title: UM-SCC-47_input_replication1

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description:
UMSCC47_WT_H3K4me1_replication1.bedgraph
UMSCC47_WT_H3K4me3_replication1.bedgraph
UMSCC47_WT_H3K27ac_replication1.bedgraph

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: HPV(+) head and neck cancer cell line

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated. The sonicated nuclear fraction was used as input.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

tag: cell line

value: HPV(+) head and neck cancer cell line

value: WT

tag: chip antibody


title: C6

status: Public on Jan 06 2023

type: RNA

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description: miRNA array serum Parkinson

hyb_protocol: In the discovery genome-wide miRNA expression analysis, serum miRNA samples were hybridized individually and blind to operator for 42 hours onto Affymetrix GeneChip miRNA 4.0 Array (Applied Biosystems #902411; product datasheet), which contains probes for more than 4,603 human miRNAs (2,578 mature miRNAs and 2,025 pre-miRNAs) following manufacturer instructions.

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner 3,000 7G following the manufacturer's recommendations. Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality.

data_processing:
Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality. Microarray raw data were analysed using Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model, which allows the relative comparison of miRNA abundance in different arrays.Only miRNAs with fluorescence detection values above 2.4 arbitrary units and a significant expression P-value below 0.05 compared to background were considered expressed in human serum samples
Normalized gene level expression values. Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: serum

label_protocol: standard Affymetrix protocol

extract_protocol: A total of 5ml peripheral blood was collected in tubes without anticoagulant (BD Vacutainer) and centrifuged 10 minutes at 1500xg and 4°C. Serum was aliquoted into polypropylene CryoTubes (Greiner Bio-One) and kept at −80°C until use. Total miRNA enriched RNA was extracted using the miRNeasy Serum/Plasma Kit (QIAGEN #217184) following manufacturer recommendations. As a carrier for miRNA isolation, we added 2ul of diluted yeast tRNA (Invitrogen #AM7119) into 200ul of serum for a final concentration of 10ug/ml. RNA concentration was determined for all samples on a NanoDrop ND-3300 fluorospectrometer (Thermo Fisher Sci.), and miRNA quality was evaluated for a subset of randomly selected samples by electropherogram using an Bioanalizer Small RNA Kit (Agilent #5067-1548).

tag: group

value: Control

tag: Sex

value: H

tag: age


title: Clinical_sample_HPV(-)HNSCC_no1

type: SRA

city: Chiba

country: Japan

library_source: transcriptomic

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HPV(–) head and neck cancer tissue

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃. Clinical samples were immediately frozen in liquid nitrogen and stored at −80℃.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: UPCI-SCC-090 was treated with 2.5nM siRNAs (siControl, siITPR3), using Lipofectamine RNAiMAX Transfection Reagent, according to the manufacturer’s instructions. RNA was extracted 48 hours after RNAi treatment.

tag: tissue

value: HPV(–) head and neck cancer tissue

tag: genotype


title: Clinical_sample_HPV(-)HNSCC_no2


title: LPD12

description: miRNA array serum Parkinson

treatment_protocol: A total of 5ml peripheral blood was collected in tubes without anticoagulant (BD Vacutainer) and centrifuged 10 minutes at 1500xg and 4°C. Serum was aliquoted into polypropylene CryoTubes (Greiner Bio-One) and kept at −80°C until use.


title: Clinical_sample_HPV(+)HNSCC_no3

source_name: HPV(+) head and neck cancer tissue

value: HPV(+) head and neck cancer tissue


title: C8

description: miRNA array serum Parkinson

value: M


title: Sentinel lymph node, OSNA S26

city: Coimbra

first: Henriqueta

middle: A. M. B. L. Coimbra

last: Silva

address: Azinhaga Santa Comba, Celas

department: Coimbra Institute for Clinical and Biomedical Research - Center of Investigation on Environment, Genetics and Oncobiology (iCBR-CIMAGO)

country: Portugal

institute: Faculty of Medicine, University of Coimbra

description: Sentinel lymph node, OSNA

data_processing:
Pre-base calling calibration, base calling and alignment arguments, including trim quality cutoff of 15, barcode filtering minimum number of reads set to 10 and wells files normalization, performed automatically and according to manufacturer's default pipeline for the Ion S5 System.
Raw count extraction were obtained by Torrent Suite ImmuneResponseRNA plugin (immuneResponseRNA v5.16.0.0)
Assembly: hg19
Supplementary files format and content: raw_counts_by_oncomine.csv refers to a comma-separated values (csv) file that includes the the raw counts values for each sample.
Supplementary files format and content: normalized_counts_DESeq2.txt refers to a tab-delimited text file that includes normalized counts values using the median of ratios method by DESeq2 R package (version 1.36.0) (Love et al., 2014) for each sample.
Supplementary files format and content: normalized_rlog_.txt refers to a tab-delimited text file that includes normalized counts values using regularized logarithm data transformation (rlog) by DESeq2 R package (version 1.36.0) (Love et al., 2014) for each sample.

source_name: Sentinel lymph node

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit (Quiagen). gDNA decontamination was confirmed. Reverse transcription was performed with 10.5 ng of total RNA using Ion TorrenTM NGS Reverse transcription kit (ThermoFisher Scientific)
The Oncomine Immune Response Research Assay – Chef Ready library preparation kit (Thermo Fisher Scientific, Carlsbad, CA, USA) was used for library construction. Automated library preparation, template preparation and subsequent chip loading were performed on the Ion Chef System using the Ion 530 Chef chip kit (ThermoFisher Scientific). For the sequencing step, 25 µl of libraries yielding 50pM were run using the Ion S5 System (ThermoFisher).

value: Sentinel lymph node


title: T4_FH3

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

data_processing:
base-calling and demultiplexing
adapter clipping and quality filtering with Trimmomatic 0.39
alignments were performed with TopHat
read counts with featureCounts
Differential expression analysis usignDESeq2 (v1.30)
Assembly: Vitis vinifera genome based on the pinot noir genome (Genoscope 12X; Jaillon et al. 2007)
Supplementary files format and content: raw_counts.txt

organism: Vitis vinifera

source_name: berry

extract_protocol:
Total RNA was extracted using perchlorate method
Illumina TruSeq Stranded mRNA Library

treatment_protocol: During the summer, in correspondence with the pre-veraison phase, it was induced for the plants of the second tunnel a gradual reduction of the water supply, up to one state of drought stress (30% of field capacity), followed by the application of a heat wave (+ 5 ° C) lasting one week. The samplings were carried out at T0 (27/06) on controls plants before the gradual cut of irrigation, at T1 (6/07) with overt water stress, immediately before the heat wave, at T2 (10/07) in the middle of the heat wave, at T3 (12/07) at the end of the heat wave, at T4 (21/07) one week after the end of stress, the "recovery" and at T5 (25/07) a technological maturation of the berry, the so called "harvest".

value: berry

tag: variety

value: Sauvignon Blanc

tag: treatment

value: drought+heat wave+spring flooding


title: C5

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S27

description: Sentinel lymph node, OSNA


title: T4_FH2


title: Clinical_sample_HPV(+)HNSCC_no2


title: C40

description: miRNA array serum Parkinson


title: T4_FH1


title: HS_0_B

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: heat stressed rep2

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were mapped to Arabidopsis reference genome (TAIR10 version) by TopHat2 (Kim et al., 2013).
Picard tools (available from http://broadinstitute.github.io/picard/) was used to discard duplicated reads.
Mapped reads from TopHat2 analysis were subsequently counted using htseq-count (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes between control and Tenofovir-treated samples using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seedlings were grown in plates on ½ MS media (1% sucrose and 0.8% agar, pH5.7) at 20°C under 12h light conditions (12h light/12h dark)

extract_protocol:
Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer's instructions. The RNA quality and integrity were assessed on the Agilent 2200 Tape Station.
Libraries for RNA expression analysis were prepared in tripicate from 1 µg of  high-integrity total RNA (RIN>8) using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA)  following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.

treatment_protocol: In drug treated plants, Tenofovir (Cayman Chemical, N 13874), was dissolved in DMSO and added to the medium at 10 µM.  One-week old seedlings have been primed by cold treatment for 24°C and immediately transferred to normal growth conditions (Control plants or CS) or to 37°C for 24hr (Heat Stressed or HS) plants. Plants have been collected 24h after heat application (HS0). Tenofovir-treated and control Arabidopsis plants have been subsequently grown at 21°C for the remaining time, and samples have been collected 3 days after heat-stress.

tag: ecotype

value: seedling

value: 9 days

value: wild-type

value: mock

value: heat stress


title: CC_0_C

description: control rep3

value: not stressed


title: Clinical_sample_HPV(+)HNSCC_no1


title: Sentinel lymph node, OSNA S24

description: Sentinel lymph node, OSNA


title: T4_H3

value: drought+heat wave


title: Sentinel lymph node, OSNA S23

description: Sentinel lymph node, OSNA


title: Clinical_sample_normal_no2

source_name: Normal tissue of the head and neck

value: Normal tissue of the head and neck

value: WT


title: C39

description: miRNA array serum Parkinson

value: Control

value: H


title: T4_H2


title: Clinical_sample_normal_no1


title: C38

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S22

description: Sentinel lymph node, OSNA


title: C37

description: miRNA array serum Parkinson


title: UM-SCC-47

library_source: genomic

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Target enrichment sequencing reads were aligned to hg19 reference human genome.
The number of reads for each target site was calculated using bedtools.
The number of reads from FaDu, an HPV(-) head and neck cancer cell line, was used as a negative control.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include mapped reads at target site for each sample.

molecule: genomic DNA

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
An HPV custom panel was created by designing 132 probes comprehensively against the HPV16 reference genome, and a backbone panel was created because of the need for read correction to compare between samples. We used 100 randomly selected locations from “xGen Human CNV Backbone Hyb panel probes” as backbone panel. We used these panels to perform hybridization captures and created DNA libraries.
The hybridization capture was performed using the provided assay kit according to the manufacturer's protocol (Integrated DNA Technologies, Inc., Coralville, IA, USA).

tag: cell type

value: HPV(+) head and neck cancer cell line


title: T4_H1


title: T4_C3


title: Sentinel lymph node, OSNA S20

description: Sentinel lymph node, OSNA


title: Sentinel lymph node, OSNA S25

description: Sentinel lymph node, OSNA


title: C36

description: miRNA array serum Parkinson


title: T4_C2


title: T4_C1


title: Sentinel lymph node, OSNA S19

description: Sentinel lymph node, OSNA


title: UPCI-SCC-090_WT_input_replication1

description:
UPCI-SCC-090_WT_H3K4me1_replication1.bedgraph.gz
UPCI-SCC-090_WT_H3K4me3_replication1.bedgraph.gz
UPCI-SCC-090_WT_H3K27ac_replication1.bedgraph.gz

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.


title: UM-SCC-104_WT_H3K4me1_replication1

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: UM-SCC-104_WT_input_replication1

description:
UM-SCC-104_WT_H3K4me1_replication1.bedgraph.gz
UM-SCC-104_WT_H3K4me3_replication1.bedgraph.gz
UM-SCC-104_WT_H3K27ac_replication1.bedgraph.gz


title: C4

description: miRNA array serum Parkinson

value: M


title: C35

description: miRNA array serum Parkinson


title: FaDu WT

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Target enrichment sequencing reads were aligned to hg19 reference human genome.
The number of reads for each target site was calculated using bedtools.
The number of reads from FaDu, an HPV(-) head and neck cancer cell line, was used as a negative control.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include mapped reads at target site for each sample.

source_name: HPV(-) head and neck cancer cell line

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-104 and FaDu was cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

value: HPV(-) head and neck cancer cell line

value: FaDu


title: C34

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S17

description: Sentinel lymph node, OSNA

value: Sentinel lymph node


title: T3_F3

value: berry

value: Sauvignon Blanc

value: Flooded


title: Sentinel lymph node, OSNA S16

description: Sentinel lymph node, OSNA


title: UM-SCC-104 WT


title: Sentinel lymph node, OSNA S21

description: Sentinel lymph node, OSNA


title: T3_F1


title: C33

description: miRNA array serum Parkinson


title: C32

description: miRNA array serum Parkinson


title: T3_F2


title: Sentinel lymph node, OSNA S15

description: Sentinel lymph node, OSNA


title: UPCI-SCC-090 WT


title: C368

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S18

description: Sentinel lymph node, OSNA


title: T3_FH3

value: drought+heat wave+spring flooding


title: C31

description: miRNA array serum Parkinson


title: Healthy control 23

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

description: SKB-counts.csv

data_processing:
Fastq files were aligned to the human genome (hg38) using Tophat2 (v2.1.1). Read counts were generated using featureCounts (Rsubread v2.0) and statistical analysis was carried out using edgeR (v3.28.1) with sva (v3.34) batch correction and TMM normalisation and applying a significance threshold of FDR < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: SKB-counts.csv is a matrix of gene counts for all samples

source_name: Peripheral blood neutrophils

extract_protocol:
Neutrophils were isolated from peripheral blood using HetaSep followed by Ficoll-Paque. RNA was extracted using Trizol chloroform and cleaned up using the Qiagen RNeasy kit including an on-column DNase digestion step. RNA was eluted in water and frozen at -80 degC.
SMRTseq2 or standard DNBseq library protocols

tag: gender

value: Male

tag: disease state

value: Healthy control

tag: library preparation protocol

value: Standard


title: Sentinel lymph node, OSNA S14

description: Sentinel lymph node, OSNA


title: T3_FH2


title: Healthy control 15

description: SKB-counts.csv

value: Female


title: C30

description: miRNA array serum Parkinson


title: C3

description: miRNA array serum Parkinson


title: T3_H3

value: drought+heat wave


title: Sentinel lymph node, OSNA S12

description: Sentinel lymph node, OSNA


title: Healthy control 1

description: SKB-counts.csv


title: Healthy control 7

description: SKB-counts.csv


title: T3_H2


title: C28

description: miRNA array serum Parkinson

value: Control


title: Patient 1036 post-SKB

description: SKB-counts.csv

value: Psoriatic arthritis

value: 12-weeks Secukinumab + DMARDs


title: Sentinel lymph node, OSNA S10

description: Sentinel lymph node, OSNA


title: Sentinel lymph node, OSNA S9

description: Sentinel lymph node, OSNA


title: T3_C3


title: T3_C2


title: C27

description: miRNA array serum Parkinson

value: H


title: Patient 1029 post-SKB

description: SKB-counts.csv

value: 12-weeks Secukinumab


title: C29

description: miRNA array serum Parkinson

value: M


title: MM2_01-24-17 (WT)

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

country: USA

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

organism: Mus musculus

source_name: Primary mouse rib chondrocytes

growth_protocol: Mouse rib primary chondrocytes were collected immidetely after isolation to retain the chondrocyte phenotypes

extract_protocol:
Cells were scraped in TRIzol reagent total RNA was isolated using phenol-chloroform extraction using Invitrogen PureLink RNA Mini Kit (#12183018A)
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). This protocol provides strand specific data while
Simultaneously removing both cytoplasmic and mitochondrial rRNA. Libraries were sequenced on the HiSeq 2500 instruments and 50 million 50 base pair single end
Reads were produced per sample. Data was extracted, de-convoluted based on dual index reads and analyzed using CLC Genomics Workbench software (Qiagen).

treatment_protocol: Wild type (WT) and mutant (MUT) mouse primary rib chondrocytes were isolated following a sequential digestion by pronase (2 mg/ml in PBS) for 30 min at 37°C, collagenase D (3 mg/ml in DMEM) for 1.5 h at 37°C, and overnight at 37°C in collagenase D (1.5 mg/ml in DMEM). Collagenase D digestion was stopped next day by adding FBS. Chondrocytes were washed twice with PBS and cells were collected.

value: Wild-type primary chondrocytes

value: E18.5 mouse rib tissue


title: Sentinel lymph node, OSNA S8

description: Sentinel lymph node, OSNA

value: Sentinel lymph node


title: Sentinel lymph node, OSNA S7

description: Sentinel lymph node, OSNA


title: T3_FH1

value: berry

value: Sauvignon Blanc


title: Patient 1036 pre-SKB

description: SKB-counts.csv

value: Standard DMARDs


title: C25

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S6

description: Sentinel lymph node, OSNA


title: Sentinel lymph node, OSNA S13

description: Sentinel lymph node, OSNA


title: C24

description: miRNA array serum Parkinson


title: C26

description: miRNA array serum Parkinson


title: T2_F3

value: Flooded


title: Patient 1029 pre-SKB

description: SKB-counts.csv


title: T3_C1


title: Patient 1028 post-SKB

description: SKB-counts.csv


title: C23

description: miRNA array serum Parkinson


title: Healthy control 6

description: SKB-counts.csv

value: Male

value: Healthy control


title: Sentinel lymph node, OSNA S5

description: Sentinel lymph node, OSNA


title: T3_H1


title: Sentinel lymph node, OSNA S11

description: Sentinel lymph node, OSNA


title: T2_F2


title: Patient 1028 pre-SKB

description: SKB-counts.csv

value: Female


title: Sentinel lymph node, OSNA S4

description: Sentinel lymph node, OSNA


title: Patient 1027 post-SKB

description: SKB-counts.csv

value: Standard


title: C21

description: miRNA array serum Parkinson

value: Control


title: T2_F1


title: Sentinel lymph node, OSNA S3

description: Sentinel lymph node, OSNA


title: Patient 1027 pre-SKB

description: SKB-counts.csv

value: Psoriatic arthritis


title: T2_FH3

value: drought+heat wave+spring flooding


title: T2_FH2


title: Patient 1008 post-SKB

description: SKB-counts.csv

value: 12-weeks Secukinumab + DMARDs


title: C13

description: miRNA array serum Parkinson

value: H


title: Sentinel lymph node, OSNA S1

description: Sentinel lymph node, OSNA


title: T2_FH1


title: C12

description: miRNA array serum Parkinson


title: BBMI3

city: Zhengzhou

first: liang

middle: nian

last: nian

address: 100 Science Avenue

country: China

institute: Zhengzhou University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from Brassicadb database (http://brassicadb.org). Bowtie v1.0.1 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Brassica_juncea_v1.5(http://brassicadb.org)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica nigra

source_name: anther

growth_protocol: B. rapa ♀×B. nigra ♂, haploid

extract_protocol:
Flower buds from meiosis and tetrad to maturity were collected and RNA was collected with Trizol reagent. Rna-seq library was constructed with 5 ~ 10 μg total RNA as template
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anther(pollen)

tag: Stage

value: MI(mitosis(gametogenesis))

tag: genomes

value: BB


title: Patient 1008 pre-SKB

description: SKB-counts.csv


title: BBMI2


title: T2_H2

value: drought+heat wave


title: T2_H1

value: berry


title: C22

description: miRNA array serum Parkinson


title: C10

description: miRNA array serum Parkinson


title: BBMI1


title: BBME3

value: young anther(pollen)

value: ME(meiosis(sporogenesis))


title: T2_C3

value: Sauvignon Blanc


title: B13

description: miRNA array serum Parkinson

value: DaT-negative L2NMCal


title: BBME2


title: B1054

description: miRNA array serum Parkinson


title: T2_C2


title: BBME1


title: T1_F3

value: Flooded


title: B10176

description: miRNA array serum Parkinson

value: DaT-positive L2NMCered


title: C11

description: miRNA array serum Parkinson

value: M


title: B10 42

description: miRNA array serum Parkinson


title: C2

description: miRNA array serum Parkinson

value: Control


title: Post_challenge vYF D271 CO331_D271

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

country: France

institute: Sanofi

description:
Post_challenge vYF D271
post challenge (vaccinated animals)

data_processing:
OmicSoft Array Studio software (v9.0 -v10.0).
The reads were aligned with OmicsSoft Aligner (OSA4) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations
Multiple mappings reads and first-read-forward-strand reads were discarded from the analysis
Read counts were then subsequently analyzed using R scripts (R version 3.3.3).
All samples were scale-normalized according to their library size by the TMM method of edgeR package (v3.16.5) and transformed with voom (Limma R package v3.30.13).
For the linear modeling of differential gene expression, a model was built with Limma using the treatment condition (vaccination group and sampling time point) as a factor (relatively to the vaccination day defined as a baseline). Contrasts were set up in order to compare for every vaccination group each time point post-vaccination with baseline (Day –29)). Contrasts were also set up to compare directly vaccination groups for each time point post-vaccination relatively to their own group baseline
The tmod R package (v0.31) was used to detect functional enrichment directly on the Limma object (i.e. inference test result from the Limma R package) on the full genes list (ordered using default "minimal significant difference" ranking) coming from each contrast
Assembly: Cyno.WashU2013
Supplementary files format and content: Raw read counts from Array Studio software

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Whole Blood

extract_protocol:
Whole blood from NHPs was collected in PAXgene tubes (BD762165 –Ozyme) and stored according to the manufacturer's protocol. Total RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation
Extracted RNA samples were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300 ng of total globin-depleted RNA according to manufacturer’s instructions.

treatment_protocol: 36 male NHPs were randomized into groups of nine to receive subcutaneous injection in the deltoid muscle region of the upper arm with a single commercial dose of Stamaril (4 LogCCID50) or YF-VAX (6 LogCCID50), or 4 or 5 LogCCID50 vYF at WSL stage. Nine months after vaccination, NHPs along with six additional unvaccinated controls were challenged by a single sub-cutaneous injection of 3.0 LogCCID50 wild-type YFV Asibi strain in the scapula region.

value: Whole Blood

value: male

value: vYF

tag: time


title: T1_F2


title: Post_challenge vYF D275 CO331_D275

description:
Post_challenge vYF D275
post challenge (vaccinated animals)


title: T1_F1


title: Post_challenge vYF D296 CO331_D296

description:
Post_challenge vYF D296
post challenge (vaccinated animals)


title: T2_H3


title: T1_FH3

value: drought+heat wave+spring flooding


title: Post_challenge vYF D259 CO331_D259

description:
Post_challenge vYF D259
post challenge (vaccinated animals)


title: B02_1

description: miRNA array serum Parkinson

value: H


title: 076-01

description: miRNA array serum Parkinson


title: T1_FH2


title: Post_challenge vYF D296 CO314_D296


title: 071 02

description: miRNA array serum Parkinson


title: T1_FH1


title: Post_challenge vYF D271 CO314_D271


title: 069 01

description: miRNA array serum Parkinson


title: T2_C1


title: T1_H3


title: Post_challenge vYF D259 CO314_D259


title: T1_H2


title: B10 202

description: miRNA array serum Parkinson


title: Post_challenge vYF D296 CO306_D296


title: 055-01

description: miRNA array serum Parkinson


title: T1_H1


title: 050 02

description: miRNA array serum Parkinson


title: Post_challenge vYF D275 CO306_D275


title: 033-01

description: miRNA array serum Parkinson


title: Post_challenge vYF D271 CO306_D271


title: T1_C1


title: Post_challenge vYF D275 CO314_D275


title: Post_challenge vYF D296 CN998_D296


title: T1_C2


title: 048 01

description: miRNA array serum Parkinson


title: Post_challenge vYF D259 CO306_D259


title: Post_challenge vYF D275 CN998_D275


title: T0_F3


title: 029-01

description: miRNA array serum Parkinson


title: 023-09

description: miRNA array serum Parkinson


title: T0_F1


title: T0_F2


title: 023-08

description: miRNA array serum Parkinson


title: 058 04

description: miRNA array serum Parkinson


title: Post_challenge vYF D259 CN998_D259


title: T0_C3


title: T1_C3


title: 023-07

description: miRNA array serum Parkinson


title: Post_challenge vYF D296 CN774_D296


title: T0_C2


title: Post_challenge vYF D275 CN774_D275


title: 023 03

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S2

description: Sentinel lymph node, OSNA

value: Sentinel lymph node


title: 012-03

description: miRNA array serum Parkinson


title: T0_C1


title: 031-02

description: miRNA array serum Parkinson


title: Post_challenge vYF D271 CN774_D271


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep2

city: Toulouse

first: Celine

last: GALES

address: 1 Avenue du Pr. Jean Poulhès

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 37042 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 34370 rows each corresponding to a unique ProbeName.

source_name: Cardiac left ventricle

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a chow diet.

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. RNA amounts were determined by NanoDrop®ND-1000 and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

value: Male

value: Cardiac left ventricle


title: 006 03

description: miRNA array serum Parkinson


title: Post_challenge vYF D271 CN998_D271


title: Post_challenge vYF D296 CN705_D296


title: Post_challenge vYF D259 CN774_D259


title: Post_challenge vYF D275 CN705_D275


title: Mix2(hashtag)

city: Shanghai

first: Yucui

last: Zhao

state: Please Select

address: No. 650 Xinsongjiang Road, Hongkou District, Shanghai

department: cancer center

institute: Shanghai general hospital

description:
10x Genomics
4016_mix2_F_20200116NP

library_source: transcriptomic single cell

data_processing:
raw sequencing data were filtrated and aligned to the   reference genome GRCh38 using CellRanger pipeline (10x Genomics, v3.1.0).
For   downstream processing, Seurat package (v.2.3) (https://satijalab.org/seurat) was used for   quality control, cellular filtration, data normalization, clustering and DEG analysis. Only cells   that expressed at least 200 genes and had less than 10% of mitochondrial unique molecular   identifiers (UMI) counts were kept for further processing.
After removing low-quality data, the   filtered matrix was performed log2 standardization.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
An input of estimated 10,000 cells for Mix1 and estimated 12,000 cells for Mix2 (10,000 of IR, 1000 of NC and 1000 of R) were respecitvely transfer to 10xChrominum instrument (10x Genomics) per the user instructions.
Single-cell libraries were constructed using the Single Cell 3’ Reagent Kit (10x Genomics, v3.1).Libraries were then performed quality control using Bioanalyzer High Sensitivity DNA kit (Agilent) and sequenced on an Illumina NextSeq 500 platform.

treatment_protocol: HCT116 RTP cells in different stages of budding were mixed up as “Mix1”, consisting of 4 groups: giant cells isolated on D8 and cultivated till D10 (group1), giant cells isolated on D8 and cultivated till D11 (group2), giant cells isolated on D5 and cultivated till D10 (group3) and giant cells isolated on D5 and cultivated till D11 (group4)； “Mix2” were performed with irradiated RTP cells (the same process as "Mix1", incorporated with antibody hasgtags  “tag8”), non-irradiated with “tag6” and repopulated cells with “tag7”.

tag: cell line

value: colorectal cancer cells


title: 006 01

description: miRNA array serum Parkinson


title: 005-01

description: miRNA array serum Parkinson


title: UM-SCC-47_WT_3

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro.
Assembly: hg19
Supplementary files format and content: hic

extract_protocol:
Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: HPV(+) head and neck cancer cell line

value: WT

tag: restricion enzyme

value: MboI


title: FaDu_WT_3

source_name: FaDu

value: FaDu

value: HPV(-) head and neck cancer cell line


title: Post_challenge vYF D259 CN705_D259


title: Post_challenge vYF D271 CN705_D271


title: UM-SCC-47_WT_2


title: 004-07

description: miRNA array serum Parkinson

tag: group


title: Post_challenge YF-VAX D296 CO464_D296

description:
Post_challenge YF-VAX D296
post challenge (vaccinated animals)

tag: Sex

value: YF-VAX


title: UM-SCC-47_WT_1


title: 003-01

description: miRNA array serum Parkinson

tag: age


title: Post_challenge YF-VAX D271 CO464_D271

description:
Post_challenge YF-VAX D271
post challenge (vaccinated animals)

tag: tissue


title: Mix2

description:
10x Genomics
4016_mix2_20200116NP

tag: genotype

value: 0Gy & 8Gy


title: Post_challenge YF-VAX D259 CO464_D259

description:
Post_challenge YF-VAX D259
post challenge (vaccinated animals)


title: 011 01

description: miRNA array serum Parkinson

value: M


title: UM-SCC-47_baitE6E7_replication1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
4C-seq reads were aligned to hg19 reference human genome, using w4Cseq.
Assembly: hg19
Supplementary files format and content: bedgraph

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47 and UM-SCC-104 were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
Cells were lysed and cross-linked DNA was digested with the primary restriction enzyme. Next, digested DNA was subjected to proximity ligation using T4 DNA ligase (EL0013, Thermo Scientific), followed by cross-link removal using Proteinase K (P8107S, New England Biolabs), which resulted in 3C libraries. The 3C libraries were then subjected to a second restriction enzyme digestion, followed by a circularization reaction using T4 DNA ligase.
The 4C template was used to perform a scaled-up inverse nested PCR. Inverse primers were designed and appropriate adaptors and index sequences were then added to the inverse primer pair.

tag: restricion enzymes

value: Csp6I, NlaIII


title: UM-SCC-47_H3K4me1_replication1

description: UMSCC47_WT_H3K4me1_replication1.bedgraph

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

tag: chip antibody

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: Post_challenge YF-VAX D296 CO226_D296

value: Whole Blood

value: male

tag: treatment


title: Mix1

description:
10x Genomics
4016mix20191111NA

tag: cell type


title: BM332_TiJ_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

city: Bethesda

first: Massimiliano

last: Bissa

state: MD

address: 9000 Rockville Pike, bldg 41/ room c303

department: NCI/CCR

institute: National Institutes of Health

description: Chromatin accessibility

data_processing:
An average number of reads of 50 million/sample were acquired with a read length of 51 bp and with a paired-end read.
Raw sequencing data were demultiplexed by Bcal2fastq v2.17. Adaptor sequence trimming was done by Cutadapt 1.18.
Bowtie2 was used to map to the rheMac10 reference genome.
PICARD tool was used to remove duplicated reads.
Peak calling was performed using MACS2.
Raw counts of mapped reads were obtained using Homer tools for the called peaks
Assembly: rheMac10
Supplementary files format and content: peak files

organism: Macaca mulatta

source_name: PBMCs/CD14+ cells

growth_protocol: Twelve juvenile (average age 3.91 years, 0.155 SD), female macaques were enrolled in the study. All twelve macaques were immunized twice with V1-deleted DNA-SIV at weeks 0 and 4. At weeks 8 and 12 all macaques were boosted with intramuscular inoculations of 10^8 Plaque Forming Units (PFU) of recombinant ALVAC (vCP2432). At week 12, vaccinated macaques also received 400 μg of v1-delted SIVmac251–M766 protein formulated in alum Alhydrogel. The isolation of CD14+ cells was performed from freshly isolated PBMCs collected at weeks 13. PBMCs were isolated from freshly collected blood.

extract_protocol:
Omni-ATAC protocol (Corces, M.R., et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959-962 (2017) & Fujiwara, S. et al.. High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue. Sci Rep 9, 516 (2019)), with a minor modification. Following isolation of CD14+ cells, for each sample 50,000 viable cells resuspended in RPMI were briefly transferred in 1.5 ml vials. Cells were pelleted and then washed with 50 µl cold PBS- 1X by centrifugation at 3000 rpm for 5 min at 4ºC. Cell pellets were added to 50 µl cold ATAC resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin, gently resuspended, and incubated for 3 min in ice. Following incubation, 1 mL cold RSB containing 0.1% Tween-20 was added to cells and centrifuged at 3000 rpm for 10 min at 4ºC. Supernatants were carefully removed, and pelleted nuclei were resuspended in 50 µl of transposition mixture containing 5 µl TDE1 Tagment DNA Enzyme (Ref #20034197, Illumina, Inc.) 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 10% dimethyl formamide in water and PBS- 1X and incubated for 30 min at 37ºC in a thermomixer with 1000 RPM mixing. Following incubation, the transposed DNA was purified by MinElute PCR Purification kit (Ref #28004, Qiagen) following manufacturer instructions, eluted in 11 µl of buffer provided by the kit, and stored at -20ºC.
Libraries for sequencing were generated as previously described (Corces, M.R., et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959-962 (2017) & Fujiwara, S. et al.. High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue. Sci Rep 9, 516 (2019)). Briefly, following a first step of amplification by PCR performed on 10 µl of eluted DNA with 2.5 µM of each primer, 1X NEBNext® high-fidelity PCR master mix and water (5 min at 72ºC; 30 s at 98ºC; 5 cycles of 10 s at 98ºC, 30 s at 63ºC, 1 min at 72ºC), the numbers of additional amplification cycles required to reach the correct amount of DNA was performed by real-time PCR conducted using 5 µl/sample of amplified DNA . Following the assessment, each sample was further amplified with the additional cycles of PCR and size selection was performed using SPRIselect (Ref #B23317, Beckman coulter) to eliminate fragments shorter than 200 bp and longer than 1000 bp. Two samples collected at weeks 64-65 from 1 animal of the vaccinated and 1 animal of the vaccinated+ALVAC/gp120/Alum boost groups of Study 2 were lost. Before sequencing, the DNA quality of the libraries was assessed by regular and high sensitivity D5000 ScreenTape® (Agilent Technologies).

treatment_protocol: The isolation of the CD14+ cells was performed from freshly isolated PBMCs (30x10^6) collected at weeks 13 in 12 vaccinated animals.        The isolation was performed by using non-human primate CD14 MicroBeads (#130-091-097, Miltenyi Biotec) and following manufacturer instructions. Briefly, 30x10^6 Ficoll Plaque isolated PBMCs were incubated with 60 µl microbeads and 240 µl buffer at 4ºC for 15 min. At the end of incubation, cells were washed with 3 ml buffer and resuspended in 500 µl of buffer. Positive selection was performed using the AutoMACSpro (Miltenyi Biotec) using the Possel program (positive selection). At the end of the separation, cells were resuspended in R10 (RPMI media, 10% FBS and 1X antibiotic/antimycotic; GIBCO) and counted for the assay.

tag: animal id

value: TiJ

tag: vaccination

tag: time point

value: basal

tag: week

value: Week 0

tag: protocol

tag: study

value: Study 2

tag: time of acquisition

tag: date of collection


title: Post_challenge YF-VAX D275 CO226_D275

description:
Post_challenge YF-VAX D275
post challenge (vaccinated animals)

tag: time


title: Clinical_sample_HPV(-)HNSCC_no4

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: HPV(–) head and neck cancer tissue


title: Clinical_sample_HPV(-)HNSCC_no3


title: 004-08

description: miRNA array serum Parkinson

data_processing:
Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality. Microarray raw data were analysed using Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model, which allows the relative comparison of miRNA abundance in different arrays.Only miRNAs with fluorescence detection values above 2.4 arbitrary units and a significant expression P-value below 0.05 compared to background were considered expressed in human serum samples
Normalized gene level expression values. Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model

tag: group

value: DaT-positive L2NMCered

tag: Sex

value: H


title: Post_challenge YF-VAX D271 CO226_D271

tag: tissue


title: BM314_TK3_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: BM318_TT7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: Post_challenge YF-VAX D259 CO226_D259


title: Clinical_sample_HPV(+)HNSCC_no4

value: HPV(+) head and neck cancer tissue

tag: genotype

value: WT


title: BM300_TK1_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: Post_challenge YF-VAX D275 CO464_D275


title: UPCI-SCC-090_siITPR3_replication1

value: HPV(+) head and neck cancer cell line

value: ITPR3 knockdown


title: UM-SCC-47_H3K4me3_replication1

description: UMSCC47_WT_H3K4me3_replication1.bedgraph

tag: cell line

value: H3K4me3_ChIP (Active Motif, 39159, lot 31420006)


title: UPCI-SCC-090_siControl_replication1

value: Non-targeting negative control


title: BM267_Ti7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: BM278_TiD_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility

value: TiD


title: PMN cells, treated with R848 plus CU-CPT9a , donor 3

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using kallisto
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analysed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sample specific read counts per gene in FPKM

source_name: blood

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

value: blood

value: neutrophils

value: R848 plus CU-CPT9a

value: 6 hours


title: PMN cells, treated with R848 plus CU-CPT9a , donor 4


title: Post_challenge YF-VAX D275 CO225_D275

value: Whole Blood

value: male

value: YF-VAX


title: Post_challenge YF-VAX D259 CO225_D259


title: Post_challenge YF-VAX D271 CO225_D271


title: BM248_TBL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility

value: TBL

value: basal

value: Week 0

value: Study 2


title: PMN cells, treated with R848 plus CU-CPT9a , donor 2


title: BM282_TV9_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: PMN cells, treated with R848 plus CU-CPT9a , donor 1


title: BM244_T96_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: BM225_06BA_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: PMN cells, treated with R848, donor 4


title: Post_challenge YF-VAX D271 CO104_D271


title: Post_challenge YF-VAX D275 CO104_D275


title: Post_challenge YF-VAX D296 CO104_D296


title: BM-RNA-186_Ti7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

data_processing:
average number of reads of 114 million/sample were acquired with a read length of 151 bp and with a paired-end read
Raw sequencing data were demultiplexed by Bcal2fastq v2.17. Adaptor sequence trimming was done by Cutadapt 1.18.
The trimmed RNA-Seq reads were aligned against rheMac10 using STAR 2.7.
Raw counts of mapped reads were obtained using the featureCounts program. Normalized data using default DESeq2 size factors were used for further analysis.
Supplementary_files_format_and_content: rheMac10

extract_protocol:
RNA isolation was performed using RNeasy Micro Kit (Cat#74004, Qiagen) following manufacturer instructions. Briefly, CD14+ cells in RNAlater were thawed on ice, 500 µl PBS was added to each vial, and centrifuged at 3000 rpm for 10 min at 4ºC. Supernatants were discarded while cell pellets were processed following manufacturer protocol and resuspended in a final volume of 14 µl of water.
The library preparation was done using the NEBNext Ultra II Directional RNA Library Prep for Illumina kit (cat # E7760L, New England BioLabs) and following manufacturer instructions. The final product was quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: The isolation of the CD14+ cells was performed from freshly isolated PBMCs (30x10^6) collected at weeks 13 in 12 vaccinated animals.        The isolation was performed by using non-human primate CD14 MicroBeads (#130-091-097, Miltenyi Biotec) and following manufacturer instructions. Briefly, 30x10^6 Ficoll Plaque isolated PBMCs were incubated with 60 µl microbeads and 240 µl buffer at 4ºC for 15 min. At the end of incubation, cells were washed with 3 ml buffer and resuspended in 500 µl of buffer. Positive selection was performed using the AutoMACSpro (Miltenyi Biotec) using the Possel program (positive selection). At the end of the separation, cells were resuspended in R10 (RPMI media, 10% FBS and 1X antibiotic/antimycotic; GIBCO) and counted for the ATAC-seq assay (50,000 cells). Leftover cells were resuspended in 500 µl RNAlater (Invitrogen, Waltham, MA) and stored at -80ºC.

value: post ALVAC+gp120

value: Week 13


title: BM229_T63_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility


title: Post_challenge YF-VAX D296 CO225_D296


title: BM-RNA-183_T96_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: PMN cells, treated with R848, donor 3


title: Post_challenge YF-VAX D259 CO104_D259


title: Post_challenge YF-VAX D296 CN700_D296


title: PMN cells, treated with R848, donor 2


title: PMN cells, treated with R848, donor 1


title: Post_challenge YF-VAX D275 CN700_D275


title: BM-RNA-182_T63_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: PMN cells, treated with SCV2-RNA2 plus CU-CPT9a , donor 4

value: SCV2-RNA2 plus CU-CPT9a


title: BM-RNA-184_TiD_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: BM263_TEL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

description: Chromatin accessibility

value: TEL


title: Post_challenge YF-VAX D271 CN700_D271


title: BM-RNA-190_TBL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: PMN cells, treated with SCV2-RNA2 plus CU-CPT9a , donor 3


title: BM-RNA-189_TV9_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Post_challenge YF-VAX D259 CN700_D259


title: PMN cells, treated with SCV2-RNA2 plus CU-CPT9a , donor 2


title: BM-RNA-188_TT7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Post_challenge YF-VAX D296 CN685_D296


title: PMN cells, treated with SCV2-RNA2 plus CU-CPT9a , donor 1


title: BM-RNA-179_TEL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: PMN cells, treated with SCV2-RNA2, donor 4


title: Post_challenge YF-VAX D275 CN685_D275


title: BM-RNA-181_06BA_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Post_challenge YF-VAX D271 CN685_D271


title: PMN cells, treated with SCV2-RNA2, donor 2


title: BM-RNA-185_TiJ_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

value: TiJ


title: Post_challenge YF-VAX D259 CN685_D259


title: Post_challenge Stamaril D296 CO433_D296

description:
Post_challenge Stamaril D296
post challenge (vaccinated animals)

value: Stamaril


title: PMN cells, treated with SCV2-RNA2, donor 3

value: blood


title: BM-RNA-180_TK1_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Post_challenge Stamaril D271 CO433_D271

description:
Post_challenge Stamaril D271
post challenge (vaccinated animals)


title: BM-RNA-054_Ti7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0


title: Post_challenge Stamaril D259 CO433_D259

description:
Post_challenge Stamaril D259
post challenge (vaccinated animals)


title: PMN cells, control plus CU-CPT9a , donor 4

value: neutrophils

value: control plus CU-CPT9a


title: PMN cells, control plus CU-CPT9a , donor 3

value: 6 hours


title: Post_challenge Stamaril D275 CO433_D275

description:
Post_challenge Stamaril D275
post challenge (vaccinated animals)

value: Whole Blood


title: BM-RNA-050_T63_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0


title: BM-RNA-051_T96_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0


title: PMN cells, control plus CU-CPT9a , donor 2


title: Post_challenge Stamaril D275 CO401_D275

value: male


title: Post_challenge Stamaril D296 CO401_D296


title: BM-RNA-052_TiD_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: TiD


title: Post_challenge Stamaril D271 CO401_D271


title: PMN cells, control, donor 4

value: control


title: PMN cells, control, donor 3


title: BM-RNA-057_TV9_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: basal


title: Post_challenge Stamaril D259 CO401_D259


title: BM-RNA-187_TK3_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: PMN cells, control, donor 2


title: PMN cells, control plus CU-CPT9a , donor 1


title: PMN cells, treated with SCV2-RNA2, donor 1


title: BM-RNA-056_TT7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: Week 0


title: Post_challenge Stamaril D296 CO382_D296


title: PMN cells, control, donor 1


title: Post_challenge Stamaril D275 CO382_D275


title: CI0000035270, cell line

city: Little Rock

first: Analiz

last: Rodriguez

state: AR

address: 4301 W. Markham St Slot 507

department: College of Medicine, Department of Neurosurgery

institute: University of Arkansas for Medical Sciences

description: 10X Genomics

data_processing:
Cell barcodes and UMI (unique molecular identifiers) barcodes were demultiplexed and single-end reads aligned to the reference genome, GRCh38, using the CellRanger pipeline (10X Genomics).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

growth_protocol: Cells from primary tumor specimens were cultured in Roswell Park Memorial Institute culture medium (RPMI) containing 10% fetal bovine serum (FBS) and 1% (v/v) antibiotic/antimitotic.  Early passage cells (<P3) were grown to confluency and then harvested for single cell RNA sequencing analysis.

extract_protocol:
Cellular suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197): 55 °C for 2 h, 85 °C for 5 min; held at 4 °C. After RT, GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D) and SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter; P/N B23318). cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 3 min; cycled 14 × : 98 °C for 15 s, 67 °C for 20 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6 × SPRI). The cDNA was subsequently sheared to ∼200 bp using a Covaris M220 system (Covaris; P/N 500295).
A single-cell RNA library was generated using the GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) and Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (P/N 120236 P/N 120237 10x Genomics). The sequencing ready library was purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin Elmer), and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824).

value: Brain

tag: disease

value: melanoma

value: female

tag: age (years)


title: CI0000035270

description: 10X Genomics


title: BM-RNA-047_TEL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: Study 2


title: C1

description: miRNA array serum Parkinson

extract_protocol: A total of 5ml peripheral blood was collected in tubes without anticoagulant (BD Vacutainer) and centrifuged 10 minutes at 1500xg and 4°C. Serum was aliquoted into polypropylene CryoTubes (Greiner Bio-One) and kept at −80°C until use. Total miRNA enriched RNA was extracted using the miRNeasy Serum/Plasma Kit (QIAGEN #217184) following manufacturer recommendations. As a carrier for miRNA isolation, we added 2ul of diluted yeast tRNA (Invitrogen #AM7119) into 200ul of serum for a final concentration of 10ug/ml. RNA concentration was determined for all samples on a NanoDrop ND-3300 fluorospectrometer (Thermo Fisher Sci.), and miRNA quality was evaluated for a subset of randomly selected samples by electropherogram using an Bioanalizer Small RNA Kit (Agilent #5067-1548).

value: Control

value: H

tag: age


title: BM-RNA-049_06BA_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

tag: animal id


title: BM-RNA-053_TiJ_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: TiJ

tag: vaccination


title: BM-RNA-048_TK1_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

tag: time point


title: BM-RNA-055_TK3_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

tag: week


title: Post_challenge Stamaril D296 CO369_D296

tag: treatment

value: Stamaril


title: CI0000035650, cell line

description: 10X Genomics


title: Post_challenge Stamaril D271 CO382_D271


title: Post_challenge Stamaril D275 CO369_D275


title: CI0000035650

description: 10X Genomics


title: Post_challenge Stamaril D271 CO369_D271


title: Post_challenge Stamaril D259 CO369_D259


title: Riboseq - RKO cells - arg fed rep 3

city: Pittsburgh

first: Dennis

last: Hsu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

description:
ribosome footprints
RKO_400uM_3

data_processing:
cutadapt was used to remove the linker sequence and the FastX-Tooolkit used to split reads by barcodes.
Reads aligning to ribosomal RNA sequences were discarded using STAR, and remaining reads aligned to the human transcriptome (GRCh38.p13). Only the longest transcript for each gene was used for alignment.
For ribosome profiling experiments, UMI-tools were used to extrat unique molecular identifiers and de-duplicate the reads.
Statistical analysis was conduced using DESeq2 (RNASeq) and Ribolog software package for ribosome profiling (https://github.com/goodarzilab/Ribolog)
Assembly: GRCh38.p13
Supplementary files format and content: Two tab delimited files containing raw counts obtained from STAR. One corresponds to the RNA seq experiments and the other to ribosome protected footprints.
Library strategy: Ribo-seq

source_name: epithelial

growth_protocol: Cells were grown in arginine-null DMEM supplemented with 10% dialyzed FBS. Arginine was supplemented to either 400 uM or 12.5 uM based on treatment conditions.

extract_protocol:
Cell lysis, ribosome footpring purification, and downstream library construction were performed according to previously published protocols (PMID 28579404). RiboCop rRNA Depletion Kit for Human/Mouse/Rate (HMR) V2 (Lexogen) were used to deplete ribosomal RNA.
RNA sequencing was prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) and following manufacturer's protocols.

treatment_protocol: Cells were first plated in full media and then later washed with media containing either full (400 uM arginine) or low (12.5 uM) arginine.

value: epithelial

value: RKO

tag: cell type

value: cancer

value: WT

value: 400 uM Arg


title: Riboseq - RKO cells - arg fed rep 2

description:
ribosome footprints
RKO_400uM_2


title: BM335_TiJ_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

data_processing:
An average number of reads of 50 million/sample were acquired with a read length of 51 bp and with a paired-end read.
Raw sequencing data were demultiplexed by Bcal2fastq v2.17. Adaptor sequence trimming was done by Cutadapt 1.18.
Bowtie2 was used to map to the rheMac10 reference genome.
PICARD tool was used to remove duplicated reads.
Peak calling was performed using MACS2.
Raw counts of mapped reads were obtained using Homer tools for the called peaks
Genome_build: rheMac10
Supplementary_files_format_and_content: peak files

value: post ALVAC+gp120

value: Week 13

tag: protocol

tag: study

value: Study 3

tag: time of acquisition


title: Post_challenge Stamaril D275 CN777_D275

value: Whole Blood

value: male

tag: time


title: BM-RNA-058_TBL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 0

value: TBL

value: basal

value: Week 0


title: Riboseq - RKO cells - arg fed rep 1

description:
ribosome footprints
RKO_400uM_1


title: Post_challenge Stamaril D296 CN777_D296

tag: Sex


title: BM321_TT7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

tag: date of collection


title: Riboseq - RKO cells - arg starved rep 3

description:
ribosome footprints
RKO_12.5uM_3

tag: tissue

tag: genotype

value: 12.5 uM Arg


title: BM303_TK1_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Riboseq - RKO cells - arg starved rep 2

description:
ribosome footprints
RKO_12.5uM_2

tag: cell line


title: Post_challenge Stamaril D259 CO382_D259


title: Post_challenge Stamaril D271 CN777_D271


title: Riboseq - RKO cells - arg starved rep 1

description:
ribosome footprints
RKO_12.5uM_1


title: Post_challenge Stamaril D259 CN777_D259


title: BM285_TV9_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: RNAseq- RKO cells - arg fed rep 3

data_processing:
cutadapt was used to remove the linker sequence and the FastX-Tooolkit used to split reads by barcodes.
Reads aligning to ribosomal RNA sequences were discarded using STAR, and remaining reads aligned to the human transcriptome (GRCh38.p13). Only the longest transcript for each gene was used for alignment.
For ribosome profiling experiments, UMI-tools were used to extrat unique molecular identifiers and de-duplicate the reads.
Statistical analysis was conduced using DESeq2 (RNASeq) and Ribolog software package for ribosome profiling (https://github.com/goodarzilab/Ribolog)
Assembly: GRCh38.p13
Supplementary files format and content: Two tab delimited files containing raw counts obtained from STAR. One corresponds to the RNA seq experiments and the other to ribosome protected footprints.


title: Post_challenge Stamaril D296 CN657_D296


title: Post_challenge Stamaril D275 CN657_D275


title: RNAseq- RKO cells - arg fed rep 2


title: RNAseq- RKO cells - arg fed rep 1


title: Post_challenge Stamaril D271 CN657_D271


title: BM270_Ti7_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: BM266_TEL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

description: Discarded in downstream analysis

value: TEL


title: BM317_TK3_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: RNAseq- RKO cells - arg starved rep 3


title: BM251_TBL_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: Post_challenge Stamaril D259 CN657_D259


title: Post_infection Asibi D273 CO569_D273

description:
Post_infection Asibi D273
post challenge (naive animals)

value: Asibi


title: RNAseq- RKO cells - arg starved rep 2


title: Post_infection Asibi D271 CO569_D271

description:
Post_infection Asibi D271
post challenge (naive animals)


title: BM247_T96_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: BM228_06BA_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: NP69SV40T_WT_input_replication2

description:
NP69SV40T_WT_H3K4me1_replication2.bedgraph.gz
NP69SV40T_WT_H3K4me3_replication2.bedgraph.gz
NP69SV40T_WT_H3K27ac_replication2.bedgraph.gz

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: nasopharyngeal epithelial cell line

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated. The sonicated nuclear fraction was used as input.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: nasopharyngeal epithelial cell line


title: RNAseq- RKO cells - arg starved rep 1

value: epithelial


title: NP69SV40T_WT_H3K27ac_replication2

tag: chip antibody

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: Post_infection Asibi D259 CO569_D259

description:
Post_infection Asibi D259
post challenge (naive animals)


title: BM232_T63_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13


title: LRB458 daf-2(e1370); irld-39(duk1); irld-52(duk17) rep4

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.2.2 was used to map reads with the following settings: bowtie -I 0 -X 500 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset (file name c_elegans.PRJNA13758.WS273.canonical_geneset.gtf downloaded from Wormbase)
edgeR version 3.24.4 was used for differential expression analysis. Count data was restricted to include protein-coding genes, and further restricted to include only genes with CPM greater than 1 in at least four libraries.
Interaction analysis to determine whether irld-39(duk1); irld-52(duk17) differentially affected gene expression in N2 and daf-2(e1370) backgrounds was done using glmQLFit and glmQLFtest functions.
Genome_build: WS273
Supplementary_files_format_and_content: Count files for each library; these are the non-normalized input into edgeR for differential expression analysis. An excel final with edgeR output from differential expression is also included.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: N2, LRB444 [irld-39(duk1); irld-52(duk17)], CB1370 [daf-2(e1370)], LRB457 and LRB458 [independent lines of daf-2(e1370); irld-39(duk1); irld-52(duk17)] were bleached as well-fed gravid adults to obtain embryos. Embryos were re-suspended in S-basal at 1/uL and placed at 20C in a shaker at 180 rpm. 24 hours later (12 hours after hatch), starved L1 larvae were collected for each condition. 10,000 starved L1s were collected for each biological replicate and strain. To collect, samples were spun down at 3,000 rpm in a 15 mL conical tube, then aspirated down to < 100 uL. This volume was transfered to an Eppenforf tube, spun down at 3,000 rpm again, then excess liquid was aspirated down to 10 uL. Samples were flash frozen in liquid nitrogen and placed at -80C until RNA isolation.

extract_protocol:
RNA was isolated using TRIzol following the manufacturer's protocol with notable exceptions. Only 100 uL of Trizol was used, and 5 ug linear polyacrylamide (Sigma Aldrich) was included as a neutral carrier for RNA precipitation. RNA was eluted in nuclease-free water and incubated at 55°C for approximately four minutes to resuspend the pellet.
NEBNext Ultra II RNA Library Prep kit was used to perform polyA selection on total RNA and prepare libraries for sequencing. ThermoFisher ERCC Spike-In mix was added based on total RNA. The libraries were enriched with PCR

tag: strain/genotype


title: Post_infection Asibi D275 CO504_D275

description:
Post_infection Asibi D275
post challenge (naive animals)

data_processing:
OmicSoft Array Studio software (v9.0 -v10.0).
The reads were aligned with OmicsSoft Aligner (OSA4) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations
Multiple mappings reads and first-read-forward-strand reads were discarded from the analysis
Read counts were then subsequently analyzed using R scripts (R version 3.3.3).
All samples were scale-normalized according to their library size by the TMM method of edgeR package (v3.16.5) and transformed with voom (Limma R package v3.30.13).
For the linear modeling of differential gene expression, a model was built with Limma using the treatment condition (vaccination group and sampling time point) as a factor (relatively to the vaccination day defined as a baseline). Contrasts were set up in order to compare for every vaccination group each time point post-vaccination with baseline (Day –29)). Contrasts were also set up to compare directly vaccination groups for each time point post-vaccination relatively to their own group baseline
The tmod R package (v0.31) was used to detect functional enrichment directly on the Limma object (i.e. inference test result from the Limma R package) on the full genes list (ordered using default "minimal significant difference" ranking) coming from each contrast
Assembly: Cyno.WashU2013
Supplementary files format and content: Raw read counts from Array Studio software


title: CB1370 daf-2(e1370) rep4

treatment_protocol: N2, LRB444 [irld-39(duk1); irld-52(duk17)], CB1370 [daf-2(e1370)], LRB457 and LRB458 [independent lines of daf-2(e1370); irld-39(duk1); irld-52(duk17)]


title: BM281_TiD_V1-deleted-DNA/DNA/ALVAC/ALVAC+gp120_Week 13

tag: animal id

value: TiD


title: NP69SV40T_WT_H3K4me3_replication2

value: H3K4me3_ChIP (Active Motif, 39159, lot 31420006)


title: Post_infection Asibi D296 CO504_D296

description:
Post_infection Asibi D296
post challenge (naive animals)


title: Post_infection Asibi D271 CO504_D271


title: NP69SV40T_WT_H3K4me1_replication2

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: LRB444 irld-39(duk1); irld-52(duk17) rep4

value: LRB444 irld-39(duk1); irld-52(duk17)


title: N2 rep4


title: Post_infection Asibi D259 CO504_D259


title: Post_infection Asibi D296 CO427_D296


title: NP69SV40T_WT_input_replication1

description:
NP69SV40T_WT_H3K4me1_replication1.bedgraph.gz
NP69SV40T_WT_H3K4me3_replication1.bedgraph.gz
NP69SV40T_WT_H3K27ac_replication1.bedgraph.gz


title: LRB457 daf-2(e1370); irld-39(duk1); irld-52(duk17) rep3


title: NP69SV40T_WT_H3K27ac_replication1


title: Post_infection Asibi D275 CO427_D275


title: NP69SV40T_WT_H3K4me3_replication1


title: CB1370 daf-2(e1370) rep3


title: LRB444 irld-39(duk1); irld-52(duk17) rep3


title: Post_infection Asibi D271 CO427_D271


title: N2 rep3


title: FaDu_WT_input_replication1

description:
FaDu_WT_H3K4me1_replication1.bedgraph.gz
FaDu_WT_H3K4me3_replication1.bedgraph.gz
FaDu_WT_H3K27ac_replication1.bedgraph.gz

value: HPV(-) head and neck cancer cell line


title: NP69SV40T_WT_H3K4me1_replication1


title: FaDu_WT_H3K27ac_replication1


title: FaDu_WT_H3K4me3_replication1


title: FaDu_WT_H3K4me1_replication1


title: Post_infection Asibi D271 CO278_D271


title: Post_infection Asibi D273 CO278_D273


title: Post_infection Asibi D274 CO278_D274

description:
Post_infection Asibi D274
post challenge (naive animals)


title: LRB458 daf-2(e1370); irld-39(duk1); irld-52(duk17) rep1


title: CB1370 daf-2(e1370) rep2


title: LRB444 irld-39(duk1); irld-52(duk17) rep2


title: Post_infection Asibi D275 CO090_D275


title: LRB457 daf-2(e1370); irld-39(duk1); irld-52(duk17) rep1


title: Post_infection Asibi D271 CO090_D271


title: LRB444 irld-39(duk1); irld-52(duk17) rep1


title: NP69SV40T_WT_replication1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).


title: NP69SV40T_WT_replication2


title: FaDu_WT_replication2

source_name: HPV(–) head and neck cancer cell line

value: FaDu


title: N2 rep1


title: irld39_52_60hr_rep1

data_processing:
Bowtie version 1.2.2 was used to map reads with the following settings: bowtie -I 0 -X 500 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset (file name c_elegans.PRJNA13758.WS273.canonical_geneset.gtf downloaded from Wormbase)
edgeR version 3.24.4 was used for differential expression analysis. Count data was restricted to include protein-coding genes, and further restricted to include only genes with CPM>1 in at least three libraries.
An interaction analysis was performed in edgeR to determine genes with significantly different gene expression between the two time series (N2 and LRB444). This was done using glmQLFit and glmQLFTest functions. Log2 fold changes were used to determine gene expression patterns of DAF-16 targets.
Genome_build: WS273
Supplementary_files_format_and_content: Count files for each library; these are the non-normalized input into edgeR for differential expression analysis. An excel final with edgeR output from differential expression is also included.

growth_protocol: N2 and LRB444 [irld-39(duk1); irld-52(duk17)] were bleached and resuspended in S-basal at 1/uL at 20C in the shaker at 180 rpm. Approximately 2-10K starved L1s were collected at 18, 24, 36, 60, and 84 hours after bleach for each genotype, by spinning down, flash freezing, and storing at -80C. 3 biological replicates were collected for each condition.

extract_protocol:
RNA was isolated using TRIzol following the manufacturer's protocol with notable exceptions. Only 100 uL of Trizol was used, and 5 ug linear polyacrylamide (Sigma Aldrich) was included as a neutral carrier for RNA precipitation. RNA was eluted in nuclease-free water and incubated at 55°C for approximately four minutes to resuspend the pellet.
NEBNext Ultra II RNA Library Prep kit was used to perform polyA selection on total RNA and prepare libraries for sequencing. 50 ng of total RNA was used for each library. ThermoFisher ERCC Spike-In mix was added based on total RNA. The libraries were enriched with PCR.

tag: hours of l1 arrest

value: 48 hr

value: irld-39(duk1); irld-52(duk17)


title: Post_infection Asibi D275 CO069_D275

value: Whole Blood

value: male


title: FaDu_WT_replication1


title: Post_infection Asibi D271 CO069_D271


title: UM-SCC-104_WT_replication2

source_name: HPV(+) head and neck cancer cell line


title: UM-SCC-104_WT_H3K4me3_replication1

value: HPV(+) head and neck cancer cell line


title: Post_infection Asibi D259 CO069_D259


title: Post_infection Asibi D259 CO278_D259


title: UM-SCC-104_WT_replication1


title: UPCI-SCC-090_WT_replication1


title: Post_Vaccination vYF D27 CO331_D27

description:
Post_Vaccination vYF D27
post vaccination

value: vYF


title: irld39_52_24hr_rep1

treatment_protocol: N2 and LRB444 [irld-39(duk1); irld-52(duk17)]

value: 12 hr


title: Post_Vaccination vYF D7 CO331_D7

description:
Post_Vaccination vYF D7
post vaccination


title: Post_Vaccination vYF D3 CO331_D3

description:
Post_Vaccination vYF D3
post vaccination


title: N2_60hr_rep1


title: N2_84hr_rep1

value: 72 hr


title: UPCI-SCC-090_WT_replication2


title: N2 rep2


title: Post_infection Asibi D259 CO427_D259

value: Asibi


title: Post_infection Asibi D259 CO090_D259


title: irld39_52_18hr_rep1

value: 6 hr


title: Post_Vaccination vYF D-29 CO331_D-29

description:
Post_Vaccination vYF D-29
post vaccination


title: irld39_52_84hr_rep3


title: UM-SCC-104_baitE6E7_replication1

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
4C-seq reads were aligned to hg19 reference human genome, using w4Cseq.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-104 was cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

tag: restricion enzymes

value: Csp6I, NlaIII


title: Post_Vaccination vYF D27 CO314_D27


title: N2_36hr_rep1

value: 24 hr


title: CONTROL SIRNA + DEX 2 [ATAC-seq]

city: Bristol

first: Felicity

last: Stubbs

address: Whitson St

institute: University of Bristol

data_processing:
Basecalling  Software: RTA 2.4.6 Parameters: Illumina instrument run time analysis software
Demultiplexing, Software: Bcl2fastq 2.17 Parameters: Barcode demultiplexed allowing 1 mismatch
Adapter and Quality Trimming Software: Trimmomatic 0.36 Parameters: Paired-end: PE -threads 16 -phred33 ILLUMINACLIP: adapters.fa:2:36:10 LEADING:10 TRAILING:10 MAXINFO:50:0.97 MINLEN:20 Single-end: SE -threads 16 -phred33 ILLUMINACLIP: adapters.fa:2:36:10 LEADING:10 TRAILING:10 MAXINFO:50:0.97 MINLEN:20
Alignment Software: Bowtie2  2.2.6 Parameters: Paired-end: -p 8 -x ref_genome -1 read1.fastq -2 read2.fastq --un-conc Single-end: -p 8 -x ref_genome -U read1.fastq --un
Duplication Statistics Software: Picard 1.84 Parameters: MarkDuplicates.jar INPUT=sample.bam OUTPUT=sample.MKDUP.bam METRICS_FILE=sample.bam.metric ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 VALIDATION_STRINGENCY=LENIENT.  ATAC-Seq peaks were identified using MACS2. Tag Density was normalized to 10 million tags by makeTagDirectory for cross comparison and visualization (HOMER v4.9.1)
Assembly: Human - hg19 reference
Supplementary files format and content: Bigwig files
Supplementary files format and content: Bigwig files

source_name: HeLa

growth_protocol: DMEM, 10% FCS.

extract_protocol:
HeLa cells were detached from flasks using Accutase, then resuspended in PBS at 6 million cells/ml. Nuclei were isolated and ATAC was performed following methods previously described. Transposition was achieved using Nextera Tn5 Transposase (Nextera kit).
ATAC-Seq samples were pooled and sequenced on NextSeq using TruSeq Chip Samples Prep Kit (IP-202-1012) and paired-end sequencing.
All the samples have percent of Q30 bases above 87%. All the samples have yields between 89 and 135 million pass filter reads. Samples were trimmed for adapters using trimmomatic software before the alignment. The trimmed reads were aligned with Human - hg19 reference using Bowtie2 alignment. Overall alignment percentage for the samples is 98%. Unique alignment is above 53%. There are 1.79 to 2.17% unmapped reads. Library complexity is measured by uniquely aligned reads using picard’s markduplicate utility. All the samples have library complexity with percent non-duplicated reads ranging from 47 to 61%.

treatment_protocol: 100nM Dex

value: HeLa

value: Cervical cancer

value: Dex

tag: time (mins)


title: irld39_52_36hr_rep1


title: Post_Vaccination vYF D7 CO314_D7

tag: treatment


title: CONTROL SIRNA - DEX 2 [ATAC-seq]

tag: cell type


title: irld39_52_60hr_rep3


title: UPCI-SCC-090_baitE6E7_replication1

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba University


title: Post_Vaccination vYF D3 CO314_D3


title: irld39_52_36hr_rep3


title: Post_Vaccination vYF D-29 CO314_D-29


title: CB1370 daf-2(e1370) rep1


title: CONTROL SIRNA + DEX 1 [ATAC-seq]


title: irld39_52_24hr_rep3


title: ARID1a KNOCKDOWN +DEX 2 [ATAC-seq]


title: CONTROL SIRNA - DEX 1 [ATAC-seq]


title: Post_Vaccination vYF D3 CO306_D3


title: ARID1a KNOCKDOWN -DEX 2 [ATAC-seq]


title: irld39_52_18hr_rep3


title: N2_60hr_rep3


title: N2_84hr_rep3


title: Post_Vaccination vYF D27 CO306_D27


title: Post_Vaccination vYF D27 CN998_D27


title: Post_Vaccination vYF D-29 CO306_D-29


title: N2_24hr_rep3


title: Post_Vaccination vYF D7 CN998_D7


title: N2_18hr_rep3


title: irld39_52_84hr_rep2


title: Post_Vaccination vYF D3 CN998_D3


title: Post_Vaccination vYF D27 CN774_D27


title: N2_24hr_rep1


title: Post_Vaccination vYF D3 CN774_D3


title: UM-SCC-47_WT_4

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro.
Assembly: hg19
Supplementary files format and content: hic

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

value: WT

tag: restricion enzyme

value: MboI


title: irld39_52_60hr_rep2

value: 48 hr


title: Post_Vaccination vYF D7 CO306_D7


title: irld39_52_24hr_rep2

value: irld-39(duk1); irld-52(duk17)


title: Post_Vaccination vYF D-29 CN774_D-29

value: Whole Blood


title: UM-SCC-47_H3K27ac_replication2

description: UMSCC47_WT_H3K27ac_replication2.bedgraph

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: N2_36hr_rep3


title: irld39_52_18hr_rep2


title: irld39_52_36hr_rep2


title: Post_Vaccination vYF D3 CN705_D3

value: male


title: Post_Vaccination vYF D27 CN705_D27

value: vYF


title: ARID1a KNOCKDOWN -DEX 1 [ATAC-seq]


title: UM-SCC-47_input_replication2

description:
UMSCC47_WT_H3K4me1_replication2.bedgraph
UMSCC47_WT_H3K4me3_replication2.bedgraph
UMSCC47_WT_H3K27ac_replication2.bedgraph

value: HPV(+) head and neck cancer cell line


title: UM-SCC-47_H3K4me3_replication2

description: UMSCC47_WT_H3K4me3_replication2.bedgraph

value: H3K4me3_ChIP (Active Motif, 39159, lot 31420006)


title: UM-SCC-47_H3K4me1_replication2

description: UMSCC47_WT_H3K4me1_replication2.bedgraph

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: N2_84hr_rep2

value: 72 hr


title: Post_Vaccination vYF D-29 CN705_D-29


title: UM-SCC-47_H3K27ac_replication1

description: UMSCC47_WT_H3K27ac_replication1.bedgraph


title: N2_36hr_rep2


title: Post_Vaccination vYF D-29 CN998_D-29


title: ARID1a KNOCKDOWN +DEX 1 [ATAC-seq]


title: UPCI-SCC-090_siITPR3_replication2

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃. Clinical samples were immediately frozen in liquid nitrogen and stored at −80℃.

value: ITPR3 knockdown


title: Post_Vaccination YF-VAX D27 CO464_D27

description:
Post_Vaccination YF-VAX D27
post vaccination

value: YF-VAX


title: UPCI-SCC-090_siControl_replication2

value: Non-targeting negative control


title: Post_Vaccination YF-VAX D7 CO464_D7

description:
Post_Vaccination YF-VAX D7
post vaccination


title: N2_24hr_rep2

value: 12 hr


title: N2_18hr_rep2

value: 6 hr


title: Post_Vaccination vYF D7 CN705_D7


title: irld39_52_84hr_rep1


title: Post_Vaccination YF-VAX D-29 CO464_D-29

description:
Post_Vaccination YF-VAX D-29
post vaccination


title: Post_Vaccination YF-VAX D3 CO226_D3

description:
Post_Vaccination YF-VAX D3
post vaccination


title: exp8_miRNA

first: Liying

last: Jiang

address: 279 zhouzhugong road

institute: Shanghai University of Medicine and Health Sciences

data_processing:
Analysis of count data was performed using the DESeq2 (differential gene expression analysis based on the negative binomial distribution) pipeline (version 1.0.19) (Anders and Huber, 2010).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample ...

source_name: pregnant female

extract_protocol:
Total RNA  was extracted  using the RNeasy micro kit (Qiagen) according to manufacturer’s protocol  and determined by Bioanalyzer 2100 (Agilent, santa Clara, CA, USA).
miRNA-Seq libraries  were performed using the Small RNA Library Prep（NEB E7300L/E7580L）.

value: female

value: peripheral blood

value: lymphocyte

tag: disease state

value: gestational diabetes (GDM)


title: Post_Vaccination YF-VAX D27 CO226_D27

extract_protocol:
Whole blood from NHPs was collected in PAXgene tubes (BD762165 –Ozyme) and stored according to the manufacturer's protocol. Total RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation
Extracted RNA samples were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300 ng of total globin-depleted RNA according to manufacturer’s instructions.

value: Whole Blood


title: N2_18hr_rep1


title: exp9_miRNA


title: UM-SCC-47_replication1

value: WT


title: N2_60hr_rep2

value: 48 hr