title: OH17_vdj

first: Oscar Junhong

last: Luo

state: Guangdong Province

address: 601 Huangpu Ave West

institute: Jinan University

data_processing:
The 10x Genomics Cell Ranger software suite (v3.1.0) with Human reference GRCh38 (v1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build) was used to process the scRNA-Seq, scTCR-Seq and cell surface protein sequencing fastq files, with default parameter settings.
Genome_build: hg38
Supplementary_files_format_and_content: MTX: Sparse matrix for gene quantification.
Supplementary_files_format_and_content: TSV: Metadata describing the gene and feature names of the sparse matrix.
Supplementary_files_format_and_content: CSV: TCR clonetype annotation.

source_name: PBMC

extract_protocol:
Fresh whole blood was collected in 2 ml tubes that treated with diamine tetraacetic acid (EDTA). Peripheral Blood Mononuclear Cells (PBMCs) were isolated from whole blood of samples with Ficoll (GE Healthcare Life Sciences) following the manufacture’s protocol. Briefly, blood sample was diluted with D-Hanks (NaCl 8 g/L, KCl 0.4 g/L, Na2HPO4 0.16 g/L, KH2HPO4 0.06 g/L, glucose 1 g/L) in a ratio of 1:1, and then add Ficoll and centrifuged at 2000 rpm for 20 min at room temperature. Enriched PBMCs were washed with D-Hanks plus 2% fetal calf serum (FBS), and then centrifuged at 400 g for 10 min, repeat twice. Then cell numbers and viability were assessed.
Cell number and viability were checked after surface protein staining (cell viability > 80%). Then droplet-encapsulation single-cell sequencing experiments were performed, and 10,000 living single cells were loaded onto each of the Chromium Controller (10x Genomics). After droplet-encapsulation, single-cell cDNA synthesis, amplification and sequencing libraries were generated using Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics), Chromium Single Cell 5' Library & Gel Bead Kit (10x Genomics), and Chromium Single Cell V(D)J Enrichment Kit (Human T Cell, 10x Genomics) according to the manufacturer’s instructions. The libraries from each loaded channel (up to eight channels) were multiplexed together and sequenced on an Illumina Novaseq 6000.

tag: cell type

value: mononuclear cell

tag: age group

value: Old

tag: assay

value: single-cell RNA


title: Selected pop. 3 on poor diet

status: Public on Jan 12 2022

type: SRA

city: Lausanne

first: Tadeusz

middle: J.

last: Kawecki

address: Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

library_source: transcriptomic

data_processing:
fastq files from the two lanes for each sample were pooled
Reads were aligned to Dmel genome BDGP6.79 using kallisto v. 0.46.2 with options --single -l 101 -s 10 -b 100 -t 8; the output files are provided ("kallisto_abundance_sample…")
Raw counts per transcript were converted to raw counts per gene with tximport Bioconductor package
Genes with read count greater than 2 per million in at least 6 samples were retained, the rest were filtered out
Abundances were analyzed with limma-voom with implicit EdgeR normalization; normalized log2 expression values (eList$E) are provided as the expression matrix
Genome_build: BDGP6.79
Supplementary_files_format_and_content: Tab-delimited text files "kallisto_abundance_sample??.tsv" contain, for each sample, the FGtr ID of each transcript, its length and effective length, the absolute estimated number of counts (est_counts) and the counts per million (tpm)
Supplementary_files_format_and_content: CarcassesVoomNormlizedLog2Counts.txt: matrix table or voom log2-normalized expression values for each gene (row) and sample (columns)

molecule: total RNA

organism: Drosophila melanogaster

source_name: carcass mated females

growth_protocol: "Standard" diet consisted of 12.5 g dry brewer’s yeast, 30 g sucrose, 60 g glucose, 50 g cornmeal, 0.5 g CaCl2, 0.5 g MgSO4, 10 ml 10% Nipagin, 6 ml propionic acid, 20 ml ethanol and 15 g of agar per liter of water.   The "poor" diet contained 1/4 of the concentrations of yeast, sugars and cornmeal, but the same concentrations of the other ingredients. Flies were raised in bottles seeded with about 200 eggs per 40 ml of food medium.   Adults of all populations and of both sexes were transferred to standard diet on day 1 post-emergence. Females were collected three days later, i.e., they were aged about 4 days.

extract_protocol:
RNA was extracted from the carcass samples using "Total RNA Purification Plus" by Norgen Biotek (#48300, 48400).
cDNA libraries (TrueSeq Standard RNA) were generated and sequenced on two lanes of Illumina HiSeq4000 (single read, 150 bp)

treatment_protocol: Female flies were collected in the morning and dissected in PBS. The abdomen was separated, and the gonads, the gut and the bulk of Malpighian tubes were removed, producing the "carcass", consisting of the abdominal fat body attached to the body wall, as well as any hemolymph, oenocytes, neurons and fragments of Malpighian tubes that remained embedded in the fat body.

tag: larval diet

value: standard

tag: evolutionary regime

value: Control

tag: replicate population

tag: age

value: 4 days

tag: tissue

value: carcass

tag: Sex

value: female


title: OH15_vdj

city: Guangzhou

country: China

molecule: polyA RNA

organism: Homo sapiens


title: Brg1_KD_D1_Etv2_Repeat_rep1

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

country: USA

institute: University of Minnesota

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ChIP-seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: MEF

extract_protocol:
EB or MEF cells were harvested as described above. ChIP assays for ETV2 and H3K27ac were performed from 2 x 106 MEFs or 1 x 107 EB cells, respectively. Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M.  For the BRG1 ChIP-seq, cells were first crosslinked in 2 mM disuccinimidyl glutarate (DSG; Life Technologies: Cat. #20593) for 30 min then in 1% formaldehyde for 10 min, quenched with glycine for 5 min.  The remainder of the ChIP protocol was performed following the protocol described by Magli et al19. We used antibodies against H3K27ac (Abcam, ab4729), ETV2 (Abcam, ab181847), and BRG1 (Abcam ab110641) for the respective pulldowns. For both of the pulldowns, protein A Dynabeads were added to the ChIP reactions and incubated for 30 minutes at room temperature. Magnetic beads were washed and chromatin was eluted. After crosslinking reversal, RNase A, and proteinase K treatment, ChIP DNA was extracted with the Min-Elute PCR purification kit (Qiagen). ChIP DNA was quantified with Quant-it PicoGreen dsDNA Assay Kit (Life Technologies). Sequencing libraries were prepared using equal amount of ChIP DNA per sample as per instructions of SMARTer® ThruPLEX® DNA-Seq Kit (Takara R400675) and SMARTer® DNA Unique Dual Index Kit - 24U Set A (Takara R400665). Sequencing was performed at the University of Minnesota Genome Center with the The NextSeq 550 high-throughput benchtop sequencer.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: day 1

tag: dox or no dox

value: Dox


title: M5_Lung_C2

city: Heidelberg

first: Delphine

last: Merino

state: Victoria

address: Level 5, ONJ Centre, 145 Studley Rd, Heidelberg

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

data_processing:
Base calling used Real-Time Analysis on board software v2.4.6
Demultiplexed into fastq files using bcl2fastq software v2.15.0.4
Reads were filtered using cutadapt
Reads were mapped to GRCh38 genome using STAR
Reads were quantified using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files with raw gene counts for every gene and every sample

source_name: Sorted subclone 2 - Lung metastasis, Retransplantation experiment

extract_protocol:
Qiagen miRNeasy micro Kit with in column DNAse treatment
Illumina TruSeq RNA Library Prep Kit v2

tag: sample type

value: Sorted metastatic subclone

tag: subclone

tag: organ

value: Lung metastasis

tag: cell line

tag: mouse number

tag: retransplantation

value: TRUE


title: Peromyscus_polionotus_burrowing_rep2

city: San Francisco

first: Ryan

last: York

state: CA

address: 1328 6th Avenue

institute: Stanford University

data_processing:
To compare gene expression both across treatments and species, we first removed low-quality and adaptor sequences using SeqPrep (https://github.com/jstjohn/SeqPrep).
The P. maniculatus genome was masked at sites with SNPs using the perl script MaskReferencefromBED (https://github.com/TheFraserLab/ASEr) to avoid reference genome mapping bias. Reads from all F1 hybrid samples were aligned to this masked genome using STAR v 2.4.2a (Dobin et al., 2013) in 2-pass mode.
We determined ASE at the read-level using the script GetGeneASEbyReads in the ASEr package (https://github.com/TheFraserLab/ASEr).
To test for allele-specific expression differences, we first filtered ASE calls from GetGeneASEbyReads requiring at least 1 count per allele from all genes per sample.
After filtering we computed an ASE ratio for each gene by calculating the log2 ratio of P. maniculatus allelic counts compared to P. polionotus allelic counts. Positive values correspond to a P. maniculatus allelic bias while negative values reflect a P. polionotus bias.
Genome_build: pman 1.0
Supplementary_files_format_and_content: Matrix table with allele counts

organism: Peromyscus polionotus

source_name: Whole brain

growth_protocol: All experimental animals were males and housed in standard polysulfone cages (19.7 x 30.5 cm and 16.5 cm high; Allentown, New Jersey, USA) in same sex and genotype groups, until testing adults at approximately 50-80 days of age. Housing cages contained enrichment as previously described (Lewarch and Hoekstra, 2018). We maintained animals at 22 ºC with a 16:8h light:dark cycle and provided them with standard rodent food and water ad libitum. All procedures were approved by the Harvard University Institutional Animal Care and Use Committee (protocol 27-09-3)

extract_protocol:
To capture behavior-relevant gene expression, we focused on the brain. Therefore, at the conclusion of the test trial, we immediately euthanized animals using CO2 inhalation and rapidly dissected whole brains in chilled PBS, flash-froze the sample in liquid nitrogen, and stored it at -80 °C. Later, we homogenized tissues using a TissueLyser (Qiagen, Venlo, Netherlands) in Trizol (ThermoFisher Scientific, Waltham, MA, USA), and extracted total RNA using 5Prime Phase Lock Gel Tubes Heavy (Quantabio, Beverly, MA, USA), followed by clean-up with RNeasy columns (Qiagen, Venlo, Netherlands).
We prepared RNA-seq libraries with a TruSeq Stranded mRNA Library Prep Kit, following manufacturer’s instructions (Illumina, San Diego, CA, USA), and assessed library quality prior to sequencing using a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: We measured burrowing behavior using large sand-filled (Scott Pharma, Marlborough, MA, USA) enclosures (1.2 x 1.5 x 1.1 m) set up as previously described (Weber et al., 2013). We first ran all experimental animals through two “pretest” trials in the enclosures to allow them to acclimate and to confirm individuals burrowed in a species- (or hybrid-) typical manner. Next, we randomly assigned animals to a test trial cohort, “burrowing” or “control”.

value: Whole brain

tag: condition

value: Burrowing


title: Selected pop. 2 on poor diet

value: Selected


title: M5_Liver_C2

source_name: Sorted subclone 2 - Liver metastasis, Retransplantation experiment

value: Liver metastasis


title: OH14_vdj

tag: cell type

value: mononuclear cell

tag: age group


title: M4_Lung_C2


title: Selected pop. 1 on poor diet

tag: larval diet


title: OH17_scRNA

value: Old

tag: assay


title: Control pop. 6 on poor diet

tag: evolutionary regime

tag: replicate population


title: Brg1_KD_D1_Input_Repeat

value: input


title: M3_Tumor_C2

source_name: Sorted subclone 2 - Primary tumor

value: Primary tumour

value: FALSE


title: PFC Foxp2+ WT H3K4me3 CUT&RUN Sample2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
Library strategy: CUT&RUN
Raw reads were first preprocessed to remove low quality reads and adaptor sequences using Trimgalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameter “--paired”. The trimmed reads were then aligned to the mm10 genome using Bowtie2 (v2.3.4.3) [PMID: 19261174]  with parameters “‘--no-unal --no-mixed --no-discordant -I 150 -X 2000”. Samtools (v1.9) [PMID: 19505943]  was used to remove low mapping quality (mapq <10) and unmapped reads. Only uniquely mapped reads were kept for downstream analysis. Bigwig tracks were generated using “bamCoverage” command from deepTools (v3.0.2) [PMID: 24799436]  with parameters “--binSize 20 --extendReads 250 --normalizeUsing RPKM --outFileFormat bigwig  --minMappingQuality 30 --scaleFactor 1”. The bigwigs of the CUT&RUN samples with yeast spiked-in data were scaled based on the number of uniquely mapped reads to the yeast genome normalized to 100,000 reads (saling factor=10^5/[#uniquely mapped spikein reads]). The differential peaks were detected using the R/Bioconductor package Linnorm (v.2.16.0) [PMID: 28981748] for non-spikein CUT&RUN data, and we used the R/Bioconductor package csaw (v1.20.0) [PMID: 26578583] for comparison between spiked-in samples
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: PFC

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
FACS sorted nuclei were used for CUT&RUN experiments. Briefly, Foxp2-Cre or Foxp2-Cre/Setd1a+/- mice were euthanized by inhalation of CO2. Brains were rapidly removed and the prefrontal cortex was dissected and immediately frozen with dry ice and then stored at −80 °C until processing for nuclear isolation. Frozen brain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 20 times with pestle A, followed by 20 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 μm cell strainer (Fisher) and added 1 ml dilution buffer [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6000×g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for FACS. The GFP+ nuclei were directly sorted into CUT&RUN wash buffer with Sony SH800 sorter. The sorted nuclei were immediately used for CUT&RUN experiments.
CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).

tag: strain

tag: tissue

value: PFC

value: male

tag: age

value: 8-10 weeks

tag: treatment

tag: chip antibody

value: H3K4me3 (Cell Signaling 9727S)


title: PFC Foxp2+ WT H3K4me3 CUT&RUN Sample1

tag: Sex


title: OH14_scRNA

value: single-cell RNA


title: Karpas-422 Input DNA

city: Shanghai

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

department: Biochemistry and Molecular Cell Biology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Cluster Generation:The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the Illumina cBot, following NovaSeq 6000 S4 Reagent Kit manufacturer’s instructions.
Sequencing on Illumina NovaSeq 6000: Sequencing was performed on Illumina NovaSeq 6000 using NovaSeq 6000 S4 Reagent Kit (300 cycles), according to the manufacturer’s instructions.
Data Collection and Analysis: Images analysis and base calling à Solexa CHASTITY quality filter à Human genome (UCSC HG19) alignment à Peak detection à Peak annotation.
Genome_build: UCSC HG19

source_name: Karpas-422 cells

growth_protocol: Karpas-422 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
Karpas-422 cell pellet was wash twice with ice cold PBS and DNA was extracted using DNeasy Blood & Tissue Kit (#69504, Qiagen) per instruction manual
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina)

value: Diffuse large B cell lymphoma cells

value: untreated


title: OH15_scRNA


title: M4_Liver_C2

tag: sample type

value: Sorted metastatic subclone

tag: subclone

tag: organ

value: TRUE


title: Control pop. 4 on poor diet

value: standard

value: Control

value: 4 days

value: carcass

value: female


title: Control pop. 3 on poor diet

value: Selected


title: Control pop. 5 on poor diet


title: M3_Lung_C13

source_name: Sorted subclone 13 - Lung metastasis

value: Lung metastasis

tag: cell line

tag: mouse number

tag: retransplantation


title: Karpas-422 IP

tag: cell type

value: Karpas-422 IP (anti-Sox9 anitbody ab3697, Abcam)


title: PFC Foxp2 Setd1+/- Bulk RNA-Seq Sample2

data_processing:
Raw reads were first preprocessed to remove low quality reads and adaptor sequences using Trimgalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameter “--paired” for paired-end samples. Reads were mapped to the reference genome was performed with STAR (v.2.7.3a) (PMID: 23104886) software. Gene level quantification was done using RSEM (v.1.3.0) (PMID: 21816040). Differential gene expression were performed using the R/Bioconductor package edgeR (3.28.0) (PMID: 19910308).
Bigwig files were generated using deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
For Foxp2+ neuron-specific RNA-Seq, Foxp2-Cre or Foxp2-Cre/Setd1a+/- mice were euthanized by inhalation of CO2. Brains were rapidly removed and the prefrontal cortex was dissected and immediately frozen with dry ice and then stored at −80 °C until processing for nuclear isolation. Frozen brain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 20 times with pestle A, followed by 20 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 μm cell strainer (Fisher) and added 1 ml dilution buffer [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6000×g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for FACS. The GFP+ nuclei were directly sorted into Trizol (Thermo Fisher) with Sony SH800 sorter. The RNA was extracted with Direct-zol RNA Microprep Kits (Zymo) and store at −80 °C upon use.
The RNA-seq library were constructed with Smart-seq V4 reagents following the manufacturer's protocol

value: PFC

value: Setd1a CRISPR-Cas9


title: M3_Lung_C2

source_name: Sorted subclone 2 - Lung metastasis

value: FALSE


title: Control pop. 2 on poor diet

tag: larval diet


title: ZNI_T

city: Beijing

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Genome_build: hg19
Supplementary_files_format_and_content: filtered mRNA expression files

source_name: invasive malignant pleomorphic adenoma tissue

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: treatment type

value: Surgery

tag: vital status

value: Alive


title: PFC Foxp2 Setd1+/- Bulk RNA-Seq Sample1

value: male

value: 8-10 weeks


title: Control pop. 1 on poor diet

tag: evolutionary regime

tag: replicate population


title: ZNI_G

source_name: normal salivary gland

tag: tissue

value: normal salivary gland


title: PFC Foxp2+ WT Bulk RNA-Seq Sample2

tag: strain

tag: age


title: M3_Liver_C13

source_name: Sorted subclone 13 - Liver metastasis

value: Sorted metastatic subclone

value: Liver metastasis


title: M3_Liver_C2

source_name: Sorted subclone 2 - Liver metastasis


title: ZMK_T

value: invasive malignant pleomorphic adenoma tissue


title: PFC Foxp2+ WT Bulk RNA-Seq Sample1

tag: treatment


title: Pex25BirA_2minCHX_5minBiotin_pulldown

city: Cambridge

first: Jonathan

middle: S

last: Weissman

state: MA

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

description:
pex25::PEX25-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2Δ0 met15Δ0 ura3Δ0
Ribosome-protected mRNA fragments.

data_processing:
Library strategy: Ribo-seq
Base calls were called with Illumina CASAVA software.
3' adaptor was trimmed using fastx_clipper with -l 24 -a CTGTAGGCACCATCAAT.
5' nucleotide was removed using fastx_trimmer -f 2.
Reads were aligned to rRNA, tRNA and cloning oligos using Bowtie v1.1.2. Unaligned (filtered) reads were aligned to a genomic index (sacCer3) using Tophat v2.1.1 with the following parameters: --bowtie1 --read-mismatches 0 --no-novel-juncs. Only uniquely-mapped reads were used for subsequent analysis.
Each alignment was assigned a specific P-site nucleotide using a 15 nt offset from the 3' end of the read. Gene level counts and rpkm were calculated using plastid cs count using a positions file that masks regions to which reads cannot uniquely align. For rpkm calculations, all reads mapping to any annotated exon (transcript) were used for the denominator for total reads mapped.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing count and rpkm data.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.
Footprinting was performed with RNase I, monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads. RNA was extracted with Trizol and protected fragments gel purified. Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2. Unligated linkers were enzymatically removed and ligated fragments were gel purified, reverse transcribed and gel purified. The cDNA was circularized then PCR amplified.

treatment_protocol: For harvesting, cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction with 10 nM biotin for the times shown.

tag: strain/background

tag: genotype/variation

value: pex25::PEX25-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2<delta>0 met15<delta>0 ura3<delta>0

tag: biotin induction duration

value: pulldown


title: Pex25BirA_2minCHX_5minBiotin_input

tag: sample type

value: input


title: PFC Foxp2 Setd1a+/- H3K4me3 CUT&RUN Sample2

tag: Sex

tag: chip antibody

value: H3K4me3 (Cell Signaling 9727S)


title: PFC Foxp2 Setd1a+/- H3K4me3 CUT&RUN Sample1


title: EB_Etv2_Dox_3h_rep2

description:
EB_Dox_3h_Etv2_FE.bw
EB_Dox_3h_Etv2_summits.bed

source_name: EB

extract_protocol:
EB or MEF cells were harvested as described above. ChIP assays for ETV2 and H3K27ac were performed from 2 x 10e6 MEFs or 1 x 10e7 EB cells, respectively. Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M.  For the BRG1 ChIP-seq, cells were first crosslinked in 2 mM disuccinimidyl glutarate (DSG; Life Technologies: Cat. #20593) for 30 min then in 1% formaldehyde for 10 min, quenched with glycine for 5 min.  The remainder of the ChIP protocol was performed following the protocol described by Magli et al19. We used antibodies against H3K27ac (Abcam, ab4729), ETV2 (Abcam, ab181847), and BRG1 (Abcam ab110641) for the respective pulldowns. For both of the pulldowns, protein A Dynabeads were added to the ChIP reactions and incubated for 30 minutes at room temperature. Magnetic beads were washed and chromatin was eluted. After crosslinking reversal, RNase A, and proteinase K treatment, ChIP DNA was extracted with the Min-Elute PCR purification kit (Qiagen). ChIP DNA was quantified with Quant-it PicoGreen dsDNA Assay Kit (Life Technologies). Sequencing libraries were prepared using equal amount of ChIP DNA per sample as per instructions of SMARTer® ThruPLEX® DNA-Seq Kit (Takara R400675) and SMARTer® DNA Unique Dual Index Kit - 24U Set A (Takara R400665). Sequencing was performed at the University of Minnesota Genome Center with the The NextSeq 550 high-throughput benchtop sequencer.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: ETV2 (Abcam, ab181847)

value: Dox

value: EB

tag: paired or single

value: single


title: M2_Tumor_C13

source_name: Sorted subclone 13 - Primary tumor

tag: subclone

tag: organ

value: Primary tumour

tag: cell line

tag: mouse number

tag: retransplantation

value: FALSE


title: ZMK_G

tag: tissue

tag: treatment type

value: Surgery

tag: vital status

value: Alive


title: M2_Tumor_C2


title: Pex25BirA_2minCHX_2minBiotin_pulldown


title: M3_Tumor_C13


title: XK_G


title: M2_Lung_C13

value: Lung metastasis


title: XK_T


title: EB_input_Dox_3h, rep2

tag: treatment

tag: cell type


title: EB_Etv2_Dox_3h_rep1


title: NMO_T


title: Pex25BirA_2minCHX_2minBiotin_input

tag: strain/background

tag: genotype/variation


title: M2_Lung_C2

tag: sample type


title: Pex11BirA_2minCHX_5minBiotin_input

description:
pex11::PEX11-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2Δ0 met15Δ0 ura3Δ0
Ribosome-protected mRNA fragments.

value: pex11::PEX11-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI leu2<delta>0 met15<delta>0 ura3<delta>0

tag: biotin induction duration


title: M2_Liver_C13

value: Sorted metastatic subclone


title: EB_Etv2_Dox_12h_rep1

description:
EB_Dox_12h_Etv2_FE.bw
EB_Dox_12h_Etv2_summits.bed

tag: chip antibody


title: NMO_G

value: normal salivary gland


title: Pex11BirA_2minCHX_2minBiotin_pulldown


title: M2_Liver_C2

value: Liver metastasis


title: EB_Etv2_Dox_12h_rep2

tag: time


title: KTI_T

value: invasive malignant pleomorphic adenoma tissue


title: EB_input_Dox_12h, rep2

tag: paired or single


title: M1_Tumor_C2

tag: subclone


title: EB_input_NoDox_12h, rep2

value: NoDox


title: KTI_G


title: Pex11BirA_2minCHX_2minBiotin_input

value: input


title: Wild-type RNA-seq rep 3

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Adapter sequences from raw RNA-Seq reads were trimmed using the “ILLUMINACLIP” function from the Trimmomatic software package using standard paired-end parameters. Trimmed reads were then mapped to the SL3.0 build of the tomato genome using the Spliced Transcripts Alignment to a Reference (STAR) aligner using default parameters.
Mapped reads were annotated to genes using the “featureCounts” function from the Subread software package. Differential gene expression analysis was calculated by using DeSeq2 package.
Genome_build: SL3.0
Supplementary_files_format_and_content: DeSeq2 output of RNA-seq

organism: Solanum lycopersicum

source_name: shoot apex of 28 day old plants

growth_protocol: Plants were grown on soil under 16 hrs of light/8 hrs dark cycles for 28 days after germination. Shoot apices, (0.8 g for each replicate and two replicates per genotype) containing approximately three visible expanding leaves, were harvested  into liquid nitrogen aand stored at -80 prior to RNA extraction.

extract_protocol:
Frozen shoot tissues were processed with the Qiagen RNeasy Mini Plant kit according to the manufacturer’s instructions.
RNA-seq libraries were prepared with the Zymo RiboFree Total RNA Library Kit according to the manufacturer’s instructions.

value: Shoot apex with three expanding leaves


title: M1_Tumor_C13_rep3

source_name: Sorted subclone 13 - Primary tumor, technical replicate

tag: organ


title: N6

city: Wuhan

first: Gang

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of human using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: reads count
Supplementary_files_format_and_content: rpkm value

source_name: Normal tissue adjacent to the prostate cancer

extract_protocol:
Total RNAs were extracted from samples using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on NovaSeq 6000 sequencer (Illumina) with PE150 model.

value: prostate

tag: age


title: Wild-type RNA-seq rep 2


title: N3


title: MEF_Brg1_NoDox_d0_rep2

description:
MEF_NoDox_d0_Brg1_FE.bw
MEF_NoDox_d0_Brg1_summits.bed

source_name: MEF

value: BRG1 (Abcam ab110641)

value: MEF


title: M1_Tumor_C13_rep1

tag: cell line

tag: mouse number


title: Wild-type RNA-seq rep 1

tag: tissue


title: Pex11BirA_2minCHX_5minBiotin_pulldown

value: pulldown


title: crel-3 RNA-seq rep 2


title: MEF_Brg1_NoDox_d0_rep1

value: single


title: MEF_Brg1_Dox_d7_rep1

description:
MEF_Dox_d7_Brg1_FE.bw
MEF_Dox_d7_Brg1_summits.bed

value: Dox


title: M1_Lung_C13_rep3

tag: retransplantation

value: FALSE


title: MEF_input_Dox_d2, rep2


title: T5

source_name: Prostate Cancer Tissue


title: crel-1 RNA-seq rep 3


title: M1_Lung_C13_rep2

source_name: Sorted subclone 13 - Lung metastasis, technical replicate


title: T6


title: crel-3 RNA-seq rep 1


title: M1_Lung_C13_rep1


title: T3


title: MEF_Brg1_Dox_d2_rep2

description:
MEF_Dox_d2_Brg1_FE.bw
MEF_Dox_d2_Brg1_summits.bed


title: M1_Lung_C2


title: N5


title: M1_Liver_C13_rep3

source_name: Sorted subclone 13 - Liver metastasis, technical replicate


title: 3D_CAF_st_C

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using STAR
Gene count tables were generated using the --quantMode GeneCounts argument in STAR
DESeq2 was used to identify significant differential expression between control and experimental samples
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including per sample: Ensembl gene ID, total counts

source_name: MRC5 + tgfb1  (1% BDDGE scaffold)

growth_protocol: NFs were seeded on the St and So scaffold dor 7 days and then retrieved from the scaffolds using trypsin.

extract_protocol:
At day7 of culture cells were detached from the scaffolds using trypsin. Trypsin inactivation was performed using DMEM-F12 media an total RNA extraction was performed using Qiagen kit.
cDNA libraries were prepared at Novogene

treatment_protocol: NFs were treated with tgfb1 to be converted in CAFs. Both cells were grown on 3D collagen I-based scaffolds

value: cancer-associated fibroblasts (CAFs)

value: TGFB

tag: surface


title: MEF_input_Dox_d1, rep2

tag: treatment


title: M1_Liver_C13_rep1


title: crel-1 RNA-seq rep 1


title: 3D_CAF_st_B

tag: cell type


title: MEF_Brg1_Dox_d1_rep1

description:
MEF_Dox_d1_Brg1_FE.bw
MEF_Dox_d1_Brg1_summits.bed


title: crel-2 RNA-seq rep 2


title: M1_Tumor_C13_rep2

value: Primary tumour


title: EB_Brg1_NoDox_3h_rep1

value: EB


title: 3D_NF_st_A

source_name: MRC5 (1% BDDGE scaffold)

value: Normal fibroblasts (NFs)

value: Control


title: 3D_CAF_so_C

source_name: MRC5 + tgfb1 (0.01% BDDGE scaffold)


title: MEF_Brg1_Dox_d1_rep2


title: 3D_CAF_st_A


title: crel-1 RNA-seq rep 2


title: crel-2 RNA-seq rep 1


title: PGC_RNA2

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
To generate clean reads, we trimmed adapter sequences and removed low quality reads from the raw paired-end sequenced files using Trimmomatic v.0.39.
The quality of the clean reads was quality-checked (QC) whether read lengths were longer than 75 bp and Phred scores were higher than 30 using FastQC v.0.11.9.
We mapped the clean reads to the galGal6a reference genome (GRCg6a) through HISAT2 v.2.2.0.
We converted the sequence alignment/map files (.SAM files) into binary alignment/map files (.BAM files) using SAMtools v.1.10.
To quantify gene expression, we used HTSeq-count and counted the number of reads mapped to Ensembl genomic GTF of galGal6a release 101.
Genome_build: galGal6a
Supplementary_files_format_and_content: tab-delimited table with raw gene counts for every gene and each sample
Supplementary_files_format_and_content: tab-delimited matrix table with normalized read counts as trimmed mean of M values (TMM) for every gene and every sample

organism: Gallus gallus

source_name: Primordial germ cell

growth_protocol: The freshly laid White Leghorn (WL) eggs were incubated with intermittent rocking at 37.5 °C under 60–70% relative humidity until the day of sample collection. For the collection of CEF, all internal organs and limbs were removed from the embryos at Hamburger and Hamilton (HH) stage 28 / embryonic day 6 (N = 5 for each replication). The remaining embryonic body was then dissociated using 0.05% trypsin-EDTA in Hanks’ Balanced Salt Solution (HBSS) at 37°C for 10 min. After adding 10% fetal bovine serum (FBS) for inactivation of trypsin-EDTA and briefly centrifuging at 1200 rpm for 5 min, cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM/High Glucose) supplemented with 10% FBS and 1% antibiotic–antimycotic at 37°C in an atmosphere with 5% CO2 and 60-70% relative humidity. The adherent CEF cells were subcultured at 3 - 4 days intervals via trypsin-EDTA treatment until passage 2. Blastoderm cells were collected by gentle dissociation of EGK.X blastoderm (N = 10 for each replication) from freshly laid eggs in phosphate buffered saline (PBS). For the collection of PGC, gonads at HH stage 28 embryos (N = 484, 658, or 684 for each replication) were dissociated using 0.05% trypsin-EDTA in HBSS. After adding 10% FBS for inactivation of trypsin-EDTA and briefly centrifuging at 1200 rpm for 5 min, cells were incubated for 20 min with anti-stage specific embryonic antigen (SSEA-1). The cells were washed with 1 mL of magnetic-activated cell-sorter (MACS) buffer (0.5% BSA and 2 mM EDTA), and the supernatant was completely removed by centrifugation. The pellet was mixed with 100 μL MACS buffer supplemented with 20 μL rat anti-mouse IgM microbeads for 15 min at 4°C. The cells were washed by the addition of 500 μL MACS buffer and loaded into a MACS column. After several batches of cell preparation, the PGC-enriched fraction was separated. In total, three biological replications were made for each sample.

extract_protocol:
Total RNA was isolated from CEF, EGK.X blastoderm and PGC using Trizol reagent (Invitrogen, Carlsbad, CA, USA). The quality and quantity of the extracted total RNA were determined using the DropSense96 system (Trinean, Gentbrugge, Belgium), Ribogreen (Invitrogen) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Total RNA was used to construct cDNA libraries using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Gold (Illumina, San Diego, CA, USA). The resulting libraries were subjected to whole-transcriptome sequencing (WTS) analysis using the Illumina Nextseq 500 platform to produce 150 bp paired-end reads.

treatment_protocol: Not applicable

tag: breed

value: White Leghorn

value: Primordial germ cell

tag: differentiation

value: Undifferentiated progenitor gamete cells

tag: Stage

value: Hamburger and Hamilton stage 28


title: MEF_Brg1_Dox_d7_rep2


title: 3D_NF_st_B


title: 3D_NF_st_C


title: EB_Brg1_NoDox_12h_rep2

value: NoDox


title: Z1 at L-10

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and basecalling.
The 3′ adaptor sequences were removed, and reads with the trimmed length <18 bp were discarded using Cutadapt v2.7. Read quality control was performed with FastQC v0.11.9 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
MiRNA analysis: Trimmed and filtered reads were mapped with bowtie (v1.1.1) to the reference genome (GRCh38.p12), allowing a maximum of one mismatch. Calculation of the raw read counts and reads per million (RPM) values was performed using miRDeep2 (miRBase v22.0).
Small-RNA analysis:  Trimmed and filtered reads were mapped with STAR aligner (v2.7.5b) allowing for reads multi-mapping to different parts of the reference genome (GRCh38.p12). GENCODE release 38 was used for gene and transcript annotations.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: raw miRNA counts for every gene and every sample produced with miRDeep2
Supplementary_files_format_and_content: CPM counts for every gene and every sample produced with edgeR
Supplementary_files_format_and_content: raw small RNA counts for every gene and every sample produced with STAR aligner

source_name: peripheral blood sEVs

extract_protocol:
sEVs were isolated from peripheral blood (PB) samples of 14 astronauts at L-10, R-0, and R+3 using the ExoQuick Plasma preparation and sEV precipitation kit (Cat # EXOQ5TM, System Biosciences, CA, USA). 400 μl of plasma was mixed with thrombin and kept at room temperature (RT) for 5 minutes. Subsequently, samples were centrifuged at 10,000 rpm for 5 minutes. Samples were then incubated with the exosome precipitation solution and refrigerated at 4ºC for 30 minutes. After centrifugation at 1,500 x g for 30 minutes at 4ºC, a beige-colored pellet was observed and dissolved in 100 μl of sterile 1xPBS. NS-300 Nanosight instrument (Malvern Instruments Ltd., Malvern, UK) equipped with an sCMOS camera (Hamamatsu Photonics, Hamamatsu, Japan) and a 405 nm laser was used. Data acquisition and processing were performed using NTA software version 2.3 build 0025. Background extraction was applied, and automatic settings were employed to determine the minimum expected particle size, minimum track length, and blur settings. Data were obtained at camera level 12 (shutter: 600, gain: 350). Three movies of 30 seconds at 25 frames per second were recorded and assigned a single measurement in triplicates.
Total RNA from sEVs was isolated from PB samples using miRNeasy kit following manufacturer's protocol (Cat#217084, Qiagen). RNA quality was assessed using an Agilent TapeStation (Agilent, Palo Alto, CA, USA), and RNA concentration was quantified by Qubit 4.0 spectrophotometer. The library for small RNA-sequencing (RNA-Seq) was prepared using the Smarter smRNAseq kit for Illumina (Takara Bio Inc., USA). The quantity and quality of amplified libraries were evaluated using Qubit (Invitrogen, Carlsbad, CA, USA) and Agilent TapeStation high sensitivity D1000 Screen Tape. Small RNA-seq libraries were sequenced using single-end 75 base pairs (SE75) sequencing chemistry on NextSeq 500 instruments following the manufacturer's protocols (Illumina).

value: peripheral blood sEVs

tag: time point

tag: Sex

value: not collected


title: EB_input_Dox_12h, rep1

tag: time

tag: chip antibody


title: Z1 at R-0


title: 3D_CAF_so_A


title: Pancreatic Islets, HPAP035

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Pancreatic Islets

extract_protocol:
Fresh pancreatic islets were dissociated to single cells, Chromium Single Cell 3’ Library & Gel Bead Kit v2 was used to construct the sequencing libraries.
Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2
single cell RNA-Seq

value: Pancreas

tag: gender

value: 35 years


title: EB_input_NoDox_3h, rep2

tag: paired or single

value: single


title: MEF_Brg1_Dox_d2_rep1

value: BRG1 (Abcam ab110641)

value: Dox

value: MEF


title: Z1 at R+3


title: 3D_NF_so_C

source_name: MRC5 (0.01% BDDGE scaffold)


title: MEF_input_NoDox_d0, rep2


title: EGKX_RNA3

source_name: EGK.X blastoderm

value: EGK.X blastoderm

value: Eyal-Giladi and Kochav stage X


title: 3D_NF_so_B

value: Normal fibroblasts (NFs)


title: 3D_CAF_so_B

value: cancer-associated fibroblasts (CAFs)

value: TGFB


title: PGC_RNA1

value: White Leghorn

value: Primordial germ cell


title: EGKX_RNA1


title: 3D_NF_so_A

value: Control


title: EB_Brg1_NoDox_12h_rep1

description:
EB_NoDox_12h_Brg1_FE.bw
EB_NoDox_12h_Brg1_summits.bed

source_name: EB

value: NoDox

value: EB


title: Z2 at R-0

value: peripheral blood sEVs

value: not collected


title: M1_Liver_C2

source_name: Sorted subclone 2 - Liver metastasis

tag: sample type

value: Sorted metastatic subclone

tag: subclone

tag: organ

value: Liver metastasis

value: FALSE


title: Z2 at R+3

tag: tissue


title: CEF_RNA1

source_name: Embryonic fibroblast

value: Embryonic fibroblast

value: Differentiated somatic cells

value: Hamburger and Hamilton stage 28


title: CEF_RNA2


title: CEF_RNA3


title: EGKX_RNA2

value: EGK.X blastoderm

value: Eyal-Giladi and Kochav stage X


title: Z3 at R+3


title: 2D_CAF_B

source_name: MRC5 + tgfb1

value: cancer-associated fibroblasts (CAFs)


title: EB_input_Dox_3h, rep1

value: Dox

value: single


title: Z3 at R-0


title: Z2 at L-10


title: Z3 at L-10


title: 2D_CAF_C

value: TGFB


title: EB_Brg1_NoDox_3h_rep2

description:
EB_NoDox_3h_Brg1_FE.bw
EB_NoDox_3h_Brg1_summits.bed

value: BRG1 (Abcam ab110641)


title: PGC_RNA3

value: White Leghorn

value: Primordial germ cell

value: Undifferentiated progenitor gamete cells


title: EB_Brg1_Dox_3h_rep1

description:
EB_Dox_3h_Brg1_FE.bw
EB_Dox_3h_Brg1_summits.bed

value: EB


title: MEF_input_Dox_d7, rep2

value: MEF


title: EB_Brg1_Dox_3h_rep2


title: EB_Brg1_Dox_12h_rep2

description:
EB_Dox_12h_Brg1_FE.bw
EB_Dox_12h_Brg1_summits.bed


title: 2D_NF_C

value: Normal fibroblasts (NFs)

value: Control


title: 2D_CAF_A


title: 2D_NF_B


title: 2D_NF_A


title: MEF_input_Dox_d7, rep1


title: EB_Brg1_Dox_12h_rep1


title: Z4 at L-10

value: peripheral blood sEVs

value: not collected


title: MEF_input_Dox_d2, rep1


title: MEF_Etv2_Dox_d2_rep2

description:
MEF_Dox_d2_Etv2_FE.bw
MEF_Dox_d2_Etv2_summits.bed

value: ETV2 (Abcam, ab181847)


title: Z5 at R-0


title: RNA_Pol_II_D458_with THZ1

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of fastq files was accessed using FastQC
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v. 2.3.2).
Samtools (v. 1.9) was used to convert the sam files into bam files, to filter out unmapped reads and to sort the bam files.
The total number of reads used for peak calling was normalized using samtools view -hs (random extraction of a specified percentage of reads).
Samtools sort was used to sort the bam files after read extraction.
Bam files were indexed using samtools index.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files from the bedgraph files.
Peaks were called using macs2 (v. 2.1.1.20160309) with default parameters using python (v. 2.7.14).
Peak locations were further annotated using the clusterProfiler, ChIPseeker and ngs.plot.r R packages.
Genome_build: hg38
Supplementary_files_format_and_content: The tdf files were generated with igvtools toTDF.

source_name: Medulloblastoma

growth_protocol: D458 cell lines were cultured in DMEM (Gibco, Carlsbad, CA) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and 1× L-glutamine (Cellgro). Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
The growth medium was aspirated from cells (70% confluence) and replaced with a 1% formaldehyde in 1X DPBS for 10 min at room temperature. The cross-linking was terminated by addition of glycine to a final concentration of 0.125 M and incubation for 5 min. The cells were washed twice with cold PBS and scraped in ChIP lysis buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl pH 8.1) containing COmplete EDTA free protease inhibitors (Sigma). The cell lysates were sonicated with a Bioruptor Plus (Diagenode) for 25 cycles (30 seconds ON and 30 seconds OFF). The size of the sonicated DNA fragments was checked on an 1X TAE1 % agarose gel electrophoresis and ranged between 250 to 500 bp. After removing the debris via centrifugation, chromatin extracts were collected and protein concentration was determined by BCA protein assay reagents (Pierce).  For immunoprecipitation, chromatin extracts with 1 mg of total protein for each sample were incubated with primary antibodies (dilution 1:50) overnight at 4ºC. Primary antibodies used are included in table under “Western blotting” below. After incubation with the primary antibody, 20 uL of pre-washed magnetic beads (Magna ChIP Protein A+G Magnetic Beads, Millipore Sigma) were added to each sample for 2 hours at 4ºC. Using a magnetic rack, the immunoprecipitates were washed successively with 1 ml of low salt buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), high salt buffer (20 mM Tris-HCl [pH 8.0], 500 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), LiCl washing buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, , 1.0% NP40, 1.0% deoxycholate, 1 mM EDTA) and twice with TE buffer. The DNA-protein complexes were eluted with 300 μl of IP elution buffer (1% SDS, 0.1 M NaHCO3). The eluents were pooled together and the cross-links were reversed by adding NaCl (a final concentration 0.2 M) into the eluents and incubating them at 65 ºC overnight. The DNAs were recovered by proteinase K and RNase A digestion, followed by phenol/chloroform extraction and ethanol precipitation. Pellets were resuspended in 50 μl of 10 mM Tris-HCl [pH 8.0]. ChIP-DNA was quantified using the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific).
Libraries were prepared according to Nugen's instructions accompanying their Ovation Ultralow System V2 kit.

treatment_protocol: Cells were treated for 48 hours with either DMSO or 10 nM THZ1.

tag: cell line

value: THZ1 (10nM)

value: RNA Pol II CTD; Abcam Cat. #ab817; RRID:AB_306327


title: MEF_Etv2_Dox_d1_rep2

description:
MEF_Dox_d1_Etv2_FE.bw
MEF_Dox_d1_Etv2_summits.bed

source_name: MEF


title: H3_histone_D458_with_DMSO

value: DMSO

value: H3_histone; Abcam Cat. #ab1791


title: Z5 at L-10


title: RNA_Pol_II_D458_with_DMSO


title: Myc_D458_with_THZ1

value: Myc; Cell Signaling Technology; Cat. #13987;RRID:AB_2631168


title: Myc_D458_with_DMSO


title: MEF_Etv2_Dox_d2_rep1

value: Dox

value: single


title: F023_protein

description: processed data available on GSM4750311

data_processing:
The 10x Genomics Cell Ranger software suite (v3.1.0) with Human reference GRCh38 (v1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build) was used to process the scRNA-Seq, scTCR-Seq and cell surface protein sequencing fastq files, with default parameter settings.
Genome_build: hg38
Supplementary_files_format_and_content: MTX: Sparse matrix for gene quantification.
Supplementary_files_format_and_content: TSV: Metadata describing the gene and feature names of the sparse matrix.
Supplementary_files_format_and_content: CSV: TCR clonetype annotation.

source_name: PBMC

extract_protocol:
Fresh whole blood was collected in 2 ml tubes that treated with diamine tetraacetic acid (EDTA). Peripheral Blood Mononuclear Cells (PBMCs) were isolated from whole blood of samples with Ficoll (GE Healthcare Life Sciences) following the manufacture’s protocol. Briefly, blood sample was diluted with D-Hanks (NaCl 8 g/L, KCl 0.4 g/L, Na2HPO4 0.16 g/L, KH2HPO4 0.06 g/L, glucose 1 g/L) in a ratio of 1:1, and then add Ficoll and centrifuged at 2000 rpm for 20 min at room temperature. Enriched PBMCs were washed with D-Hanks plus 2% fetal calf serum (FBS), and then centrifuged at 400 g for 10 min, repeat twice. Then cell numbers and viability were assessed.
Cell number and viability were checked after surface protein staining (cell viability > 80%). Then droplet-encapsulation single-cell sequencing experiments were performed, and 10,000 living single cells were loaded onto each of the Chromium Controller (10x Genomics). After droplet-encapsulation, single-cell cDNA synthesis, amplification and sequencing libraries were generated using Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics), Chromium Single Cell 5' Library & Gel Bead Kit (10x Genomics), and Chromium Single Cell V(D)J Enrichment Kit (Human T Cell, 10x Genomics) according to the manufacturer’s instructions. The libraries from each loaded channel (up to eight channels) were multiplexed together and sequenced on an Illumina Novaseq 6000.

tag: subject id

value: mononuclear cell

tag: age group

value: Old

tag: assay

value: single-cell surface protein


title: MEF_Etv2_Dox_d1_rep1

tag: treatment

tag: cell type


title: Z6 at R-0


title: Z6 at R+3


title: MEF_H3K27ac_Dox_d7_rep2

description:
MEF_Dox_d7_H3K27ac_FE.bw
MEF_Dox_d7_H3K27ac_peaks.broadPeak

value: H3K27ac (Abcam, ab4729)


title: Z6 at L-10


title: Z4 at R+3


title: Z4 at R-0


title: MEF_H3K27ac_Dox_d7_rep1

value: MEF


title: F021_protein

description: processed data available on GSM4750310


title: Z7 at R+3


title: Peromyscus_maniculatus_control_rep3

organism: Peromyscus maniculatus

source_name: Whole brain

value: Whole brain

tag: condition


title: Peromyscus_maniculatus_control_rep2

value: Control


title: F020_protein

description: processed data available on GSM4750309


title: Z7 at R-0

value: peripheral blood sEVs

tag: time point


title: MEF_Etv2_Dox_d7_rep2

description:
MEF_Dox_d7_Etv2_FE.bw
MEF_Dox_d7_Etv2_summits.bed


title: Peromyscus_maniculatus_control_rep1


title: F024_protein

description: processed data available on GSM4750308

source_name: Cord blood

value: Cord blood


title: Z7 at L-10

tag: Sex

value: not collected


title: MEF_Etv2_Dox_d7_rep1

tag: time

value: ETV2 (Abcam, ab181847)


title: Peromyscus_maniculatus_burrowing_rep3

value: Burrowing


title: Z5 at R+3


title: Peromyscus_maniculatus_burrowing_rep2


title: MEF_H3K27ac_Dox_d2_rep1

description:
MEF_Dox_d2_H3K27ac_FE.bw
MEF_Dox_d2_H3K27ac_peaks.broadPeak

tag: chip antibody


title: MEF_H3K27ac_Dox_d2_rep2


title: Z8 at R-0


title: Peromyscus_maniculatus_burrowing_rep1


title: F016_protein

description: processed data available on GSM4750306


title: F017_protein

description: processed data available on GSM4750307


title: M1_Liver_C13_rep2

source_name: Sorted subclone 13 - Liver metastasis, technical replicate

value: Sorted metastatic subclone

value: Liver metastasis

tag: mouse number

tag: retransplantation

value: FALSE


title: Z8 at L-10


title: F014_protein

description: processed data available on GSM4750305

value: Young


title: MEF_H3K27ac_Dox_d1_rep2

description:
MEF_Dox_d1_H3K27ac_FE.bw
MEF_Dox_d1_H3K27ac_peaks.broadPeak

value: Dox

tag: paired or single

value: single


title: Z9 at R+3


title: Z9 at R-0


title: F013_protein

description: processed data available on GSM4750304

value: mononuclear cell


title: MEF_input_NoDox_d0, rep1

value: NoDox


title: F012_protein

description: processed data available on GSM4750303

value: single-cell surface protein


title: MEF_H3K27ac_Dox_d1_rep1

value: H3K27ac (Abcam, ab4729)

value: MEF


title: MEF_H3K27ac_NoDox_d0_rep2

description:
MEF_NoDox_d0_H3K27ac_FE.bw
MEF_NoDox_d0_H3K27ac_peaks.broadPeak


title: F008_protein

description: processed data available on GSM4750302

value: Frail


title: Z9 at L-10

value: peripheral blood sEVs


title: Z8 at R+3


title: Z10 at R+3


title: MEF_H3K27ac_NoDox_d0_rep1


title: F007_protein

description: processed data available on GSM4750301


title: F006_protein

description: processed data available on GSM4750300


title: MEF_input_Dox_d1, rep1


title: F004_protein

description: processed data available on GSM4750299


title: Z10 at R-0


title: EB_input_NoDox_3h, rep1

value: EB

value: Paired


title: Z10 at L-10

value: not collected


title: Z11 at R-0


title: F002_protein

description: processed data available on GSM4750298


title: Z11 at R+3


title: F023_vdj

value: Old

value: single-cell TCR


title: WholeBlood_HVTN087158520046_Day7

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

institute: Imperial College London

description: Whole blood gene expression of participant HVTN087158520046 on day 7 after treatment: PLACEBO

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: female

tag: age

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

tag: group

value: PLACEBO

tag: vaccinations received

tag: day

value: whole blood


title: EB_input_NoDox_12h, rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.2.4 with default parameters.
The ChIP-seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files

tag: treatment

tag: cell type


title: EB_H3K27ac_NoDox_3h_rep1

description:
EB_NoDox_3h_H3K27ac_FE.bw
EB_NoDox_3h_H3K27ac_peaks.broadPeak


title: WholeBlood_HVTN087158520046_Day3

description: Whole blood gene expression of participant HVTN087158520046 on day 3 after treatment: PLACEBO

tag: tissue


title: WholeBlood_HVTN087134520041_Day14

description: Whole blood gene expression of participant HVTN087134520041 on day 14 after treatment: PLACEBO

value: male

value: other

value: hispanic or latino


title: Z11 at L-10

tag: time point

tag: Sex


title: WholeBlood_HVTN087123520203_Day14

description: Whole blood gene expression of participant HVTN087123520203 on day 14 after treatment: PLACEBO


title: WholeBlood_HVTN087158520046_Day14

description: Whole blood gene expression of participant HVTN087158520046 on day 14 after treatment: PLACEBO


title: WholeBlood_HVTN087158520046_Day0

description: Whole blood gene expression of participant HVTN087158520046 on day 0 after treatment: PLACEBO


title: F020_vdj

first: Oscar Junhong

institute: Jinan University

tag: subject id

value: mononuclear cell

tag: age group

tag: assay


title: WholeBlood_HVTN087158520046_Day1

description: Whole blood gene expression of participant HVTN087158520046 on day 1 after treatment: PLACEBO


title: F021_vdj


title: WholeBlood_HVTN087123520203_Day7

description: Whole blood gene expression of participant HVTN087123520203 on day 7 after treatment: PLACEBO


title: Z12 at R-0


title: WholeBlood_HVTN087134520041_Day0

description: Whole blood gene expression of participant HVTN087134520041 on day 0 after treatment: PLACEBO


title: EB_H3K27ac_NoDox_12h_rep1

description:
EB_NoDox_12h_H3K27ac_FE.bw
EB_NoDox_12h_H3K27ac_peaks.broadPeak

tag: time

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

value: NoDox

tag: paired or single


title: EB_H3K27ac_NoDox_3h_rep2


title: EB_H3K27ac_NoDox_12h_rep2


title: EB_H3K27ac_Dox_3h_rep2

description:
EB_Dox_3h_H3K27ac_FE.bw
EB_Dox_3h_H3K27ac_peaks.broadPeak

value: Dox


title: Z12 at R+3

value: peripheral blood sEVs


title: F016_vdj

value: Cord blood


title: Z12 at L-10

value: not collected


title: Z13 at R+3


title: WholeBlood_HVTN087123520203_Day1

description: Whole blood gene expression of participant HVTN087123520203 on day 1 after treatment: PLACEBO

tag: participant

tag: gender

tag: age


title: WholeBlood_HVTN087123520203_Day3

description: Whole blood gene expression of participant HVTN087123520203 on day 3 after treatment: PLACEBO

tag: race

tag: ethnicity

tag: group


title: EB_H3K27ac_Dox_3h_rep1

tag: treatment

value: EB

value: Paired


title: F014_vdj

tag: cell type

value: Young

value: single-cell TCR


title: F017_vdj


title: EB_H3K27ac_Dox_12h_rep2

description:
EB_Dox_12h_H3K27ac_FE.bw
EB_Dox_12h_H3K27ac_peaks.broadPeak


title: WholeBlood_HVTN087123520203_Day0

description: Whole blood gene expression of participant HVTN087123520203 on day 0 after treatment: PLACEBO

value: female

value: white

value: not hispanic or latino

tag: vaccinations received

tag: day

tag: tissue


title: Z13 at R-0

tag: time point

tag: Sex


title: F013_vdj

tag: subject id

tag: age group

tag: assay


title: N3 input

city: Nanjing

first: Ruifeng

last: Zhang

address: 87Dingjiaqiao Road

institute: Zhongda Hospital of Southeast University

data_processing:
Illumina HiSeq 4000 sequencer was used for basecalling.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality reads were aligned to the reference genome (UCSC RN5) with hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA and LncRNA were figured out and chosen by home-made scripts.
Genome_build: UCSC RN5
Supplementary_files_format_and_content: excel format include FPKM values for each Sample

organism: Rattus norvegicus

source_name: lung

extract_protocol:
The mRNA was isolated from total RNA with oligo(dT) magnetic beads (ThermoFisher), and then subjected to immunoprecipitation with the GenSeqTM m7G-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Briefly, RNA was decapping with Tobacco Decapping Enzyme, and then randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m7G antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a HiSeq platform (Illumina).

value: lung

value: 21% fractional inspired oxygen

tag: antibody


title: WholeBlood_HVTN087132520201_Day7

description: Whole blood gene expression of participant HVTN087132520201 on day 7 after treatment: NONE

tag: participant

value: male

value: black or african american

value: whole blood


title: Z14 at R-0


title: Z14 at R+3


title: N3 IP


title: Z14 at L-10


title: N2 input


title: F007_vdj

city: Guangzhou

last: Luo

address: 601 Huangpu Ave West

value: mononuclear cell

value: Frail


title: F006_vdj


title: WholeBlood_HVTN087132520201_Day14

description: Whole blood gene expression of participant HVTN087132520201 on day 14 after treatment: NONE

tag: gender


title: WholeBlood_HVTN087132520201_Day3

description: Whole blood gene expression of participant HVTN087132520201 on day 3 after treatment: NONE

tag: age


title: N2 IP


title: F004_vdj


title: SCP32C

city: Boston

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

data_processing:
Adapter sequence was trimmed from raw RNA-seq reads using Cutadapt v1.8.

Rsubread v. 1.32.4 was used to quantify raw counts per gene.
The threshold for expression detection was > 1 logCPM in at least 2 samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes transcript per million (TPM) values for every gene in each sample.

source_name: Xenograft tumor derived from MDA-MBA-468 subclone

growth_protocol: On the day of transplantation, cells were collected by treatment with 0.25% trypsin (Corning, Cat. No. 25-053-CI) for approximately 10 minutes. The Z-Series Coulter Counter (Beckman) was used to determine the number of cells per mL cell suspension.  Next, 2x10^6 cells were injected orthotopically into the fourth mammary gland of anesthetized mice. Tumors were harvested after two months in vivo.

extract_protocol:
RNA lysates were prepared using the PureLinkTM RNA Mini Kit (Life Technologies, Cat. No. 12183025). The RNA concentration was measured using the Epoch microplate spectrophotometer (BioTek). Prior to library generation for RNA-sequencing, the quality of the RNA was determined using a 2200 TapeStation and RNA screen tapes (Agilent Technologies).
The mRNA libraries were generated by the Bauer core facility at Harvard University using the KAPA Stranded RNA Hyperprep kit (Roche) and included polyA enrichment. The quality of these libraries was assessed by a 2200 TapeStation analyzer using D1000 screen tapes (Agilent Technologies), and q-PCR.

tag: growth condition

value: in vivo xenograft tumor


title: N1 input


title: MDA-MBA-468

data_processing:
Sequencing reads were converted to fastq files using bcl2fastq v.2.20.0.422.
Reads from two sequencing runs of the same sample were merged, aligned, and counted with cellranger v3.0.2 using refdata-cellranger-hg19-3.0.0 provided by 10x Genomics, Inc.
Genes detected in <10% of cells were removed. Cells with <500 or >8000 unique gene counts,  >10% mitochondrial genes, or <1000 unique unique molecular identifiers (UMI) were excluded.
The Adaptively-Thresholded Low Rank Approximation (ALRA) method was used to impute missing values.
Data were normalized with a scale factor of 10000 and scaled (linear model), regressing out mitochondrial content, proliferation and number of UMI.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for every gene in each cell.

source_name: MDA-MBA-468 cell line

growth_protocol: The MDA-MB-468 cell line was acquired from ATCC and authenticated by STR profiling. 293T, MDA-MB-468 and SCP cell lines were maintained in DMEM with high glucose (Life Technologies, Cat. No. 11965118) + 10% heat-inactivated FBS (Sigma, Cat. No. 12306C-500mL) + 5 units/mL penicillin and 5 µg/mL streptomycin (Life Technologies, Cat. No. 15070-63). Cells were plated at 2x10^6 cells per 10 cm dish and left to propagate for 48 hours. This process was repeated one additional time.

extract_protocol:
To generate the single cell suspension, cells were washed with 1X PBS and treated with 0.25% Trypsin EDTA for 5 minutes. The cells were then washed 3 times with 1X PBS + 0.04% BSA and resuspended in 1X PBS + 0.04% BSA at approximately 1 x 106 cells/mL.
Single cell capturing and cDNA library generation were performed by the Bauer core facility at Harvard University using the 10X Chromium 3’ library construction kit v2 following the manufacturer’s instruction. The library was sequenced (paired-end, 150 cycles) using two NextSeq High Output flow cells (Illumina).
Other: single-cell RNA-Seq

tag: cell line


title: WholeBlood_HVTN087132520201_Day0

description: Whole blood gene expression of participant HVTN087132520201 on day 0 after treatment: NONE

tag: race

tag: ethnicity

tag: group


title: WholeBlood_HVTN087158520281_Day7

description: Whole blood gene expression of participant HVTN087158520281 on day 7 after treatment: VSVHIVGAG

tag: vaccinations received

value: D-DV

tag: treatment

value: VSVHIVGAG


title: WholeBlood_HVTN087158520281_Day3

description: Whole blood gene expression of participant HVTN087158520281 on day 3 after treatment: VSVHIVGAG

tag: day

tag: tissue


title: N1 IP


title: F002_vdj

tag: cell type


title: Z13 at L-10

source_name: peripheral blood sEVs

value: peripheral blood sEVs

tag: time point

tag: Sex

value: not collected


title: EB_H3K27ac_Dox_12h_rep1

city: Minneapolis

first: Daniel

last: Garry

address: 2231 6th Street SE, 4th Floor

institute: University of Minnesota

tag: time

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

value: Dox

value: EB

tag: paired or single

value: Paired


title: F024_vdj

tag: subject id

tag: age group

value: Cord blood

tag: assay

value: single-cell TCR


title: WholeBlood_HVTN087158520281_Day1

description: Whole blood gene expression of participant HVTN087158520281 on day 1 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: female

tag: age

value: white

value: not hispanic or latino


title: F012_vdj

value: Young


title: SCP32A

tag: growth condition


title: F008_vdj

value: mononuclear cell


title: F023_scRNA

value: Old

value: single-cell RNA


title: HPH4 input

value: lung

value: 10% fractional inspired oxygen

tag: antibody


title: WholeBlood_HVTN087158520281_Day0

description: Whole blood gene expression of participant HVTN087158520281 on day 0 after treatment: VSVHIVGAG

tag: race

tag: ethnicity

tag: group

tag: vaccinations received

value: D-DV

tag: treatment

value: VSVHIVGAG

value: whole blood


title: F021_scRNA

tag: cell type


title: HPH4 IP

tag: tissue


title: HPH3 input


title: SCP29B

value: in vivo xenograft tumor


title: SCP32B


title: F020_scRNA


title: SCP29A


title: WholeBlood_HVTN087158520281_Day14

description: Whole blood gene expression of participant HVTN087158520281 on day 14 after treatment: VSVHIVGAG

tag: day


title: F024_scRNA


title: HPH3 IP


title: SCP03C


title: SCP29C


title: F017_scRNA


title: WholeBlood_HVTN087125520056_Day14

description: Whole blood gene expression of participant HVTN087125520056 on day 14 after treatment: VSVHIVGAG

value: DD-V


title: HPH2 IP


title: HPH2 input


title: F016_scRNA


title: SCP03B


title: SCP03A


title: SCP01C


title: N2

data_processing:
Illumina HiSeq 4000 sequencer was used for basecalling.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality reads were aligned to the reference genome (UCSC RN5) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM(Fragments per kilobase of exon per million fragments mapped) as the expression profiles of LncRNA and mRNA
Genome_build: UCSC RN5
Supplementary_files_format_and_content: excel format include FPKM values for each Sample

extract_protocol:
total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: condition

value: 21% fractional inspired oxygen


title: N3


title: F014_scRNA

tag: subject id


title: WholeBlood_HVTN087125520056_Day7

description: Whole blood gene expression of participant HVTN087125520056 on day 7 after treatment: VSVHIVGAG


title: F013_scRNA

tag: age group


title: WholeBlood_HVTN087125520056_Day1

description: Whole blood gene expression of participant HVTN087125520056 on day 1 after treatment: VSVHIVGAG


title: N1


title: F012_scRNA

tag: assay


title: F008_scRNA

value: Frail


title: WholeBlood_HVTN087123520052_Day7

description: Whole blood gene expression of participant HVTN087123520052 on day 7 after treatment: NONE

tag: participant

value: hispanic or latino

value: DDD-


title: WholeBlood_HVTN087125520056_Day3

description: Whole blood gene expression of participant HVTN087125520056 on day 3 after treatment: VSVHIVGAG

tag: gender

value: female

value: white


title: WholeBlood_HVTN087125520056_Day0

description: Whole blood gene expression of participant HVTN087125520056 on day 0 after treatment: VSVHIVGAG

tag: age

value: not hispanic or latino


title: WholeBlood_HVTN087123520052_Day0

description: Whole blood gene expression of participant HVTN087123520052 on day 0 after treatment: NONE


title: SCP01A

tag: growth condition


title: SCP01B


title: HPH4


title: WholeBlood_HVTN087158520266_Day14

description: Whole blood gene expression of participant HVTN087158520266 on day 14 after treatment: VSVHIVGAG

value: male

value: multiple

value: DDDV


title: Parental_replicate2

growth_protocol: The MDA-MB-468 cell line was acquired from ATCC and authenticated by STR profiling. MDA-MB-468 and SCP cell lines were maintained in DMEM with high glucose (Life Technologies, Cat. No. 11965118) + 10% heat-inactivated FBS (Sigma, Cat. No. 12306C-500mL) + 5 units/mL penicillin and 5 µg/mL streptomycin (Life Technologies, Cat. No. 15070-63). Each cell line was plated at 2x10^6 cells per 10 cm dish and left to propagate for 48 hours. This process was repeated at least once before collecting RNA samples through direct lysis on the 10 cm dishes.

extract_protocol:
RNA was extracted using the PureLinkTM RNA Mini Kit (Life Technologies, Cat. No. 12183025). The RNA concentration was measured using the Epoch microplate spectrophotometer (BioTek). Prior to library generation for RNA-sequencing, the quality of the RNA was determined using a 2200 TapeStation and RNA screen tapes (Agilent Technologies). The mRNA libraries were generated by the Biopolymers Facility at Harvard Medical School using the KAPA mRNA HyperPrep kit (Roche) and included poly-A enrichment. The quality of these libraries was assessed by a 2200 TapeStation analyzer using D1000 screen tapes (Agilent Technologies), and q-PCR.
mRNA libraries were generated by the Biopolymers Facility at Harvard Medical School using the KAPA mRNA HyperPrep kit (Roche) and included poly-A enrichment. The quality of these libraries was assessed by a 2200 TapeStation analyzer using D1000 screen tapes (Agilent Technologies), and q-PCR. Libraries were multiplexed into two pools and subsequently sequenced (paired-end, 50 cycles) using two NextSeq Mid Output flow cells per library (Illumina).

value: in vitro cell culture


title: HPH3

value: lung

value: 10% fractional inspired oxygen


title: F007_scRNA

value: mononuclear cell

value: single-cell RNA


title: WholeBlood_HVTN087158520266_Day7

description: Whole blood gene expression of participant HVTN087158520266 on day 7 after treatment: VSVHIVGAG

value: VSVHIVGAG

value: whole blood


title: WholeBlood_HVTN087158520266_Day3

description: Whole blood gene expression of participant HVTN087158520266 on day 3 after treatment: VSVHIVGAG


title: Parental_replicate1


title: HPH2


title: F006_scRNA


title: SCP33

source_name: MDA-MBA-468 subclone


title: WholeBlood_HVTN087158520266_Day1

description: Whole blood gene expression of participant HVTN087158520266 on day 1 after treatment: VSVHIVGAG


title: Site#1_Legacy_5 [BiSulfite-seq]

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the bowtie2 sequence analysis programs. Reads were mapped to the ensembl reference human genome.
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.
Methylation percentage for each CpG sites were calcualted by methylKit
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited coverage files created by Bismark aligner for each sample.

source_name: hippocampal

extract_protocol:
Tissues [hippocampal  (flash frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
Briefly, DNA was digested with the MspI restriction enzyme and purified using phenol:chloroform extraction and ethanol precipitation, blunt-end digested, phosphorylated, and ligated into an adapter duplex with methylated cytosines. The ligated fragments were cleaned and size selected by an agarose gel. Bisulfite conversion was performed for selected fragments followed by PCR amplification and cleanup using AMPure XP beads. The Qubit assay and Agilent’s High Sensitivity D1000 assay were used to quantify the libraries.

value: hippocampal

tag: strain

value: Sprague Dawley


title: F004_scRNA

value: Frail


title: Site#2_Trinity_6 [BiSulfite-seq]


title: SCP32_replicate2


title: SCP32_replicate1


title: SCP31


title: Site#3_UAB_6 [BiSulfite-seq]


title: Site#2_Trinity_5 [BiSulfite-seq]


title: SCP29


title: Site#3_UAB_5 [BiSulfite-seq]


title: F002_scRNA


title: SCP30


title: WholeBlood_HVTN087158520266_Day0

description: Whole blood gene expression of participant HVTN087158520266 on day 0 after treatment: VSVHIVGAG

tag: race


title: SCP27


title: SCP26


title: Site#1_Legacy_4 [BiSulfite-seq]


title: Site#2_Trinity_4 [BiSulfite-seq]


title: Site#2_Trinity_3 [BiSulfite-seq]


title: Site#3_UAB_4 [BiSulfite-seq]


title: Site#1_Legacy_3 [BiSulfite-seq]


title: WholeBlood_HVTN087158520225_Day7

description: Whole blood gene expression of participant HVTN087158520225 on day 7 after treatment: VSVHIVGAG

tag: ethnicity


title: WholeBlood_HVTN087158520225_Day1

description: Whole blood gene expression of participant HVTN087158520225 on day 1 after treatment: VSVHIVGAG

tag: group


title: SCP28


title: WholeBlood_HVTN087158520225_Day14

description: Whole blood gene expression of participant HVTN087158520225 on day 14 after treatment: VSVHIVGAG

tag: vaccinations received


title: SCP25


title: WholeBlood_HVTN087158520225_Day0

description: Whole blood gene expression of participant HVTN087158520225 on day 0 after treatment: VSVHIVGAG

tag: treatment


title: WholeBlood_HVTN087158520225_Day3

description: Whole blood gene expression of participant HVTN087158520225 on day 3 after treatment: VSVHIVGAG


title: Site#1_Legacy_2 [BiSulfite-seq]


title: SCP23


title: TYESA-Blood_a

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

hyb_protocol: Samples (1.2 µg) were hybridized on SurePrint G3 Custom GE 8x60K microarrays (Agilent technologies, design n° 071137) at 65°C using Agilent's GE Hybridization kit. Washes were conducted as recommended by the manufacturer using Agilent's Gene Expression Wash Pack.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides. Spot intensities and other quality control features were extracted with Agilent's Feature Extraction software version 10.7.3.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 071137_D_F_20141113) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The “gProcessedSignal” produced by Agilent Feature Extraction software served as probe-level raw expression values. An aggregated raw expression value was computed for each feature as the median of probe-level values. CDS expression values were quantile-normalized between all experiments (64 hybridizations data) using the R package ‘limma’ and this transformation was propagated to all other types of regions.

organism: Flavobacterium psychrophilum

source_name: Bacteria

label_protocol: 10 µg of DNase-treated RNA were converted into Cy3-labeled cDNA using Fairplay III Microarray labelling kit (Agilent technologies) with random priming and 50 µg/mL actinomycin D as described for strand-specific hybridization (Rasmussen et al., 2009).

extract_protocol: Total RNA was extracted as described in Rochat T. et al (2019) (PMID:30635380).

treatment_protocol: Colonies grown in the presence of blood. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 2. Twenty µL of culture were then striked on TYES agar plates with an overlay of 10% defibrinated horse blood-agar [TYESA-Blood] or on plates made with 10% defibrinated horse blood solidified with 1.5% agar [Blood]. Plates were inubated at 18°C until colonies appeared and cells were then harvested, 4 and 10 days after inoculation for [TYESA-Blood] and [Blood], respectively.

value: OSU THCO2-90

tag: blood

value: TYSEA blood


title: Site#2_Trinity_2 [BiSulfite-seq]

tag: tissue


title: Blood_a

value: blood


title: WholeBlood_HVTN087158520128_Day14

description: Whole blood gene expression of participant HVTN087158520128 on day 14 after treatment: VSVHIVGAG

value: female

value: white

value: not hispanic or latino

tag: day


title: TYESA-Blood_b


title: Blood_b


title: Plasma_a

treatment_protocol: Exposure to plasma of rainbow trout. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 1. Cultures (8 mL) were harvested by centrifugation 3 min at 4000g, washed twice in sterile 1% peptone water and split in two halves. One of the pellets was resuspended in 300 µL of plasma [Plasma] and the other one in 300 µL of peptone water [EP2]. Plasma was prepared as following: whole blood was collected from 4 juvenile rainbow trout and pooled in a pre-cooled collection tube containing heparin. Cells were removed by centrifugation 5 min at 200g at 4°C.

tag: trout plasma

value: yes


title: WholeBlood_HVTN087158520128_Day3

description: Whole blood gene expression of participant HVTN087158520128 on day 3 after treatment: VSVHIVGAG

value: DDDV


title: Plasma_b


title: WholeBlood_HVTN087158520128_Day1

description: Whole blood gene expression of participant HVTN087158520128 on day 1 after treatment: VSVHIVGAG


title: SCP20

value: in vitro cell culture


title: Site#3_UAB_3 [BiSulfite-seq]


title: EP2_a

value: no


title: SCP19


title: SCP22


title: Site#1_Legacy_1 [BiSulfite-seq]


title: SCP24


title: WholeBlood_HVTN087158520128_Day7

description: Whole blood gene expression of participant HVTN087158520128 on day 7 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087158520128_Day0

description: Whole blood gene expression of participant HVTN087158520128 on day 0 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087158520095_Day7

description: Whole blood gene expression of participant HVTN087158520095 on day 7 after treatment: VSVHIVGAG


title: MUC_b

treatment_protocol: Exposure to skin mucus of rainbow trout. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 1. Cultures (8 mL) were harvested by centrifugation 3 min at 4000g, washed in sterile 1% peptone water, then resuspended in 400 µL of the same buffer. This bacterial suspension was split in two halves then mixed (v:v) with skin mucus recovered from juvenile rainbow trout [MUC] or 1% peptone water [EP].  Cells were harvested after 15 min of incubation under orbital shaking at 18°C.

tag: trout mucus


title: WholeBlood_HVTN087158520095_Day0

description: Whole blood gene expression of participant HVTN087158520095 on day 0 after treatment: VSVHIVGAG


title: EP2_b


title: Site#2_Trinity_1 [BiSulfite-seq]


title: WholeBlood_HVTN087158520095_Day14

description: Whole blood gene expression of participant HVTN087158520095 on day 14 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087158520095_Day1

description: Whole blood gene expression of participant HVTN087158520095 on day 1 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087158520052_Day14

description: Whole blood gene expression of participant HVTN087158520052 on day 14 after treatment: VSVHIVGAG

value: male


title: SCP17


title: Site#3_UAB_1 [BiSulfite-seq]


title: EP_a


title: Site#3_UAB_2 [BiSulfite-seq]


title: MUC_a


title: EP_b


title: SCP16


title: SCP15


title: WholeBlood_HVTN087158520052_Day7

description: Whole blood gene expression of participant HVTN087158520052 on day 7 after treatment: VSVHIVGAG


title: SCP18


title: HCl_b

treatment_protocol: Exposure to acid stress. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 0.5. Cultures were then split in two halves and HCl 0.1N solution was diluted 133x in one of them [HCl] or not [CS4]. Cells were harvested from the cultures after 5 min of incubation.

tag: acid stress


title: SCP14


title: Site#2_Trinity_6 [RNA-seq]

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence alignment programs. Reads were mapped to the hg19 genome reference to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each Sample.

extract_protocol:
Tissues [hippocampal  (flash frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Site#3_UAB_6 [RNA-seq]


title: CS4_b


title: Site#2_Trinity_5 [RNA-seq]


title: WholeBlood_HVTN087158520052_Day1

description: Whole blood gene expression of participant HVTN087158520052 on day 1 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087158520052_Day3

description: Whole blood gene expression of participant HVTN087158520052 on day 3 after treatment: VSVHIVGAG


title: SCP13


title: CS4_a


title: HCl_a


title: Site#1_Legacy_5 [RNA-seq]


title: Site#3_UAB_5 [RNA-seq]


title: SCP12


title: Site#1_Legacy_4 [RNA-seq]


title: SCP09


title: SCP11


title: Site#2_Trinity_4 [RNA-seq]


title: SCP08


title: WholeBlood_HVTN087134520164_Day7

description: Whole blood gene expression of participant HVTN087134520164 on day 7 after treatment: VSVHIVGAG

value: other

value: hispanic or latino


title: WholeBlood_HVTN087134520164_Day14

description: Whole blood gene expression of participant HVTN087134520164 on day 14 after treatment: VSVHIVGAG

value: VSVHIVGAG

value: whole blood


title: Water_c

treatment_protocol: Expression of cells in water. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) until OD600nm of 1. Cultures were then diluted 100-times in 15 L dechlorinated water maintained at 10°C with vigorous aeration in aquarium containing 10 juveniles rainbow trout [FishWater] or no fish [Water]. Bacteria were harvested after 24 h of incubation by vacuum filtration of 1 L of water on TPP® Filtermax rapid bottle-top filter with 0.22 micron pore size. Cultures used for inoculation of aquarium water were harvested at OD600 of 1 using the same procedure of vacuum filtration.

tag: freshwater

value: water


title: FishWater_a

value: fish water


title: Site#2_Trinity_3 [RNA-seq]

value: hippocampal

value: Sprague Dawley


title: Water_a

value: OSU THCO2-90


title: Site#3_UAB_4 [RNA-seq]


title: SCP07


title: SCP05


title: Site#1_Legacy_2 [RNA-seq]


title: SCP04


title: WholeBlood_HVTN087134520164_Day0

description: Whole blood gene expression of participant HVTN087134520164 on day 0 after treatment: VSVHIVGAG

tag: participant

value: female


title: LAB_a

value: control


title: Site#2_Trinity_2 [RNA-seq]


title: LAB_c


title: Anaer_b

treatment_protocol: Adaptation to stress conditions. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 0.4. Cultures were then split in three parts. Control cultures were maintained in the same growth conditions [CS2]. For amoxicillin exposure, cultures were supplemented with amoxicillin at a final concentration of 0.4 µg/mL [AMOX]. For oxygen limitation [Anaer], cultures were transfered in a 15-mL tube completely filled and maintained under orbital shaking at 18°C. Cells were harvested from the cultures after 1 h after of incubation.

tag: stress

value: oxygen limitation


title: SCP06


title: WholeBlood_HVTN087134520123_Day1

description: Whole blood gene expression of participant HVTN087134520123 on day 1 after treatment: VSVHIVGAG

tag: gender

tag: age


title: AMOX_b

tag: strain

value: amoxicillin


title: Anaer_a


title: WholeBlood_HVTN087134520123_Day14

description: Whole blood gene expression of participant HVTN087134520123 on day 14 after treatment: VSVHIVGAG

tag: race

value: DDDV


title: WholeBlood_HVTN087134520164_Day1

description: Whole blood gene expression of participant HVTN087134520164 on day 1 after treatment: VSVHIVGAG

tag: ethnicity


title: WholeBlood_HVTN087134520123_Day0

description: Whole blood gene expression of participant HVTN087134520123 on day 0 after treatment: VSVHIVGAG

tag: group


title: AMOX_a


title: WholeBlood_HVTN087134520123_Day7

description: Whole blood gene expression of participant HVTN087134520123 on day 7 after treatment: VSVHIVGAG

tag: vaccinations received


title: Site#3_UAB_3 [RNA-seq]


title: SCP03

tag: growth condition

value: in vitro cell culture


title: SCP02


title: Site#3_UAB_2  [RNA-seq]


title: CS2_b

value: no


title: SCP01


title: Total RNA from Stage6_blood_G3

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

institute: The Ohio State University

data_processing:
For fresh/frozen samples, alignment to human genome (hg38) was done using TopHat. Transcriptome assembly and analysis was performed using Cufflinks and expression was reported as FPKM
For FFPE-derived samples, low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64.  Samples were aligned to Ensemble Human reference GRCh37.97 using the RNA-Seq aligner STAR version 2.6.0c. Features were identified from Ensemble (grch37/release-97). Feature coverage counts were calculated using featureCounts, FPKMs values were generated based on overall alignment. Expression was normalized using DESeq2.
Genome_build: FFPE mapped to GRCh37.97 and fresh/frozen mapped to hg38
Supplementary_files_format_and_content: csv files include FPKM values for each sample

source_name: peripheral blood

extract_protocol:
For fresh-frozen samples, total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen). Total RNA was extracted from FFPE samples using the RNeasy FFPE kit (Qiagen).
For fresh-frozen samples, directional poly-A RNA sequencing libraries were prepared and sequenced as 42-bp paired-end reads on an Illumina NextSeq 500 instrument (Illumina) to a depth of 33.2-48.0 million read pairs. For FFPE samples, directional RNA sequencing libraries were prepared and sequenced as 150-bp paired-end reads to a depth of ~50 million read pairs per sample.

tag: disease state

value: Normal

tag: sample type

value: NKDI

tag: isolation type

value: fresh-frozen

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: Site#1_Legacy_1 [RNA-seq]

tag: tissue


title: Site#2_Trinity_1 [RNA-seq]


title: Total RNA from Stage6_blood_G2


title: WholeBlood_HVTN087158520052_Day0

description: Whole blood gene expression of participant HVTN087158520052 on day 0 after treatment: VSVHIVGAG

tag: participant

value: male

value: white

value: not hispanic or latino

tag: treatment

value: VSVHIVGAG

tag: day

value: whole blood


title: Total RNA from Stage6_blood_G1


title: Site#3_UAB_1 [RNA-seq]

value: hippocampal

value: Sprague Dawley


title: CS2_a

value: OSU THCO2-90

tag: stress


title: Total RNA from Stage5_tonsil_G3

source_name: tonsil


title: SGA-3_MSP

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

description: processed data file: Methyl_HELP-Tag_Processeddata.xlsx

data_processing:
Library strategy: HELP
Raw sequence reads were quality checked, trimmed, and mapped to rn6 genome. Tag count was calculated and normalized as described in Greally JM. The HELP-Based DNA Methylation Assays. Methods Mol Biol. 2018;1708:191‐207. doi:10.1007/978-1-4939-7481-8_11.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: Methyl_HELP-Tag_Processeddata.xlsx

extract_protocol:
Genomic DNA were isolated with phenol-chloroform-isoamyl alcohol (25:24:1), then followed by dialysis with 2x SSC.
Multiplexed libraries were created using the published protocol by Greally JM (The HELP-Based DNA Methylation Assays. Methods Mol Biol 2018;1708:191-207).
TruSeq-HELP Tagging

value: Pancreatic islets

tag: age

value: 2 weeks

tag: condition

value: IUGR


title: LYSO_a

treatment_protocol: Adaptation to stress conditions. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 0.8. Cultures were then split in three parts and hydrogen peroxide [HP] or lysozyme [LYSO] was added to one of them at a final concentration of 100 µM or 100 µg/mL, respectively. The third part was used as an unstressed control [CS1]. Cells were harvested from the three cultures 10 min after addition of the chemicals.

tag: strain

value: lysozyme


title: WholeBlood_HVTN087134520112_Day14

description: Whole blood gene expression of participant HVTN087134520112 on day 14 after treatment: VSVHIVGAG

tag: gender

tag: race

value: other

tag: ethnicity

value: hispanic or latino

tag: group

value: DDDV


title: WholeBlood_HVTN087134520112_Day0

description: Whole blood gene expression of participant HVTN087134520112 on day 0 after treatment: VSVHIVGAG

tag: vaccinations received


title: WholeBlood_HVTN087134520112_Day3

description: Whole blood gene expression of participant HVTN087134520112 on day 3 after treatment: VSVHIVGAG


title: LYSO_b