title: ES_only_ES_d3_rep2

source_name: ES monoculture

value: ES


title: viviparous species N. micrantha denoted as X-species, Leaf X2 rep1 [X2-1]

status: Public on Dec 31 2021

type: SRA

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

country: China

institute: The Second Affiliated Hospital of Xinjiang Medical University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. colorata genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Genome_build: Nymphaea_colorata_Nym_GWHAAYW00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Nymphaea micrantha

growth_protocol: The plants of two Nymphaea species N. micrantha (X) and N. colorata (L) (Figure 1A and 1B) were grown in a planting container of 100 cm diameter and 60 cm depth, with 30 cm soil thickness at Water Lily Resource Garden of the Floriculture Institute of Guangxi Academy of Agricultural Sciences, Guangxi, China during the growth season of 2019. Six disease free plants with robust growth for each genotype were selected for the transcriptome study

extract_protocol:
The total RNA was extracted by CTAB method from leaf tissues of each sample using the three biological repeats.
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 M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

treatment_protocol: The harvested leaves were immediately frozen in liquid nitrogen and stored at -80 °C.

tag: genotype

value: viviparous species

value: wild type

tag: developmental stage

value: Development stage

tag: age

value: the leaves are submerged and completely rolled leaves with 4-6 cm length

tag: tissue

value: leaf


title: viviparous species N. micrantha denoted as X-species, Leaf X1 rep1 [X1-1]

value: the leaves are submerged and completely rolled with 1-2 cm length


title: P93_Baseline_CD154

city: Cambridge

first: Ang

middle: Andy

last: Tu

state: MA

address: 500 Main Street

department: Biological Engineering

country: USA

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: scRNA + TCR-Seq
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: hg19
Supplementary_files_format_and_content: gene expression count (genes by cells)

organism: Homo sapiens

source_name: Transcriptome of single cells

extract_protocol: Seq-Well

tag: timepoint

value: Baseline

value: Partial tolerance

tag: sequencing platform

value: NovaSeq S2 100 cycles


title: M03_Stomach_24M_F0_3

city: Chicago

first: Alexander

last: Misharin

state: IL

address: SQBRC 303 E Superior St 5-404

department: Medicine (Pulmonary Division)

institute: Northwestern University

description: mRNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.36) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (GRCm38.p3y) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

organism: Mus musculus

growth_protocol: Male C57BL/6J mice were provided by NIA NIH

extract_protocol:
RNA was isolated using an RNeasy DNA/RNA kit after homogenization and lysis in guanidine thiocyanate buffer supplemented with β-mercaptoethanol. RNA concentration and quality were assessed using an Agilent TapeStation. RNAseq libraries were prepared using an NEB Next RNA Ultra kit with polyA enrichment module using an Agilent Bravo NGS Automated fluidics handling platform as described elsewhere (Misharin et al., 2017, J Exp Med 214). Libraries were multiplexed and sequenced on an Illumina NextSeq 500 platform using 75 cycles of high-output flow cells and a dual indexing strategy.
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) using 75 cycles of high-output flow cells and a dual indexing strategy.

treatment_protocol: Mice were housed at Northwestern University Feinberg School of Medicine Center for Comparative Medicine for 4 weeks prior to sacrifice.

tag: strain

tag: Sex

value: male

tag: organ

value: Stomach

tag: age (months)

tag: pfu (influenza)


title: M03_Kidney_24M_F0_3

description: mRNA-seq

value: Kidney


title: ES-TS-XEN_XEN_d1_rep2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Base calling was performed using bcl2fastq v2.20.0.422 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: plain text (tab-separated values)

source_name: XEN coculture ES-TS-XEN

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.

extract_protocol:
RNA was extracted follwing Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were observed in monoculture (without different cells) or co-culture conditions.

tag: cell type

value: XEN


title: M03_MuscSat_24M_F0_3

description: mRNA-seq

value: Muscle


title: ES-TS-XEN_TS_d1_rep2

source_name: TS coculture ES-TS-XEN

value: TS


title: M03_GutEP_24M_F0_3

description: mRNA-seq

value: Gut epithelium


title: P90_Buildup_CD137

value: Buildup


title: M03_Esophagus_24M_F0_3

description: mRNA-seq

value: Esophagus


title: ES-TS-XEN_ES_d1_rep2

source_name: ES coculture ES-TS-XEN

value: ES


title: ES-TS-PrES_PrES_d1_rep2

source_name: PrES coculture ES-TS-PrES

value: PrES


title: P90_Baseline_CD137


title: ES-TS-PrES_TS_d1_rep2

source_name: TS coculture ES-TS-PrES


title: M03_Cerebellum_24M_F0_3

description: mRNA-seq

value: Cerebellum


title: P90_Avoidance_CD154

value: Avoidance


title: ES-TS-PrES_ES_d1_rep2

source_name: ES coculture ES-TS-PrES


title: M03_Brain_24M_F0_3

description: mRNA-seq

value: Frontal cortex


title: M03_Blood_24M_F0_3

description: mRNA-seq

value: Blood


title: P90_Maintenance_CD154

value: Maintenance

value: Partial tolerance


title: P90_Avoidance_CD137

value: NovaSeq S2 100 cycles


title: M03_Heart_24M_F0_3

description: mRNA-seq

value: male

value: Heart


title: TS-XEN_XEN_d1_rep2

source_name: XEN coculture TS-XEN

value: XEN


title: M03_BAT_24M_F0_3

description: mRNA-seq

value: Brown adipose tissue


title: TS-XEN_TS_d1_rep2

source_name: TS coculture TS-XEN

value: TS


title: P90_Buildup_CD154


title: NHEK_siRNA_IL-37_3

type: RNA

city: Fukuoka

first: Gaku

last: Tsuji

address: Maidashi

institute: Kyushu University

hyb_protocol: The cRNA samples were hybridized onto the array chip at 45 °C for 16 h and stained with streptavidin-phycoerythrin using GeneChip™ Fluidics Station 450 (Applied Biosystem).

scan_protocol: The imaging data were obtained with GeneChip™ Scanner 3000 (Affymetrix).

data_processing: The data were converted to CEL file format using Affymetrix GeneChip® Command Console. The data were normalized with Transcriptome Analysis Console (Applied Biosystems).

label: biotin

source_name: Human keratinocytes transfected with siRNA IL-37

label_protocol: Five hundred nanograms of pooled RNA isolated from NHEKs transfected with either control siRNA or IL-37 siRNA was used for microarray analysis with Clariom™ S Array, human (Applied Biosystem, Waltham, MA, USA). RNA samples derived from the NHEKs were reverse-transcribed to single-stranded cDNA using Genechip™ WT Amplification Kit (Affymetrix). The synthesis of double-stranded cDNA and cRNA was performed in accordance with the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using an RNeasy Plus Micro Kit (Qiagen).

value: Normal Human Epidermal Keratinocytes (NHEK)

value: IL-37 knockdown


title: NHEK_siRNA_IL-37_2


title: NHEK_siRNA_control_2

source_name: Human keratinocytes transfected with siRNA Control

value: control


title: P90_Baseline_CD154

value: Baseline


title: P90_Maintenance_CD137


title: NHEK_siRNA_control_3


title: NHEK_siRNA_IL-37_1


title: M03_Adrenal_24M_F0_3

description: mRNA-seq

value: Adrenal Gland


title: ES-XEN_XEN_d1_rep2

source_name: XEN coculture ES-XEN


title: KO biological rep2

city: Guangzhou

first: Liu

last: Qiuzhen

address: No.1023,South Shatai Road, Baiyun District

country: Zimbabwe

institute: Southern Medical University

description: Gene expression data from NOS1-KO A375 melanoma cell line

hyb_protocol: Sample was hybridized to the Affymetrix Clariom S Assay,human (Cat No 902926) for 16-18 h at 45°C.

scan_protocol: Microarrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method Values presented are log2 RMA signal intensity.

source_name: NOS1-KO A375

label_protocol: Sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT)

extract_protocol: Total RNA was extracted by Trizol, and then purified with NucleoSpin® miRNA (Cat No 740971.250,Macherey-Nagel).

tag: cell line

value: melanoma


title: P84_Maintenance_CD137

value: Placebo


title: ES-XEN_ES_d1_rep2

source_name: ES coculture ES-XEN

value: ES


title: KO biological rep3


title: M02_WAT_24M_F0_2

description: mRNA-seq

value: White adipose tissue


title: P84_Buildup_CD137

value: Buildup


title: M02_Stomach_24M_F0_2

description: mRNA-seq

value: Stomach


title: M02_Skin_24M_F0_2

description: mRNA-seq

value: Skin


title: P84_Baseline_CD137

value: NovaSeq S2 100 cycles


title: P84_Maintenance_CD154_2

description: Maintenance CD154 replicate 2

value: Maintenance


title: TS-PrES_TS_d1_rep2

source_name: TS coculture TS-PrES


title: M02_SI_24M_F0_2

description: mRNA-seq

value: male

value: Small intestine


title: P84_Maintenance_CD154

description: Maintenance CD154 replicate 1


title: ES-PrES_PrES_d1_rep2

source_name: PrES coculture ES-PrES

value: PrES


title: M06_Skin_18M_F0_3

description: mRNA-seq


title: M02_MuscSat_24M_F0_2

description: mRNA-seq

value: Muscle


title: ES-PrES_ES_d1_rep2

source_name: ES coculture ES-PrES


title: NHEK_siRNA_control_1

value: Normal Human Epidermal Keratinocytes (NHEK)


title: KO biological rep1


title: WT biological rep2

description: Gene expression data from WT A375  melanoma cell line

source_name: WT A375

value: WT


title: P84_Buildup_CD154

source_name: Transcriptome of single cells


title: M02_Lung_24M_F0_2

description: mRNA-seq

value: Lung


title: WT biological rep3


title: ES-TS_TS_d1_rep2

source_name: TS coculture ES-TS

value: TS


title: WT biological rep1

value: melanoma


title: JO12

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymtetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed using the Transcriptome Analysis Console (ThermoFisher)

source_name: Patient n.6, Case, Metastatic HNSCC HPV positive patient, post- ICI treatment

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (ClariomS  Assay Guide, Affymetrix, ThermoFisher).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: blood


title: M02_Liver_24M_F0_2

description: mRNA-seq

value: Liver


title: IF71


title: M02_LI_24M_F0_2

description: mRNA-seq

value: Large intestine


title: TS-PrES_PrES_d1_rep2

source_name: PrES coculture TS-PrES


title: XEN_only_XEN_d1_rep2

source_name: XEN monoculture

value: XEN


title: P84_Baseline_CD154

value: Baseline

value: Placebo


title: ES-TS_ES_d1_rep2

source_name: ES coculture ES-TS

value: ES


title: M02_Kidney_24M_F0_2

description: mRNA-seq

value: Kidney


title: P69_Maintenance_CD137

value: Maintenance

value: Treatment failure

value: NovaSeq S2 100 cycles


title: TS_only_TS_d1_rep2

source_name: TS monoculture


title: P69_Buildup_CD137

value: Buildup


title: M02_GutEP_24M_F0_2

description: mRNA-seq

value: male

value: Gut epithelium


title: M02_Heart_24M_F0_2

description: mRNA-seq

value: Heart


title: XEN_only_XEN_d0_rep2


title: P69_Baseline_CD137


title: IF55

source_name: Patient n.6, Case, Metastatic HNSCC HPV positive patient, during- ICI treatment


title: IF64


title: TS_only_TS_d0_rep2

value: TS


title: HY51

source_name: Patient n.5, Control, HNSCC-free after first line treatment


title: P69_Avoidance_CD137

value: Avoidance


title: ES_only_ES_d1_rep2

source_name: ES monoculture


title: FH44

source_name: Patient n.4, Control, HNSCC-free after first line treatment

value: blood


title: M02_Esophagus_24M_F0_2

description: mRNA-seq

value: Esophagus


title: M02_Cerebellum_24M_F0_2

description: mRNA-seq

value: Cerebellum


title: IF46

source_name: Patient n.6, Case, Metastatic HNSCC HPV positive patient, pre- ICI treatment


title: M02_Brain_24M_F0_2

description: mRNA-seq

value: Frontal cortex


title: ES-TS-XEN_XEN_d3_rep1

source_name: XEN coculture ES-TS-XEN

value: XEN


title: FH39

source_name: Patient n.3, Control, HNSCC-free after first line treatment


title: P69_Baseline_CD154

value: Baseline


title: P69_Buildup_CD154


title: ES_only_ES_d0_rep2

value: ES


title: ES-TS-XEN_TS_d3_rep1

source_name: TS coculture ES-TS-XEN


title: M02_Blood_24M_F0_2

description: mRNA-seq

value: Blood


title: M02_BAT_24M_F0_2

description: mRNA-seq

value: Brown adipose tissue


title: FH29

source_name: Patient n.2, Control, HNSCC-free after first line treatment


title: ES-TS-XEN_ES_d3_rep1

source_name: ES coculture ES-TS-XEN


title: FG61

source_name: Patient n.1, Control, HNSCC-free after first line treatment


title: M02_Adrenal_24M_F0_2

description: mRNA-seq

value: Adrenal Gland


title: P69_Maintenance_CD154

source_name: Transcriptome of single cells

value: Maintenance

value: Treatment failure

value: NovaSeq S2 100 cycles


title: P33_Maintenance_Double_negative

value: Partial tolerance


title: P69_Avoidance_CD154


title: breast carcinoma JL97

hyb_protocol: Standard Affymetrix hybridization protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

source_name: breast carcinoma

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: disease state

value: HER2-positive breast cancer

tag: er

value: POS

tag: pgr

tag: response

value: PR

tag: n

value: NEG


title: M01_WAT_24M_F0_1

description: mRNA-seq

value: male

value: White adipose tissue


title: ES-TS-PrES_PrES_d3_rep1

source_name: PrES coculture ES-TS-PrES

value: PrES


title: P33_Buildup_Double_negative

value: Buildup


title: M01_Stomach_24M_F0_1

description: mRNA-seq

value: Stomach


title: P33_Baseline_Double_negative

value: Baseline


title: ES-TS-PrES_TS_d3_rep1

source_name: TS coculture ES-TS-PrES

value: TS


title: breast carcinoma JL96

value: PCR


title: P33_Avoidance_CD137

value: Avoidance


title: ES-TS-PrES_ES_d3_rep1

source_name: ES coculture ES-TS-PrES

value: ES


title: breast carcinoma JL95


title: M01_Skin_24M_F0_1

description: mRNA-seq

value: Skin


title: P33_Avoidance_Double_negative

value: NovaSeq S2 100 cycles


title: TS-XEN_TS_d3_rep1

source_name: TS coculture TS-XEN


title: M01_SI_24M_F0_1

description: mRNA-seq

value: Small intestine


title: breast carcinoma JL94

value: HER2-positive breast cancer


title: P33_Buildup_CD137

value: Partial tolerance


title: M01_MuscSat_24M_F0_1

description: mRNA-seq

value: Muscle


title: M01_Lung_24M_F0_1

description: mRNA-seq

value: Lung


title: breast carcinoma JL92

value: POS

value: PR


title: ES-XEN_ES_d3_rep1

source_name: ES coculture ES-XEN


title: breast carcinoma JL93

value: NEG


title: P33_Baseline_CD137


title: M01_Liver_24M_F0_1

description: mRNA-seq

value: male

value: Liver


title: breast carcinoma JL90


title: P33_Avoidance_CD154


title: M01_LI_24M_F0_1

description: mRNA-seq

value: Large intestine


title: TS-PrES_PrES_d3_rep1

source_name: PrES coculture TS-PrES

value: PrES


title: P33_Maintenance_CD154

value: Maintenance


title: TS-XEN_XEN_d3_rep1

source_name: XEN coculture TS-XEN

value: XEN


title: TS-PrES_TS_d3_rep1

source_name: TS coculture TS-PrES

value: TS


title: P33_Maintenance_CD137


title: M01_Kidney_24M_F0_1

description: mRNA-seq

value: Kidney


title: ES-PrES_PrES_d3_rep1

source_name: PrES coculture ES-PrES


title: P33_Baseline_CD154

value: Baseline

value: NovaSeq S2 100 cycles


title: P33_Buildup_CD154

value: Buildup


title: ES-PrES_ES_d3_rep1

source_name: ES coculture ES-PrES

value: ES


title: M01_Heart_24M_F0_1

description: mRNA-seq

value: Heart


title: P111_Avoidance_Double_negative

value: Avoidance

value: Full tolerance


title: ES-XEN_XEN_d3_rep1

source_name: XEN coculture ES-XEN


title: M01_GutEP_24M_F0_1

description: mRNA-seq

value: Gut epithelium


title: breast carcinoma JL91

value: HER2-positive breast cancer

value: POS

value: PR

value: NEG


title: breast carcinoma JL89

value: PCR


title: ES-TS_TS_d3_rep1

source_name: TS coculture ES-TS


title: ES-TS_ES_d3_rep1

source_name: ES coculture ES-TS


title: M01_Esophagus_24M_F0_1

description: mRNA-seq

value: male

value: Esophagus


title: P111_Maintenance_Double_negative

value: Maintenance


title: breast carcinoma JL85


title: XEN_only_XEN_d3_rep1

source_name: XEN monoculture

value: XEN


title: breast carcinoma JL84


title: P111_Baseline_Double_negative

value: Baseline


title: PrES_only_PrES_d3_rep1

source_name: PrES monoculture

value: PrES


title: P111_Avoidance_CD137

source_name: Transcriptome of single cells

value: NovaSeq S2 100 cycles


title: M01_Blood_24M_F0_1

description: mRNA-seq

value: Blood


title: M01_BAT_24M_F0_1

description: mRNA-seq

value: Brown adipose tissue


title: TS_only_TS_d3_rep1

source_name: TS monoculture

value: TS


title: P111_Maintenance_CD137

value: Full tolerance


title: breast carcinoma JL88

source_name: breast carcinoma


title: M01_Adrenal_24M_F0_1

description: mRNA-seq

value: Adrenal Gland


title: breast carcinoma JL83

value: HER2-positive breast cancer


title: CC849_s12h

city: Beijing

first: Zhenzhen

last: Yang

address: Building 104,Beichen West Road No.1,Chaoyang District

institute: Beijing Institute of Genomics,CAS

data_processing:
FastQC is used to check the sequencing quality
remove adapter, low quality reads, bacterial reads, rRNA reads, Chloroplast reads and mitochondrial reads of CC849 by BWA
nuclear clean reads are mapped to C. reinhardtii genome (JGI v5.5) by using Tophat 2.0.14 with default parameters.
FPKM were calculated using Cufflinks with default parameters
differential genes are found by DEGseq packages of R
Genome_build: Creinhardtii_281_v5.5.gene.gff3
Supplementary_files_format_and_content: tab-delimited text files; including gene_id, gene_short_name, locus, FPKM, FPKM_status, etc

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

source_name: C. reinhardtii cells

growth_protocol: grow in TAP medium

extract_protocol:
according to QIAGEN RNeasy Plant Mini Kit
according to Truseq RNA sample preparation kit

treatment_protocol: The experiment team was transferred to sulfur-depleted TAP, and pump argon for 5 min to achieve anaerobic condition quickly in the bottle, then put the bottles in the dark for 3 hours, and then cultured in the light condition the same as control team.

tag: time

value: at 12 hour

tag: culture conditions

value: anaerobic, sulfur-depleted TAP


title: CC849_s4h

value: at 4 hour


title: P111_Buildup_CD137

value: Buildup


title: breast carcinoma JL87

value: POS

value: PCR


title: breast carcinoma JL81

value: NEG


title: breast carcinoma JL82


title: breast carcinoma JL86

value: PR


title: P111_Buildup_Double_negative


title: ES-TS-XEN_XEN_d1_rep1

source_name: XEN coculture ES-TS-XEN

value: XEN


title: breast carcinoma JL80


title: M01_Brain_24M_F0_1

description: mRNA-seq

value: male

value: Frontal cortex


title: M116_ATII_HC21d_5

first: Ziyou

last: Ren

address: 303 E Chicago Ave

description: mRNA-seq

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.33) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (with mm10 assembly) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

growth_protocol: 9-11 weeks old male mice were obtained from Jackson Laboratories

extract_protocol:
Total RNA from alveolar type 2 cells was extracted using Qiagen RNeasy Plus Mini kit (Qiagen) and quality and quantity were assessed 4200 TapeStation  Agilent
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs); DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) of the average dept of 5–7.5 million aligned reads per sample

treatment_protocol: 3 mice were kept at room air, 3 mice were kept at room air for 14 days and  exposed to 10%CO2 for 7 days,  3 mice were exposed to 10% CO2 for 21 days. At the end of the exposure, mice were ansthetized and both lungs were harvested for flow-sorting of alveolar type 2 cells

tag: treatment

value: flow-sorted alveolar type 2 cells

tag: tissue

value: Lung


title: CC849_c12h

value: aerobic, TAP with sulfur


title: ES-TS-XEN_TS_d1_rep1

source_name: TS coculture ES-TS-XEN

value: TS


title: M115_ATII_HC21d_4

description: mRNA-seq


title: CC849_c4h


title: P111_Avoidance_CD154

tag: timepoint

value: Avoidance

value: Full tolerance

tag: sequencing platform

value: NovaSeq S2 100 cycles


title: ES-TS-XEN_ES_d1_rep1

source_name: ES coculture ES-TS-XEN

value: ES

tag: strain


title: M114_ATII_HC21d_3

description: mRNA-seq

tag: Sex


title: M113_ATII_HC21d_2

description: mRNA-seq


title: M112_ATII_HC21d_1

description: mRNA-seq


title: ES-TS-PrES_PrES_d1_rep1

source_name: PrES coculture ES-TS-PrES

value: PrES


title: ES_only_ES_d3_rep1

source_name: ES monoculture


title: P111_Maintenance_CD154

value: Maintenance


title: ES-TS-PrES_TS_d1_rep1

source_name: TS coculture ES-TS-PrES


title: M111_ATII_HC7d_5

description: mRNA-seq


title: P111_Baseline_CD154

value: Baseline


title: P107_Maintenance_Double_negative

value: Placebo


title: ES-TS-PrES_ES_d1_rep1

source_name: ES coculture ES-TS-PrES


title: P107_Buildup_Double_negative

value: Buildup


title: M110_ATII_HC7d_4

description: mRNA-seq


title: M109_ATII_HC7d_3

description: mRNA-seq


title: ES-XEN_XEN_d1_rep1


title: P111_Baseline_CD137


title: TS-XEN_XEN_d1_rep1

source_name: XEN coculture TS-XEN


title: P107_Baseline_Double_negative


title: M108_ATII_HC7d_2

description: mRNA-seq


title: P107_Maintenance_CD137


title: P107_Buildup_CD137


title: TS-PrES_PrES_d1_rep1

source_name: PrES coculture TS-PrES


title: M107_ATII_HC7d_1

description: mRNA-seq


title: P107_Baseline_CD137


title: ES-XEN_ES_d1_rep1

source_name: ES coculture ES-XEN


title: M105_ATII_NC_5

description: mRNA-seq

value: Naive (Room Air exposure)


title: M106_ATII_NC_6

description: mRNA-seq


title: ES-PrES_PrES_d1_rep1

source_name: PrES coculture ES-PrES


title: P107_Maintenance_CD154


title: P111_Buildup_CD154


title: M104_ATII_NC_4

description: mRNA-seq


title: ES-PrES_ES_d1_rep1

source_name: ES coculture ES-PrES


title: M103_ATII_NC_3

description: mRNA-seq


title: P107_Buildup_CD154


title: ES-TS_TS_d1_rep1

source_name: TS coculture ES-TS


title: ES-TS_ES_d1_rep1

source_name: ES coculture ES-TS


title: M102_ATII_NC_2

description: mRNA-seq


title: M101_ATII_NC_1

description: mRNA-seq


title: P107_Baseline_CD154

source_name: Transcriptome of single cells


title: P106_Buildup_CD154_2

description: Buildup CD154 replicate 2


title: MET∆14Ex_HGF_24h_3

city: Bronx

first: Feng

last: Wang

address: 1300 Morris Park Ave

institute: albert einstein college of medicine

data_processing:
RNA-seq was performed by DNBseq (MGISEQ-2000 PE150)
Sequence reads were aligned to human genome (GRCh38.primary_assembly.genome.fa and gencode.v30.primary_assembly.annotation.gtf) by STAR (v2.6.1b) with default parameters (--readFilesCommand zcat --twopassMode Basic --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapNmax 20 --outSAMtype BAM SortedByCoordinate)
The STAR output Bam files were called to raw counts by HTSeq (v0.6.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts

growth_protocol: NCI-H292 cells were maintained in RPMI 1640 medium supplemented with 10% FBS and 1× Antibiotic/Antimycotic (Thermo Fisher Scientific).

extract_protocol:
The cells were collected and total RNA was extracted using an RNeasy mini kit (QIAGEN, CA). RNA libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit.
The RNA libraries were prepared using DNBseq RNA-seq protocol of BGI

treatment_protocol: Following incubation in serum-free medium for 18h, the cells were treated with HGF (100 ng/mL) for 0, 6 and 24h.

tag: genotype

value: mucoepidermoid carcinoma cells

tag: agent

value: HGF


title: MET∆14Ex_HGF_24h_2

tag: cell type


title: MET∆14Ex_HGF_24h_1


title: XEN_only_XEN_d1_rep1

source_name: XEN monoculture

value: XEN


title: P106_Baseline_CD154_2

description: Baseline CD154 replicate 2


title: TS-PrES_TS_d1_rep1

source_name: TS coculture TS-PrES


title: TS_only_TS_d1_rep1

source_name: TS monoculture


title: MET∆14Ex_HGF_6h_3


title: ES_only_ES_d1_rep1


title: MET∆14Ex_HGF_6h_2


title: MET∆14Ex_HGF_6h_1


title: Winnie/APCmin/5540_rep2

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

data_processing:
The quality control of the obtained reads was checked using the FastQC package
The mapping of paired-end reads was performed using the bioinformatics tool STAR (version 2.5.1a) with the standard parameters. The reference track was the assembly mm10 obtained from ENSEMBL.
The quantification of transcripts expressed for each sequenced samples was performed using featureCount algorithm
Genome_build: mm10
Supplementary_files_format_and_content: File named "rawCount all samples" is a matrix table that contains data about transcripts raw count  for all samples

source_name: ACF macrodissected

extract_protocol:
Total RNA was isolated from ACF macrodissected by using RNeasy FFPE kit (Qiagen) according to the manufacturer instructions.
Indexed libraries were prepared from 20ng/ea purified RNA with TruSeq RNA Exome Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 (Agilent Technologies) and Invitrogen Qubit fluorometer (Thermo Fisher Scientific), then pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM.

value: Colon

tag: age

value: 8 weeks


title: P106_Maintenance_Double_negative


title: Winnie/APCmin/5540_rep1


title: XEN_only_XEN_d0_rep1


title: Winnie/APCmin/5540_rep3


title: P106_Avoidance_Double_negative


title: TS_only_TS_d0_rep1


title: P106_Buildup_Double_negative


title: MET∆14Ex_HGF_0h_3

value: Lung


title: MET∆14Ex_HGF_0h_2


title: ES_only_ES_d0_rep1


title: P107_Baseline_CD154_2

description: Baseline CD154 replicate 2


title: Winnie/APCmin_rep2

value: Winnie/APCmin


title: P106_Baseline_Double_negative


title: MET∆14Ex_HGF_0h_1


title: Winnie/APCmin_rep1


title: TS-XEN_TS_day1_rep1

source_name: TS coculture TS-XEN

value: TS


title: P106_Avoidance_CD137

value: Avoidance

value: Full tolerance


title: G1E-ER4_75nM_rep2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using STAR.
Gene count abundances were estimated using the geneCounts flag with STAR
NA
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw gene counts matrix

source_name: cell line

growth_protocol: IMDM, 15% FBS, 1xPen/Strep, 4.5E-5M mono-thio-glycerate, 50ng/ml murine SCF and 2U/ml erythropoietin

extract_protocol:
Qiagen RLT lysis buffer
Smart-seq2

treatment_protocol: indicated concentrations of beta-estradiol

tag: cell line

value: beta estradiol

tag: agent amount


title: PrES_only_day1_rep2

source_name: PrES monoculture

value: PrES


title: MET_HGF_24h_3

value: WT


title: PrES_only_day1_rep1


title: G1E-ER4_75nM_rep1


title: MET_HGF_24h_2


title: G1E-ER4_50nM_rep2


title: Winnie/APCmin_rep3


title: PrES_only_day0_rep2


title: MET_HGF_24h_1


title: G1E-ER4_50nM_rep1


title: P106_Buildup_CD137

value: NovaSeq S2 100 cycles


title: PrES_only_day0_rep1


title: G1E-ER4_25nM_rep2


title: XEN-like#4Wnt3a

description: XEN-like

source_name: XEN-like

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum alb

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

treatment_protocol: No treatments were performed.


title: MET_HGF_6h_3


title: P106_Baseline_CD137

value: Baseline


title: MET_HGF_6h_2


title: P106_Maintenance_CD154

value: Maintenance


title: G1E-ER4_25nM_rep1


title: P106_Buildup_CD154

value: Buildup


title: P106_Maintenance_CD137


title: MET_HGF_6h_1

value: mucoepidermoid carcinoma cells


title: XEN-like#3Wnt3a

description: XEN-like


title: P106_Baseline_CD154


title: MET_HGF_0h_3

value: HGF


title: MET_HGF_0h_2


title: G1E-ER4_200nM_rep1


title: XEN-like#1Wnt3a

description: XEN-like


title: P106_Avoidance_CD154


title: G1E-ER4_150nM_rep2


title: PBF1 PrEStoXEN#1F

description: PrES to XEN

source_name: PrES to XEN


title: PBF1 PrES#2F

description: PrES

source_name: PrES


title: PBF1 PrEStoXEN#2F

description: PrES to XEN


title: G1E-ER4_12.5nM_rep2


title: MET_HGF_0h_1


title: HCC patients

first: Yifang

last: Gao

address: NO.58 zhongshan 2nd road, YueXiu district

institute: sun yat-sen University

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMC

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

value: peripheral blood

tag: disease state

value: HCC


title: expanded healthy donor5

value: healthy expanded


title: G1E-ER4_12.5nM_rep1


title: XEN#2F Serum/C3L

description: XEN

source_name: XEN


title: P105_Avoidance_CD154


title: PBF1 PrES#1F

description: PrES


title: expanded healthy donor4


title: XEN#2F Serum/L

description: XEN


title: G1E-ER4_200nM_rep2


title: G1E-ER4_100nM_rep1


title: P105_Maintenance_CD154


title: P105_Buildup_CD154

description: Buildup CD154 replicate 1


title: expanded healthy donor2


title: XEN#1M Serum/C3L

description: XEN


title: G1E-ER4_100nM_rep2


title: G1E-ER4_0nM_rep2

value: control


title: XEN#1M Serum/L

description: XEN


title: T48_2

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) were calculated using a protocol from Trapnell et al., Nature protocol, 2014. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI Jatropha curcas Annotation Release 101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Jatropha curcas

source_name: 48-h after GA3 treatment

extract_protocol:
Total RNA from all samples was extracted separately using TIANDZ Plant RNA Kit (TIANDZ column type RNAout 2.0, Beijing). The quantity and purity of total RNA were examined using agarose gel electrophoresis and Nanodrop 2100 (Agilent, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: Nujiang city, Yunnan province, China

value: three years

value: inflorescence meristem

value: 48-h after GA3 treatment


title: T48_1


title: G1E-ER4_0nM_rep1


title: PrES#7-2MP41

description: PrES


title: G1E-ER4_150nM_rep1

value: beta estradiol


title: T24_2

source_name: 24-h after GA3 treatment

value: 24-h after GA3 treatment


title: G1E-R307H_input

library_source: genomic

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using bowtie2
Duplicate reads were removed using Picard and peaks were called with macs2. A consensus peak file was generated using a strategy discussed in the DiffBind workflow (input samples were used in the inference of peak summits).
Bigwig files were generated using macs2 on the merged treated and input bam files and normalized using the SPMR flag.
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw peak / counts matrix; bigwig track views of merged replicates

molecule: genomic DNA

extract_protocol:
1% formaldehyde fixation followed by sonication to shear chromatin
chromatin-immunoprecipitation-sequencing using ChIP-grade anti-HA antibody (ab9110)

tag: gata1 protein construct

tag: chip antibody


title: PrES#5-3MP38

description: PrES


title: H3K27M_IgG_Input

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads (.fastq.gz) were aligned to human genome build hg19 using bwaversion 0.7.12-r1039 using the bwa mem command with default parameters and then sorted using samtools (version 1.6-8-g83bfde1) sort
Sorted alignments (.bam) were quantified using methylQA (Version: 0.2.1 (r052)) density function to generate bigwig tracks for visualization
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: H1 ESC

growth_protocol: H1 human embryonic stem cell (hESC) lines were grown under feeder-free conditions on Matrigel (Catalog  # 354277, Corning) in mTeSR1 Medium (catalog #85850, STEMCELL Technologies) and regularly passaged as aggregates with ReLeSR (STEMCELL Technologies, Cat# 05872). The H1-ESC differentiated colonies were carefully cleaned by manually scratching the colonies with a pipette tip under the microscope.  PSC colonies often exhibited increased differentiation; as this was associated with the presence of the H3K27M mutation these were not removed when the line was maintained. Experiments adhered to protocols approved by the Washington University hESC Research Oversight Committee (#12-002). As this work was designated “nonhuman subjects research” by Washington University’s Institutional Review Board, informed consent was not required. Cells were regularly checked for Mycoplasma contamination (Mycoalert Mycoplasma Detection Kit, Lonza, Cat# LT07-118). The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from the H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC) at Washington University in St. Louis. Prior to transfection the cells were treated with 10 µmol Rock (Y-27632) inhibitor for at least 1 hr. Approximately 1.5X10^6 H1ESC cells were resuspended in P3 primary buffer and electroporated using a 4D-Nucleofector (Lonza) with 1 μg of the H3F3a-K28M-KI-Puromyocin donor plasmid (GeneArt), 1 μg of the gRNA SM928.H3F3a.g37, which targets the sequence 5’- atgctggtaggtaagtaagg agg-3’, and 1.2 μg Cas9 vectors. Nucleofected cells were plated in media containing Rock inhibitor for 24 hrs post nucleofection and then returned to regular E8-Flex media. Following nucleofection, cells were screened with PCR using primer sets specific to the 5' and 3' junctions of the donor plasmid and the target gene. After confirmation of donor plasmid knock-in into the nucleofected pool the cells were treated with 0.2 µg/ml of Puromycin for 72 hrs. Surviving cells were then passaged and treated with 0.5 µg/ml of Puromycin for 72 hrs and Sanger sequencing was used to confirm the heterozygous knockin of the K27M mutation in the 5' junction PCR product of the subclones. Karyotyping of H3F3a-K28M line was performed by Cell Line Genetics.

extract_protocol:
The cell pellets were resuspended in 3 ml cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IPGAL including protease inhibitors) and incubated on ice for 10 minutes, spun at 5000 rpm for 5 min, and the supernatant was aspirated. Nuclei were resuspended in 1ml nuclear lysis buffer (50 mM Tris.HCl pH8.0, 10 mM EDTA, 1% SDS plus protease inhibitors) and incubated on ice for 10 minutes’ cold room rocker. Chromatin was then sonicated with a Biorupter (diagenode) 30 seconds on/off, repeated for 12 cycles total. After sonication, thcells were centrifuged at maximum rpm at RT for 3 minutes, and the supernatant was collected in a new tube. The sheared chromatin was confirmed to be between 300 - 500 bp by agarose gel electrophoresis, and the samples were stored at -80C until used. The 100 µg of chromatin was diluted in ChIP dilution buffer (16.7 mM Tris–HCl (pH 8.1), 167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA)was incubated overnight at 4°C with primary antibodies H3K27me3 (#07-449, Millipore Sigma), and IgG (#PP64-10-KC, Millipore Sigma) in the cold room. The next day, Protein A Dynabeads (Invitrogen) was washed three times in ChIP dilution buffer and added to the IP chromatin, and then the incubation was further continued for 4 hours. After a 4-h incubation, the beads were washed sequentially with 1× low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8), 150 mM NaCl], 1× high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8), 500 mM NaCl), 2× LiCl buffer (0.25 M LiCl, 1% IGEPAL CA- 630 (Sigma), 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris, pH 8.0]. The beads pellet was resuspended in 125 µl of elution buffer (1% SDS, 5 mM DTT, and 150 mM NaCl in Tris-EDTA buffer) and incubated at 65°C for 10 minutes. The supernatant was collected in a new tube, and the elution was repeated again. The DNA was reverse cross-linked (with 200mM NaCl, 1% SDS, 5 mM DTT) at 65°C overnight and 250 µg Protenease K was added and incubated at 37°C for 1 hour. The DNA samples were purified using the NucleoSpin gel/PCR purification kit (Takara). DNA quantification was performed using the Qubit 2.0 fluorometer (Invitrogen), and DNA quality was further confirmed using an Agilent Bioanalyzer 2100 system and high-sensitivity DNA chips. For each library preparation, 1.5 ng of immunoprecipitated chromatin was used for Illumina sequencing-compatible library preparation with the DNA Smart ChIP-seq kit (Takara), as recommended in the manufacturer’s protocol. To assess ChIP enrichment by qPCR, 200–300 pg ChIP and input DNA were used as starting material for amplicon amplification with the 7500 Fast Real-Time PCR System (Applied Biosystems). Enrichment was calculated from at least four biological replicates, with four technical replicates per biological replicate performed.
DNA sizing was determined using an Agilent Bioanalyzer, with the concentration determined by Qubit assay.  Library preparation was performed with up to 10ng of DNA. DNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Size selection was performed with Ampure XP beads (Beckman Coulter) to select for fragments between 150-700bp. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: The cells were maintained in mTeSR medium and harvested for ChIP assay when they reached 80 - 100% confluently. The hESCs were dissociated with Accutase to single cells, and then the Accutase was neutralized with three-volume of mTeSR medium, spun at 1200 rpm for 5 minutes at room temperature. The cell pellets re-suspended in 7.5 ml of mTeSR, and the cells were counted and collected 25M cells in a 15 ml conical tube. The cells DNA-histones were crosslinked with paraformaldehyde (1% final concentration, Electron Microscopy Sciences, #15710) on a rotator for 10 minutes at RT 125mM Glycine quenched it. The cells were washed twice with 1x PBS with protease inhibitor (Roche, #11836170001) and frozen at -80C until they were sonicated.

tag: genotype/variation

value: H3K27M mutant

tag: antibody

value: IgG


title: G1E-GATA1_input


title: H3K27M_IgG_rep2


title: G1E-R307C_input


title: PrES#8-3FP12

description: PrES


title: PrES#8-2MP12

description: PrES


title: H3K27M_IgG_rep1


title: T12_1

source_name: 12-h after GA3 treatment

tag: tissue

value: 12-h after GA3 treatment


title: G1E-GATA1_ChIP_rep2

value: anti-HA antibody (ab9110)


title: H3K27M_H3K27me3_rep4


title: PrES#6-5MP21

description: PrES


title: T6_2

source_name: 6-h after GA3 treatment

tag: timepoint

value: 6-h after GA3 treatment


title: G1E-GATA1_ChIP_rep1


title: PrES#8-1FP12

description: PrES


title: H3K27M_H3K27me3_rep2


title: T6_1


title: P105_Baseline_CD154

description: Baseline CD154 replicate 1

source_name: Transcriptome of single cells

extract_protocol: Seq-Well

value: Baseline

value: Full tolerance

tag: sequencing platform

value: NovaSeq S2 100 cycles


title: G1E-R307H_ChIP_rep2


title: PrES#5-3MP20

description: PrES

tag: strain


title: T0_1

source_name: 0-h after GA3 treatment

value: 0-h after GA3 treatment


title: G1E-R307H_ChIP_rep1


title: H3K27M_H3K27me3_rep1


title: T24_1


title: T12_2


title: G1E-R307C_ChIP_rep2


title: WT_IgG_Input

value: WT


title: WT_IgG_rep2


title: TS#1F

description: TS

source_name: TS


title: G1E-R307C_ChIP_rep1


title: H3K27M_H3K27me3_rep3


title: WT_IgG_rep1


title: LFM2 RNA-seq

city: Qingdao

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

data_processing:
Transcript assemblies were conducted with Cuffinks and the reference annotation based transcripts (RABT) program to obtain a comprehensive set of transcripts.
Then, a comprehensive set of transcripts were obtained by transcript assembly and the reference annotation.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method and the edgeR package were employed to identify DEGs, which were next subjected to GO and KEGG enrichment analysis.
Genome_build: Cynoglossus semilaevis genome
Supplementary_files_format_and_content: PFKM of genes for Cynoglossus semilaevis 30 libraries

organism: Cynoglossus semilaevis

source_name: the muscle of large female Cynolossus semilaevis

extract_protocol:
To increase biological reproducibility, for each tissue, two individuals from large females or small females were firstly combined into one sample, and three samples for each tissue were employed for the following experiment. Subsequently, total RNAs of 30 samples named as SFB-1~3, SFP-1~3, SFL-1~3, SFG-1~3, SFM-1~3, LFB-1~3, LFP-1~3, LFL-1~3, LFG-1~3, and LFM-1~3 were prepared by Trizol (Invitrogen, USA) and assessed by the Agilent 2100 RNA 6000 Nano kit (Agilent, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle

tag: genetic sex

value: large female


title: LFM1 RNA-seq


title: G1E-GATA1_ATAC_rep2

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using bowtie2
Duplicate reads were removed using Picard and peaks were called with macs2. A consensus peak file was generated using a strategy discussed in the DiffBind workflow.
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw peak / counts matrix

extract_protocol: After washing with PBS, around 10,000 cells were lysed and tagmented in 1x TD buffer, 2.5 µl Tn5 (Illumina), 0.1% NP40, 0.3x PBS in a 50 µl reaction volume. Samples were incubated at 37C for 30 min at 300 rpm. Tagmented DNA was purified using the MinElute PCR kit (Qiagen). The complete eluate underwent PCR, as follows. After initial extension, 5 cycles of pre-amplification using indexed primers and NEBNext® High-Fidelity 2X PCR Master Mix (NEB) were conducted, before the number of additional cycles was assessed by quantitative PCR using SYBR Green. Typically, 7-9 additional cycles were run. The final library was purified using a MinElute PCR kit (Qiagen) and quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).

tag: vector

tag: genotype

value: wildtype GATA1


title: WT_H3K27me3_rep4


title: TS#2-2M

description: TS


title: LFG3 RNA-seq

source_name: the gonad of large female Cynolossus semilaevis

value: gonad


title: TS#1-4M

description: TS


title: WT_H3K27me3_rep3


title: G1E-GATA1_ATAC_rep1

source_name: cell line


title: TS#8M

description: TS


title: WT_H3K27me3_rep2


title: G1E-R307H_ATAC_rep1

value: GATA1 point mutant p.R307H


title: LFG2 RNA-seq


title: T0_2

value: Nujiang city, Yunnan province, China

value: three years

value: inflorescence meristem


title: ES#6M NB/2iL

description: ES

source_name: ES


title: LFG1 RNA-seq


title: LFM3 RNA-seq


title: G1E-R307C_ATAC_rep2

value: GATA1 point mutant p.R307C


title: WT_H3K27me3_rep1


title: G1E-R307C_ATAC_rep1


title: ES#1M NB/2iL

description: ES


title: ES#6M FBS/2iL

description: ES


title: TS#2-3F

description: TS


title: RNA_451Lu_parental_rep2

city: Rochester

first: Steven

last: Offer

state: MN

address: 200 First Street Southwest

institute: Mayo Clinic

data_processing:
Realtime base calling was performed on the instrument
Bowtie2 was used to align ChIP-seq reads to the genome
Dulicate reads were filtered using Picard
MACS2 was used for peak calling in H3K27ac and ATAC data
SICER was used for peakcalling in H3K9me3 data
STAR v2.5.3 was usedfor RNAseq alignment and annotation
deepTools was used to transform mapped reads to BigWig files for visualization
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (.bw) files were generated using deepTools
Supplementary_files_format_and_content: .bed files contain peak data for ATAC and ChIP

source_name: Melanoma cell line

extract_protocol: RNA was extracted using the Direct-zol RNA kit (Zymo). Library preparation and sequencing was performed by Novogene using a NovaSeq 6000.

tag: parental or resistant

value: parental


title: TS#2-4F

description: TS

data_processing:
Base calling was performed using bcl2fastq v2.20.0.422 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: plain text (tab-separated values)


title: RNA_451Lu_resistant_rep2

value: Vemurafenib-resistant


title: G1E-R307H_ATAC_rep2


title: LFL2 RNA-seq

source_name: the liver of large female Cynolossus semilaevis

value: liver

tag: age


title: RNA_451Lu_resistant_rep1

tag: cell line


title: ES#1M FBS/2iL

description: ES


title: LFL1 RNA-seq


title: LFL3 RNA-seq


title: LFP3 RNA-seq

source_name: the pituitary gland of large female Cynolossus semilaevis

value: pituitary gland


title: RNA_451Lu_parental_rep1


title: G1E-GATA1_RNA_rep2

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the mm10 reference genome using STAR.
Gene count abundances were estimated using the geneCounts flag with STAR.
NA
Genome_build: mm10
Supplementary_files_format_and_content: Per-sample raw gene counts matrix


title: G1E-HMD_ATAC_rep2

value: HMD (empty vector)

value: control


title: Sample2_016_brain cerebral cortex cells from WT mice

city: Uppsala

first: Ying

last: Sun

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: brain cerebral cortex from 9wk mice

data_processing:
The raw sequence reads were analyzed by Cell Ranger 3.0.1 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with read counts for each sample

source_name: brain cerebral cortex

extract_protocol:
Single cell sequencing was performed at the eukaryotic single cell genomics facility(ESCG) using the 10× Genomics Chromium method (Hochgerner et al., 2018).
Chromium  Single Cell 3' Solution V3 chemistry.

value: cerebral cortex


title: G1E-GATA1_RNA_rep1


title: G2-3, miRNA-seq (Exosome)

city: Wuhan

first: Guoliang

address: 1095# Jiefang Avenue

institute: Tongji Hospital

data_processing: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 18 nt or longer than 32 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.

growth_protocol: A498 cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 supplemented with 10% fetal bovine serum (FBS) and 2 mmol/L L-glutamine.

extract_protocol:
The supernatant of the two groups was filtered by ultrafiltration tube and the ultracentrifugation (UC) method was optimized. After thawing at 37°C, plasma samples were centrifugated at 3,000 × g for 15min to remove cell debris. Then, the supernatant was diluted by seven-fold volume of PBS, centrifuged at 13,000 × g for 30min, and processed through a0.22μm filtertoremovelarge particles. The supernatant was ultracentrifuged using a P50AT2-986 rotor (CP100NX; Hitachi, Brea, CA, USA) at 150,000 × g, 4°C for 4h to pellet the sEVs. The pellet was resuspended in phosphate-buffered saline (PBS) and centrifuged again at 150,000 × g 4°C for 2h. After PBS washing, thesEVs enrichedfraction pellet was re-suspended in 100µL PBS.
A total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. For small RNA libraries, a total amount of 1ng-500ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. At last, library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
miRNA-seq (Exosome)

treatment_protocol: siSETD2 (siSETD2 sequence: TAGTACACCAAGACTCCAG) or si-NC.

value: Clear cell renal carcinoma cell line A498

value: si-NC


title: LFP2 RNA-seq

value: large female


title: LFP1 RNA-seq


title: Sample1_015_brain cerebral cortex cells from WT mice

description: brain cerebral cortex from 9wk mice

value: WT


title: G2-2, miRNA-seq (Exosome)


title: G1E-R307H_RNA_rep2


title: LFB3 RNA-seq

source_name: the brain of large female Cynolossus semilaevis

value: brain


title: G2-1, miRNA-seq (Exosome)


title: G1E-R307H_RNA_rep1

value: GATA1 point mutant p.R307H


title: RubWT-notxt-rep3

city: Research Triangle Park

first: Jennifer

last: Martinez

state: NC

address: 111 TW Alexander Dr.

institute: NIEHS

data_processing:
Raw reads were filtered to retain only those with mean base quality score >20.
Filtered reads were aligned to the mm10 reference genome via STAR v2.5 with parameters "--outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000".
Subread featureCounts v1.5.0-p1 was used to collect read per gene for all gene models in RefSeq as downloaded from UCSC as of November 7, 2017.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Unstranded --outWigNorm None", followed by normalization by size factors as reported by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth as bigWig; counts per gene as tab-delimited text

source_name: Differentiated bone marrow cells

growth_protocol: BMDCs were differentiated for 6-7 days in complete media supplemented with 200 ng/ml FLT3L.

extract_protocol:
Cells were harvested and washed with PBS. The RNA was extracting using Trizol and RNAeasy step kit with DNAse digestion as per manufacturer's instructions.
Libraries were prepared according to Illumina's instructions using TruSeq RNA Library Prep Kit v2;

treatment_protocol: On day 6-7, the BMDCs were incubated with Jurkat cells. Appropriate controls were used for different timepoints and treatment conditions.

tag: cell type

value: FLT3L-derived bone marrow dendritic cells

value: Rubcn WT

tag: treatment

value: No treatment


title: LFB2 RNA-seq


title: G1-3, miRNA-seq (Exosome)


title: RubWT-notxt-rep2


title: G1E-HMD_ATAC_rep1


title: G1E-R307C_RNA_rep2

value: GATA1 point mutant p.R307C


title: LFB1 RNA-seq


title: RubWT-notxt-rep1


title: Sample3_017_brain cerebral cortex cells from WT mice

description: brain cerebral cortex from 9wk mice


title: G1-2, miRNA-seq (Exosome)


title: G1E-R307C_RNA_rep1


title: RubWT-4hr_OVA-rep3

value: OVA protein (4 hrs)


title: G1E-HMD_RNA_rep2


title: SFM3 RNA-seq

source_name: the muscle of small female Cynolossus semilaevis

value: muscle

value: small female


title: RubWT-4hr_OVA-rep2


title: SFM2 RNA-seq


title: G1E-HMD_RNA_rep1


title: H11_Med2

city: New Delhi

first: Rahul

last: Pal

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

data_processing:
Raw reads are filtered based on length (read length should be greater than 50) and quality using Trimmomatic-0.39
Filtered reads are aligned using STAR-Aligner v 2.5.4b
HTSeq v0.11.2 is used to get read count of genes
Insert size and SD are calculated from BAM files using RSeQC v3.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab deliminated files include gene name and their raw counts in each sample

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from human blood using Ficoll (Amersham) gradient separation at 18°C, 400g for 40 min
The sequencing library was prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: Human PBMCs derived from a normal subject cultured with Medium (Med) or Medium supplemented with human hemoglobin (Hb) for 24 hours.

value: Peripheral blood mononuclear cells

tag: condition

value: cultured with medium


title: H11_Med1


title: RubWT-4hr_apopJC-rep3

value: Apoptotic Jurkat cells (4 hrs)


title: SFG3 RNA-seq

source_name: the gonad of small female Cynolossus semilaevis

value: gonad


title: SFM1 RNA-seq


title: M233

city: Canberra

first: Yeu-Yang

last: Tseng

state: ACT

address: 131 Garran Rd

country: Australia

institute: ANU

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped to mm10 whole genome using TopHat2
Aligned BAM files were further processed using Cufflinks (version 2.2.1) and Cuffmerge to produce a non-redundant set of transcripts and reads per kilobase million (RPKM) values were generated based on mm10 genome annotations.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 3-day-old female mouse skin fibroblasts_8 hpi

growth_protocol: skin fibroblasts were routinely generated from 3-day-old mice (typically 2–3 × 10^6 cells in a T75 flask) in DMEM supplemented with 10% FCS.

extract_protocol:
Infected cells were sorted and total RNA was isolated by using RNAqueous™ Total RNA Isolation Kit. llumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with HSV-1 expressing GFP at an MOI of 0.5

tag: Sex

value: female

value: skin fibroblasts

tag: infection

value: HSV-1 expressing GFP at an MOI of 0.5

tag: time point

value: 8 hpi


title: M232


title: H11_Hb2

value: cultured with medium supplemented with Hb


title: RubWT-4hr_apopJC-rep2


title: M231


title: H11_Hb1


title: RubWT-4hr_apopJC-rep1


title: M223

source_name: 3-day-old female mouse skin fibroblasts_4 hpi

value: 4 hpi


title: SFG2 RNA-seq


title: RubWT-30min_OVA-rep3

value: FLT3L-derived bone marrow dendritic cells

value: OVA protein (30 mins)


title: M222


title: SFL2 RNA-seq

source_name: the liver of small female Cynolossus semilaevis

value: liver


title: G1-1, miRNA-seq (Exosome)

value: Clear cell renal carcinoma cell line A498


title: SFG1 RNA-seq


title: RubWT-30min_OVA-rep2

value: Rubcn WT


title: SFL3 RNA-seq


title: JS19102_6

city: West Haven

first: Sarah

last: Slavoff

state: CT

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Library strategy: TimeLapse-seq
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCh38 genome using STAR aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph track
TC.0, TC.1 TC.2, etc in the tdf files reflect the number of T to C mutations identified. e.g.
TC.0 = zero
TC.1 = 1
TC.2 = 2

source_name: immortalized 293Ts

growth_protocol: 293T cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: s4U plus and minus cells had their media replaced with growth media supplemented with 500 uM s4U or left unsupplemented, respectively. An EGF concentration of 100 ng/mL was used for all treated groups. Cells were incubated with s4U and/or EGF for 2h.

value: HEK293T cells

tag: egf treatment

value: No

tag: s4u feed


title: RubWT-30min_OVA-rep1


title: M221


title: SFL1 RNA-seq

tag: tissue

value: small female


title: RubWT-4hr_OVA-rep1

value: OVA protein (4 hrs)


title: JS19102_4

value: Yes


title: JS19102_5


title: M213

source_name: 3-day-old female mouse skin fibroblasts_mock

value: mock


title: JS19102_3


title: RubWT-30min_apopJC-rep3

value: Apoptotic Jurkat cells (30 mins)


title: M212

value: female

value: skin fibroblasts


title: JS19102_2


title: SFP2 RNA-seq

source_name: the pituitary gland of small female Cynolossus semilaevis

value: pituitary gland


title: M211


title: RubWT-30min_apopJC-rep1


title: SFP1 RNA-seq


title: 78

city: Sinjuku-ku

first: Maho

last: Nakazawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Rheumatology, Department of Internal Medicine

institute: Keio University School of Medicine

data_processing:
The original sequencing data is in binary basecalling format, which is further converted into sequencing data in fastq format using bcl2fastq software.
Basecalling is performed by Illumina RTA software in sequencer.
Further demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information, the number of reads are counted.
Count data were calculated using software provided with trim_galore (0.4.0), cutadapt (1.7.1), HISAT2 (2.1.0) and featureCounts (1.5.2).
Genome_build: hs37d5
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: IIM AM 06

extract_protocol:
AMs were stained with antibodies for 15 minutes, washed with staining buffer, sorted from the BALF with an Aria III flow cytometer (BD Biosciences). AMs were defined as CD169+CD206+ cells. RNA was extracted from AMs by spin column-based purification (NucleoSpin RNA; Macherey-Nagel, Germany) and stored at -80 °C until further processing.
The cDNA libraries from the RNA were synthesized by SMART-Seq2  according to the reported method and purified with an Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA). Sequencing library were prepared using Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Resulting libraries were analyzed using Agilent 2100 Bioanalyzer (Agilent Genomics, Santa Clara, MA, USA) for length and quality and Qubit dsDNA assays (Thermo Fisher Scientific) for quantity. Sequencing were performed using illumina Novaseq Hiseq platform (Genewiz, USA) with read-lengths of 150bp paired-end.

value: Alveolar macrophage

tag: disease

value: IIM-ILD


title: RubKO-notxt-rep3

value: FLT3L-derived bone marrow dendritic cells

value: Rubcn KO

value: No treatment


title: SFB3 RNA-seq

source_name: the brain of small female Cynolossus semilaevis

value: brain


title: 28

source_name: RA AM 05

value: RA-ILD


title: M132

source_name: 3-day-old male mouse skin fibroblasts_8 hpi

tag: strain

value: male

value: HSV-1 expressing GFP at an MOI of 0.5

value: 8 hpi


title: SFB2 RNA-seq

tag: genetic sex

value: small female


title: JS19102_1

value: HEK293T cells

value: Yes


title: 23

source_name: DI AM 05

value: DI-ILD


title: RubKO-notxt-rep2


title: RubKO-notxt-rep1


title: 64

source_name: RA AM 04


title: SFB1 RNA-seq


title: M131


title: RubKO-4hr_OVA-rep3

value: OVA protein (4 hrs)


title: 35

source_name: IIM AM 05


title: M122

source_name: 3-day-old male mouse skin fibroblasts_4 hpi

value: skin fibroblasts

value: 4 hpi


title: M121


title: RubWT-30min_apopJC-rep2

source_name: Differentiated bone marrow cells

value: Rubcn WT

value: Apoptotic Jurkat cells (30 mins)


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week8 replicate 3 [SVA-SPR11]

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

country: Brazil

institute: Instituto Butantan

data_processing:
Quality check of reads was performed using FastQC (v.0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Fastp (v0.20.0) was used to trim adapters and reads with low sequencing quality
RNA-Seq reads were mapped using STAR (v 2.7.3a) against the S. mansoni genome PRJEA36577 (v7) retrieved from WormBase (schistosoma_mansoni.PRJEA36577.WBPS14.genomic_softmasked.fa)
Read counting was performed with RSEM (v1.3.1) using a previously published transcriptome annotation (https://doi.org/10.3389/fgene.2019.00823)
Genome_build: S. mansoni genome PRJEA36577 (v7)
Supplementary_files_format_and_content: RSEM output (.results) raw counts
Supplementary_files_format_and_content: Normalized counts (.txt). Read count values shown as log2CPM normalized across all conditions with “Trimmed Mean of M-values” (TMM) method implemented in the edgeR package within the R platform (v 3.6.2)

organism: Schistosoma mansoni

growth_protocol: Cercariae shed from infected snails were cooled on ice for 30 min and collected by centrifugation. Schistosomula were obtained by mechanical transformation of cercariae, and separation of their bodies as previously described71. The newly transformed schistosomula (NTS) were maintained for 72 h, before co-culture, in M169 medium (Vitrocell, cat number 00464) supplemented with penicillin/streptomycin, amphotericin, gentamicin (Vitrocell, cat number 00148), 1 µM serotonin, 0.5 µM hypoxanthine, 1 µM hydrocortisone and 0.2 µM triiodothyronine at 37 °C and 5% CO2.

extract_protocol:
Total RNA from schistosomula was extracted using the RNeasy Micro Kit (Qiagen, 74004). RNA samples were quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Q32852); purity was evaluated using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies) and the integrity was verified using the Agilent RNA 6000 Pico Kit (Agilent Technologies, 5067-1513) in the 2100 Bioanalyzer Instrument (Agilent Technologies)
Stranded tagged cDNA libraries were prepared by BGI Genomics using the Strand-Specific Transcriptome Library Construction Protocol (DNBSEQ, SOP-SS-115) and quantification and quality were performed on a 2100 Bioanalyzer (Agilent).
Libraries were pooled and sequenced (300 cycles, paired-end sequencing) on a MGISEQ-2000 instrument

treatment_protocol: The 12 rhesus macaque females used in this study had a mean age 13.9 ± 2.8 years and a mean weight 9.3 ± 1.9 kg at the outset. Each animal was exposed to 700 S. mansoni cercariae from a BH isolate (Parasitology Laboratory, Butantan Institute, Brazil) maintained by passage through golden hamsters (Mesocricetus auratus) and Biomphalaria glabrata snails. Exposure of macaques to cercariae was performed via a metal ring placed on the shaved abdominal skin, for 30 min, under ketamine hydrochloride (10 mg/kg body weight) and xylazine (0.5 mg/kg body weight) (Sespo, Sao Paulo, Brazil) anaesthesia. Blood was collected at Wk0, Wk8 or Wk43. For RNA-Seq assays, 3-day-old schistosomula were co-cultured for 72 h with a pool of plasma from all rhesus macaques self-curing collected at Wk0, Wk8 or Wk43 (i.e., Wk1pc). Schistosomula not exposed to plasma were used as controls. Three biological replicates from each condition were assayed

value: BH strain

tag: tissue/cell type

value: somula


title: SFP3 RNA-seq

value: pituitary gland


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week1pc replicate 3 [SVA-SPR12]


title: 51

source_name: DI AM 04

value: Alveolar macrophage


title: RubKO-4hr_OVA-rep2

value: FLT3L-derived bone marrow dendritic cells

tag: genotype

value: Rubcn KO


title: RubKO-4hr_OVA-rep1


title: M133

value: male

value: HSV-1 expressing GFP at an MOI of 0.5


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week0 replicate 3 [SVA-SPR10]


title: 26

source_name: DI AM 03


title: RubKO-4hr_apopJC-rep3

value: Apoptotic Jurkat cells (4 hrs)


title: RNA-Seq of control somula replicate 3 [SVA-SPR9]

source_name: RNA-Seq of control somula

value: control


title: 24

source_name: IIM AM  04

value: IIM-ILD


title: M113

source_name: 3-day-old male mouse skin fibroblasts_mock

value: mock


title: RubKO-4hr_apopJC-rep2


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week1pc replicate 2 [SVA-SPR8]


title: 6

source_name: IIM AM  03


title: RubKO-4hr_apopJC-rep1


title: M123


title: M111


title: 25

source_name: DI AM 02

value: DI-ILD


title: RubKO-30min_OVA-rep3

value: OVA protein (30 mins)


title: RubKO-30min_OVA-rep2


title: 18

source_name: IIM AM  02


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week0 replicate 2 [SVA-SPR6]


title: RNA-Seq of control somula replicate 2 [SVA-SPR5]


title: 82

source_name: IIM AM  01


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week1pc replicate 1 [SVA-SPR4]


title: 62

source_name: DI AM 01


title: Intermittent donor 3

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and Trimmomatic.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Gingival fibroblast derived induced pluripotent stem cells

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: Intermittent donor 3


title: RubKO-30min_OVA-rep1


title: RubKO-30min_apopJC-rep3


title: Control-Intermittent donor 3

value: Gingival fibroblast derived induced pluripotent stem cells

value: Control-Intermittent donor 3


title: M112

tag: age

value: skin fibroblasts


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week8 replicate 1 [SVA-SPR3]

value: BH strain

value: somula


title: Control-Intermittent donor 2

value: Control-Intermittent donor 2


title: 53

source_name: RA AM 03

value: Alveolar macrophage

value: RA-ILD


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week0 replicate 1 [SVA-SPR2]


title: RubKO-30min_apopJC-rep2

value: FLT3L-derived bone marrow dendritic cells

value: Rubcn KO

value: Apoptotic Jurkat cells (30 mins)


title: RubKO-30min_apopJC-rep1


title: Control-Intermittent donor 1

value: Control-Intermittent donor 1


title: 47

source_name: RA AM 02


title: 20

source_name: RA AM 01


title: RNA-Seq of control somula replicate 1 [SVA-SPR1]

value: control


title: RNA-Seq of somula co-cultured with plasma rhesus collected at week8 replicate 2 [SVA-SPR7]


title: Intermittent donor 2

value: Intermittent donor 2


title: Intermittent donor 1

value: Intermittent donor 1


title: Si_24_3

status: Public on Dec 30 2021

first: shuang

last: liu

address: 7 Nanhai Road

department: CAS Key Laboratory of Experimental Marine Biology

institute: Institute of Oceanology, Chinese Academy of Sciences

description: microRNA

data_processing:
50bp single-end sequencing was performed on an Illumina Hiseq2500 (LC-Bio, China) according to the vendor’s recommended protocol.
Raw reads were subjected to an in-house program, ACGT101-miR (LC-Bio, China) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed using Student t test.
The significance threshold was set to be 0.01 and 0.05 in each test. Fold-change of≥ 2 or ≤ 0.5 (P < 0.05) indicated a statistical significance of the differentially expressed miRNA.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_001904815.2
Supplementary_files_format_and_content: raw and normalized counts

organism: Paralichthys olivaceus

source_name: spleen

growth_protocol: During acclimation, the water temperature was maintained at ~22°C and the fish were kept under a natural photoperiod with continuous aeration.

extract_protocol:
Small RNA isolation, library construction, and high-throughput sequencing were all carried out by LC-Bio (Hangzhou, China). Briefly, total RNA was isolated and purified using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Approximately 1 g of total RNA was used to prepare small RNA library with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Japanese flounder (~250 g) were randomly assigned to two groups. One group was intramuscularly injected with 5×10^8 CFU S. iniae suspension, and the other group (control) was similarly injected with the same volume of PBS.

value: spleen

tag: time post infectiion

value: infected group


title: Si_24_1

description: microRNA


title: Si_24_2

description: microRNA


title: C_24_3

description: microRNA

value: Control group


title: Si_6_3

description: microRNA


title: Si_6_2

description: microRNA


title: C_6_3

description: microRNA


title: C_24_2

description: microRNA


title: Anagen

city: baltimore

first: Yingchao

last: Xue

state: MD

address: 1500 orleans st, room 216

institute: johns hopkins university

description:
Anagen
Normal skin in growing hair cycle.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
We calculated the gene expression fold changes after expansion in Excel, by calculating the ratios of the linear gene expression values of E/NE for each time point. Then we get a list of the top 100 up-regulated genes for each time point. We put these gene list into DAVID bioinformatics database for pathway analysis. We choose the genes with a fold change over 1.5 or below 0.75 for plotting the heatmap.
probe group file: Clariom_S_Mouse.r1.pgf
meta-probeset file: Clariom_S_Mouse.na36.mm10.transcript.csv

source_name: wildtype adult mouse, with a anagen hair cycle

label_protocol: The Affymetrix WT PLUS kt was used following manufacturer's protocol in their Technical Manual.

growth_protocol: Not applicable.

extract_protocol: We take whole skin samples over the tissue expander from mice. Total RNA were extracted from the whole skin tissue by using the RNeasy Protect Mini Kit (Qiagen).

treatment_protocol: A silicon expander was implanted underneath the back skin of the adult mice. For the expanded mice, the expander was gradually enlarged by injecting PBS into it. The non-expanded mice only implanted with a expander but did not receive PBS injection.

tag: mouse age at start of experiment

value: 9 weeks

tag: expander implantation

value: no

value: normal skin in no-surgery mouse

tag: hair cycle stage

value: Anagen


title: non-expanded sample, time point 3

description:
NE3
Skin over the tissue expander on the non-expanded mice.

source_name: non-expanded mice, skin from on top of the expander

value: yes

value: 14 days post full injection of expander

value: non-expanded skin


title: C_24_1

description: microRNA


title: C_6_1

description: microRNA


title: Telogen

description:
Telogen
Normal skin in resting hair cycle.

source_name: wildtype adult mouse, with a telogen hair cycle

value: Telogen


title: Control heart

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
cellranger 2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: read counts in h5 format

source_name: Mouse embrynic heart

extract_protocol: scRNA-seq Single Cell 3' v2

value: Embryonic heart

tag: genotype/variation


title: TR9: MCoV infected+ treated 5

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

description: Treatment 5

data_processing:
fastq generation incl. demultiplexing and adapter trimming, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
count normalization and transformation, DESeq2 v1.22.2
Genome_build: GRCm38 supplemented with NC_048217.1 genome sequence
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

source_name: middle, right lung lobe

extract_protocol:
RNA was isolated from right middle lung lobe using Maxwell® RSC simplyRNA Tissue Kit (Promega, AS1340) in combination with a ball mill (Retsch)
Sequencing libraries were be prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen).

value: middle, right lung lobe

tag: disease state

value: MCoV infected+ treated


title: TR7: MCoV infected+ treated 3

description: Treatment 3


title: TR5: MCoV infected+ treated 2

description: Treatment 2


title: expanded sample, time point 3

description:
E3
Skin over the tissue expander on the expanded mice.

source_name: expanded mice, skin from on top of the expander

tag: time point

value: expanded skin


title: Ino80 cKO heart

value: Ino80 cKO


title: expanded sample, time point 2

description:
E2
Skin over the tissue expander on the expanded mice.

value: 7 days post full injection of expander


title: non-expanded sample, time point 1

description:
NE1
Skin over the tissue expander on the non-expanded mice.

value: 0 days post full injection of expander


title: non-expanded sample, time point 2

description:
NE2
Skin over the tissue expander on the non-expanded mice.


title: expanded sample, time point 1

description:
E1
Skin over the tissue expander on the expanded mice.


title: TR8: MCoV infected+ treated 4

description: Treatment 4


title: non-expanded sample, time point 4

description:
NE4
Skin over the tissue expander on the non-expanded mice.

value: 21 days post full injection of expander


title: expanded sample, time point 4

description:
E4
Skin over the tissue expander on the expanded mice.


title: TR3: MCoV infected+ treated 1

description: Treatment 1


title: V8: MCoV infected 5

description: Infected 5

value: MCoV infected


title: Si_6_1

description: microRNA

value: spleen

value: infected group


title: V4: MCoV infected 2

description: Infected 2


title: V5: MCoV infected 3

description: Infected 3


title: V7: MCoV infected 4

description: Infected 4


title: V2: MCoV infected 1

description: Infected 1


title: C_6_2

description: microRNA

value: Control group


title: CO5: healthy 5

description: Control 5

value: healthy


title: CO3: healthy 3

description: Control 3


title: D58_org

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

data_processing:
Reads were demultiplexed and fastqs were created using cellranger-atac mkfastq (1.2.0)
Reads were alligned, peaks were called, and fragment files and peak x cell matricies were created using cellranger-atac count (1.2.0)
Peaks were re-called using Macs2 (through Signac) and new peak x cell matricies were created using Signac::FeatureMatrix()
TFIDF was run on the peak x cell matricies using Signac::RunTFIDF()
Downstream processing was preformed in R using Signac, Seurat, ChromVar, and Monocle 3
Genome_build: GRCH38
Supplementary_files_format_and_content: filtered_peak_bc_matrix.tar.gz files 10x filtered_peak_bc_matrix files (peak x cell matricies), fragments.tsv.gz (10x Tn5 fragment files), Macs2_TFIDF.mtx files (cells x Macs2 peaks), metadata.csv.gz (metadata for samples)

source_name: retinal organoid

extract_protocol:
Fresh tissue, from both fetal retina or cultured organoids and retinospheres, was dissociated in papain and DNAse (#LK003170 and #LK00316, Worthington) for 20 to 30 minutes on a nutator at 37°C until a single cell suspension was achieved.
10x Single Cell ATAC v1.1

tag: treatment

value: control

tag: culture

value: retinal organoid


title: FD89 peripheral retina

source_name: fetal retal

value: fetal retal


title: FD74 + 4DIV + PF4014


title: FD87 peripheral retina + 4DIV


title: FD74 + 4DIV


title: FD78 repeat


title: H7_D77_org + Pf4014


title: CO2: healthy 2

description: Control 2

tag: tissue


title: CO4: healthy 4

description: Control 4


title: H7_D77_org


title: 12_P4_JEP1375

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street

institute: Purdue university

data_processing:
Data quality control was performed using FastQC v0.11.8. RNA expression levels in each library were estimated by “rsem-calculate-expression” from RSEM v1.3.0 (PMID: 21816040) using default parameters except “--bowtie-n 1 –bowtie-m 100 –seed-length 28”.
The bowtie index required by RSEM software was generated by “rsem-prepare-reference” on all RefSeq genes, obtained from UCSC table browser on April 2017.
EdgeR v3.24.3 (PMID: 19910308) package was used to identify differentially expressed genes among samples with following constraints: fold change > 2, FDR < 0.05 and TPM > 2.
Gene set enrichment analysis (GSEA) was performed using GSEA version 3.0 (PMID: 16199517). Genesets for testing were sourced from “hallmark genesets” curated by the MSigDB v7.0 (GSEA). Heatmaps were drawn using Morpheus (Broad Institute).
Genome_build: hg19
Supplementary_files_format_and_content: txt file contains the RPKM value for each gene in each sample. It is generated by EdgeR v3.24.3

source_name: Human carotid plaques

growth_protocol: Atherosclerotic carotid plaques were collected during carotid endarterectomy. Biopsies from atherosclerotic carotid plaques were placed in Dulbecco’s modified Eagle’s medium (D-MEM/F12; Gibco) enriched with 30 mg/ml endotoxin-free and fatty acid-free bovine serum albumin (Sigma Aldrich).

extract_protocol:
Supernatant was and snap frozen plaques were harvested for multiplex cytokine analysis and stored at -80 °C .
RNA sequencing libraries were generated using SENSE mRNA-Seq library prep kit according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria).In brief, up to 200 ng of total RNA was prepared and incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. Library preparation was then initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly-synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (15 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 180-600 bp with average library size 240 bp. Libraries were normalized and pooled to 2.6 pM and subjected to clustering on two NextSeq 500 high output flowcells. Finally single read sequencing was performed for 75 cycles on a NextSeq 500 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions. Base calling were done on the NextSeq 500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.17 (Illumina, Inc. San Diego, CA, USA).

treatment_protocol: The biopsies containing atherosclerotic plaques of each patient were split into macroscopically equal pieces and treated with non-cell permeable C5aR1 antagonist PMX53 (10 μg/ml), cell permeable C5aR1 antagonist JEP1375 (10 μg/ml) or PBS for 6 hrs.

value: Atherosclerotic carotid plaques

value: JEP1375 for 6 hours

tag: patients

value: Patient 4

tag: sequencing method

value: SE 86bp RNAseq, NextSeq 500


title: H1_D77_org + Pf4014


title: H1_D77_org


title: CO1: healthy 1

description: Control 1

value: middle, right lung lobe

tag: strain


title: FD87 central retina + 4DIV + PF4014


title: FD53


title: FD87 central retina + 4DIV


title: FD89 central retina


title: 7_P3_NT

value: PBS for 6 hours

value: Patient 3


title: FD87 peripheral retina + 4DIV  + PF4014


title: 10_P4_NT


title: 6_P2_JEP1375

value: Patient 2


title: FD78


title: FD59


title: 3_P1_JEP1375

value: Patient 1


title: 11_P4_PMX53

value: PMX53 for 6 hours


title: 9_P3_JEP1375


title: 5_P2_PMX53


title: 4_P2_NT


title: 1_P1_NT


title: 2_P1_PMX53


title: 8_P3_PMX53