 Extra-embryonic ectoderm


title: E7.5 Endoderm,rep2


title: E7.5 Ectoderm,rep2


title: EXP51 plasma (exposed)


title: EXP50 plasma (exposed)


title: BG88_1

description: Library name: Sample 12

value: Liver

value: Het:BRAF +/+, TRP53 flx/flx, ICMT flx/+

value: B6[ICMT tm1MbrgB6.129P2-(Trp53tm1Brn)(Mmcm)(Braftm1WT)J X(Zc3h12atm1c WT)(Speer6-ps1Tg(Albcre)21Mgn]/J X B6[129P2-(Trp53tm1Brn)(Braftm1Mmcm)/J Icmt tm1Mbrg]


title: E6.5 Epiblast,Kmt2b Ctr,rep1


title: E6.5 Epiblast,rep1


title: R2

value: Overexpressing rocR (low cdGMP)


title: P3


title: BG183_1

description: Library name: Sample 18

value: Hom:BRAF +/+, TRP53 flx/flx, ICMT flx/flx


title: EXP49 plasma (exposed)

value: Female


title: EXP43 plasma (exposed)


title: BG175_2

description: Library name: Sample 15


title: BG30_1

description: Library name: Sample 16


title: BG175_1

description: Library name: Sample 14


title: BG40

description: Library name: Sample 10


title: EXP44 plasma (exposed)


title: EXP55 plasma (exposed)


title: E6.5 Visceral endoderm,rep1


title: BG30_2

description: Library name: Sample 17


title: RNA-Seq_KYSE140_siSF3B3

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

description: Library name: Sample 2

data_processing:
Basecalling from raw data (FAST5 format) was performed using the Guppy software (version 3.0.3) (Oxford Nanopore)
Reads were aligned to the hg38 genome assembly using minimap2
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: KYSE140 cells were cultured in RPMI1640 medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using TRIzol following the manufacturer’s protocol.
cDNA libraries were constructed using the Ligation Sequencing Kit (SQK-LSK109) (Oxford Nanopore) and sequenced with SpotON FlowCell MKⅠ (R9.4) (Oxford Nanopore) according to the manufacture’s protocol.

treatment_protocol: KYSE140 cells were transfected with control siRNA (siCTL) or siRNA specifically against SF3B3 (siSF3B3) for two days, followed by Nanopore sequencing.

tag: cell line

value: WT


title: E6.5 Epiblast,Kmt2b ko,rep1


title: EXP45 plasma (exposed)


title: P1


title: E6.5 Epiblast,Kmt2b ko,rep2


title: EXP46 plasma (exposed)


title: E6.5 Epiblast,Jarid2 Ctr,rep2


title: R1


title: BG88_2

description: Library name: Sample 13


title: RNA-Seq_KYSE140_siCTL

description: Library name: Sample 1

value: siCTL


title: E6.5 Epiblast,Kmt2b Ctr,rep2


title: EXP40 plasma (exposed)


title: EXP39 plasma (exposed)


title: BG31

description: Library name: Sample 11


title: E6.5 Epiblast,Jarid2 Ctr,rep1


title: BG55_2

description: Library name: Sample 9


title: EXP42 plasma (exposed)


title: malpa459

description: Library name: Sample 6

value: Ctrl :BRAF wt, TRP53 flx/flx, ICMT flx/+

value: B6-ICMT tm1MbrgB6.129P2-(Trp53tm1Brn)(Mmcm)(Braftm1WT)J  X(Zc3h12atm1c WT)(Speer6-ps1Tg(Albcre)21Mgn/J


title: E6.5 Epiblast,Eed Ctr,rep2

value: E6.5 epiblast


title: EXP41 plasma (exposed)


title: R3


title: malpa454

description: Library name: Sample 4


title: BG55_1

description: Library name: Sample 8


title: EXP36 plasma (exposed)


title: Liver, HF, STZ, 8 weeks, rep5

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description:
Library name: STZ_8w_HF_5
S_S_08_65

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.4a
calling done with STRINGTIE v2.1.3b
Assembly: GRCm39.103
Supplementary files format and content: file containing gene counts for each sample

extract_protocol:
total RNA was extracted using a miRNeasy kit (Qiagen, Germany) as per the manufacturer’s instructions
done by BGI (Shenzhen, China)

treatment_protocol: At age of two days male mice were injected with single subcutaneous dose of 200 µg streptocotozin dissolved in 0.1 M citrate buffer (pH 4.5) (STZ, S).  At 4 weeks of age mice were switched to ad libitum feeding of a high-fat diet (HF; Ssniff) or a cholesterol-enriched high-fat diet (HFHC; Altromin). Mice were sacrificed after a 6-hour fast at 8 or 12 weeks of age.

value: liver

value: male

tag: diet

value: HF

value: 8 weeks


title: Liver, HF, STZ, 12 weeks, rep2

description:
Library name: STZ_12w_HF_2
S_S_12_20

tag: tissue

value: 12 weeks


title: E6.5 Epiblast,Jarid2 ko,rep2


title: Liver, HF, STZ, 12 weeks, rep3

description:
Library name: STZ_12w_HF_3
S_S_12_40


title: Liver, HF, STZ, 12 weeks, rep4

description:
Library name: STZ_12w_HF_4
S_S_12_41


title: EXP38 plasma (exposed)

value: Exposed


title: malpa458

description: Library name: Sample 5

value: Liver


title: E6.5 Epiblast,Eed Ctr,rep1


title: malpa462

description: Library name: Sample 7


title: Liver, HF, STZ, 12 weeks, rep1

description:
Library name: STZ_12w_HF_1
S_S_12_137


title: EXP37 plasma (exposed)

value: Male


title: EXP35 plasma (exposed)


title: BG3 _2

description: Library name: Sample 3

value: B6[ICMT tm1MbrgB6.129P2-(Trp53tm1Brn)(Mmcm)(Braftm1WT)J X(Zc3h12atm1c WT)(Speer6-ps1Tg(Albcre)21Mgn]/J X B6[129P2-(Trp53tm1Brn)(Braftm1Mmcm)/J Icmt tm1Mbrg]


title: E6.5 Epiblast,Eed ko,rep2


title: Liver, HF, STZ, 8 weeks, rep4

description:
Library name: STZ_8w_HF_4
S_S_08_63


title: E6.5 Epiblast,Eed ko,rep1


title: Liver, HF, STZ, 8 weeks, rep2

description:
Library name: STZ_8w_HF_2
S_S_08_51


title: HCC22-088-P3-S2

city: Pittsburgh

first: Alexander

middle: Chih-Chieh

last: Chang

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

description:
Library name: HCC22-088-P3-S2
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture

library_source: other

data_processing:
Raw sequencing data was processed using the 10x Genomics Spaceranger pipeline to generate fastq files
Sequences were aligned to the hg38 genome using Spaceranger's default settings
Gene expression of refseq coding genes were quanitfied using Spaceranger's default settings.
Assembly: GrCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes, each corresponding to a spot on the Visium slide.
Supplementary files format and content: features.tsv.gz: List of gene or protein features, including their unique identifiers and names.
Supplementary files format and content: matrix.mtx.gz: Sparse matrix containing counts of each feature (gene or protein) per barcode (spot).
Supplementary files format and content: aligned_fiducials.jpg: Image of the slide with fiducial markers aligned to aid in spatial registration.
Supplementary files format and content: aligned_tissue_image.jpg: Processed image of the tissue with alignment corrections applied.
Supplementary files format and content: cytassist_image.tiff: High-resolution raw image captured by the CytAssist instrument before alignment.
Supplementary files format and content: detected_tissue_image.jpg: Image showing the detected tissue region on the slide after preprocessing.
Supplementary files format and content: scalefactors_json.json: JSON file containing scale factors for converting between different image resolutions.
Supplementary files format and content: spatial_enrichment.csv: CSV file containing spatial enrichment scores for various features across spots.
Supplementary files format and content: tissue_hires_image.png: High-resolution image of the tissue captured from the slide.
Supplementary files format and content: tissue_lowres_image.png: Lower-resolution version of the tissue image used for visualization and analysis.
Supplementary files format and content: tissue_positions.csv: CSV file mapping spatial barcodes to their corresponding X, Y coordinates in the tissue.
Supplementary files format and content: feature_reference.csv: Reference file containing feature annotations, including gene or protein names and identifiers.
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5-formatted file containing the filtered feature-barcode matrix for gene or protein expression.
Supplementary files format and content: isotype_normalization_factors.csv: CSV file containing normalization factors for isotype control correction in antibody capture data.
Supplementary files format and content: molecule_info.h5: HDF5 file containing detailed molecule-level information, including UMI counts and feature assignments.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Breast

extract_protocol:
Prior to sectioning, samples were assessed for RNA quality, and all samples had a DV200 score above the minimum threshold (\(\geq30\%\)). Spatial transcriptomic and proteomic libraries were generated with Visium CytAssist for FFPE v2 gene expression kit (10x Genomics: 1000520) with the Human Immune Cell Profiling Panel (10x Genomics: PN-1000607).
Five-micron FFPE sections were placed on Schott Nexterion Hydrogel Coated Slides (Schott North America: 1800434) or Fisherbrand Superfrost Plus Slides (Fisher: 22-037-246) and processed through the 10x CytAssist for FFPE v2 protocol according to the manufacturer’s instructions. Library QC was completed with an Agilent TapeStation 4150. Libraries were normalized and pooled to 2 nM prior to loading on an Illumina NextSeq 2000, using a P3 100 flow cell. The pooled library was loaded at 650 pM, and sequencing was carried out with a 28/10/10/50 bp read structure, targeting 125 million reads per sample for transcriptomic libraries and 25 million reads per sample for proteomic libraries.

value: Breast

value: post primary endocrine therapy


title: Liver, HF, STZ, 8 weeks, rep1

description:
Library name: STZ_8w_HF_1
S_S_08_1


title: Liver, HF, STZ, 8 weeks, rep3

description:
Library name: STZ_8w_HF_3
S_S_08_53


title: EXP34 plasma (exposed)


title: EXP33 plasma (exposed)

value: Female


title: BG3 _1

description: Library name: Sample 2


title: malpa387

description: Library name: Sample 1


title: Human cardiac microvascular endothelial cell EVs, HCMVEC-EVs, rep 3

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: HCMVECEV3

data_processing:
CM-, CF-, HCMVEC-EVs: Libraries were sequenced using a NextSeq500 (Illumina) at 1x 75 (bp) and an average depth of 30 million reads. Mac-EVs: Libraries were sequenced using a NovaSeq 6000 S4 (Illumina) at  2× 150 (bp) and an average depth of 12 million reads.
For Mac-EVs, R1 reads were trimmed to 75 bp before analysis and these were the files used for further analyses consistent with CM-, CF-, and HCMVEC-EVs.
CM-, CF-, HCMVEC-EVs: The Bio-Rad SeqSense pipeline employing STARaligner (v2.7.0 f) was used to aligned reads to the human genome (GRCh38.p12) and generate miRNA count files. Mac-EVs: The Qiagen RNA-seq Analysis Portal 3.0 (workflow version 1.2) was used to align trimmed R1 sequencing data to the human genome (GRCh38.103) via the miRbase v22 database and generate raw miRNA count files for each sample. Count file format was harmonized between the alignment pipelines for compatibility with downstream analyses; miRNAs absent in one pipeline with non-zero counts in the other were manually added as entries with zero counts as needed, while miRNAs missing -3p/-5p delineation in the BioRad pipeline were determined based on the solely expressed form in the Qiagen pipeline as well as the provided chromosome location.
Assembly: hg38, miRbase v22
Supplementary files format and content: CardiacEVs_rawcounts.txt: tab-delimited text file including raw counts for each sample

source_name: ABM T0514

growth_protocol: To produce primitive macrophages, the H1 hESC line was first differentiated into CD43+ primitive hematopoietic progenitors according to a previously published protocol1, which were isolated via magnetic-activated cell sorting and frozen. To complete primitive macrophage differentiation, cells were thawed then cultured in suspension for 3 days in poly-HEMA coated 6 well plates at a density of approximately 500,000 cells per well. Cells were cultured in supplemented StemPro-34 base medium (2ml per well, containing transferrin (ROCHE 10652202001, 150µg/ml), ascorbic acid (Sigma Aldrich A4544, 50µg/ml), L-glutamine (ThermoFisher 25040081, 2mM), and monothioglycerol (Sigma Aldrich M6145, 50µg/ml)) with the addition of MCSF (R&D Systems 216-MC, 30ng/mL), IL3 (R&D Systems 203IL, 50ng/mL) and SCF (R&D Systems 255SC, 100ng/mL). Then, for 18+ days, cells were cultured in the same supplemented StemPro-34 base medium with the addition of MCSF (30ng/mL) alone and medium was changed weekly.  CMs were differentiated from BJ1D human iPSCs as described previously.2 Briefly, iPSCs cultured in mTeSR Plus medium (STEMCELL Technologies) were passaged at 0.75 million cells per well onto 12-well Matrigel (Corning) coated plates. When confluent, medium was changed to RPMI supplemented with B27 minus insulin (Gibco), 1% Pen-Strep, and 8 µM CHIR99021 (Cayman Chemical) for 24 h. On day 3, medium was changed to the same RPMI based medium (without CHIR) plus 5µM IWP4 (Stemgent) for 48 h. After this, cells were cultured in RPMI with B27 minus insulin until day 7 then RPMI with B27 supplement (Gibco) thereafter. After at least day 14, CMs were harvested by 30 min treatment with 10x TrypLE Express (Gibco) at 37°C, media was added to neutralize TrypLE and rinse wells, then cells were centrifuged for 5 min at 300 g, resuspended in medium, and live cells counted with the addition of trypan blue.  Human ventricular cardiac fibroblasts (CFs) (Lonza, CC-2904) were cultured in Fibroblast Growth Medium 3 (FGM3; PromoCell, C-23025) with 1% 10,000 U/ml penicillin/streptomycin in T75 or T175 flasks.  Human cardiac microvascular endothelial cells (HCMVECs) (Applied Biological Materials Inc, T0514) were cultured in Endothelial Cell Growth Medium 2 (EGM2; PromoCell, C-22011) with 1 % 10,000 U/ml penicillin/streptomycin in T75 or T175 flasks. 1. Atkins MH, Scarfò R, McGrath KE, Yang D, Palis J, Ditadi A, Keller GM. Modeling human yolk sac hematopoiesis with pluripotent stem cells. J Exp Med. 2021;219(3). doi:10.1084/jem.20211924 2. Lian X, Zhang J, Azarin SM, Zhu K, Hazeltine LB, Bao X, Hsiao C, Kamp TJ, Palecek SP. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nat Protoc. 2013;8(1):162-175. doi:10.1038/nprot.2012.150

extract_protocol:
miRNA was isolated from lysed EV pellets using the miRNeasy Micro Kit (Qiagen, 217084) according to the manufaturer's protocol. Samples were treated with DNase.
CM-, CF-, HCMVEC-EVs: SEQuoia Complete Stranded RNA Library Prep Kit and Dual Indexed Primers (Bio-Rad 17005726 and 12011928) Mac-EVs: Library preparation was performed using the QIAseq miRNA Library Kit (Qiagen, catalog no. 331502).

treatment_protocol: Following macrophage differentiation as outlined above, supplemented StemPro-34 base medium with the addition of MCSF (30ng/mL) was prepared as before then depleted of background particles via ultrafiltration: media was centrifuged in Amicon Ultra-15 100kDa centrifugal filters (MilliporeSigma, UFC910024) at 4000g for 30 min at room temperature. Macrophage cells in suspension were pelleted via centrifugation at 200g for 5 minutes, supernatant was removed, and cells were resuspended in 1ml of medium for counting in the presence of trypan blue. Cells were then centrifuged and resuspended in 4ml ultrafiltered medium per well of cells collected from 6 well plate. After 48h of culture, conditioned media was collected and centrifuged to pellet cells. Supernatant was collected and frozen at -20°C until EV isolation.  Following CM differentiation, between days 14-22, conditioned media (RPMI with B27 supplement) was collected from culture plates after 72h of culture (in accordance with the regular media change timeline for CM differentiation protocol) until the timepoint where CMs were dissociated and counted. Conditioned media was frozen at -20°C until EV isolation.  For CFs, when cells reached 80% confluence, flasks were washed briefly with PBS then media was changed to un-supplemented basal FGM3 medium with the addition of 10% exosome-depleted FBS (ThermoFisher Scientific, A2720803) and 1% 10,000 U/ml penicillin/streptomycin. 15ml of media was used in T75 flasks and 35ml in T175 flasks. After 48h of culture, conditioned media was collected and frozen at -20°C until EV isolation. Cells were detached from flasks with trypsin, centrifuged, and resuspended for counting in the presence of trypan blue. HCMVEC conditioned media was collected using the exact same protocol as CFs except that un-supplemented basal EGM2 with the addition of 2% exosome-depleted FBS and 1% 10,000 U/ml penicillin/streptomycin was employed. Thawed conditioned media was centrifuged at 3200g for 10min to pellet cell debris. Supernatant was collected. The PEG-based miRCURY exosome isolation kit (Qiagen, 76743) was utilized for EV isolation. PEG-media solutions were rotated overnight at 4°C then centrifuged for 30min at 3200g and 21°C to pellet EVs. Pellets were rinsed superficially with PBS without resuspension. EV pellets were resuspended directly in Qiazol lysis buffer for total RNA extraction.

value: ABM T0514

value: endothelial cell

tag: batch


title: EXP32 plasma (exposed)


title: Human cardiac microvascular endothelial cell EVs, HCMVEC-EVs, rep 2

description: Library name: HCMVECEV2


title: Cardiac fibroblast EVs, CF-EVs, rep 3

description: Library name: CFEV3

source_name: Lonza CC-2904

value: Lonza CC-2904

value: cardiac fibroblast


title: Human cardiac microvascular endothelial cell EVs, HCMVEC-EVs, rep 1

description: Library name: HCMVECEV1


title: Cardiac fibroblast EVs, CF-EVs, rep 2

description: Library name: CFEV2


title: Liver, HFHC, STZ, 12 weeks, rep5

description:
Library name: STZ_w12_HFHC_5
S_A_12_54

source_name: liver

value: HFHC


title: Cardiac fibroblast EVs, CF-EVs, rep 1

description: Library name: CFEV1


title: Crskip rep 2

city: Beijing

first: Yan

last: Li

address: Haidian

institute: Capital Normal University

description: Library name: Crskip-2

data_processing:
Reads were mapped to the Chlamydomonas reinhardtii genome using bowtie2. Only the uniquely mapped reads were saved.
Assembly: Chlamydomonas reinhardtii CC-4532 v6.1
Supplementary files format and content: txt file of gene expression count from featurecounts

organism: Chlamydomonas reinhardtii

source_name: single cells

extract_protocol:
Wild-type Chlamydomonas reinhardtii, crpaf1-1, and crskip-1 mutants were cultured in TAP liquid medium under a 14 h light/10 h dark cycle at 22°C for two generations and harvested at late G1 phase for RNA extraction.
mRNA-seq libraries were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit (Illumina) according to manufacturer’s instructions. Briefly, polyadenylated RNAs were enriched from total RNA with oligo(dT) beads, followed by adapter ligation and PCR amplification. The libraries were sequenced on Illumina NovaSeq 6000 platform (PE150).

value: single cells

value: skip


title: EXP31 plasma (exposed)


title: Liver, HFHC, STZ, 12 weeks, rep4

description:
Library name: STZ_12w_HFHC_4
S_A_12_50

value: liver

value: male


title: Crskip rep 1

description: Library name: Crskip-1


title: Liver, HFHC, STZ, 12 weeks, rep3

description:
Library name: STZ_12w_HFHC_3
S_A_12_38

value: 12 weeks


title: CTRL29 plasma (control)

description: Plasma sample from an unexposed control professional, matched by age and sex, without occupational exposure to anesthetic gases.

value: Control


title: CTRL30 plasma (control)


title: Cardiomyocyte EVs, CM-EVs, rep 3

description: Library name: CMEV3

source_name: BJ1D hiPSC

value: BJ1D hiPSC

value: cardiomyocyte


title: CrWT rep 2

description: Library name: CrWT-2

value: WT


title: CTRL28 plasma (control)


title: CrWT rep 3

description: Library name: CrWT-3


title: Liver, HFHC, STZ, 12 weeks, rep1

description:
Library name: STZ_12w_HFHC_1
S_A_12_17


title: Liver, HFHC, STZ, 12 weeks, rep2

description:
Library name: STZ_12w_HFHC_2
S_A_12_36


title: CTRL27 plasma (control)


title: Cardiomyocyte EVs, CM-EVs, rep 2

description: Library name: CMEV2


title: Crpaf1 rep 3

description: Library name: Crpaf1-3


title: Cardiomyocyte EVs, CM-EVs, rep 1

description: Library name: CMEV1


title: Crpaf1 rep 2

description: Library name: Crpaf1-2


title: CTRL26 plasma (control)


title: Liver, HFHC, STZ, 8 weeks, rep3

description:
Library name: STZ_8w_HFHC_3
S_A_08_52

value: 8 weeks


title: AAV DNA, PGK library, input

city: Biberach

first: Martin

last: Oti

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim

description: Library name: vDNA_Virus_Input_PGK_Input_Input_1

data_processing:
The NGS paired-end reads were mapped to the human genome (assembly hg38) using bowtie2 (v2.2.9). Mapped reads were filtered for those mapping to a single genomic location using samtools (v1.2), and those mapping to the capture library target regions were quantified using the ‘featureCounts’ tool of the Subread NGS alignment suite (v1.6.2)
For fragment-level analyses, the fragments were processed using the BEDTools suite v2.26.0. First, they were extracted from the name-sorted paired-end BAM files (sorted with ‘samtools sort -n’) using the ‘bedtools bamtobed’ command with the ‘-bedpe’ flag, and their overall start and end coordinates were stored in the normal BED file format, with the mapping quality (MAPQ) placed in the score field and the read name in the name field. They were then filtered for MAPQ >= 30 using the Linux ‘awk’ command, their coordinates were rounded to the nearest 10 bp to account for reads with slightly trimmed ends, they were quantified using ‘bedtools groupby –c 4 –o count’, and finally they were intersected with the capture library target regions using ‘bedtools intersect’.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each cellular DNA & RNA sample

source_name: Virus

growth_protocol: HepG2 and HaCaT cells were cultured at 37°C in a humidified atmosphere containing 5% CO2. Growth medium consisted of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen Life Technology, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, Waltham, USA).

extract_protocol:
DNA and RNA were extracted using the ALLprep 96 DNA/RNA kit (QIAGEN, Hilden, Germany).
2 µg of total RNA were used for mRNA enrichment utilizing the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, USA) followed by cDNA synthesis and amplicon PCR using enhancer cassette-specific primers. 20 ng of PCR product as well as 20 ng of DNA were used for index PCR with UDI primers (New England Biolabs, Ipswich, USA), which bind inside the enhancer cassette. Additionally, 5 ng and 10 ng of plasmid and viral input DNA were used for index PCR, respectively.

treatment_protocol: HepG2 and HaCaT cells were grown to 80% confluency in 12 well plates. Cells were transduced with the STARR-CRAAVT AAV libraries using a multiplicity of infection (MOI) of 100,000 viral genomes per cell. The minP plasmid library was also transfected using 1 ug of DNA and Lipofectamine 3000. Cells were harvested after 72h.

value: Virus


title: Liver, HFHC, STZ, 8 weeks, rep4

description:
Library name: STZ_8w_HFHC_4
S_A_08_70


title: Liver, HFHC, STZ, 8 weeks, rep5

description:
Library name: STZ_8w_HFHC_5
S_A_08_72


title: Liver, HFHC, STZ, 8 weeks, rep2

description:
Library name: STZ_8w_HFHC_2
S_A_08_139


title: AAV DNA, minP library, input

description: Library name: vDNA_Virus_Input_minP_Input_Input_1


title: CTRL23 plasma (control)

source_name: Human plasma

value: Female


title: AAV DNA, AFP library, input

description: Library name: vDNA_Virus_Input_AFP_Input_Input_1


title: E6.5 Epiblast,Jarid2 ko,rep1

value: E6.5 epiblast


title: SKMEL5 SC10 day 8 bulk RNA-seq, replicate 3

city: Nashville

first: Blake

last: Baleami

state: TN

address: 1161 21st Ave S

department: Human Genetic PhD Program

institute: Vanderbilt University

description:
Library name: SC10_day8_rep3_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.

data_processing:
For bulk RNA-seq, reads were aligned to the hg38 human reference genome using HISAT2 and gene counts were generated using featureCounts. For scRNA-seq, reads were processed using Cell Ranger v3.0.2 with the GRCh38 reference transcriptome to generate gene expression count matrices. For bulk ATAC-seq, reads were trimmed with cutadapt, aligned to hg38 using bwa-mem, deduplicated, and peaks were called using MACS2. Processed files deposited in GEO include gene expression matrices and chromatin accessibility peak files used for downstream analyses.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include RNA-seq gene expression matrices, ATAC-seq peak files, and single-cell RNA-seq count matrices.
Supplementary files format and content: Bulk RNA-seq: Gene-level expression counts generated using featureCounts. The file is a comma-separated values (CSV) matrix where rows correspond to genes and columns correspond to samples. Entries represent raw read counts assigned to each gene.
Supplementary files format and content: ATAC-seq: Chromatin accessibility peaks identified from aligned reads. Peak regions are provided in BED/narrowPeak format with genomic coordinates and associated peak scores.
Supplementary files format and content: scRNA-seq: Processed count matrices generated from single-cell RNA-seq data. Each dataset contains the standard three files used by common single-cell analysis pipelines (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). The matrix.mtx file contains the sparse gene-by-cell count matrix, features.tsv.gz lists gene identifiers, and barcodes.tsv.gz lists cell barcodes.

source_name: skin

growth_protocol: SKMEL5 melanoma cells were obtained from ATCC and maintained in a 1:1 mixture of Dulbecco’s Modified Eagle Medium (DMEM) and Ham’s F-12 medium supplemented with 10% fetal bovine serum at 37°C in 5% CO2. Cells were passaged twice weekly using TrypLE and confirmed to be mycoplasma-free. Single cell-derived SKMEL5 subclones were generated by limiting dilution as described previously.

extract_protocol:
For bulk RNA-seq, total RNA was isolated using the TRIzol extraction method according to the manufacturer’s instructions. For scRNA-seq, cells were washed and resuspended in 0.04% BSA in PBS prior to single-cell capture. For ATAC-seq, cells were lysed and nuclei prepared using Omni-ATAC lysis and resuspension buffers prior to transposition.
Bulk RNA-seq libraries were prepared following mRNA enrichment and cDNA library construction using the Illumina TruSeq stranded mRNA sample preparation kit. Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium 3′ gene expression protocol (version 2 chemistry). Bulk ATAC-seq libraries were generated using the Omni-ATAC protocol with Tn5 transposition followed by PCR amplification.

treatment_protocol: Cells were treated with the BRAF inhibitor PLX4720 at a final concentration of 8 µM for the indicated durations. For drug-treated samples, media and drug were replaced every 3 days. Cells treated with PLX4720 for 8 days are referred to as idling cells.

value: skin

value: SKMEL5 melanoma cells

value: melanoma cell line


title: plasmid DNA, PGK library, input

description: Library name: pDNA_Plasmid_Input_PGK_Input_Input_1

source_name: Plasmid

value: Plasmid


title: Crpaf1 rep 1

description: Library name: Crpaf1-1

value: single cells


title: Crskip rep 3

description: Library name: Crskip-3

value: skip


title: SKMEL5 SC10 day 8 bulk RNA-seq, replicate 2

description:
Library name: SC10_day8_rep2_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: SKMEL5 SC10 day 8 bulk RNA-seq, replicate 1

description:
Library name: SC10_day8_rep1_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: RaxCre_Sun1GFP_p90_rna

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust St.

department: Ophthalmology

description:
Library name: RaxCre_Sun1GFP_p90_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

data_processing:
Multiomic and scRNA were processed through the Cell Ranger ARC and Cell Ranger pipeline respectively (10x Genomics) with default parameters. Seurat and Signac was used to perform downstream analysis.
Assembly: GRCm38
Supplementary files format and content: Cell-by-gene and Cell-by-peak count matrix for each sample as .h5 format

source_name: Retina

extract_protocol:
0.01% Nonidet P40 lysis buffer to prepare single nuclei suspension or papain dissociation to prepare single cell suspension
scATAC-Seq and scRNA-Seq following 10x multiome guideline or 10x 3' ver3.1 or ver4 guidelines

value: Retina

value: whole tissue

tag: library protocol

tag: library type

value: mRNA


title: CTRL20 plasma (control)

value: Control


title: CrWT rep 1

description: Library name: CrWT-1


title: CTRL19 plasma (control)


title: CTRL21 plasma (control)

value: Male


title: RaxCre_Sun1GFP_Sox8/Sox9_cKO_p90_rna

description:
Library name: RaxCre_Sun1GFP_Sox8/Sox9_cKO_p90_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

tag: age


title: CTRL18 plasma (control)


title: plasmid DNA, AFP library, input

description: Library name: pDNA_Plasmid_Input_AFP_Input_Input_1


title: SKMEL5 SC10 day 3 bulk RNA-seq, replicate 3

description:
Library name: SC10_day3_rep3_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: Chx10Cre_Sox9_cKO_p120_rna

description:
Library name: Chx10Cre_Sox9_cKO_p120_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Liver, HFHC, STZ, 8 weeks, rep1

description:
Library name: STZ_8w_HFHC_1
S_A_08_138

value: liver

value: male

value: HFHC


title: plasmid DNA, minP library, input

description: Library name: pDNA_Plasmid_Input_minP_Input_Input_1


title: CTRL22 plasma (control)


title: SKMEL5 SC10 day 3 bulk RNA-seq, replicate 1

description:
Library name: SC10_day3_rep1_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: HepG2 cells RNA, PGK AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HepG2_PGK_Transduction_2

value: liver cancer

value: PGK enhancer candidate AAV library


title: CTRL15 plasma (control)

value: Female


title: CTRL16 plasma (control)


title: GlastCre_Sun1GFP_p17_GFP+_atac

description:
Library name: GlastCre_Sun1GFP_p17_GFP+_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq

library_source: genomic single cell

value: Flowsorted GFP+ cells

value: 10x Multiome

value: ATAC


title: Chx10Cre_Sox9_cKO_p14_rna

description:
Library name: Chx10Cre_Sox9_cKO_p14_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: CTRL17 plasma (control)

description: Plasma sample from an unexposed control professional, matched by age and sex, without occupational exposure to anesthetic gases.


title: SKMEL5 SC10 day 3 bulk RNA-seq, replicate 2

description:
Library name: SC10_day3_rep2_bulkRNA
SKMEL5 melanoma subclone SC10 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.

value: skin

value: SKMEL5 melanoma cells

value: melanoma cell line


title: SKMEL5 SC10 day 0 bulk RNA-seq, replicate 3

description:
Library name: SC10_day0_rep3_bulkRNA
Untreated SKMEL5 melanoma subclone SC10 cells used for bulk RNA sequencing.

value: untreated


title: HepG2 cells RNA, PGK AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HepG2_PGK_Transduction_1


title: GlastCre_Sun1GFP_p17_GFP+_rna

description:
Library name: GlastCre_Sun1GFP_p17_GFP+_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Retina


title: HepG2 cells RNA, PGK AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HepG2_PGK_Transduction_3


title: CTRL13 plasma (control)


title: SKMEL5 SC07 day 8 bulk RNA-seq, replicate 3

description:
Library name: SC07_day8_rep3_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: CTRL12 plasma (control)


title: HepG2 cells RNA, minP plasmid candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HepG2_minP_Transfection_3

value: minP enhancer candidate plasmid library


title: HepG2 cells RNA, AFP AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HepG2_AFP_Transduction_1

value: AFP enhancer candidate AAV library


description:
Library name: GlastCre_Sun1GFP_Sox8/Sox9_cKO_p17_GFP+_rna
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: mRNA


title: SKMEL5 SC10 day 0 bulk RNA-seq, replicate 1

description:
Library name: SC10_day0_rep1_bulkRNA
Untreated SKMEL5 melanoma subclone SC10 cells used for bulk RNA sequencing.


title: HepG2 cells RNA, AFP AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HepG2_AFP_Transduction_3


title: HepG2 cells RNA, AFP AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HepG2_AFP_Transduction_2


title: CTRL14 plasma (control)

value: Control


description:
Library name: GlastCre_Sun1GFP_Sox8/Sox9_cKO_p17_GFP+_atac
ATAC: BAM file which can be converted to fastq files using bamtofastq


title: HepG2 cells RNA, minP AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HepG2_minP_Transduction_3

value: minP enhancer candidate AAV library


title: SKMEL5 SC07 day 3 bulk RNA-seq, replicate 2

description:
Library name: SC07_day3_rep2_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: SKMEL5 SC10 day 0 bulk RNA-seq, replicate 2

description:
Library name: SC10_day0_rep2_bulkRNA
Untreated SKMEL5 melanoma subclone SC10 cells used for bulk RNA sequencing.


title: SKMEL5 SC07 day 8 bulk RNA-seq, replicate 1

description:
Library name: SC07_day8_rep1_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: CTRL10 plasma (control)

description: Plasma sample from an unexposed control professional, matched by age and sex, without occupational exposure to anesthetic gases.

value: Male


title: CTRL11 plasma (control)


title: SKMEL5 SC07 day 8 bulk RNA-seq, replicate 2

description:
Library name: SC07_day8_rep2_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: p17_h3k4me3_rep2

description:
Library name: p17_h3k4me3_rep2
paired-end fastq files

data_processing:
Sequencing reads were trimmed to remove adaptors before aligning the reads to the mouse GRCm38 reference genome using bowtie2. Spike-in normalization was performed using E. coli–aligned (K12-MG1655) read counts to generate sample-specific scaling factors. Fragment files and normalized coverage tracks were produced. Peaks were called with SEACR (stringent mode) using matched IgG controls.
Assembly: GRCm38
Supplementary files format and content: bigWig and bed files containing genomic coordinates of enriched binding
Library strategy: CUT&RUN

source_name: retina

extract_protocol:
0.01% Nonidet P40 lysis buffer to prepare single nuclei suspension
600,000 nuclei were processed using the Epicypher CUT&RUN v5 kit with antibodies against H3k4me3, H3k27ac, Sox8, Sox9 and IgG. The cleaved DNA fragments were prepared for sequencing using the Epicypher CUT&RUN library prep kit v1.

value: retina

tag: antibody

value: H3k4me3 (EpiCypher 13-0060K)


title: p17_sox8_ab5_rep2

description:
Library name: p17_sox8_ab5_rep2
paired-end fastq files

value: SOX8 (Proteintech 20627-1-AP)


title: SKMEL5 SC07 day 0 bulk RNA-seq, replicate 2

description:
Library name: SC07_day0_rep2_bulkRNA
Untreated SKMEL5 melanoma subclone SC07 cells used for bulk RNA sequencing.


title: HaCaT cells RNA, PGK AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HaCaT_PGK_Transduction_3

source_name: HaCaT

value: HaCaT

value: keratinocyte

value: PGK enhancer candidate AAV library


title: CTRL09 plasma (control)


title: SKMEL5 SC07 day 3 bulk RNA-seq, replicate 3

description:
Library name: SC07_day3_rep3_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.

value: skin


title: SKMEL5 SC07 day 0 bulk RNA-seq, replicate 1

description:
Library name: SC07_day0_rep1_bulkRNA
Untreated SKMEL5 melanoma subclone SC07 cells used for bulk RNA sequencing.

value: SKMEL5 melanoma cells


title: p17_sox8_ab3_rep2

description:
Library name: p17_sox8_ab3_rep2
paired-end fastq files

value: SOX8 (GeneTex GTX129949)


title: HaCaT cells RNA, PGK AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HaCaT_PGK_Transduction_1


title: p17_h3k27ac_rep2

description:
Library name: p17_h3k27ac_rep2
paired-end fastq files

value: H3K27ac (EpiCypher 13-0059)


title: CTRL07 plasma (control)

value: Female


title: CTRL03 plasma (control)


title: HepG2 cells RNA, minP AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HepG2_minP_Transduction_2

value: liver cancer


title: p17_sox8_ab3_rep1

description:
Library name: p17_sox8_ab3_rep1
paired-end fastq files


title: p17_sox8_ab5_rep1

description:
Library name: p17_sox8_ab5_rep1
paired-end fastq files


title: HepG2 cells RNA, minP plasmid candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HepG2_minP_Transfection_1

value: minP enhancer candidate plasmid library


title: HaCaT cells RNA, AFP AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HaCaT_AFP_Transduction_2

value: AFP enhancer candidate AAV library


title: p17_sox9_ab4_rep1

description:
Library name: p17_sox9_ab4_rep1
paired-end fastq files

value: SOX9 (Millipore Sigma ab5535)


title: HaCaT cells RNA, AFP AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HaCaT_AFP_Transduction_3


title: CTRL08 plasma (control)

description: Plasma sample from an unexposed control professional, matched by age and sex, without occupational exposure to anesthetic gases.

value: Control


title: p17_igg_ctrl_rep2

description:
Library name: p17_igg_ctrl_rep2
paired-end fastq files

value: IgG (EpiCypher 13-0042K)


title: SKMEL5 SC01 day 8 bulk RNA-seq, replicate 1

description:
Library name: SC01_day8_rep1_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.

value: melanoma cell line


title: SKMEL5 SC01 day 8 bulk RNA-seq, replicate 3

description:
Library name: SC01_day8_rep3_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: SKMEL5 SC07 day 0 bulk RNA-seq, replicate 3

description:
Library name: SC07_day0_rep3_bulkRNA
Untreated SKMEL5 melanoma subclone SC07 cells used for bulk RNA sequencing.

value: untreated


title: CTRL06 plasma (control)


title: CTRL05 plasma (control)


title: HaCaT cells RNA, PGK AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HaCaT_PGK_Transduction_2


title: p17_sox9_ab4_rep2

description:
Library name: p17_sox9_ab4_rep2
paired-end fastq files

value: retina


title: HepG2 cells RNA, minP AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HepG2_minP_Transduction_1

value: minP enhancer candidate AAV library


title: SKMEL5 SC01 day 3 bulk RNA-seq, replicate 3

description:
Library name: SC01_day3_rep3_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: SKMEL5 SC07 day 3 bulk RNA-seq, replicate 1

description:
Library name: SC07_day3_rep1_bulkRNA
SKMEL5 melanoma subclone SC07 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: p2_sox9_ab4_rep2

description:
Library name: p2_sox9_ab4_rep2
paired-end fastq files


title: SKMEL5 SC01 day 3 bulk RNA-seq, replicate 1

description:
Library name: SC01_day3_rep1_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: CTRL02 plasma (control)


title: p2_sox8_ab5_rep2

description:
Library name: p2_sox8_ab5_rep2
paired-end fastq files

value: SOX8 (Proteintech 20627-1-AP)


title: SKMEL5 SC01 day 0 bulk RNA-seq, replicate 3

description:
Library name: SC01_day0_rep3_bulkRNA
Untreated SKMEL5 melanoma subclone SC01 cells used for bulk RNA sequencing.


title: HaCaT cells RNA, minP AAV candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HaCaT_minP_Transduction_3

value: HaCaT

value: keratinocyte


title: p17_h3k27ac_rep1

description:
Library name: p17_h3k27ac_rep1
paired-end fastq files


title: SKMEL5 SC01 day 0 bulk RNA-seq, replicate 1

description:
Library name: SC01_day0_rep1_bulkRNA
Untreated SKMEL5 melanoma subclone SC01 cells used for bulk RNA sequencing.

value: skin

value: SKMEL5 melanoma cells


title: CTRL04 plasma (control)

description: Plasma sample from an unexposed control professional, matched by age and sex, without occupational exposure to anesthetic gases.


title: CTRL01 plasma (control)


title: p17_h3k4me3_rep1

description:
Library name: p17_h3k4me3_rep1
paired-end fastq files

value: H3k4me3 (EpiCypher 13-0060K)


title: SKMEL5 SC01 day 8 bulk RNA-seq, replicate 2

description:
Library name: SC01_day8_rep2_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to bulk RNA sequencing.


title: Control vs. OsSGS3b mutant 2

city: Matsuyama

first: Masamichi

last: Nishiguchi

address: 3-5-7 Tarumi

country: Japan

institute: Ehime University

description: Biological replicate 2 of 2.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: the Agilent G2505C DNA microarray scanner.

data_processing: Signal intensities were extracted by Feature Extraction software version 10.5.1.1

organism: Oryza sativa

source_name: leaf

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Rice seedlings were transferred to small plastic boxes containing commercial soil for rice cultivation (Iseki, Matsuyama, Japan) and placed in growth chambers (temperature ranged between 23 and 26C under 16 h daylight and 8 h dark)

extract_protocol: Total RNA extracted using Total RNA purification kit (Jene Bioscience) following manufacturer's instructions

treatment_protocol: No particular treatment

tag: Stage

value: 4 weeks

tag: genotype/variation

value: control

source_name: mutant leaf

value: OsSGS3b mutant


title: p2_h3k4me3_rep2

description:
Library name: p2_h3k4me3_rep2
paired-end fastq files


title: p17_igg_ctrl_rep1

description:
Library name: p17_igg_ctrl_rep1
paired-end fastq files


title: SKMEL5 SC01 day 3 bulk RNA-seq, replicate 2

description:
Library name: SC01_day3_rep2_bulkRNA
SKMEL5 melanoma subclone SC01 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 3 days prior to bulk RNA sequencing.


title: Arabidopsis thaliana,output replicate 2

city: Shenzhen

first: Yongzhou

last: Bao

address: BuxinRoad NO. 97, Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description: Library name: Arabidopsis thaliana,output replicate 2

data_processing:
MACS2, v2.1.4, "callpeak -c <STARR-Seq input library bam> -t <STARR-Seq output library bam> --keep-dup all -q 0.05 --gsize 119667750 –nomodel"
Assembly: TAIR10
Supplementary files format and content: narrowPeak

organism: Arabidopsis thaliana

source_name: mature leaves

extract_protocol:
2%CTAB was used to extract 3 μg of Arabidopsis thaliana Col-0 genomic DNA
First, Arabidopsis thaliana genomic DNA fragmented using ultrasonication. The fragmented DNA was size-selected (450–500 bp). DNA fragments underwent end repair, adapter ligation, and purification. Adapter-ligated DNA was then amplified using PCR, incorporating homologous arms for cloning. The purified PCR products, now containing homologous arms, were inserted into the linearized vector backbone. After recombination, all products were pooled, and DNA constructs were subsequently transformed into MegaX DH10B™ T1R electrocompetent cells. All transformed Escherichia coli cultures were pooled and grown in LB medium. The input plasmid library was extracted. The input plasmid library was introduced into Agrobacterium tumefaciens strain GV3101 carrying the helper plasmid pSoup via electroporation. The transformed Agrobacterium culture was grown in YEP medium. The bacteria were harvested and resuspended in infiltration buffer. The suspension was then infiltrated into the leaves of Nicotiana benthamiana plants. The plants were maintained under normal growth conditions for 72 hours. Total RNA was extracted from the transformed Nicotiana benthamiana leaves. Polyadenylated  mRNA was then isolated. The mRNA was treated. First-strand cDNA was synthesized using SuperScript III. Target-specific reverse transcription (RT) was performed. After RT, the reaction was treated with RNase A and H, followed by pooling. In the final PCR amplification, cDNA reaction was used as a template for PCR reaction. Each index PCR was performed. The PCR products were size-selected (450–500 bp) and submitted for Illumina sequencing.The input library for sequencing was generated using a similar PCR setup.

value: mature leaves


title: HepG2 cells DNA, PGK AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HepG2_PGK_Transduction_3

value: liver cancer

value: PGK enhancer candidate AAV library


title: p2_sox9_ab4_rep1

description:
Library name: p2_sox9_ab4_rep1
paired-end fastq files

value: SOX9 (Millipore Sigma ab5535)


title: Arabidopsis thaliana,output replicate 1

description: Library name: Arabidopsis thaliana,output replicate 1


title: HaCaT cells RNA, minP plasmid candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HaCaT_minP_Transfection_2

value: minP enhancer candidate plasmid library


title: HDAC3 KO-AC, bio rep 3

city: Little Rock

first: Rami

middle: Ahmad Nawaf

last: Shahror

state: AR

address: APT 277, 11800 Pleasent Ridge Rd.

institute: University of Arkansas for Medical Sciences

description: Library name: Sample 18

data_processing:
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Macrophages

growth_protocol: Bone marrow was obtained from femurs and differentiated in vitro into macrophages as we previously described.11 Briefly,  bone marrow cells were isolated in cold PBS, filtered, and resuspended in a DMEM high glucose medium containing 20% FBS with 20% L929 conditioned media and 1% penicillin-streptomycin to induce macrophage differentiation. Cells were seeded in  100 mm dishes and allowed to adhere. After 4 days, the media was replaced with fresh differentiation media.

extract_protocol:
Machrophages were homogenized in TRIzol reagent
NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: the suspended  K562 cells were subjected to UV-B irradiation for 15 minutes using a UV crosslinker ). then the cells were resuspended in fresh DMEM media with 10% FBS  and incubated them in a 5% CO2 incubator at 37°C for two hours. Macrophages were co-cultured with apoptotic K562 cells for 45 minutes at 37°C. Non-apoptotic cells were used in control groups. After incubation, the suspended K562 cells were removed and washed with PBS. The BMDMs were maintained for 5 hours for total RNA isolation

value: Macrophages

tag: genotype

value: HDAC3 KO

value: Apototic cells


title: HaCaT cells RNA, minP plasmid candidate enhancer library, biol rep 3

description: Library name: RNA_Cell_HaCaT_minP_Transfection_3

tag: cell type


title: HDAC3 KO-NAC, bio rep 3

description: Library name: Sample 15

tag: treatment

value: Non apototic cells


title: HaCaT cells RNA, AFP AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HaCaT_AFP_Transduction_1

value: HaCaT

value: AFP enhancer candidate AAV library


title: p2_sox8_ab5_rep1

description:
Library name: p2_sox8_ab5_rep1
paired-end fastq files

value: retina

value: SOX8 (Proteintech 20627-1-AP)


title: HepG2 cells DNA, PGK AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HepG2_PGK_Transduction_2


title: SKMEL5 SC01 day 0 bulk RNA-seq, replicate 2

description:
Library name: SC01_day0_rep2_bulkRNA
Untreated SKMEL5 melanoma subclone SC01 cells used for bulk RNA sequencing.

value: skin

value: SKMEL5 melanoma cells

value: melanoma cell line

value: untreated


title: p2_h3k27ac_rep2

description:
Library name: p2_h3k27ac_rep2
paired-end fastq files

value: H3K27ac (EpiCypher 13-0059)


title: p2_sox8_ab3_rep2

description:
Library name: p2_sox8_ab3_rep2
paired-end fastq files

value: SOX8 (GeneTex GTX129949)


title: HaCaT cells RNA, minP plasmid candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HaCaT_minP_Transfection_1

value: keratinocyte


title: HaCaT cells RNA, minP AAV candidate enhancer library, biol rep 2

description: Library name: RNA_Cell_HaCaT_minP_Transduction_2

value: minP enhancer candidate AAV library


title: HDAC3 KO-AC, bio rep 1

description: Library name: Sample 16


title: HepG2 cells DNA, PGK AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HepG2_PGK_Transduction_1

value: liver cancer

value: PGK enhancer candidate AAV library


title: HaCaT cells RNA, minP AAV candidate enhancer library, biol rep 1

description: Library name: RNA_Cell_HaCaT_minP_Transduction_1


title: HDAC3 KO-NAC, bio rep 1

description: Library name: Sample 13

value: Macrophages

value: HDAC3 KO


title: HDAC3 KO-AC, bio rep 2

description: Library name: Sample 17

value: Apototic cells


title: p2_sox8_ab3_rep1

description:
Library name: p2_sox8_ab3_rep1
paired-end fastq files


title: p2_igg_ctrl_rep2

description:
Library name: p2_igg_ctrl_rep2
paired-end fastq files

value: IgG (EpiCypher 13-0042K)


description: Library name: Arabidopsis thaliana, Agrobacterium input library

value: mature leaves


title: cutlured embryo WRI1 and DGAT1 overexpression 5

city: Upton

first: Jorg

last: Schwender

state: NY

address: 50 Bell Ave.

department: Biology

institute: Brookhaven National Laboratory

description: Library name: LG33

data_processing:
Transcriptomic paired-end read data were aligned to a reference Thlaspi arvense genome (GenBank Acc.: GCA_911865555.2, (Nunn et al., 2022, https://doi.org/10.1111/pbi.13775) using HISAT2 v. 2.2.1 (Kim et al., 2019, https://doi.org/10.1038/s41587-019-0201-4).
StringTie v. 2.2.1 (Pertea et al., 2016, https://doi.org/10.1038/nprot.2016.095) was used to assemble reads into transcripts using GenBank Acc.: GCA_911865555.2 as the reference annotation to guide assembly. Novel transcript isoforms were not allowed.
A read count matrix was generated using prepDE.py in the stringtie package.
Assembly: GCA_911865555.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Thlaspi arvense

source_name: cultured embryos

growth_protocol: Developing embryos were dissected from seed pods under sterile conditions approximately 15 days after flowering. 15 dissected embryos were placed in a tissue culture flask with 30 mL filter sterilized growth medium (20% (w/v) polyethylene glycol 4000, 120 mM glucose, 35 mM Gln, 10 mM Ala, pH 5.8; inorganic nutrients see Schwender et al., 2015, https://doi.org/10.1104/pp.15.00385) at 20 °C, at a continuous light condition of 50 μmol m−2 s−1 for 10 days.

extract_protocol:
RNA was extracted using the Spectrum™ Plant Total RNA Kit (Sigma).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: cultured embryos

value: WRI1 and DGAT1 overexpression

value: developing embryo


title: HepG2 cells DNA, AFP AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HepG2_AFP_Transduction_3

value: AFP enhancer candidate AAV library


title: HDAC3 KO-NAC, bio rep 2

description: Library name: Sample 14

value: Non apototic cells


title: cutlured embryo WRI1 and DGAT1 overexpression 4

description: Library name: LG32


description: Library name: Arabidopsis thaliana, plasmid input library


title: HepG2 cells DNA, AFP AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HepG2_AFP_Transduction_2


title: p2_h3k4me3_rep1

description:
Library name: p2_h3k4me3_rep1
paired-end fastq files

value: retina

value: H3k4me3 (EpiCypher 13-0060K)


title: HDAC3 KO-NO Treatment, bio rep 3

description: Library name: Sample 12

value: No treatment


title: HepG2 cells DNA, AFP AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HepG2_AFP_Transduction_1


title: HDAC3 KO-NO Treatment, bio rep 2

description: Library name: Sample 11


title: HDAC3 KO-NO Treatment, bio rep 1

description: Library name: Sample 10


title: p2_h3k27ac_rep1

description:
Library name: p2_h3k27ac_rep1
paired-end fastq files

value: H3K27ac (EpiCypher 13-0059)


title: HepG2 cells DNA, minP plasmid candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HepG2_minP_Transfection_3

value: minP enhancer candidate plasmid library


title: IgG_Immunoprecipitation_rep1

city: Washington

first: Aykut

last: Uren

state: DC

address: 3970 Reservoir Road, N.W.

department: Department of Oncology

institute: Georgetown University

description: Library name: aigg1

data_processing:
Data was analyzed using CLC Genomics Workbench 20 software (Qiagen). Ezrin-bound mRNAs were identified with a fold change absolute value of >1.5; a false discovery rate (FDR) p-value of <0.05; and a max group mean of >1 over IgG control.
CLC Genomcs Workbench 20.0.4 was used for mapping the reads to mouse genome.
Assembly: GRCm38
Supplementary files format and content: CSV files include raw counts for each sample
Supplementary files format and content: CSV files include RPKM values for each sample

source_name: Bone

growth_protocol: Mouse OS cell line K7M2 and its derivatives were cultured in DMEM (Gibco, #11875) supplemented with 10% FBS (Sigma-Aldrich #F0926). Cells were maintained at 37C in a humidified atmosphere with 5% CO2 and regularly tested for mycoplasma with MycoAlertTM Mycoplasma Detection kit (Lonza, #75860). K7M2 cell line was fingerprinted with a CellCheck 19 mouse panel by IDEXX BioAnalytics Inc and its STR profile was authenticated by comparing them to the available profile of K7M2 wt (ATCC, Inc., #CRL-2836).

extract_protocol:
Magna RIP (Millipore, #17-700) according to the manufacturer’s instructions. Normal mouse IgG (Millipore, #CS200621) and 𝛼-Ezrin (Sigma-Aldrich, #E8897) were used for the immunoprecipitation. rRNA was depleted with NEBNext rRNA Depletion Kit v2 (NEB, #E7400S) according to the manufacturer’s instructions
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required. RNA libraries were sequenced for 6 G of raw data per sample with PE 150bp read length on NovaSeq platform

treatment_protocol: No treatment was performed.

value: Bone

value: Mouse Osteoblast Osteosarcoma

value: Ezrin -/- transfected with Ezrin T567A


title: Control vs. OsRDR1 mutant 2

description: Biological replicate 2 of 2.

source_name: control leaf

growth_protocol: Rice seedlings were transferred to small plastic boxes containing commercial soil for rice cultivation (Iseki, Matsuyama, Japan) and placed in growth chambers (temperature ranged between 23 and 26C under 16 h daylight and 8 h dark)

value: 4 weeks seedlings

value: wild type

value: leaf

value: OsRDR1 mutant


title: WT-AC, bio rep 3

description: Library name: Sample 9

value: Macrophages

value: WT

value: Apototic cells


title: cutlured embryo WRI1 and DGAT1 overexpression 3

description: Library name: LG31

value: cultured embryos

value: WRI1 and DGAT1 overexpression

value: developing embryo


title: Ezrin_Immunoprecipitation_rep2

description: Library name: aezrin2


title: cutlured embryo WRI1 and DGAT1 overexpression 1

description: Library name: LG29


title: p2_igg_ctrl_rep1

description:
Library name: p2_igg_ctrl_rep1
paired-end fastq files

value: retina

value: IgG (EpiCypher 13-0042K)


title: HepG2 cells DNA, minP plasmid candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HepG2_minP_Transfection_1

value: liver cancer


title: cutlured embryo WRI1 and DGAT1 overexpression 2

description: Library name: LG30


title: WT-AC, bio rep 2

description: Library name: Sample 8


title: WT-AC, bio rep 1

description: Library name: Sample 7


title: HepG2 cells DNA, minP AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HepG2_minP_Transduction_3

value: minP enhancer candidate AAV library


title: cutlured embryo WT 5

description: Library name: LG28


title: Control vs. OsRDR1 mutant l

description: Biological replicate 1 of 2.


title: Ezrin_Immunoprecipitation_rep1

description: Library name: aezrin1

value: Bone


title: Control vs. OsSGS3b mutant 1

description: Biological replicate 1 of 2.

value: 4 weeks

value: control

value: OsSGS3b mutant


title: WT-NAC, bio rep 3

description: Library name: Sample 6

value: Non apototic cells


title: HepG2 cells DNA, minP AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HepG2_minP_Transduction_2


title: Nicotiana benthamiana,RNA replicate 1

description: Library name: Nicotiana benthamiana,RNA replicate 1

data_processing:
follow the bioinformatic pipeline of ATAC-STARR-seq
Assembly: Niben261
Supplementary files format and content: bed

organism: Nicotiana benthamiana

source_name: 4-weeks old leaves

extract_protocol:
We spun 500g Nicotiana benthamiana leaf to prepare nuclei.
First，assay for transposase-accessible chromatin (ATAC) was conducted.Then，adapter-ligated DNA was then amplified using PCR, incorporating homologous arms for cloning. The purified PCR products, now containing homologous arms, were inserted into the linearized vector backbone. After recombination, all products were pooled, and DNA constructs were subsequently transformed into MegaX DH10B™ T1R electrocompetent cells. All transformed Escherichia coli cultures were pooled and grown in LB medium. The input plasmid library was extracted. The input plasmid library was introduced into Agrobacterium tumefaciens strain GV3101 carrying the helper plasmid pSoup via electroporation. The transformed Agrobacterium culture was grown in YEP medium. The bacteria were harvested and resuspended in infiltration buffer. The suspension was then infiltrated into the leaves of Nicotiana benthamiana plants. The plants were maintained under normal growth conditions for 72 hours. Total RNA was extracted from the transformed Nicotiana benthamiana leaves. Polyadenylated  mRNA was then isolated. The mRNA was treated. First-strand cDNA was synthesized using SuperScript III. Target-specific reverse transcription (RT) was performed. After RT, the reaction was treated with RNase A and H, followed by pooling. In the final PCR amplification, cDNA reaction was used as a template for PCR reaction. Each index PCR was performed. The PCR products were size-selected (450–500 bp) and submitted for Illumina sequencing.The input library for sequencing was generated using a similar PCR setup.

value: 4-weeks old leaves


title: HepG2 cells DNA, minP AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HepG2_minP_Transduction_1


title: Nicotiana benthamiana,RNA replicate 2

description: Library name: Nicotiana benthamiana,RNA replicate 2


title: HaCaT cells DNA, PGK AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HaCaT_PGK_Transduction_2

value: HaCaT

value: keratinocyte

value: PGK enhancer candidate AAV library


title: HaCaT cells DNA, PGK AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HaCaT_PGK_Transduction_3


title: Nicotiana benthamiana, DNA replicate 2

description: Library name: Nicotiana benthamiana, DNA replicate 2


title: cutlured embryo WT 1

description: Library name: LG24

value: WT


title: cutlured embryo WT 3

description: Library name: LG26

value: cultured embryos


title: cutlured embryo WT 2

description: Library name: LG25


title: WT-NO Treatment, bio rep 3

description: Library name: Sample 3

value: Macrophages

value: No treatment


description: Library name: Nicotiana benthamiana, plasmid  replicate 2


title: Nicotiana benthamiana, DNA replicate 1

description: Library name: Nicotiana benthamiana, DNA replicate 1


title: cutlured embryo WT 4

description: Library name: LG27

value: developing embryo


title: Overexpressing pleD* (high cdGMP), rep1

description: Library name: 57P1

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)
Read mapping was performed with HISAT2. Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R4 were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s glmQLFTest.
Assembly: NC_011586.2
Supplementary files format and content: raw_counts.tsv includes a tab-delimited matrix with headers with the raw read values for each gene in each sample and condition
Supplementary files format and content: normalised_counts.tsv includes a tab-delimited matrix with headers with the normalised read values for each gene in each sample and condition

organism: Acinetobacter baumannii AB0057

source_name: bacterial cell

growth_protocol: A. baumannii AB0057 derivatives carrying either rocR or pleD* inserted in a miniTn7 transposon  were grown in LB supplemented with IPTG 1 mM (3 biological replicates per strain) until reaching mid-exponential phase (approx. OD600 0.6).

extract_protocol:
Cultures were harvested by centrifugation (or direct resuspension for desiccated cells) in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: Induction pof the expression of either rocR of pleD* by addition of IPTG 1 mM.

value: bacterial cell


title: WT-NO Treatment, bio rep 2

description: Library name: Sample 2


title: Nicotiana benthamiana, ATAC-seq library

description: Library name: Nicotiana benthamiana, ATAC-seq library


title: WT-NAC, bio rep 2

description: Library name: Sample 5


title: Overexpressing pleD* (high cdGMP), rep3

description: Library name: 57P3


title: HaCaT cells DNA, AFP AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HaCaT_AFP_Transduction_2

value: AFP enhancer candidate AAV library


title: HaCaT cells DNA, AFP AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HaCaT_AFP_Transduction_3


title: A549 cells, TGFβ1, bio rep 3

city: Guangzhou

first: Xingyu

last: Lv

address: No. 107, West Jiangxi Road

department: Sun Yat-Sen Memorial Hospital

institute: Sun Yat-sen University

description: Library name: Sample 6

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

source_name: cell line

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

value: cell line

value: alveolar epithelial cells

value: TGFβ1 10ng/mL for 48 hours


title: Overexpressing pleD* (high cdGMP), rep2

description: Library name: 57P2


title: HaCaT cells DNA, PGK AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HaCaT_PGK_Transduction_1


title: Overexpressing rocR (low cdGMP), rep3

description: Library name: 57R3