title: KΔ75_4

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Cell Ranger Software Suite (v3.1.0) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: brain

extract_protocol:
Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
single nucleus RNA sequencing

value: cortex

value: 2 years


title: NCI-H2023-CDDP-R_miR-455-5p_REP2

status: Public on Dec 31 2022

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: NCI-H2023-CDDP-R cells subjected to treatment cycles (n=11) of Cisplatin and then transfected with a miR-455-5p mimic

hyb_protocol: Samples were then hybridized ON, washed, stained, and scanned using the GeneChip Hybridization Oven 640, Fluidic Station 450.

scan_protocol: Scanner 3000 7G (Thermo Fisher Scientific) were used to generate the raw data files (.CEL files) according to the manufacturer's instruction.

data_processing: Quality control and normalization of CEL files were performed using Transcriptome Analysis Console (TAC) software v4.0 (Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38. The analyses were performed in two independent biological experiments and gene expression data were Log2 transformed before analyses.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cell line, overexpressing a miR-455-5p mimic

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (GeneChip® Human Clarion S Array; ThermoFisher Scientific).

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 5% FBS and 1% penicillin/streptomycin (Gibco). Cells were maintained at 37°C and 5% CO2 in a humidified incubator. Cells were routinely verified as free of mycoplasma contamination.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Hilden, Germany), treated with DNase-RNase free (Qiagen, Hilden, Germany) and quantified by Nanodrop (Thermo Fisher Scientific).

treatment_protocol: Negative control mimic (Qiagen, cat. 1027281) and miR-455-5p mimic (Qiagen, cat. 219600) were transiently transfected at a concentration of 5nM using Lipofectamine RNAiMAX (Invitrogen). To obtain NCI-H2023-Parental and NCI-H2023-CDDP-R cells,  NCI-H2023 cells were subjected prior transfection to treatment cycles (n=11) consisting of 3-4 days of either NaCl 0.9% vehicle solution or cisplatin (sigma) treatment and 1-2 weeks of culture in RPMI 5% FBS 1% penicillin/streptomycin .

tag: cell line id

tag: tissue

value: Lung adenocarcinoma cell line from lymph node of stage IIIA NSCLC


title: NCI-H2023-CDDP-R_miR-455-5p_REP1


title: Smart-HCT-52

type: SRA

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

country: China

institute: HKUST

description: HCT116 single cell 052

library_source: transcriptomic

data_processing:
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

source_name: HCT116 cell line

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics

value: Colon

tag: method


title: NCI-H1993_miR-455-5p_REP2

description: NCI-H1993 cells transfected with miR-455-5p mimic


title: NCI-H1993_CTRL_REP2

description: NCI-H1993 cells transfected with a negative control mimic

source_name: cell line, overexpressing a negative control mimic


title: NCI-H1993_miR-455-5p_REP1


title: KΔ75_1

country: USA

organism: Mus musculus

tag: strain

tag: age

tag: genotype


title: Smart-HCT-51

description: HCT116 single cell 051


title: NCI-H1993_CTRL_REP1


title: LNmet_pN0_POOL1

description: pool of 5 lymph nodal metastasis collected before treatment from stage IIIA NSCLC patients who responded to neoadjuvant chemotherapy (pN0)

source_name: lymph nodal metastasis

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (GeneChip® Pico reagent Kit and GeneChip® Human Clarion S Array; ThermoFisher Scientific).

extract_protocol: Two FFPE tissue sections (5–10μm thick) on glass slides with adequate tumor cellularity (>60%) were selected by a certified pathologist and microdissected by scraping with a scalpel prior to RNA isolation. Total RNA was extracted using AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany), treated with DNase-RNase free (Qiagen, Hilden, Germany) and quantified by Nanodrop (Thermo Fisher Scientific). For any sample, RNA from 5 individual patients balanced for sex, age and hystotype were pooled.

value: FFPE  tissue

tag: tumor type

value: NSCLC

tag: tumor stage

value: stage IIIA

tag: metastatic site

value: mediastinal lymph node

tag: response to neoadjuvant chemotherapy

value: sensitive (pN0)


title: LNmet_pN0_POOL2


title: KΔ75_3


title: Smart-HCT-50

description: HCT116 single cell 050


title: KΔ75_2


title: Smart-HCT-47

description: HCT116 single cell 047


title: WT3

value: WT


title: Smart-HCT-46

description: HCT116 single cell 046


title: Batch2_Oleanolic acid(Medium dose)_rep3

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description:
Batch2_Oleanolic acid(Medium dose)_rep3
935

data_processing:
Quality of raw sequence data was checked via the FastQC and adapter or low quality bases were trimmed with TrimGalore
After trimming, the reads were aligned to the human reference genome (hg38) using the STAR aligner
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation GRCh38.84 Gene Transfer Format (GTF) file
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

tag: cell line

tag: dose

value: 2 uM


title: Smart-HCT-49

description: HCT116 single cell 049


title: genomic DNA from peripheral blood leukocyte DNA 29

type: genomic

city: Beijing

first: Pei

last: Cao

address: No 2 Building Guangqu Road Chaoyang District

institute: China National Center for Food Safety Rsik Assessment

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412123

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K Beadchip using standard Illumina protocol

scan_protocol: The raw image intensities of the hybridized arrays were scanned using an Illumina iScan SQ scanner (iScan System, Illumina)

data_processing: The obtained raw image intensity data (including original signal values and detection P values) were processed by GenomeStudio v1.9 software (Illumina)

molecule: genomic DNA

source_name: peripheral blood leukocyte DNA 29

label_protocol: Standard Illumina Protocol

growth_protocol: A total of 32 health children aged between 2 to 15 years (13 males, 19 females) were recruited as respondents from each household. According to the internal exposure of DON, sex, age and BMI, 32 participants were divided into two groups (the low and high DON exposure group).

extract_protocol: Genomic DNA was extracted and purified from peripheral blood WBCs using the QIAamp DNA Mini Kit according to the manufactures' instructions.

treatment_protocol: About 3 ml of peripheral blood was taken for DNA extraction.White blood cells were isolated from blood specimens using the GMS10038.1 Blood Leukocyte Separation Kit.

value: peripheral blood


title: genomic DNA from peripheral blood leukocyte DNA 30

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411213

source_name: peripheral blood leukocyte DNA 30


title: genomic DNA from peripheral blood leukocyte DNA 28

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412235

source_name: peripheral blood leukocyte DNA 28


title: genomic DNA from peripheral blood leukocyte DNA 27

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411252

source_name: peripheral blood leukocyte DNA 27


title: Smart-HCT-48

description: HCT116 single cell 048


title: LNmet_pN2_POOL2

description: pool of 5 lymph nodal metastasis collected before treatment from stage IIIA NSCLC patients who did not respond to neoadjuvant chemotherapy (pN2)

value: resistant (pN2)


title: Smart-HCT-45

description: HCT116 single cell 045


title: genomic DNA from peripheral blood leukocyte DNA 31

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411352

source_name: peripheral blood leukocyte DNA 31


title: LNmet_pN2_POOL1


title: WT4


title: Batch2_Oleanolic acid(Low dose)_rep3

description:
Batch2_Oleanolic acid(Low dose)_rep3
936


title: genomic DNA from peripheral blood leukocyte DNA 25

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411443

source_name: peripheral blood leukocyte DNA 25


title: Smart-HCT-44

description: HCT116 single cell 044


title: genomic DNA from peripheral blood leukocyte DNA 32

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412074

source_name: peripheral blood leukocyte DNA 32


title: WT2


title: Batch2_Oleanolic acid(High dose)_rep3

description:
Batch2_Oleanolic acid(High dose)_rep3
934

value: 10 uM


title: WT1


title: Batch2_Oleanolic acid(Low dose)_rep2

description:
Batch2_Oleanolic acid(Low dose)_rep2
926


title: Smart-HCT-42

description: HCT116 single cell 042


title: Smart-HCT-41

description: HCT116 single cell 041


title: Batch2_Paeoniflorin(Medium dose)_rep3

description:
Batch2_Paeoniflorin(Medium dose)_rep3
932


title: Smart-HCT-40

description: HCT116 single cell 040


title: Smart-HCT-39

description: HCT116 single cell 039


title: genomic DNA from peripheral blood leukocyte DNA 24

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412274

source_name: peripheral blood leukocyte DNA 24


title: genomic DNA from peripheral blood leukocyte DNA 26

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411342

source_name: peripheral blood leukocyte DNA 26


title: genomic DNA from peripheral blood leukocyte DNA 17

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412373

source_name: peripheral blood leukocyte DNA 17


title: genomic DNA from peripheral blood leukocyte DNA 23

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411362

source_name: peripheral blood leukocyte DNA 23


title: Smart-HCT-38

description: HCT116 single cell 038


title: genomic DNA from peripheral blood leukocyte DNA 21

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411553

source_name: peripheral blood leukocyte DNA 21


title: genomic DNA from peripheral blood leukocyte DNA 16

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_411452

source_name: peripheral blood leukocyte DNA 16


title: Smart-HCT-43

description: HCT116 single cell 043


title: genomic DNA from peripheral blood leukocyte DNA 22

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411433

source_name: peripheral blood leukocyte DNA 22


title: Smart-HCT-37

description: HCT116 single cell 037

source_name: HCT116 cell line


title: genomic DNA from peripheral blood leukocyte DNA 20

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412282

source_name: peripheral blood leukocyte DNA 20


title: Batch2_Paeoniflorin(High dose)_rep2

description:
Batch2_Paeoniflorin(High dose)_rep2
921


title: Batch2_Oleanolic acid(Medium dose)_rep2

description:
Batch2_Oleanolic acid(Medium dose)_rep2
925


title: genomic DNA from peripheral blood leukocyte DNA 19

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_412205

source_name: peripheral blood leukocyte DNA 19


title: ATAC-seq_ST3

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

library_source: genomic

data_processing:
ATAC-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Bowtie2 v2.3.4.3. After removing duplications, Samtools v1.9 was used to sort and build the alignment file index. MACS2 was used for peak calling. Parameters were used as follows: --keep-dup 1 --shift -100 --extsize 200 –nomodel.
RNA-seq: Raw data was first processed by FastQC for quality control, and cleaned using Trim-galore. Clean data were then aligned to the Mouse (mm10) reference genome using default settings of Tophat2 v2.1.1. Then, samtools v1.9 was used to sort and build the alignment file index. Gene expression counts were generated using FeatureCounts v1.6.3. Differential analysis was conducted using DESeq2 and significant genes were selected with padj < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq: ATAC_peak text files
Supplementary_files_format_and_content: RNA-seq: raw gene counts text files

source_name: microglia from whole brain (cerebellum and olfactory bulb removed)

extract_protocol:
Nuclei was extracted from isolated microglia in 5 ml of lysis buffer (0.32M sucrose, 5 mM CaCl2, MgAce2, EDTA, Tris-HCl pH=8, w/o 0.1% NP-40) and collected by centrifugation.
ATAC-seq library was generated using reagents from TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-02) according to the manuscript’s instruction with modifications.

tag: gender

value: male

value: 5 month


title: genomic DNA from peripheral blood leukocyte DNA 18

description:
peripheral blood sample from low DON exposure  group
SAMPLE A_411212

source_name: peripheral blood leukocyte DNA 18


title: Batch2_Paeoniflorin(Low dose)_rep3

description:
Batch2_Paeoniflorin(Low dose)_rep3
933


title: Smart-HCT-35

description: HCT116 single cell 035


title: ATAC-seq_ST2


title: Batch2_Oleanolic acid(High dose)_rep2

description:
Batch2_Oleanolic acid(High dose)_rep2
924


title: Batch2_Paeoniflorin(Medium dose)_rep2

description:
Batch2_Paeoniflorin(Medium dose)_rep2
922


title: Batch2_Paeoniflorin(Low dose)_rep2

description:
Batch2_Paeoniflorin(Low dose)_rep2
923


title: Batch2_Paeoniflorin(High dose)_rep3

description:
Batch2_Paeoniflorin(High dose)_rep3
931


title: genomic DNA from peripheral blood leukocyte DNA 14

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412152

source_name: peripheral blood leukocyte DNA 14


title: ATAC-seq_CO3


title: genomic DNA from peripheral blood leukocyte DNA 12

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412054

source_name: peripheral blood leukocyte DNA 12


title: Smart-HCT-36

description: HCT116 single cell 036


title: Batch2_Oleanolic acid(Low dose)_rep1

description:
Batch2_Oleanolic acid(Low dose)_rep1
916


title: genomic DNA from peripheral blood leukocyte DNA 13

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412113

source_name: peripheral blood leukocyte DNA 13


title: genomic DNA from peripheral blood leukocyte DNA 15

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_411472

source_name: peripheral blood leukocyte DNA 15


title: Batch2_Oleanolic acid(Medium dose)_rep1

description:
Batch2_Oleanolic acid(Medium dose)_rep1
915


title: Batch2_Paeoniflorin(Medium dose)_rep1

description:
Batch2_Paeoniflorin(Medium dose)_rep1
912


title: Smart-HCT-32

description: HCT116 single cell 032


title: Smart-HCT-34

description: HCT116 single cell 034


title: ATAC-seq_ST1


title: Smart-HCT-31

description: HCT116 single cell 031


title: genomic DNA from peripheral blood leukocyte DNA 9

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412213

source_name: peripheral blood leukocyte DNA 9


title: Batch2_Oleanolic acid(High dose)_rep1

description:
Batch2_Oleanolic acid(High dose)_rep1
914


title: Smart-HCT-30

description: HCT116 single cell 030


title: RNA_seq_ST3

extract_protocol:
Immediately after microglia purification, total RNA was extracted by using Direct-zol RNA Microprep kit (Zymoresearch Cat#R2062) following manufactory’s instruction.
RNA-seq library was generated using QIAseq® Stranded RNA Library Kit (Qiagen,180743) according to the manuscript’s instruction.


title: Smart-HCT-33

description: HCT116 single cell 033


title: genomic DNA from peripheral blood leukocyte DNA 11

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412393

source_name: peripheral blood leukocyte DNA 11


title: Smart-HCT-28

description: HCT116 single cell 028


title: Smart-HCT-29

description: HCT116 single cell 029


title: Batch2_Paeonol(High dose)_rep3

description:
Batch2_Paeonol(High dose)_rep3
834


title: RNA_seq_ST2


title: RNA_seq_CO3


title: Batch2_Paeoniflorin(Low dose)_rep1

description:
Batch2_Paeoniflorin(Low dose)_rep1
913


title: genomic DNA from peripheral blood leukocyte DNA 5

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412083

source_name: peripheral blood leukocyte DNA 5


title: Batch2_Hederagenin(Low dose)_rep3

description:
Batch2_Hederagenin(Low dose)_rep3
833


title: ATAC-seq_CO1


title: ATAC-seq_CO2


title: genomic DNA from peripheral blood leukocyte DNA 6

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412162

source_name: peripheral blood leukocyte DNA 6


title: Smart-HCT-26

description: HCT116 single cell 026


title: Batch2_Paeoniflorin(High dose)_rep1

description:
Batch2_Paeoniflorin(High dose)_rep1
911


title: RNA_seq_CO2


title: Batch2_Hederagenin(Medium dose)_rep3

description:
Batch2_Hederagenin(Medium dose)_rep3
832


title: genomic DNA from peripheral blood leukocyte DNA 10

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412014

source_name: peripheral blood leukocyte DNA 10


title: genomic DNA from peripheral blood leukocyte DNA 7

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412332

source_name: peripheral blood leukocyte DNA 7


title: Gastrocnemius iSAC, biological rep4

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

country: Spain

institute: CIBER

description: Gene expression data from Gastrocnemius of SAC mice.

hyb_protocol: Following fragmentation and terminal labeling,  ss-cDNA was hybridized for 17hr at 45ºC on Clariom™ S  HT, mouse array plate, using the automated GeneTitan System (Affymetrix), which includes the hybridization oven, Fluidic Station and Scanner

scan_protocol: Chips were scanned using the Scanner of the GeneTitan System

data_processing: Transcriptome Analysis Console 4.0 Software. Summarization Method: Gene Level-SST-RMA. Gene-Level Fold Change < -1,5 or > 1,5. Gene-Level P-Value < 0,05. Anova Method: ebayes

label_protocol: 150 ng of good quality RNA samples (RIN >8) with a Ratio 260/280 = 1.8-2 were used.  Fragmentation and Biotin labelling of ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit user guide, using an automated system (Biomek FX System, Beckman Coulter)

growth_protocol: 15 weeks old male mice were fed chow diet or a high-fat diet (45% lipids) or sucrose (50% in drinking water) for 6 weeks and sacrificed to isolate plasma exosomes

extract_protocol: Total RNA was extracted from frozen liver, eWAT and gastrocnemius muscle with miRNeasy Mini Kit and treated with DNAse, following standard procedures

treatment_protocol: 15 weeks old male mice maintained in chow diet were injected with the plasma exosomes described above and sacrificed 72 h after the injection

value: Gastrocnemius

tag: treatment

value: chow diet + SAC exos


title: genomic DNA from peripheral blood leukocyte DNA 8

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412233

source_name: peripheral blood leukocyte DNA 8


title: Smart-HCT-25

description: HCT116 single cell 025


title: Smart-HCT-27

description: HCT116 single cell 027


title: Batch2_Paeonol(Low dose)_rep3

description:
Batch2_Paeonol(Low dose)_rep3
836


title: Smart-HCT-24

description: HCT116 single cell 024


title: Batch2_Paeonol(Low dose)_rep2

description:
Batch2_Paeonol(Low dose)_rep2
826


title: Batch2_Paeonol(Medium dose)_rep3

description:
Batch2_Paeonol(Medium dose)_rep3
835


title: RNA_seq_ST1


title: genomic DNA from peripheral blood leukocyte DNA 4

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412273

source_name: peripheral blood leukocyte DNA 4


title: Smart-HCT-20

description: HCT116 single cell 020

source_name: HCT116 cell line


title: RNA_seq_CO1


title: Batch2_Hederagenin(High dose)_rep3

description:
Batch2_Hederagenin(High dose)_rep3
831


title: Smart-HCT-19

description: HCT116 single cell 019


title: Smart-HCT-18

description: HCT116 single cell 018


title: Batch2_Paeonol(Low dose)_rep1

description:
Batch2_Paeonol(Low dose)_rep1
816


title: Gastrocnemius iHFD, biological rep3

description: Gene expression data from Gastrocnemius of HFD mice.

value: chow diet + HFD exos


title: Smart-HCT-23

description: HCT116 single cell 023


title: Gastrocnemius iHFD, biological rep4


title: Gastrocnemius iHFD, biological rep2


title: Smart-HCT-17

description: HCT116 single cell 017


title: Batch2_Paeonol(Medium dose)_rep1

description:
Batch2_Paeonol(Medium dose)_rep1
815


title: Gastrocnemius iSAC, biological rep1


title: Batch2_Paeonol(Medium dose)_rep2

description:
Batch2_Paeonol(Medium dose)_rep2
825


title: Batch2_Paeonol(High dose)_rep2

description:
Batch2_Paeonol(High dose)_rep2
824


title: Smart-HCT-22

description: HCT116 single cell 022


title: Gastrocnemius iSAC, biological rep2


title: Gastrocnemius iCT, biological rep4

description: Gene expression data from Gastrocnemius of CT mice.

value: chow diet + CT exos


title: Smart-HCT-21

description: HCT116 single cell 021

value: Colon


title: Gastrocnemius iHFD, biological rep1


title: BMDMs, IL4_3

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Hisat2 with default parameters;
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using stringtie;
The raw count of each gene were calculated by Htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
The BMDMs were isolated from bone marrow
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Treat by 20ng/ml IL4 or/with 100ng/ml LPS

tag: cell type

value: BMDMs

value: bone marrow

value: Il4 stimulate 24h


title: Gastrocnemius iSAC, biological rep3


title: Smart-HCT-16

description: HCT116 single cell 016


title: Gastrocnemius iCT, biological rep2


title: Batch2_Hederagenin(Low dose)_rep2

description:
Batch2_Hederagenin(Low dose)_rep2
823


title: Gastrocnemius iCT, biological rep1


title: BMDMs, IL4_LPS_3

value: Il4 stimulate 24h wash out and LPS stimulate 4h


title: genomic DNA from peripheral blood leukocyte DNA 1

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412303

source_name: peripheral blood leukocyte DNA 1


title: genomic DNA from peripheral blood leukocyte DNA 3

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412293

source_name: peripheral blood leukocyte DNA 3


title: BMDMs, IL4_1


title: Batch2_Hederagenin(Medium dose)_rep2

description:
Batch2_Hederagenin(Medium dose)_rep2
822


title: Batch2_Hederagenin(Low dose)_rep1

description:
Batch2_Hederagenin(Low dose)_rep1
813


title: Smart-HCT-14

description: HCT116 single cell 014


title: BMDMs, ctrl_LPS_3

value: LPS stimulate 4h


title: Batch2_Hederagenin(High dose)_rep2

description:
Batch2_Hederagenin(High dose)_rep2
821


title: Batch2_Hederagenin(Medium dose)_rep1

description:
Batch2_Hederagenin(Medium dose)_rep1
812


title: Batch2_Hederagenin(High dose)_rep1

description:
Batch2_Hederagenin(High dose)_rep1
811


title: Smart-HCT-15

description: HCT116 single cell 015


title: Gastrocnemius iCT, biological rep3


title: eWAT iSAC, biological rep4

description: Gene expression data from eWAT of SAC mice.

value: eWAT


title: eWAT iSAC, biological rep2


title: Batch2_Paeonol(High dose)_rep1

description:
Batch2_Paeonol(High dose)_rep1
814


title: BMDMs, IL4_LPS_1


title: Smart-HCT-13

description: HCT116 single cell 013


title: Smart-HCT-10

description: HCT116 single cell 010


title: Smart-HCT-08

description: HCT116 single cell 008


title: BMDMs, ctrl_LPS_1


title: BMDMs, ctrl_3

value: Control


title: genomic DNA from CCD-19Co transfected with p16-Dnmt vector 64d

first: Baozhen

last: Zhang

address: Fuchenglu No.52

department: Dept Aetiology

institute: Peking University Cancer Hospital and Institute

description: This cell line was derived from colon tissue from a 2.5 months old female Black, stably transfected with the p16-Dnmt vector and cultured for 64 days

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: process color bias and Quantile function by R package lumi2.22.1

label: Cy3, Cy5

growth_protocol: Cultured in Eagle's Minimum Essential Medium supplemented with 15% FBS and maintained at 37°C in humidified air with 5% CO2

extract_protocol: Genomic DNA was isolated and purified with phenol/chloroform extraction, and further treated with sodium bisulfite using ZYMO EZ DNA Methylation kit

treatment_protocol: Stably transfected with the pTRIPZ empty control vector

tag: transfection

value: p16-Dnmt vector 64d

value: normal fibroblast


title: genomic DNA from CCD-19Co transfected with p16-Dnmt vector 187d

description: This cell line was derived from colon tissue from a 2.5 months old female Black, stably transfected with the p16-Dnmt vector and cultured for 187 days

value: p16-Dnmt vector 187d


title: genomic DNA from CCD-18Co transfected with pTRIPZ control vector

description: This cell line was derived from colon tissue from a 2.5 months old female Black, stably transfected with the pTRIPZ empty control vector

source_name: CCD-pTZ

value: pTRIPZ control vector


title: genomic DNA from peripheral blood leukocyte DNA 2

description:
peripheral blood sample from high DON exposure  group
SAMPLE A_412224

source_name: peripheral blood leukocyte DNA 2

value: peripheral blood


title: genomic DNA from CCD-19Co transfected with p16-Dnmt vector 135d

description: This cell line was derived from colon tissue from a 2.5 months old female Black, stably transfected with the p16-Dnmt vector and cultured for 135 days

value: p16-Dnmt vector 135d


title: Smart-HCT-11

description: HCT116 single cell 011


title: Smart-HCT-07

description: HCT116 single cell 007


title: Batch2_Gallic acid(Low dose)_rep3

description:
Batch2_Gallic acid(Low dose)_rep3
736


title: eWAT iSAC, biological rep1

value: chow diet + SAC exos


title: Dysferlin KO FAPs 1

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

data_processing:
The Illumina sequenced single cell sample fastq files were processed using10x Genomics Cell Ranger 3.0.0 (https://www.nature.com/articles/ncomms14049)
The raw base call files generated by the sequencer, were demultiplexed into fastq files by the cellranger mkfastq function
The function cellranger count was used to align the fastq to the pre-built cell ranger mouse reference (refdata-cellranger-mm10-3.0.0), filter the UMI barcodes and estimate the counts
The output for this step is the feature count matrix, which is provided as an input to Seurat, for further downstream processing
Genome_build: refdata-cellranger-mm10-3.0.0
Supplementary_files_format_and_content: mtx, tsv
Supplementary_files_format_and_content: alignment file, matrix file, barcodes, features

source_name: Fibroadipogenic Progenitors

extract_protocol:
FAPs were isolated from the hindlimb muscles of 8Mo B6A/J and WT female mice in a modified protocol from our previously published study (Hogarth et al, NComms 2019). Mice were euthanized and the tibialis anterior, extensor digitorum longus, gastrocnemius, soleus, quadriceps and psoas were immediately dissected. Non-muscle tissue including tendon, nerve and overlying fascia were carefully removed, and muscles were minced finely in a sterile dish and incubated in Collagenase II (2.5U/ml, ThermoFisher, #17101015) in PBS for 30min at 37°C. The resulting slurry was washed with sterile PBS before further digest in Collagenase D (1.5U/ml, Sigma Aldridge, #COLLD-RO) and Dispase II (2.4U/ml, Sigma Aldridge, #D4693) in PBS for 60min at 37°C. Resulting slurries were passed through 100µm and 40µm strainers and primary cells were resuspended in 1ml PBS with 2%FBS and 2nM EDTA. The suspensions were subsequently stained with anti-PDGFRα-APC (1.0 µg per 106 cells in 100 µl, Biolegend, #135908) for flow cytometry. Immediately prior to FACS, cells were stained with 7AAD viability staining solution (1:200 dilution, BioLegend #420404). Cell suspensions were then sorted on an Influx cell sorter (Becton Dickinson, #646500); live cells were enriched by gating based on forward and side scatter, and doublets were excluded using trigger pulse width gating. We gated out 7AAD+ cells to further increase sample viability, before purified PDGFRα+ FAPs were then collected for single cell sequencing.
Libraries were prepared according to 10x's instructions accompanying the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000075 ). At the 10x controller step, single-cell suspension at a density of 1000 cells/µL in 1x PBS with 0.04% BSA was added to real-time polymerase chain reaction (RT-PCR) master mix aiming for sampling around 8000 cells, and then loaded together with Single Cell 3′ v3 gel beads and partitioning oil into a Single Cell 3′ Chip according to the manufacturer’s instructions. RNA transcripts from single cell were uniquely barcoded and reverse-transcribed within droplets to generate single cell cDNAs. Single cell cDNA libraries were generated via end-repair, A tailing, ligation (Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, PN-1000075) and index PCR ( Chromium i7 Multiplex Kit, PN-120262) according to the manufacturer’s instructions (10x genomics, US). Sizes of the preamplified cDNA and sequencing libraries were determined by the DNA high sensitivity kit (Agilent, Cat #5067-4626). All single-cell libraries were sequenced with a customized paired-end with single indexing (28/8/91-bp for v3 libraries) format according to the recommendation by 10X Genomics. These libraries were sequenced on a Novaseq 6000 system using the S1 flow cell (Illumina, US).
Droplet based single cell RNA seq

value: BLA/J

tag: Sex

value: Female

value: 8 Months


title: eWAT iHFD, biological rep3

description: Gene expression data from eWAT of HFD mice.

value: chow diet + HFD exos


title: Batch2_Gallic acid(Medium dose)_rep3

description:
Batch2_Gallic acid(Medium dose)_rep3
735

value: 2 uM


title: eWAT iSAC, biological rep3


title: Smart-HCT-12

description: HCT116 single cell 012

value: Colon


title: Dysferlin KO FAPs 4


title: Smart-HCT-09

description: HCT116 single cell 009


title: Batch2_Gallic acid(high dose)_rep3

description:
Batch2_Gallic acid(high dose)_rep3
734

value: 10 uM


title: Batch2_Catechin(Low dose)_rep3

description:
Batch2_Catechin(Low dose)_rep3
733


title: Dysferlin KO FAPs 3


title: Wild type FAPs 4


title: eWAT iHFD, biological rep4


title: Wild type FAPs 3


title: BMDMs, ctrl_1

value: BMDMs

value: bone marrow


title: Wild type FAPs 2


title: Dysferlin KO FAPs 2


title: Batch2_Catechin(Medium dose)_rep3

description:
Batch2_Catechin(Medium dose)_rep3
732


title: eWAT iHFD, biological rep2

value: eWAT


title: eWAT iHFD, biological rep1


title: Smart-HCT-06

description: HCT116 single cell 006


title: Batch2_Gallic acid(Low dose)_rep2

description:
Batch2_Gallic acid(Low dose)_rep2
726


title: eWAT iCT, biological rep2

description: Gene expression data from eWAT of CT mice.

value: chow diet + CT exos


title: Smart-HCT-05

description: HCT116 single cell 005


title: Batch2_Catechin(Low dose)_rep2

description:
Batch2_Catechin(Low dose)_rep2
723


title: Smart-HCT-03

description: HCT116 single cell 003


title: Smart-HCT-02

description: HCT116 single cell 002


title: Batch2_Gallic acid(Medium dose)_rep2

description:
Batch2_Gallic acid(Medium dose)_rep2
725


title: Batch2_Catechin(Medium dose)_rep2

description:
Batch2_Catechin(Medium dose)_rep2
722


title: D10_3CI

city: Miami

first: Pei-Ciao

last: Tang

state: FL

address: 1501 NW 10th Avenue, Miami, FL 33136, 926 F2

department: Otolayrngology

institute: University of Miami

data_processing:
The single cell suspension was first counted on the Countess II FL for cell number, cell viability, and cell size.
Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000.
Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics).
Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA. The resulting library was sequenced using a custom program on Illumina NovaSeq 6000.
CellRanger 3.1.0 was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files
Genome_build: mm10
Supplementary_files_format_and_content: Processed data were analized with the Rpackage Seurat (version 2.3.1) with Rstudio version 1.1.453 and R version 3.5.1

source_name: 3D inner ear organoid

extract_protocol:
Dissociated organoids in TrypLE. Dissociated cells were filtered through 40µM cell strainer follwed by three washes in 2% BSA/DPBS. Finally, suspended in 2%BSA/DPBS.
Single cell 3’ RNA-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc).

value: R1E derived Inner ear organoid

value: 3 uM CHIR + 4 uM IWP2

tag: induction day


title: Smart-HCT-04

description: HCT116 single cell 004

tag: tissue


title: Batch2_Catechin(High dose)_rep3

description:
Batch2_Catechin(High dose)_rep3
731


title: D08_1,5CI

value: 1.5 uM CHIR + 4 uM IWP2


title: eWAT iCT, biological rep3


title: eWAT iCT, biological rep4


title: Batch2_Catechin(High dose)_rep2

description:
Batch2_Catechin(High dose)_rep2
721


title: Stripped_Bulk_MA-seq_H9

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

description: Bulk H9 gDNA that has been proteased prior to MA-seq

data_processing:
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify genomic based epigenetic marks.
For genomic based reads, read 1 sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11
For genomic based reads, a custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. Processed text files were then created using another custom Perl script that by parsed 5mCpG sites based on their genomic context (GCH vs WCG).  This code is available on request.
For RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq hg19 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: DNA accessibility files (noted in the naming of the file) list detected methylated GCH sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Endogenous 5mC files (noted in the naming of the file) list detected methylated WCG sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Transcript count files (noted in the naming of the file) is a matrix with the columns indicating cell number, and each row indicating the number of transcripts detected for a given gene.

source_name: H9 hESC

growth_protocol: All mammalian cells were culture at 37 C with 5% CO2. HEK293T cells were cultured on tissue culture treated plastic in high glucose DMEM (Gibco cat. No. 10569044) containing L-Glutamine and sodium pyruvate, supplemented with 10% FBS and 1x Penicillin-Streptomycin. H9 cells were grown feeder-free on Matrigel coated plates in mTeSR1 medium. Cells were routinely passaged 1:6 once they reached 75% confluency using 0.25% trypsin-EDTA or Versene solution for HEK293T or H9 cells respectfully. For FACS sorting, a single-cell suspension was created using 0.25% trypsin-EDTA. The trypsin was then neutralized using a serum containing medium. Afterwards, the cells were washed with 1x PBS before being passed through a cell strainer and sorted for single cells into 384 well plates. hiPSCs (Allen Cell line AICS-0024) were grown feeder-free on Matrigel coated plates in mTeSR1 medium. Cells were routinely passaged as clumps 1:6 once they reached 75% confluency using non-enzymatic agitation following manufacturer’s instructions (ReleSR, STEMCELL Tech.).

extract_protocol:
For single cell experiments, cells were sorted via FACs directly into lysis buffer.  For bulk experiments, genomic DNA was extracted using a Dneasy Blood & Tissue Kit from Qiagen.
scMAT-seq  4 µL of Vapor-Lock (QIAGEN) was manually dispensed into each well of a 384-well plate using a 12-channel pipet. All additional dispenses into the 384-well plate were added using the Nanodrop II liquid handling robot (BioNex Solutions). To each well 100 nL of uniquely barcoded 7.5 ng/uL CEL-seq primer containing 4 UMIs was added. The CEL-seq type primers used here were described previously in detail (2). Then 100 nL of lysis buffer (0.175% IGEPAL CA-630, 1.75 mM dNTPs, 1:1,250,000 ERCC RNA spike-in mix (Ambion, 4456740), and 0.19 U RNase inhibitor (Clontech, 2313A)) was added. A single cell was isolated per reaction well using FACS. Unless cryopreserved, after sorting, plates were heated to 65 C for 3 min and returned to ice to lyse the cells. Next, 150 nL of reverse transcription GC tagging mix (0.7 U RNAseOUT (Invitrogen, 10777-019), 1.17x first strand buffer, 11.67 mM DTT, 3.5 U Superscript II (Invitrogen, 18064-071), 0.19 mM SAM, 1.17x GC reaction buffer, 0.1 U M.CviPI (NEB, M0227S)) was added and the plate was heated to 37°C for 1 hr, 4°C for 5 min, 65°C for 10 min, and 70°C for 10 min. Next, 1.75 µL of second strand synthesis mix (1.74x second strand buffer (Invitrogen, 10812-014), 0.35 mM dNTP, 0.14 U E.coli DNA Ligase (Invitrogen, 18052-019), 0.56 U E.coli DNA Polymerase I (Invitrogen, 18010-025), 0.03 U RNase H (Invitrogen, 18021-071)) was added and the plate was cooled to 16°C for 2hr. Afterwards, protease mix (6 µg Protease (Qiagen, 19155), 6.25x buffer 4) was added, and the plate was heated to 50°C for 15 hrs, 70°C for 20 mins, and 80°C for 5 mins. Next, 5hmCs were blocked by adding the following mix (1 U T4-BGT (NEB, M0357L), 6x UDP-glucose, 1x buffer 4) to each well and the plate was heated to 37°C for 16 hrs. Afterwards, protease mix (2 µg Protease, 1x buffer 4) was added, and the plate was heated to 50°C for 3 hrs, 70°C for 20 mins, and 80°C for 5 mins. Next MspJI digestion mix (1x buffer 4, 8x enzyme activator solution, 0.1 U MspJI (NEB, R0661L)) was added and the plate was heated to 37°C for 4.5 hrs, and 65°C for 25 mins. Unless otherwise stated, to each well 320 uL of uniquely barcoded 125 nM MspJI double stranded adapter was added. The MspJI adapters have been described in detail previously (3). Next 680 nL of ligation mix (1.47x T4 ligase reaction buffer, 5.88 mM ATP (NEB, P0756L), 140 U T4 DNA ligase (NEB, M0202M)) was then added, and the plate was cooled to 16°C for 16 hrs. After ligation, reaction wells receiving different barcodes were pooled using a multichannel pipette, and the oil phase was discarded. This was then incubated for 30 mins with 1x AMPure XP beads (Beckman Coulter, A63881), washing twice with 80% ethanol and resuspending in 30 µL of nuclease free water. Afterwards, this was evaporated down to 6.4 µL. Following this step, library preparation was performed as previously described in the scAba-seq and scMspJI-seq protocols (3, 4). Libraries were sequenced on an Illumina NextSeq 500 or an Illumina Hiseq 4000, sequencing a minimum of 75-bp on read 1 to detect 5mC. To detect RNA transcripts, a minimum sequencing length of 25-bp on read 1 and 50-bp on read 2 was utilized. Additionally, unless otherwise stated, transcript detection as only performed on RNA enriched samples and 5mC detection was only performed on unenriched samples.

treatment_protocol: For mesodermal differentiation, the media was replaced with mTeSR1 supplemented with 5 uM of CHIR99021 (STEMCELL Tech.) for 24 hours. For gastrulating 3D stem-cell cultures, on Day 1: hiPSCs (Allen Cell line  AICS-0024) are released from well-plate surfaces using non-enzymatic agitation following manufacturer’s instructions (ReleSR, STEMCELL Tech.). Cells are resuspended as a single-cell suspension at densities of 750K-1M cells/mL in mTeSR1 containing 10μM ROCK inhibitor Y27632 (Abcam). 200μL of cell suspension is then pipetted onto prepatterned dishes (circular features 250 uM in diameter) and allowed to settle for 15 minutes before adding 1mL of mTeSR1 and allowing cells to settle for 10 additional minutes. Excess media is aspirated, leaving enough liquid to cover patterns and is replaced with fresh 2mL of mTeSR until the following day. On day 2: mTESR1 media is exchanged with mTESR1 media containing Matrigel (4%, v/v). This triggers lumen formation over 24hrs. On Day 3: micropatterned colonies have formed a lumen. mTESR1 is exchanged with the addition of 5ng/ml Recombinant Human BMP4 (Fisher Scientific 314BP010). Exposure to BMP4 triggers differentiation of cells and is considered 0 hours for experimental purposes. On Day 4 or 5: Samples were collected for single-cell sequencing at either 20, 36, or 48 hrs post BMP4 supplementation. Samples were dissociated into a single cell suspension using TrypLE reagent (Gibco), and gentle pipetting. The TrypLE reagent was then neutralized using a serum containing medium. Afterwards, the cells were washed with 1x PBS before being passed through a cell strainer and sorted for single cells into 384 well plates.

tag: single-cell

value: Bulk

tag: molecule

value: genomic DNA


title: eWAT iCT, biological rep1

tag: strain


title: Batch2_Gallic acid(high dose)_rep2

description:
Batch2_Gallic acid(high dose)_rep2
724


title: D08_IWP2

value: 0 uM CHIR + 4 uM IWP2


title: Batch2_Gallic acid(Low dose)_rep1

description:
Batch2_Gallic acid(Low dose)_rep1
716


title: PASE8_Lib2_scMAT-seq_20hr-PASE

description: scMAT-seq. 20 hr post BMP4 induction in 3D gastruloid model

data_processing:
Library strategy: scMAT-seq
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify genomic based epigenetic marks.
For genomic based reads, read 1 sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11
For genomic based reads, a custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. Processed text files were then created using another custom Perl script that by parsed 5mCpG sites based on their genomic context (GCH vs WCG).  This code is available on request.
For RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq hg19 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: DNA accessibility files (noted in the naming of the file) list detected methylated GCH sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Endogenous 5mC files (noted in the naming of the file) list detected methylated WCG sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Transcript count files (noted in the naming of the file) is a matrix with the columns indicating cell number, and each row indicating the number of transcripts detected for a given gene.

source_name: AICS-0024 (20 hr 3D gastruloid induction)

tag: cryopreservation

value: Fresh

tag: differentiation

value: 3D gastruloid

value: genomic DNA & polyA RNA


title: Batch2_Gallic acid(Medium dose)_rep1

description:
Batch2_Gallic acid(Medium dose)_rep1
715


title: D05_IWP2


title: Wild type FAPs 1

value: Female

tag: age

value: 8 Months


title: Liver iSAC, biological rep3

description: Gene expression data from liver of SAC mice.

value: Liver

value: chow diet + SAC exos


title: Batch2_Gallic acid(high dose)_rep1

description:
Batch2_Gallic acid(high dose)_rep1
714

value: 10 uM


title: Liver iSAC, biological rep2


title: D08_3CI


title: PASE13_Lib3_scRNA-seq_36hr-PASE

description: scRNA-seq. 36 hr post BMP4 induction in 3D gastruloid model

molecule: polyA RNA

source_name: AICS-0024 (36 hr 3D gastruloid induction)

value: polyA RNA


title: Batch2_Catechin(Low dose)_rep1

description:
Batch2_Catechin(Low dose)_rep1
713


title: D07_3CI


title: Liver iSAC, biological rep1


title: PASE13_Lib2_scRNA-seq_36hr-PASE


title: Smart-HCT-01

description: HCT116 single cell 001

value: Colon

tag: method


title: Liver iSAC, biological rep4


title: PASE13_Lib1_scRNA-seq_36hr-PASE


title: Liver iHFD, biological rep4

description: Gene expression data from liver of HFD mice.

value: chow diet + HFD exos


title: D06_3CI

value: R1E derived Inner ear organoid


title: Liver iHFD, biological rep3


title: Batch2_Catechin(Medium dose)_rep1

description:
Batch2_Catechin(Medium dose)_rep1
712

value: 2 uM


title: PASE16_Lib4_scMAT-seq_48hr-PASE

description: scMAT-seq. 48 hr post BMP4 induction in 3D gastruloid model

source_name: AICS-0024 (48 hr 3D gastruloid induction)


title: PASE16_Lib3_scMAT-seq_48hr-PASE


title: D05_3CI

value: 3 uM CHIR + 4 uM IWP2


title: D04_3CI


title: Batch2_Benzoic acid (Low dose)_rep3

description:
Batch2_Benzoic acid (Low dose)_rep3
636


title: LS005: MPLW515L BM stroma3

city: New York

first: Lei

last: Ding

state: NY

department: Rehabilitation & Regenerative Medicine

institute: Columbia University Irving Medical Center

description: 2 mice pooled together

data_processing:
Data were demultiplexed, aligned, and UMI-collapsed using the Cell Ranger Single-Cell Software Suite (v.4.0.0, 10x Genomics). Transcripts were aligned to a custom mm10/GRCm38 reference genome that included the sequences of GFP and tdTomato. Note that the raw data bam files are aligned to an unmodified mm10/GRCm38 reference genome whereas the processed Cell Ranger output files include GFP and tdTomato transcript counts.
Filtering, normalization, and downstream analysis were performed using the Seurat R package. Low-quality barcodes were filtered out according to the cell quality metrics: total UMI counts, genes detected, and mitochondrial proportion. The filtration process began by applying a minimum cutoff of 700 genes detected and a minimum cutoff of 1000 total UMI counts. After these cutoffs were applied, barcodes were further excluded by removing those at the extreme ends of the distributions of the three quality metrics. Data normalization was achieved by applying the R package sctransform.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: barcodes (barcodes.tsv.gz), genes (features.tsv.gz), and gene-barcode matrix (matrix.mtx.gz) are the filtered output files from Cell Ranger after alignment with a custom mm10 genome including GFP and tdTomato. The normalized_counts_summary.csv file is a summary table of the normalized raw counts for all cells included in the final analysis.

source_name: Hindlimb bone marrow

extract_protocol:
Hindlimb bones were dissected and bone marrow was carefully flushed to minimize tissue disruption using FACS buffer (HBSS + 2% FBS). Intact bone marrow plugs were digested with a mixture of Collagenase IV (200 U/ml, Worthington), Liberase DH (0.3 Wünsch units/ml, MilliporeSigma), and DNase I (200 U/ml, MilliporeSigma) diluted in HBSS (with Ca2+ and Mg2+) at 37ºC for 25 minutes. Samples were then dissociated by repetitive pipetting with a P1000 tip and filtered through a 40 µm cell strainer. Immunostaining was performed for 30 minutes on ice with anti-CD45 (30F-11) and anti-Ter119 to exclude hematopoietic cells. Incubation with Calcein Violet-AM was used to stain live cells and exclude debris. SYTOX Green was added shortly before FACS analysis to exclude dead/dying cells. FACS-isolated stromal cells (CD45/Ter119/GFP/SYTOX Green negative, Calcein Violet-AM positive) were processed using Chromium Controller (10x Genomics).
scRNA-seq libraries were constructed using Chromium Single Cell 3' v3 Reagent Kit according to manufacturer instructions. Sequencing was performed on an Illumina NovaSeq 6000.

tag: genotype

value: Lepr-Cre; tdTomato

value: bone marrow plug

tag: condition


title: Batch2_Benzoic acid (Medium dose)_rep3

description:
Batch2_Benzoic acid (Medium dose)_rep3
635

tag: cell line

tag: dose


title: LS004: Control BM stroma

description: 2 mice pooled together

extract_protocol:
Hindlimb bones were dissected and central marrow tissue was carefully flushed to minimize tissue disruption using FACS buffer (HBSS + 2% FBS). Intact bone marrow plugs were digested with a mixture of Collagenase IV (200 U/ml, Worthington), Liberase DH (0.3 Wünsch units/ml, MilliporeSigma), and DNase I (200 U/ml, MilliporeSigma) diluted in HBSS (with Ca2+ and Mg2+) at 37ºC for 25 minutes. Samples were then dissociated by repetitive pipetting with a P1000 tip and filtered through a 40 µm cell strainer. Immunostaining was performed for 30 minutes on ice with anti-CD45 (30F-11) and anti-Ter119 to exclude hematopoietic cells. Incubation with Calcein Violet-AM was used to stain live cells and exclude debris. SYTOX Green was added shortly before FACS analysis to exclude dead/dying cells. FACS-isolated stromal cells (CD45/Ter119/GFP/SYTOX Green negative, Calcein Violet-AM positive) were processed using Chromium Controller (10x Genomics).
scRNA-seq libraries were constructed using Chromium Single Cell 3' v3 Reagent Kit according to manufacturer instructions. Sequencing was performed on an Illumina NovaSeq 6000.

value: empty vector control


title: Liver iCT, biological rep4

description: Gene expression data from liver of CT mice.

tag: treatment

value: chow diet + CT exos


title: Batch2_Benzoic acid (High dose)_rep3

description:
Batch2_Benzoic acid (High dose)_rep3
634


title: PASE16_Lib2_scMAT-seq_48hr-PASE

value: Fresh

value: 3D gastruloid


title: Liver iCT, biological rep3


title: Liver iHFD, biological rep1


title: PASE15_Lib4_scMAT-seq_IPSC_CHIR_Treatment

description: scMAT-seq. Cells 1-48 untreated IPSC. Cells 49-96 24 hours of CHIR treatment.

source_name: AICS-0024 (WT and 24hr CHIR)

value: 5 uM CHIR

value: genomic DNA & polyA RNA


title: LS003: MPLW515L BM stroma2


title: PASE15_Lib3_scMAT-seq_IPSC_CHIR_Treatment


title: Batch2_Albiflorin (Low dose)_rep3

description:
Batch2_Albiflorin (Low dose)_rep3
633


title: LS002: MPLW515L BM stroma1


title: Batch2_Catechin(High dose)_rep1

description:
Batch2_Catechin(High dose)_rep1
711


title: Liver iCT, biological rep1

value: Liver


title: Liver iHFD, biological rep2


title: Plate38_Lib4_scMAT-seq_H9_RNA_Enriched_Only

description: scMAT-seq RNA Enrichment, testing C1, M270, M280, and T1 bead as well as leaving on C1 beads during library prep. Each dataset is from the same cells and the same amplified RNA was used for all enrichment tests.

value: Frozen


title: hippocampus from young mother rep4

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
raw fastq files were trimmed to remove low-quality reads
STAR was used to map the reads to the mm10 reference genome
Htseq-count was used to calculate the gene raw counts with GENCODE vM20
Genome_build: mm10
Supplementary_files_format_and_content: txt file contain two columns. The first column refers to the gene name and the second column refers to the raw counts.

source_name: hippocampus from young mother

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
The collected M2 oocyte were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences. For hippocampus, a total amount of 2 μg RNA per sample was used.RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For oocyte, after the first reaction of reverse transcription, we used template-switching oligos to obtain the yield of full-length cDNA. Then, we performed RT-PCR to maximize cDNA (After 90 min at 42 °C (the optimal conditions for Superscript II, according to the manufacturer), we raised the temperature to 50 °C for 2 min to promote the unfolding of any RNA secondary structures. We then lowered it to 42 °C again for 2 min and repeated this cycle a total of ten).After the first-strand reaction,We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The quantity of the libraries was assessed and defined by qPCR, respectively, and the libraries were sequenced by Illumina novaseq for 150-bp paired-end reads. For hippocampus, Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. 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 NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: 8-week-old female mice were intraperitoneally injected with rapamycin (2mg/kg) for 40 weeks. At the end of experiment, 4-week-old, 48-week-old and 48-week-old rapa-treated female mice were intraperitoneally injected with pregnant mare serum gonadotropin (PMSG, 5 IU for 4 wks and 10 IU for 48 wks, Ningbo Sansheng Pharmaceutical Corporation, Zhejiang, China) followed by human chorionic gonadotrophin (hCG, 5 IU for 4wk and 10 IU for 48 wks) 46-48 h later to collect M2 matured oocytes. The cumulus cells were removed by pipetting in M2 medium containing 0.1% hyaluronidase (Sigma-Aldrich). Adult female(about 10 month of age) F1 offspring were used to collect hippocampus, and one of hippocampus was fresh frozen in dry ice with RNAlater.

value: hippocampus

tag: cell type

value: 40~44 -week-old

value: wild type


title: PASE15_Lib2_scMAT-seq_IPSC_CHIR_Treatment


title: Liver iCT, biological rep2


title: PASE16_Lib1_scMAT-seq_48hr-PASE


title: Batch2_Benzoic acid (Low dose)_rep2

description:
Batch2_Benzoic acid (Low dose)_rep2
626


title: hippocampus from young mother rep2


title: Batch2_Albiflorin (Medium dose)_rep3

description:
Batch2_Albiflorin (Medium dose)_rep3
632


title: hippocampus from young mother rep1


title: Batch2_Benzoic acid (High dose)_rep2

description:
Batch2_Benzoic acid (High dose)_rep2
624

value: 10 uM


title: Plate38_Lib2_scMAT-seq_H9

description: scMAT-seq on H9 hESC cells


title: hippocampus from rapa-treated aged mother rep3

value: rapa


title: hippocampus from young mother rep3


title: Plate14_1C-3_scMspJI-seq_H9

description: scMspJI-seq on H9 hESC cells

data_processing:
Library strategy: scMspJI-seq
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify genomic based epigenetic marks.
For genomic based reads, read 1 sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11
For genomic based reads, a custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. Processed text files were then created using another custom Perl script that by parsed 5mCpG sites based on their genomic context (GCH vs WCG).  This code is available on request.
For RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq hg19 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: DNA accessibility files (noted in the naming of the file) list detected methylated GCH sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Endogenous 5mC files (noted in the naming of the file) list detected methylated WCG sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Transcript count files (noted in the naming of the file) is a matrix with the columns indicating cell number, and each row indicating the number of transcripts detected for a given gene.


title: Batch2_Albiflorin (Low dose)_rep2

description:
Batch2_Albiflorin (Low dose)_rep2
623


title: Gastrocnemius SAC, biological rep4 [GasSAC4]

description: Gene expression data from Gastrocnemius of SAC mice.

treatment_protocol: 15 weeks old male mice were fed chow diet or a high-fat diet (45% lipids) or sucrose (50% in drinking water) for 6 weeks

value: Gastrocnemius

value: chow diet + sucrose


title: Gastrocnemius SAC, biological rep3 [GasSAC3]


title: Batch2_Albiflorin (High dose)_rep3

description:
Batch2_Albiflorin (High dose)_rep3
631


title: Plate38_Lib1_scMAT-seq_H9

description: scMAT-seq on H9 hESC cells


title: Batch2_Albiflorin (Medium dose)_rep2

description:
Batch2_Albiflorin (Medium dose)_rep2
622

value: 2 uM


title: hippocampus from rapa-treated aged mother rep2


title: Gastrocnemius SAC, biological rep2 [GasSAC2]


title: Gastrocnemius HFD, biological rep3 [GasHFD3]

description: Gene expression data from Gastrocnemius of HFD mice.

value: high-fat diet


title: Plate39_Lib4_scMAT-seq_H9

description: scMAT-seq on H9 hESC cells


title: Gastrocnemius SAC, biological rep1 [GasSAC1]


title: hippocampus from rapa-treated aged mother rep1


title: Batch2_Benzoic acid (Medium dose)_rep2

description:
Batch2_Benzoic acid (Medium dose)_rep2
625


title: Plate39_Lib3_scMAT-seq_H9

description: scMAT-seq on H9 hESC cells


title: Batch2_Albiflorin (High dose)_rep2

description:
Batch2_Albiflorin (High dose)_rep2
621


title: Gastrocnemius HFD, biological rep4 [GasHFD4]


title: hippocampus from aged mother rep3

source_name: hippocampus from aged mother


title: Plate4_Lib2_scMAT-seq_HEK293T

description: scMAT-seq on HEK293T cells


title: Gastrocnemius HFD, biological rep2 [GasHFD2]


title: Gastrocnemius HFD, biological rep1 [GasHFD1]


title: Batch2_Benzoic acid (Low dose)_rep1

description:
Batch2_Benzoic acid (Low dose)_rep1
616


title: Plate3_Lib2_scMA-seq_HEK293T

description: scMA-seq on HEK293T cells

data_processing:
Library strategy: scMA-seq
Illumina bcl2fastq2 v 2.20 software used for basecalling
A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify genomic based epigenetic marks.
For genomic based reads, read 1 sequences were mapped to the hg19 genome build using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11
For genomic based reads, a custom Perl script was used to demultiplex cell barcodes and identify 5mCpG sites from the sam files. Processed text files were then created using another custom Perl script that by parsed 5mCpG sites based on their genomic context (GCH vs WCG).  This code is available on request.
For RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq hg19 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 11. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: DNA accessibility files (noted in the naming of the file) list detected methylated GCH sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Endogenous 5mC files (noted in the naming of the file) list detected methylated WCG sites. Column 1 is the cell number, column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, and column 4 is the strand of the detected mark.
Supplementary_files_format_and_content: Transcript count files (noted in the naming of the file) is a matrix with the columns indicating cell number, and each row indicating the number of transcripts detected for a given gene.

value: genomic DNA


title: Gastrocnemius CT, biological rep4 [GasCT4]

description: Gene expression data from Gastrocnemius of CT mice.

value: chow diet


title: hippocampus from aged mother rep2


title: K27me3 100µM IOX1 THP1

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

country: United Kingdom

institute: Paul O' Gorman Leukaemia Research Centre

data_processing:
First, for RNA-seq datasets, FastQC tool (release 0.11.8, 4 October, 2018) were used to check the overall   quality of the raw reads.
the quality-filtered read samples were then aligned to the Hisat2 genome index
The output SAM files were then converted into the BAM format using Samtools (release 0.1.19, 19 March 2013)
Count matrix was produced with ‘featureCounts’ from the Subread package (release 1.6.4, 14 March 2019)
Second, for ChIP-seq datasets, read quality was checked using FastQC.
Raw reads were trimmed using trim_galore and mapped to a human reference genome (hg38) using bwa.
Picard package was used to sort the reads, convert to bam files, and remove duplicates.
Macs2 was used to call peaks on the fragment sizes prediced for each sample using 'predictd' function in macs2.
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, a tab-delimited text file includes raw gene counts for every gene and every sample. And for ChIP-seq, a tab-delimited text file in a BED format storing genomic regions of coordinates and associated annotations.

source_name: THP-1 cells

growth_protocol: Cells were grown in RPMI containing 10% FBS.

extract_protocol:
Trypan blue cell counts were carried out immediately prior to treatment of cells with IOX1. RNA extraction was carried out using the QIAshredder spin columns and RNeasy Plus Micro Kit or Mini kit according to the manufacturer’s instructions. RNA quantities were assessed by Nanodrop and quality assessed using the Agilent RNA integrity 6000 nano kit. For ChIP-seq, DNA was purified using Diagenode's iPure kit v2.
RNA-seq libraries were produced using the TruSeq stranded mRNA kit (Illumina). For ChIP-seq, libraries were made using the TruSeq ChIP Library Preparation Kit according to the manufacturer's instructions.

treatment_protocol: Stock solutions (1000X) of each tested IOX1 concentration were thawed at RT and 5µl added to respective wells and agitated to ensure distribution of IOX1 throughout the medium. Cells were incubated at 37°C, 5% CO2. Every 24 hours another cell count was performed over a total period of 72 hours. As a negative control THP-1 cells were separately treated with dimethyl sulfoxide (DMSO). IOX1 was prepared in DMSO.

value: human AML cell line

tag: treatment time

value: 48 hours

tag: drug treatment

value: 100uM IOX1

tag: antibody


title: Batch2_Albiflorin (Low dose)_rep1

description:
Batch2_Albiflorin (Low dose)_rep1
613


title: Batch2_Benzoic acid (Medium dose)_rep1

description:
Batch2_Benzoic acid (Medium dose)_rep1
615


title: Batch2_Benzoic acid (High dose)_rep1

description:
Batch2_Benzoic acid (High dose)_rep1
614


title: K27me3 50µM IOX1 THP1

value: 50uM IOX1


title: young oocyte rep2

source_name: young oocyte

tag: tissue

value: oocyte

value: M2 oocyte


title: young oocyte rep1


title: Gastrocnemius CT, biological rep3 [GasCT3]


title: K27me3 DMSO THP1

value: 0.1% DMSO (control)


title: Batch2_Albiflorin (Medium dose)_rep1

description:
Batch2_Albiflorin (Medium dose)_rep1
612


title: Batch2_Albiflorin (High dose)_rep1

description:
Batch2_Albiflorin (High dose)_rep1
611


title: K9me3 DMSO THP1


title: Batch2_vehicle_rep3

description:
Batch2_vehicle_rep3
131

value: vehicle


title: K27me3 30µM IOX1 THP1

value: 30uM IOX1


title: rapa-treated aged oocyte rep3

source_name: rapa-treated aged oocyte

value: wild type


title: rapa-treated aged oocyte rep2

value: rapa


title: Gastrocnemius CT, biological rep2 [GasCT2]

value: Gastrocnemius


title: eWAT SAC, biological rep3 [eWATSAC3]

description: Gene expression data from eWAT of SAC mice.

value: eWAT

value: chow diet + sucrose


title: Batch2_vehicle_rep2

description:
Batch2_vehicle_rep2
121


title: rapa-treated aged oocyte rep1


title: hippocampus from aged mother rep1

value: hippocampus

value: 40~44 -week-old


title: aged oocyte rep2

source_name: aged oocyte


title: Gastrocnemius CT, biological rep1 [GasCT1]

value: chow diet


title: eWAT SAC, biological rep4 [eWATSAC4]


title: K9me3 50µM IOX1 THP1

value: human AML cell line


title: K9me3 100µM IOX1 THP1

value: 48 hours


title: eWAT SAC, biological rep1 [eWATSAC1]


title: eWAT SAC, biological rep2 [eWATSAC2]


title: Batch2_vehicle_rep1

description:
Batch2_vehicle_rep1
111


title: K9me3 30µM IOX1 THP1


description:
Batch1_ethanol extract of PR (Low dose)_rep3
336

value: 20 ug/mL


title: K9me2 DMSO THP1


title: aged oocyte rep1


title: scATAC_ESC_Ola_IFNb_6h_Rep1

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
ATAC-seq bam files: Raw reads were trimmed by Trimmomatic (v0.36) and mapped using Bowtie2 (v2.3.3.1). The mapped reads were with bedtools (v2.27.1) sorted, shifted by +4/-5bp to correct for transposase intragtion bias, duplicates and reads in blacklisted reads removed. Reads with quality score below 30 were removed.
ATAC-seq bed files: The sorted and quality filtered bam files were used for peak calling by MACS2 (v2.1.2).
ATAC Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control.
ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
RNA-seq raw counttable: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. STAR counted reads per genes in ReadsPerGene.out.tab files. These files were combined and the resulting raw count-table was the input for DESeq2.
RNA-seq count table TPM and FPKM: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. The  Aligned.to.Transcriptome.out.bam files from STAR were used as input for RSEM (v1.3.0) to create TPM and FPKM values.
RNA-seq DESeq result tables: Result tables for DESeq2 (1.24.0) for the comparisons of 1h IFNb with 0h; 6h IFNb with 0h and 6h with 1h IFNb.
scATAC-seq: Raw reads were applied to CellRanger (v1.1.0), a full automatic pipeline especially for scATAC-seq data done by the 10x Chromium.
scATAC-seq: The default output counttable for downstream analysis.
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq bam files: Quality filtered mapped read files
Supplementary_files_format_and_content: ATAC-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq peak list for STAT1 and STAT2 by DiffBind: Peak lists for STAT1p701 and STAT2 replicates were anaylzed by DiffBind (v2.12.0) to create list of robust binding sites over replicates. Peaks at 1h and 6h of IFNb treatment were combined
Supplementary_files_format_and_content: RNA-seq raw counttable: Counttable containing ENSEMBL gene ID and the raw read counts for each gene over the replicates in ESCs, MEFs and NPCs
Supplementary_files_format_and_content: RNA-seq count table TPM and FPKM: Counttable with normalized TPM and FPKM values for each samples of ESCs, MEFs and NPCs. In addtition, the ENSEMBL gene ID, all transcript Ids and the annotated gene length.
Supplementary_files_format_and_content: RNA-seq DESeq result tables: Results table from DESeq2 of all genes for the three compariosns of 1h vs 0h, 6h vs 0h and 6h vs 1h. Each files contains the ENSEMBL gene ID, the normalized counts for all used samples, the base mean expression, the log2 fold change of the comaprison, the standard error of the log2 fold change, the Wald statistic, pvalue and adjusted pvalue.
Supplementary_files_format_and_content: scATAC: Counttable with a the coordinates of mapped fragments, the barcode of the fragment and the counts.
Supplementary_files_format_and_content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.

growth_protocol:
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.

extract_protocol:
ATAC-seq: . For ESCs, the cell pellet was resuspended in 200 µl ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl2, 3 mM MgCl2, 0.1 % NP-40) and incubate for at room temperature for 2 min. 20 µl ATAC reaction buffer containing 10 µl 2x transposase buffer and 2.5 µl Tn5 enzyme (Illumina) was added and samples were incubated at 37 °C for 30 min. Samples were purified. For MEFs, the lysis buffer contained additionally 1 % digitonin.
ATAC-seq: Purified samples were directly amplifed, barcoded and purified.
ChIP-seq for histone marks in ESC: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in ESCs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
ChIP-seq for STATs in ESCs and MEFs: The isolation of the chromatin was done with Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003)
ChIP-seq for STATs in ESCs and MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
RNA-seq: Total RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, 740984.250). Depletion of rRNA was done with Ribo-Zero rRNA Removal Kit (Illumina, 15066012) for ESCs and MEFs and with NEBNext® rRNA Depletion Kit (New England Biolabs, E6350).
RNA-seq: Libraries were prepared using NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina (New England Biolabs, E7760).
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).

treatment_protocol: All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours

value: Embryonic stem cells


title: eWAT HFD, biological rep4 [eWATHFD4]

description: Gene expression data from eWAT of HFD mice.

value: high-fat diet


description:
Batch1_ethanol extract of PR (Medium dose)_rep3
335

value: 100 ug/mL


title: scATAC_ESC_Ola_IFNb_0h_Rep1


description:
Batch1_ethanol extract of PR (High dose)_rep3
334

value: 500 ug/mL


title: eWAT HFD, biological rep3 [eWATHFD3]


title: K9me2 50µM IOX1 THP1

value: 50uM IOX1


title: K9me2 100µM IOX1 THP1

value: 100uM IOX1


title: ATAC_MEF_Ola_IFNb_6h_Rep2

description: Resulting peak list from peak calling with MACS2 (broad peak)

value: Mouse embryonic fibroblasts


title: eWAT HFD, biological rep2 [eWATHFD2]


description:
Batch1_water extract of PR (Low dose)_rep3
333


description:
Batch1_water extract of PR (Medium dose)_rep3
332


title: Input control No IP THP1


description:
Batch1_water extract of PR (High dose)_rep3
331


title: K9me2 30µM IOX1 THP1

value: 30uM IOX1


title: eWAT HFD, biological rep1 [eWATHFD1]


title: ATAC_MEF_Ola_IFNb_1h_Rep2


title: eWAT CT, biological rep4 [eWATCT4]

description: Gene expression data from eWAT of CT mice.


description:
Batch1_ethanol extract of PR (Low dose)_rep2
326


title: 100µM IOX1 THP1 r3


title: eWAT CT, biological rep3 [eWATCT3]


title: ATAC_MEF_Ola_IFNb_1h_Rep1


title: ATAC_MEF_Ola_IFNb_0h_Rep2


title: eWAT CT, biological rep2 [eWATCT2]


description:
Batch1_ethanol extract of PR (High dose)_rep2
324


title: ATAC_MEF_Ola_IFNb_0h_Rep1


title: 100µM IOX1 THP1 r1


title: 50µM IOX1 THP1 r3


title: Liver SAC, biological rep4 [LiverSAC4]

description: Gene expression data from liver of SAC mice.

value: Liver


title: uninjured_3

city: Los Angeles

first: Weihong

last: Ge

address: 635 Charles E Young Dr South 355

institute: UCLA

data_processing:
Demux, Cell Ranger 2.2.0, 10X genomics
Alignment/counts, Cell ranger 2.2.0, 10XGenomics
Clustering, Seurat V3
Genome_build: mm10
Supplementary_files_format_and_content: filtered_gene_bc-matrices generated from Cell ranger 2.2.0

source_name: brain

extract_protocol:
Single cell suspensions of adult cortices were prepared as described previously (Wu et al., 2017, Detecting activated cell populations using single-cell RNA-seq. Neuron 96, 313-329). Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics, PN-120237) and the Chromium Single Cell A Chip Kit (10X Genomics, PN-120236) as per the manufacturer ʼs protocol.
10XGenomics Single Cell 3' Droplet-based single cell approach

treatment_protocol: C57BL/6 mice weighing 24-28g were anesthetized with isoflurane. The body temperature of animals was maintained with a heating pad at 37C during surgery and 60 mins ischemia period. MCAO mice were sacrified at 4 different time points after MCAO, otgheter with 2 uninjured wild type controls

value: 6 wks

tag: Sex

value: female

tag: brain region

value: cortical coresponding to ipsilateral perilesional area


description:
Batch1_water extract of PR (Low dose)_rep2
323

data_processing:
Quality of raw sequence data was checked via the FastQC and adapter or low quality bases were trimmed with TrimGalore
After trimming, the reads were aligned to the human reference genome (hg38) using the STAR aligner
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation GRCh38.84 Gene Transfer Format (GTF) file
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample


description:
Batch1_ethanol extract of PR (Medium dose)_rep2
325


title: ATAC_MEF_Ola_IFNb_6h_Rep1

tag: strain


title: eWAT CT, biological rep1 [eWATCT1]

value: eWAT


title: 50µM IOX1 THP1 r2


title: 100µM IOX1 THP1 r2


description:
Batch1_water extract of PR (Medium dose)_rep2
322


title: Liver SAC, biological rep3 [LiverSAC3]

value: chow diet + sucrose


title: uninjured_2

value: male


title: 50µM IOX1 THP1 r1

value: human AML cell line

value: 48 hours


title: uninjured_1


description:
Batch1_ethanol extract of PR (Low dose)_rep1
316

value: 20 ug/mL


title: 30µM IOX1 THP1 r3


title: Liver SAC, biological rep1 [LiverSAC1]


description:
Batch1_water extract of PR (High dose)_rep2
321


title: 30µM IOX1 THP1 r2


title: 7d_ipsilateral

value: cortical perilesional area


title: Liver HFD, biological rep4 [LiverHFD4]

description: Gene expression data from liver of HFD mice.

value: high-fat diet


title: Liver HFD, biological rep3 [LiverHFD3]


description:
Batch1_ethanol extract of PR (Medium dose)_rep1
315

value: 100 ug/mL


title: 7d_contralateral


title: 30µM IOX1 THP1 r1


title: Liver HFD, biological rep2 [LiverHFD2]


description:
Batch1_ethanol extract of PR (High dose)_rep1
314

value: 500 ug/mL


description:
Batch1_water extract of PR (Low dose)_rep1
313


title: 3d_contralateral


title: Liver HFD, biological rep1 [LiverHFD1]


title: 1d_ipsilateral


title: DMSO THP1 r3

value: 0.1% DMSO (control)


description:
Batch1_water extract of PR (Medium dose)_rep1
312


title: DMSO THP1 r2


title: Liver SAC, biological rep2 [LiverSAC2]


description:
Batch1_water extract of PR (High dose)_rep1
311


title: DMSO THP1 r1


title: Liver CT, biological rep4 [LiverCT4]

description: Gene expression data from liver of CT mice.

value: chow diet


title: 4hr_ipsilateral


title: crizotinib treated TS cell line

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

data_processing:
Adapters were trimmed using skewer embedded in docker4seq package (https://pubmed.ncbi.nlm.nih.gov/29069297/)
Reads were mapped with STAR  embedded in docker4seq package
Counts were generated using RSEM  embedded in docker4seq package
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited, raw counts

source_name: lymphoma

growth_protocol: RPMI with 10% FBS or RPMI with 10% FBS containing 0.5-1 μM crizotinib

extract_protocol:
RNA was purified from wild type and crizotinib resistant cell lines using RNeasy mini kit (Qiagen).
libraries generated using TruSeq RNA Access library prep kit (Illumina) following manufacturer’s instructions and starting from 40 ng of DNA-free RNA

treatment_protocol: crizotinib to the medium at a starting concentration of 10 nmol/L. Medium was replaced with fresh RPMI-1640 supplemented with crizotinib every 48 or 72 hours, and cell viability was assessed by flow cytometry after staining with 200 nM tetramethylrhodamine methyl ester (TMRM). After 2-3 passages at the same crizotinib concentration, a higher dose of crizotinib was added to the medium until a final concentration of 1 μM was achieved.

value: TS

value: crizotinib treated


title: Batch1_vehicle_rep3

description:
Batch1_vehicle_rep3
132

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

value: vehicle


title: skate_adult_pelvic_fin_MethylCseq

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Sequenced reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:50)
Trimmed reads were mapped to Leri_hhj.fasta genome reference (containing the λ phage genome as chrLambda) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
The numbers of methylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Genotype and methylation bias correction were performed using MethylDackel (MethylDackel extract Leri_hhj_lambda.fasta $input_bam -o $output --mergeContext --minOppositeDepth 5 --maxVariantFrac 0.5 --OT 10,110,10,110 --OB 40,140,40,140) (https://github.com/dpryan79/MethylDackel). (https://github.com/dpryan79/MethylDackel)
Genome_build: little skate: Leri_hhj.fasta
Supplementary_files_format_and_content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

organism: Leucoraja erinaceus

source_name: little skate adult pelvic fin DNA subjected to MethylC-seq

extract_protocol: MethylC-seq library preparation was performed as described previously (PMID: 25692984). Briefly, 1000 ng of genomic DNA extracted from embryonic and adult skate fins was spiked with unmethylated λ phage DNA (Promega) and sonicated to ~300 bp fragments using M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA was then purified, end-repaired using End-It™ DNA End-Repair Kit (Lucigen) and A-tailed using Klenow Fragment (3'→5' exo-) (New England Biolabs) followed by the ligation of NEXTFLEX® Bisulfite-Seq Adapters. Bisulfite conversion of adaptor-ligated DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research). Library amplification (13 PCR cycles) was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). Library size was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche) yielding ~10-20 nM.

treatment_protocol: no treatment

value: adult

tag: tissue type

value: pelvic fin


title: Liver CT, biological rep3 [LiverCT3]

data_processing: Transcriptome Analysis Console 4.0 Software. Summarization Method: Gene Level-SST-RMA. Gene-Level Fold Change < -1,5 or > 1,5. Gene-Level P-Value < 0,05. Anova Method: ebayes

value: Liver


title: Batch1_vehicle_rep2

description:
Batch1_vehicle_rep2
122


title: skate_st31_pelvic_fin_MethylCseq

source_name: little skate stage 31 embryonic pelvic fin DNA subjected to MethylC-seq

value: stage 31 embryo


title: 3d_ipsilateral

value: 6 wks

value: male


title: Liver CT, biological rep2 [LiverCT2]


title: Batch1_vehicle_rep1

description:
Batch1_vehicle_rep1
112


title: Liver CT, biological rep1 [LiverCT1]


title: skate_st31_pectoral_fin_MethylCseq

source_name: little skate stage 31 embryonic pectoral fin DNA subjected to MethylC-seq

value: pectoral fin


title: crizotinib treated SR786 cell line


title: crizotinib treated KARPAS cell line

value: KARPAS


title: mycelium, VOC-exposed, 72hrs, rep 3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic (Bolger et al., 2014) and the low-quality reads were removed to obtain the clean reads.
Then, about 48 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the P. myriotylum SWQ7 reference genome JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555) (Daly et al., 2022) using HISAT2 (Kim et al., 2015) and > 90% of the reads mapped to the genome from all the samples.
FPKM (Roberts et al., 2011) of each gene was calculated using Cufflinks (Trapnell et al., 2010) , and the read counts of each gene were obtained by HTSeq-count (Anders et al., 2015).
The GFF file "JAAS_PmSWQ7_1.0_assembly_augustus_MU_annots_exclud_t_posons_alt_ts.gff" available from another GEO submission (GSE174557) was used.
Assembly: JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555)
Supplementary files format and content: tab-delimited text file of read counts for all samples
Supplementary files format and content: tab-delimited text file of FPKM values for all samples

organism: Pythium myriotylum

source_name: mycelium

growth_protocol: The antimicrobial activity of the P. oligandrum strain GAQ1 was evaluated against P. myriotylum by using a bipartite plate technique. An actively growing fresh 5 mm diameter mycelial plug of P. oligandrum was inoculated on one side and P. myriotylum on the other side of the plate containing clarified V8 agar media (5% V8 juice and 1.5% agar) whereas the plates without either P. myriotylum or P. oligandrum served as control. Each treatment was applied to three replicate plates and was repeated at least three times (a polycarbonate membrane with a 0.1 µm pore size (GVS filter technology, USA) was placed on the agar). Plates were firmly sealed (at least nine times) with parafilm (PARAFILM M, Bemis, USA) to avoid the leakage of VOCs and incubated at 25°C in the dark. The entire P. myriotylum mycelia, except for the plug, was collected for RNA extraction from 48 h, 60 h, and 72 h after inoculation of the bi-partite plates in triplicate. The collected mycelia were flash-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantity were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

treatment_protocol: See the growth protocol for the description of treatments.

value: mycelium

tag: time

value: VOC-exposed


title: crizotinib treated JB6 cell line


title: 1d_contralateral

tag: age

value: cortical coresponding to ipsilateral perilesional area


title: heart_MI_7d_KO3_rep1

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: Gene expression in heart tissues after  7 days myocardial infarction

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: LV_MI_7 day

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: myocardial infarction

value: heart

value: myocardial infarction

tag: genotype/variation

value: KDM5B knock-out

tag: time point

value: 7 days after myocardial infarction

tag: gender


title: crizotinib treated DEL cell line

tag: cell line

value: DEL

value: crizotinib treated