title: Microglia_coculture_aSyn [DE06NGSUKBR117823]


title: Patient 4 followup

status: Public on Dec 01 2023

type: SRA

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

description: 10x Genomics 5'

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
Frozen PBMC samples were quickly thawed in a water bath set to 37°C, re-suspended in 10 mL of ice-cold RPMI (Sigma, cat. no. R0883) with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and incubated for 10 min on ice to allow DMSO to diffuse from the tissue. Samples were spun down at 300g for 5 min, resuspended in PBS with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and cell count and viability was assessed using Luna-FLTM cell counter (Dual Fluorescence Cell counter, Logos Biosystems Inc., cat. no. L1001) using acridine orange propidium iodide (AOPI, Logos Biosystems Inc., cat. no. F23001) live/dead staining. Cell concentration was set according to 10X Genomics recommendation to 700-1000 cells/μL and 10 000 cells were targeted per sample. Cell suspensions were loaded on Chip K (10X Genomics, PN- 1000286) and processed using the 10X Genomics Chromium platform with the 5P V(D)J immune profiling kit on 10X Genomics Chromium Single Cell Controller (10X Genomics, PN-120263).
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: Peripheral blood mononuclear cells

tag: time point

value: followup

tag: disease state

value: melanoma

tag: age


title: CHLA01, rep 3

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

country: USA

institute: Johns Hopkins All Childrens Hospital

description: small RNA

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for nextseq output.
Small RNA-seq reads were trimmed with trim_galore retaining minimum read length 16 and average read quality 20.
Reads were aligned to reference genome using STAR aligner with maximum 10 multiple alignments allowed.
Read counts for miRNA were generated using featureCounts from subread package using gff from mirbase database.
Assembly: GRCh38
Supplementary files format and content: featureCounts files

molecule: polyA RNA

source_name: Human medulloblastoma

growth_protocol: DAOY cells were cultured in DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% nonessential amino acids and 1% penicillin/streptomycin. ONS-76 cells were cultured in RPMI-1640 supplemented with 10% FBS, 1% nonessential amino acids and 1% penicillin/streptomycin. D341 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. D425 cells were cultured in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin. CHLA-01-MED and CHLA-01R-MED cells were cultured in DMEM/F12 with 10% FBS, 20 ng/mL EGF, 20 ng/mL bFGF, B-27 supplement and 1% penicillin/streptomycin.

extract_protocol:
miRNA was prepared from cell lines using the miRNeasy Mini Kit (Qiagen). The quality of RNA was determined with the High Sensitivity RNA ScreenTape assay in TapeStation (Agilent Technologies).
Small RNA libraries were prepared for sequencing using standard PerkinElmer protocols of NEXTFLEX Small RNA Sequencing Kit V4.

tag: tissue

value: Human medulloblastoma

tag: cell line

value: Medulloblastoma cell line


title: Patient 2 baseline

description: 10x Genomics 5'

value: baseline


title: plasma, subject 535274a5T1

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

hyb_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

molecule: protein

source_name: serum

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: Microglia_single_wo [DE17NGSUKBR117819]

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

country: Germany

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Flooring
Assembly: mm10
Supplementary files format and content: fastq

organism: Mus musculus

source_name: Microglia

growth_protocol: Primary microglia were generated from P0-3 pups and cultured in in DMEM (Gibco) supplemented with 10% heat-inactivated fetal calf serum (FCS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco) for 7-10 days.

extract_protocol:
RNA was isolated via Qiagen RNeasy micro kit
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)

treatment_protocol: Primary cortical neurons (DIV14) were loaded for 16 h with 0.1 µM Atto488-labelled α-syn fibrils, washed with PBS and co-cultured with or without microglia for 6 hrs. Control neurons were left untreated.

value: primary Microglia

tag: passages

tag: strain

tag: treatment group


title: Neurons_coculture_wo [DE97NGSUKBR117834]

source_name: Neurons

growth_protocol: Primary cortical neurons were isolated from E15-16 mouse embryos. Neurons were seed on PDL-coated well plates cultured in Neurobasal (NB) medium supplemented with 2% B-27 Plus and 1x L-Glutamine for 14 days.

value: primary Neurons


title: plasma, subject 511a0966T1

scan_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: Female

value: Negative

value: No


title: Patient 1 baseline

description: 10x Genomics 5'


title: Neurons_coculture_wo [DE92NGSUKBR117827]


title: Patient 4 baseline

description: 10x Genomics 5'


title: plasma, subject 534ef1bfT3

label_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf


title: Patient 5 baseline

description: 10x Genomics 5'


title: Microglia_coculture_aSyn [DE16NGSUKBR117837]


title: plasma, subject 534ef1bfT2


title: Patient 3 baseline

description: 10x Genomics 5'


title: plasma, subject 4fb7a031T8


title: Neurons_coculture_wo [DE82NGSUKBR117813]


title: plasma, subject 4fb7a031T1


title: plasma, subject 4f7c6b2fT1


title: plasma, subject 4f6fb5f1T8


title: 2755 [Sample_4]

city: Boston

first: Raymond

last: Comenzo

state: MA

address: 800 Washington Street

institute: Tufts Medical Center

data_processing:
The raw reads were mapped to human refrence genome using HISAT (v2.1.0), resulting in alignment file in BAM format.
A count table is generated using the BAM files as input, and a GTF annotation files from the reference genome.
The raw count table is used as input for differential expression analysis using DESeq2
Supplementary files format and content: tab delimited file of raw read count tables from featureCounts
Supplementary files format and content: tab delimited files of differential expression analysis from DESeq2 analysis

source_name: Bone Marrow

extract_protocol:
The bone marrow cell was sorted and then lysted in RLT Plus buffer.  The RNA is isolated on a Qiagen QIASymphony with QIASymphony RNA Kit, following the manufacturer instruction.
The RNA-Seq libraries were preparing using Illumina stranded mRNA sample preparation kit, following the manufacturer instruction.

value: Bone Marrow

value: Plasma Cell

tag: disease

value: AL Amyloidosis

value: vascular amyloid in bone marrow


title: Neurons_single_wo [DE71NGSUKBR117817]

tag: cell type


title: Patient 1 followup

description: 10x Genomics 5'

value: Peripheral blood mononuclear cells

tag: time point

value: followup

value: melanoma


title: Neurons_coculture_wo [DE87NGSUKBR117820]


title: plasma, subject 51b22678T1


title: HDF_untreated_YAP_Rep2

city: Groningen

first: Bram

last: Piersma

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen

library_source: genomic

data_processing:
For Chip-seq, reads were aligned to the human genome build hg19 using BWA (v0.7.12) with default settings. PCR duplicates and unmapped reads were removed with SAMTools (v0.1.19).
Normalized peak coverage files (bigwig) as reads per genomic content, were generated with DeepTools bamCoverage (2.5.1) with 10bp bins from merged (SamTools) with the following parameters:  --normalizeTo1x  2451960000 --extendReads 200 -bs 10 --ignoreDuplicates --bl. Blacklisted regions (downloaded from ENCODE) were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig from merged YAP Chip-seq sample replicates and input DNA

molecule: genomic DNA

source_name: HDF

growth_protocol: Primary human dermal fibroblasts (CC-2511; Lonza, Basel, Switzerland) were sub-cultured in Dulbecco’s modified Eagle medium (DMEM, 12-604F; Lonza) containing 50 U/L penicillin/streptomycin (15140122; Thermo Scientific) and 10% fetal bovine serum (FBS; Sigma-Aldrich). Before commencing experiments, cells were verified to be mycoplasm free.

extract_protocol:
Protein complexes were cross-linked with 1.5 mM ethylene glycol bis(succinimidyl succinate) (21565; Thermo Scientific) in PBS with gentle agitation at RT for 15 minutes. Cross-linking of protein complexes to DNA was performed by adding methanol-free formaldehyde to a final concentration of 1% and incubation with gentle agitation at RT for 8 minutes. Next, cross-linking was quenched by adding glycine to a final concentration of 200 mM at RT for 5 minutes. Cells were then washed three times with ice-cold PBS containing 1% protease inhibitor cocktail, collected by scraping, and pelleted by centrifugation at 2000 × g for 5 minutes at 4°C. Nuclei were purified by re-suspending pellets in buffer LB1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1% protease inhibitor cocktail) and washed in buffer LB2 (10 mM Tris HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% protease inhibitor cocktail) followed by lysis in buffer LB3 (10 mM Tris HCl p.H 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1% NP-40, 1% Triton X-100, 1% protease inhibitor cocktail) while rotating for 1 hour at 4°C. Chromatin samples were sheared twice using a BioRuptor PLUS device (B01020001; Diagenode, Liège, Belgium) for 6 minutes at 4°C. Correct chromatin fragment size was verified using gel electrophoresis. Dynabeads (10002D; Thermo Fisher Scientific) were incubated for 4 hours with primary antibodies. YAP bound chromatin was precipitated in RIPA buffer (50 mM HEPES pH 7.6, 1 mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5 M LiCL, 1% protease inhibitor cocktail) at 4°C on a rotating platform for 18 hours. Afterwards the beads were washed five times in RIPA buffer, and once with TE buffer (10 mM Tris, 1mM EDTA, pH 8.0). Immunoprecipitated chromatin was eluted with elution buffer (1% SDS, 0.1M NaHCO3), de-crosslinked overnight, and cleaned up using RNAse and Protease-K treatment, followed by purification with a PCR cleanup kit (Qiagen).
Sequencing libraries were prepared for input control and two biological replicates for YAP in each culture condition using the NEBNext Ultra II DNA Library Prep Kit according to manufacturer's instructions (E7370; New England Biolabs, USA). Library quality was verified using BioAnalzyer.

treatment_protocol: Starvation and experiments were performed in DMEM containing 50 U/L penicillin/streptomycin, 0.5% FBS and 17 mM ascorbic acid (A8960; Sigma-Aldrich). Human dermal fibroblasts (15,000/cm2) were serum starved for 16 hours and subsequently exposed to TGFβ1 for 24 hours.

value: Dermal fibroblast (LONZA CC-2511)

tag: passage

value: Passage 9

tag: treatment

value: control

tag: chip antibody

value: anti-YAP:ab52771 (Abcam), Research Resource Identifier:AB_2219141


title: plasma, subject 5006beccT1

value: Male

tag: age

value: Positive

value: Yes

value: Somascan discovery platform v4


title: HepG2_24h_4

city: Sevilla

first: Patricia

last: de la Cruz-Ojeda

address: Avda. Manuel Siurot s/n

country: Spain

institute: Institute of Biomedicine of Seville

data_processing:
Basecall, trimming and demultiplexing were carried out with DRAGEN FASTQ Generation software and Illumina FastQ generation tool
Secondary analysis, concerning alignment, mapping and differential expression analysis, was carried out using Illumina BaseSpace Apps "RNAseq Aligment" and "DESeq2"
Reads were mapped to the human genome version GRCh38 using STAR Aligner
Differential expression analysis was performed using the DESeq2 method
Assembly: GRCh38
Supplementary files format and content: 2 Matrix tables with raw and normalized gene counts for every gene and every sample
Supplementary files format and content: Text files with normalized gene counts per sample

source_name: liver tumor

growth_protocol: Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine suplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% non-essential amino acids and penicillin-streptomycin solution; cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2. Cells were plated at 50.000 cells/cm2 and transfected with Lipofectamine RNAimax after 24h with miR-200c-3p inhibitor, miR-222-5p mimic, miR-512-3p mimic and transfection controls. Media was changed 6 hours later

extract_protocol:
Total RNA was extracted using a miRNeasy mini kit with DNase treatment according to the manufacturer’s instructions(QIAGEN, Germany).
Libraries were prepared using total RNA lysates. Total RNA concentration and quality of the RNA were assessed with Qubit (Qubit™ DNA HS assay) and TapeStation 4150 with the RNA ScreenTape Assay  (Agilent Technologies Genomics, USA), respectively. RNA Integrity Number (RIN) values were assessed. Libraries were constructed from 100 ng of RNA with the Illumina Stranded TOTAL RNA prep Ligation with RIBO-ZERO PLUS. Libraries were amplified, purified and subjected to quality control with High Sensitivity DNA Qubit® Assay and High Sensitivity D100 ScreenTape Assay (average size 260-280 bp). Samples were then pooled together at 2.4 nM, diluted at 1.2 nM (PhiX included) and sequenced in NovaSEq6000 S1  instrument from Illumina (2x75 cycles)

treatment_protocol: Sorafenib was added at the concentration of 10 µM at 24 h hours after transfection, and lysates were obtained after  24 hours after treatment. Control cells were treated in parallel with dimethyl sulfoxide (DMSO), vehicle in wich Sorafenib was dissolved.

tag: tissue

value: liver tumor

tag: cell line

value: Hepatoblastoma

tag: genotype

value: p53 wild type

value: Control


title: plasma, subject 4f6fb5f1T4

tag: subject id

tag: blood sample id

tag: Sex

tag: days since first sample

value: No


title: 2738 [Sample_3]

value: Bone Marrow

value: Plasma Cell

value: AL Amyloidosis

tag: disease state

value: vascular amyloid in bone marrow


title: HDF_TGFb1_YAP_Rep2

value: Dermal fibroblast (LONZA CC-2511)

value: 5 ng TGFb1/mL for 24h


title: 2831 [Sample_2]

value: no amyloid in bone marrow


title: Neurons_coculture_aSyn [DE70NGSUKBR117835]

value: primary Neurons

tag: passages

tag: strain


title: HepG2_SF24h_4

value: Sorafenib 10 µM


title: HDF_TGFb1_YAP_Rep1

value: Passage 9

value: anti-YAP:ab52771 (Abcam), Research Resource Identifier:AB_2219141


title: HepG2_24h_3


title: 2741 [Sample_1]

value: Female

tag: disease


title: HepG2_SF24h_3

value: liver tumor

tag: cell type


title: HepG2_24h_2

value: Hepatoblastoma


title: Neurons_single_wo [DE81NGSUKBR117831]

tag: treatment group


title: HepG2_SF24h_2

value: p53 wild type


title: HepG2_SF24h_1


title: Neurons_single_wo [DE76NGSUKBR117824]


title: HDF_untreated_YAP_Rep1

tag: passage

value: control


title: plasma, subject 4f2957eeT4

value: Male

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: HepG2_24h_1

tag: tissue

tag: treatment

value: Control


title: MIN6 cells/25mM/RPF biol rep8 [RPF 16]

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

description: 75 bp

library_source: other

data_processing:
Data analyses employed the XPRESSyourself pipeline. Briefly, trimmed reads were aligned to the genome (Ensemble release version 102) with the two-pass option that removes rRNA alignments and PCR duplicates and counts reads that map to the exons or truncated coding sequences of the longest transcripts of protein-coding genes. XPRESSpipe was used for quality control analyses (RPF coverage, length and periodicity) and to obtain normalized quantification of RNA, RPF counts and TE defined as ratio of RPF to RNA. Differential expression and differential TE were performed using DESeq2. Since samples were collected in 2 separate batches, analyses were corrected for batch effects.
Assembly: Ensemble release version 102
Supplementary files format and content: Raw read counts for all the genes detected in each RNA and RPF library for each sample are provided in RNAseq counts.xls, and RPF counts.xls
Library strategy: Ribosome Profiling

molecule: other

source_name: Pancreas

growth_protocol: MIN6 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Ribosome protected footprints (RPFs) were obtained using RNase digestion and gel-extraction, as previously described (McGlincey et al. 2017) except that 1 U/20 million cells RNase 1 (Thermo Scientific) was used. Libraries were made in two batches (samples 1-8 in one batch; 9-16 in a second batch).
For RPF library, rDNA depletion was performed using biotinylated rDNA sequences to remove rRNA contamination. Input libraries were generated using polyA enrichment, and Kapa stranded mRNA Hyper Prep (Illumina). RPF and RNA libraries were sequenced using Illumina NS500 single-end 75 bp reads.
Ribosome profiling under low and high glucose conditions in MIN6 cells was designed to assay mRNA translation efficiency changes under different glucose conditions

treatment_protocol: MIN6 cells incubated in media with 5.5 mM or 25 mM glucose for 24 hours were treated with 100 µg/ml of cycloheximide for 5 minutes.

value: Pancreas

tag: cell line

value: Beta cells

tag: genotype

value: Wildtype

tag: batch


title: plasma, subject 4f6fb5f1T12

tag: subject id

tag: blood sample id

tag: Sex

tag: age


title: MIN6 cells/5.5mM/RPF biol rep8 [RPF 15]

description: 75 bp


title: HDF_Input

value: Dermal fibroblast (LONZA CC-2511)

tag: chip antibody


title: Neurons_single_wo [DE66NGSUKBR117810]

value: primary Neurons

tag: passages

tag: strain


title: MIN6 cells/5.5mM/RPF biol rep7 [RPF 13]

description: 75 bp

tag: cell type


title: plasma, subject 4ecf7ee5T1

tag: days since first sample

value: Negative

value: No


title: plasma, subject 4f6fb5f1T1

tag: patient classification at first sample


title: Neurons_coculture_aSyn [DE65NGSUKBR117828]

tag: treatment group


title: MIN6 cells/25mM/RPF biol rep6 [RPF 12]

description: 75 bp


title: Neurons_coculture_aSyn [DE60NGSUKBR117821]


title: metagenomic sample obtained from skin of Pat20, Stage: nonlesional (sample103)

city: Mainz

first: Philipp

last: Licht

address: Langenbeckstrasse 1

department: Dept. of Dermatology

institute: University Medical Center Mainz

data_processing:
Preparation steps and analysis of metagenomic samples were conducted using the bioBakery toolsuit. Raw reads were first quality checked, trimmed and human reads filtered out with KneadData version 0.7.10, which integrates the tools FastQC 0.11.9, Trimmomatic 0.33, and Bowtie2 2.4.1.
Taxonomic profiles (bacteria) were generated with MetaPhlAn 3.0.2. Relative abundances of each clades were obtained with the flag --analysis_type rel_ab. Absolute counts were inferred with the flag -t rel_ab_w_read_stats. Taxonomic tables of each sample were merged with the merge_metaphlan_tables.py script and only the species level retained.
Taxonomic profiles (viruses) were generated with MetaPhlAn 3.0.2 with the flag -add_viruses.  Taxonomic tables of each sample were merged with the merge_metaphlan_tables.py script and only the species level retained.
To profile virulence genes, protein sequences were obtained from the the Virulence Factor Database (VFDB). These were used as input to the Identify-mode of ShortBRED (X).
Strain profiling was performed with PanPhlAn 3.1. The least stringent option for profiling carried out by adding respective flags as described in the manual (--min_coverage 1 --left_max 1.70 --right_min 0.30).
Assembly: hg38
Supplementary files format and content: metaphlan: tab-delimited files showing the relative abundance (or absolute counts in the metaphlan3_absolute_counts.txt files) of species per sample
Supplementary files format and content: shortbred: tab-delimited files showing the abundance of virulence genes per sample
Supplementary files format and content: panphlan: tab-delimited file corresponding to multiple samples showing the presence/absence of genes in the pangenomes of S. aureus, S.hominis, S. epidermidis and C. acnes.
Library strategy: Whole Metagenome Sequencing (WMS)

source_name: Skin

extract_protocol:
To extract the DNA, samples were then treated with 1 μl ReadyLyse Lysozyme solution (MGP04100, Lucigen, USA) at 37 °C for 60 min on a heated shaking block. After incubation, the sample solution was separated from the swab head with the help of the semi-permeable valve in the baskets by centrifuging at 12,000 g for 2 min. The basket containing the swab head was discarded. Then, beads (Pathogen Lysis Tubes, 19092, Qiagen, Germany) were added into the collection tube to mechanically disrupt cells using a TissueLyser II (85300, Qiagen, Germany) for 10 min at 30 Hz. Samples were then incubated at 67 °C for 30 min and placed on ice for 5 min. After adding 150 μl MPC precipitation reagent from the MasterPure Yeast DNA Purification Kit, cell debris was spun down and the supernatant was transferred to a fresh DNA LoBind Tube (0030108051, Eppendorf, Germany). Samples were combined with an equal volume of 100% ethanol (15420665, Fisher BioReagents, USA) and purified using the PureLink Genomic DNA Mini Kit (K182002, Invitrogen, USA) according to the manufacturer’s instruction. Finally, DNA was eluted in 25 μl 0.1 TE.
Libraries were constructed with the  NEBNext Ultra II FS DNA Library Prep Kit (E7805L, New England Biolabs, USA) in combination with NEBNext Multiplex Oligos, Dual Index Set 1 (E7600S, New England Biolabs, USA) according to the manufacturer’s instructions.

value: Skin

tag: condition

value: nonlesional

tag: individual


title: Neurons_single_aSyn [DE49NGSUKBR117825]


title: plasma, subject 4f2957eeT1

tag: covid-19 status

tag: instrument model


title: A-SalineCre-_rep5

city: Milwaukee

first: Justin

middle: L

last: Grobe

state: WI

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Raw reads were demultiplexed and quality of pre-aligned data was computed by FastQC
Reads were aligned to the Gencode vM23 (GRCm38.p6) mouse reference genome with Star
Data was then further processed in the MAPRSeq3 workflow to obtain read counts at the gene and exon levels
Aligned data was inspected via RSeQC modules
Differential gene expression was tested in EdgeR with a pairwise approach comparing: CNO Cre+ vs. Saline Cre-, CNO Cre+ vs. CNO Cre-, and CNO+MitoQ Cre+ vs. CNO Cre+
Assembly: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: Excel file (.xlsx) with individual raw counts, individual RPKM values, and pairwise comparisons

source_name: placenta

growth_protocol: All mice were housed in a temperature and humidity-controlled facility with ad libitum access to 2029x Teklad diet and water.

extract_protocol:
RNA was harvested using Trizol in a bullet blender, chloroform was added, and aqueous phase was transferred to Invitrogen RNAeasy kit (per manufacture instructions)
RNA libraries were prepared using Takara low-input, SMART-seq stranded preparation kit according to manufacture protocol

tag: tissue

value: placenta

tag: genotype

value: hM3Dq+ Gcm1Cre-

tag: treatment

value: Saline


title: MIN6 cells/5.5mM/RPF biol rep6 [RPF 11]

description: 75 bp

tag: cell line

tag: batch


title: metagenomic sample obtained from skin of Pat19, Stage: nonlesional (sample98)


title: Neurons_coculture_aSyn [DE55NGSUKBR117814]


title: Neurons_single_aSyn [DE39NGSUKBR117811]


title: MIN6 cells/25mM/RPF biol rep7 [RPF 14]

description: 75 bp


title: metagenomic sample obtained from skin of Pat20, Stage: Plaque (sample102)

value: Plaque


title: plasma, subject 4e646f0bT4

tag: subject id

tag: blood sample id

tag: Sex

value: Female

tag: age

value: Positive


title: plasma, subject 4ee897a3T1

value: Yes

value: Somascan discovery platform v4


title: MIN6 cells/25mM/RPF biol rep5 [RPF 10]

description: 75 bp

value: Pancreas

tag: cell type


title: metagenomic sample obtained from skin of Pat19, Stage: Patch (sample97)

value: Patch


title: MIN6 cells/5.5mM/RPF biol rep5 [RPF 9]

description: 75 bp

value: Beta cells

value: Wildtype


title: Neurons_single_aSyn [DE54NGSUKBR117832]

value: primary Neurons

tag: passages

tag: strain


title: plasma, subject 4e646f0bT20

tag: days since first sample

tag: patient classification at first sample


title: plasma, subject 4eaa3021T1

value: Male


title: metagenomic sample obtained from skin of Pat19, Stage: nonlesional (sample100)

tag: condition

tag: individual


title: metagenomic sample obtained from skin of Pat19, Stage: Plaque (sample99)


title: Tumor 39

city: Shanghai

first: Yile

last: Xie

address: 145 Middle Shandong Road

country: China

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the Mus musculus genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Subcutaneous tumor

growth_protocol: MC38 C57B/L6 mice colon adenocarcinoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: The MC38 cells were inject subcutaneously into germ free C57B/L6 mice. The mice were treated with anti-PD-1 mAb (intraperitoneal injection)or F. nucleatum ATCC-25586 (gavage). The subcutaneous tumor were disected from sacrificed mice at day 23.

value: Subcutaneous tumor

value: C57BL6 murine colon adenocarcinoma cells

value: WT

value: anti-PD-1 + F. nucleatum


title: MIN6 cells/5.5mM/RPF biol rep4 [RPF 7]

description: 75 bp


title: plasma, subject 4e646f0bT8

tag: covid-19 status

tag: instrument model


title: Tumor 36

tag: tissue

tag: genotype


title: metagenomic sample obtained from skin of Pat18, Stage: Patch (sample92)

value: Skin


title: plasma, subject 4e646f0bT1

value: No


title: MIN6 cells/5.5mM/RPF biol rep3 [RPF 5]

description: 75 bp

tag: cell line

tag: treatment


title: plasma, subject 4e59b73dT12

tag: subject id


title: Tumor 19


title: metagenomic sample obtained from skin of Pat18, Stage: Patch (sample94)


title: Tumor 40


title: MIN6 cells/25mM/RPF biol rep4 [RPF 8]

description: 75 bp

tag: batch


title: Tumor 37


title: metagenomic sample obtained from skin of Pat18, Stage: nonlesional (sample95)

value: nonlesional


title: Tumor 18


title: plasma, subject 4e59b73dT4

tag: blood sample id

tag: Sex


title: MIN6 cells/5.5mM/RPF biol rep2 [RPF 3]

description: 75 bp

tag: cell type


title: Neurons_single_aSyn [DE44NGSUKBR117818]

tag: passages

tag: treatment group


title: Tumor 17


title: plasma, subject 4e59b73dT8

tag: age

tag: days since first sample


title: MIN6 cells/25mM/RPF biol rep3 [RPF 6]

description: 75 bp


title: metagenomic sample obtained from skin of Pat17, Stage: nonlesional (sample90)

tag: condition


title: MIN6 cells/25mM/RPF biol rep2 [RPF 4]

description: 75 bp


title: plasma, subject 4ba22d3cT1

value: Female

tag: patient classification at first sample


title: plasma, subject 4d1159ddT1

tag: covid-19 status

value: Positive


title: metagenomic sample obtained from skin of Pat17, Stage: Patch (sample87)

tag: individual


title: Tumor 11

tag: tissue


title: MIN6 cells/25mM/RPF biol rep1 [RPF 2]

description: 75 bp

tag: genotype


title: mESC, H3K27me3, G2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
. CUT&Flow datasets were aligned to the mm10 version of Mus musculus genome using bowtie2, with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 2000.
Duplicate reads were discarded for further analysis if the reads had same start and end coordinates. Coverage at 100 bp windows genome-wide was calculated as number of reads that mapped at that window, normalized by the factor N: N = 2800000000/(Total number of mapped reads), 2800000000 was a number chosen arbitrarily in the range of total mapped base pairs in M. musculus genome.
Assembly: mm10
Supplementary files format and content: bigwig files contain normalized read coverage at 100 bp windows genome-wide, for fragments between 120 and 1000 bp in length.
Library strategy: CUT&Tag

source_name: E14 mESC

growth_protocol: KnockOut DMEM, 20% ES-qualified fetal bovine serum, 2 mM Glutamax, 10 U/ml penicillin-streptomycin, 1X non-essential amino acids, 1X 2-mercaptoethanol and 1000 U/ml Leukemia Inhibitory Factor. Cells were culture in gelatin-coated flasks at 37C at 5% CO2.

extract_protocol:
Cells were lysed and nuclei extracted. CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher) was followed for chromatin targeting and tagmentation. Nuclei were stained with propidium iodide and sorted based on DNA content.
CUTANA Direct-to-PCR CUT&Tag protocol (Epicypher) was followed for library construction. Libraries were amplified with 18 cycles on thermocycler, size selected with AMPure XP beads and validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

value: E14 mESC

value: Mouse embryonic stem cells

value: Sorted, G2 fraction

tag: antibody


title: plasma, subject 4b09fa79T4

tag: subject id

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: plasma, subject 4b09fa79T1

tag: blood sample id


title: mESC, H3K27me3, MS

tag: treatment

value: Sorted, Mid S fraction


title: mESC, H3K27me3, LS

tag: cell type

value: Sorted, Late S fraction


title: plasma, subject 4a4e5a82T4

tag: Sex

value: Male


title: metagenomic sample obtained from skin of Pat17, Stage: Patch (sample89)

value: Patch


title: plasma, subject 4e59b73dT1


title: metagenomic sample obtained from skin of Pat15, Stage: nonlesional (sample80)


title: metagenomic sample obtained from skin of Pat16, Stage: Plaque (sample82)

value: Plaque


title: MIN6 cells/5.5mM/input RNA_biol rep8 [RNA 15]

description: 75 bp

data_processing:
Data analyses employed the XPRESSyourself pipeline. Briefly, trimmed reads were aligned to the genome (Ensemble release version 102) with the two-pass option that removes rRNA alignments and PCR duplicates and counts reads that map to the exons or truncated coding sequences of the longest transcripts of protein-coding genes. XPRESSpipe was used for quality control analyses (RPF coverage, length and periodicity) and to obtain normalized quantification of RNA, RPF counts and TE defined as ratio of RPF to RNA. Differential expression and differential TE were performed using DESeq2. Since samples were collected in 2 separate batches, analyses were corrected for batch effects.
Assembly: Ensemble release version 102
Supplementary files format and content: Raw read counts for all the genes detected in each RNA and RPF library for each sample are provided in RNAseq counts.xls, and RPF counts.xls

value: Pancreas

value: Beta cells

value: Wildtype

tag: batch


title: plasma, subject 4a4e5a82T12

tag: age


title: MIN6 cells/25mM/input RNA_biol rep7 [RNA 14]

description: 75 bp


title: mESC, H3K27me3, ES

value: Sorted, Early S fraction


title: metagenomic sample obtained from skin of Pat17, Stage: nonlesional (sample88)

value: Skin

value: nonlesional


title: MIN6 cells/5.5mM/input RNA_biol rep7 [RNA 13]

description: 75 bp


title: metagenomic sample obtained from skin of Pat15, Stage: Plaque (sample79)


title: mESC, H3K27me3, G1

value: Sorted, G1 fraction


title: plasma, subject 4a4e5a82T1

tag: days since first sample

value: Positive

value: No


title: MIN6 cells/25mM/input RNA_biol rep6 [RNA 12]

description: 75 bp


title: MIN6 cells/5.5mM/RPF biol rep1 [RPF 1]

description: 75 bp


title: plasma, subject 4a298280T1


title: DJ1_KO_OVA_266

city: Tianjin

first: Kuan

last: Li

address: Jingu road 890

institute: Department of Basic Medicine, Haihe Hospital, Tianjin University

data_processing:
Illumina NovaSeq6000 sequencing
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36)
Then clean reads were separatelyaligned to reference genome with orientation mode using hisat2 software. This software was used to map with default parameters
Use htseq to count each gene reads with default parameters
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was harvested using TRIzol® Reagent kit . 1 ug of total RNA was used for the construction of sequencing libraries.
Genomic RNA libraries have been prepared according to Illumina’s protocols using the Illumina TruseqTM RNA sample prep Kit

value: lung

value: female

tag: mouse strain_(background)

value: lung cells

value: Total lung cells from DJ-1 KO mice after OVA challenge

tag: time

value: 7 weeks


title: metagenomic sample obtained from skin of Pat16, Stage: nonlesional (sample83)

tag: condition


title: metagenomic sample obtained from skin of Pat15, Stage: Plaque (sample77)

tag: individual


title: MIN6 cells/5.5mM/input RNA_biol rep6 [RNA 11]

description: 75 bp

tag: tissue


title: metagenomic sample obtained from skin of Pat14, Stage: nonlesional (sample75)


title: MIN6 cells/25mM/input RNA_biol rep8 [RNA 16]

description: 75 bp

tag: genotype


title: plasma, subject 4a1d25b3T1

value: Female

tag: patient classification at first sample

tag: covid-19 status

value: Yes

value: Somascan discovery platform v4


title: MIN6 cells/25mM/input RNA_biol rep5 [RNA 10]

description: 75 bp

value: Pancreas

tag: cell line


title: plasma, subject 49d8bfa6T1

tag: subject id

value: Male

tag: instrument model


title: WT_OVA_WT_9

tag: treatment

value: Total lung cells from WT mice after OVA challenge


title: MIN6 cells/5.5mM/input RNA_biol rep5 [RNA 9]

description: 75 bp

tag: cell type

value: Beta cells

value: Wildtype


title: plasma, subject 492ef74fT4

tag: blood sample id

tag: Sex


title: WT_OVA_WT_6


title: metagenomic sample obtained from skin of Pat15, Stage: nonlesional (sample78)

value: Skin

value: nonlesional


title: metagenomic sample obtained from skin of Pat14, Stage: Plaque (sample72)

value: Plaque


title: plasma, subject 492ef74fT1

tag: age

value: Positive

value: No


title: MIN6 cells/25mM/input RNA_biol rep4 [RNA 8]

description: 75 bp

tag: batch


title: metagenomic sample obtained from skin of Pat13, Stage: Patch (sample69)

value: Patch


title: MIN6 cells/5.5mM/input RNA_biol rep4 [RNA 7]

description: 75 bp


title: DJ1_KO_OVA_267

value: lung

value: female

tag: mouse strain_(background)

value: lung cells


title: metagenomic sample obtained from skin of Pat13, Stage: nonlesional (sample70)


title: plasma, subject 4850aa1aT8

tag: days since first sample


title: WT_OVA_WT_5

tag: time

value: 7 weeks


title: WT_PBS_WT_3

value: Total lung cells from WT mice after PBS challenge


title: plasma, subject 4850aa1aT12

value: Yes

value: Somascan discovery platform v4


title: DJ1_KO_OVA_263

value: Total lung cells from DJ-1 KO mice after OVA challenge


title: MIN6 cells/25mM/input RNA_biol rep3 [RNA 6]

description: 75 bp

value: Pancreas


title: WT_PBS_WT_2


title: MIN6 cells/5.5mM/input RNA_biol rep3 [RNA 5]

description: 75 bp

value: Beta cells


title: metagenomic sample obtained from skin of Pat13, Stage: nonlesional (sample68)

tag: condition

tag: individual


title: metagenomic sample obtained from skin of Pat13, Stage: Patch (sample67)

tag: tissue


title: WT_PBS_WT_1


title: plasma, subject 4850aa1aT1

value: Male

tag: patient classification at first sample


title: MIN6 cells/25mM/input RNA_biol rep2 [RNA 4 ]

description: 75 bp

tag: genotype

value: Wildtype


title: metagenomic sample obtained from skin of Pat14, Stage: Plaque (sample74)

value: Skin


title: plasma, subject 484011eeT4

value: Female

tag: covid-19 status


title: plasma, subject 484011eeT1

tag: subject id

value: Positive


title: metagenomic sample obtained from skin of Pat12, Stage: nonlesional (sample65)

value: nonlesional


title: GTE-4

city: Binzhou

first: Xiuzhen

last: Liu

address: No.661, Second Huanghe Road

institute: Binzhou Medical University Hospital

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: cochlea

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Green tea extract(GTE, 0.006%) and black coffee (0.1%) were added in the drinking water given to the GTE and coffee treated group mice, respectively, from 3 months old to 12 months old; normal drinking water was provided to the control group.

tag: strain

tag: genetype

value: wild type

value: 12 months

value: cochlea

value: add GTE to drinking water


title: MIN6 cells/5.5mM/input RNA_biol rep2 [RNA 3]

description: 75 bp

tag: cell line

tag: cell type

tag: treatment


title: metagenomic sample obtained from skin of Pat12, Stage: Patch (sample64)

value: Patch


title: metagenomic sample obtained from skin of Pat18, Stage: nonlesional (sample93)


title: MIN6 cells/25mM/input RNA_biol rep1 [RNA 2]

description: 75 bp


title: plasma, subject 476283f6T1

tag: blood sample id

tag: Sex

tag: age

value: No

tag: instrument model


title: MIN6 cells/5.5mM/input RNA_biol rep1 [RNA 1]

description: 75 bp

tag: batch


title: metagenomic sample obtained from skin of Pat12, Stage: Patch (sample62)

tag: condition


title: GTE-1


title: GTE-2


title: metagenomic sample obtained from skin of Pat11, Stage: nonlesional (sample60)

tag: individual


title: plasma, subject 473aecd6T1

tag: days since first sample

value: Negative

value: Yes


title: metagenomic sample obtained from skin of Pat11, Stage: Patch (sample59)

tag: tissue


title: spleen, HSC, day 14 post 5-FU, biological replicate 4

city: Kumamoto

first: Terumasa

last: Umemoto

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
The sequence reads that passed quality filters were analyzed by CLC genomic workbench.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.12.0.4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.12.0.4
Assembly: mapped to the reference sequence GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include TPM, RPKM, and read number for each sample.

source_name: spleen

growth_protocol: Animals were housed with a 12 hour light/dark cycle in an environment conditioned to 23 degrees Celsius. Food and water were provided ad libitum. All animal experiments were performed according to the “Guidelines of Kumamoto University on Animal Use”

extract_protocol:
after obtaining a single cell suspension from either spleen or bone marrow (long bones), cells were subjected to magnetic cell separation to enrich for lineage negative cells (CD11b-/Gr-1-/CD4-/CD8-/Ter119-/B220-). Subsequently, cells were stained with hematopoietic stem cell markers and finally 100 cells of the immunophenotype Lineage-/EPCR+/Sca-1+/CD48-/CD150+ (also termed long-term HSCs) were sorted into cell lysis buffer to extract RNA. After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9).
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

treatment_protocol: mice were intravenously injected with 250 mg/kg 5-fluorouracil (5-FU)

value: spleen

value: hematopoietic stem cell

tag: genotype

value: wild-type C57BL/6

value: 5-fluorouracil treated


title: spleen, HSC, day 14 post 5-FU, biological replicate 3


title: metagenomic sample obtained from skin of Pat10, Stage: nonlesional (sample55)


title: coffee-3

value: add coffee to drinking water


title: coffee-4


title: plasma, subject 464a28c7T13

tag: patient classification at first sample

tag: covid-19 status

value: Somascan discovery platform v4


title: spleen, HSC, day 14 post 5-FU, biological replicate 2


title: metagenomic sample obtained from skin of Pat10, Stage: Patch (sample54)

value: Skin


title: coffee-2

tag: strain


title: spleen, HSC, day 14 post 5-FU, biological replicate 1


title: plasma, subject 464a28c7T12

tag: subject id

value: Female

value: Positive


title: coffee-1

tag: genetype

value: wild type


title: GTE-3

value: 12 months


title: metagenomic sample obtained from skin of Pat10, Stage: nonlesional (sample53)

value: nonlesional


title: spleen, HSC, day 8 post 5-FU, biological replicate 4

tag: cell type


title: plasma, subject 464a28c7T1


title: metagenomic sample obtained from skin of Pat10, Stage: Patch (sample52)


title: plasma, subject 476283f6T4

value: Male


title: plasma, subject 46021e50T12


title: plasma, subject 46021e50T1


title: control-4

value: cochlea

tag: treatment

value: normal drinking water


title: spleen, HSC, day 8 post 5-FU, biological replicate 2


title: metagenomic sample obtained from skin of Pat9, Stage: Plaque (sample47)

value: Plaque


title: plasma, subject 47090582T1

tag: blood sample id

value: No

value: Yes


title: plasma, subject 46021e50T0

tag: Sex


title: metagenomic sample obtained from skin of Pat9, Stage: nonlesional (sample48)


title: spleen, HSC, day 8 post 5-FU, biological replicate 1

value: spleen

value: hematopoietic stem cell


title: metagenomic sample obtained from skin of Pat8, Stage: nonlesional (sample45)


title: control-1

tag: age


title: spleen, HSC, Control, biological replicate 3

value: wild-type C57BL/6

value: untreated


title: metagenomic sample obtained from skin of Pat8, Stage: Patch (sample44)

value: Patch


title: spleen, HSC, Control, biological replicate 4


title: plasma, subject 44fc8c3bT4

tag: instrument model

value: Somascan discovery platform v4


title: ARMC5_KO_NSC 2

city: Montreal

first: Jiangping

last: Wu

address: 900 Rue Saint Denis

country: Canada

description: RPB1(NTD)-specific antibody ChIP DNA fragments

data_processing:
Base-calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.  ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic (Bolger et al., 2014). The resulting reads were mapped to the mouse reference genome (GRCm38) using BWA-MEM (Li and Durbin, 2009) in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained, and PCR duplicates were marked using Picard tools. Peaks were called and annotated using MACS2 (Zhang et al., 2008) and HOMER (Heinz et al., 2010) software suites, respectively.
Genes that lacked RPB1 ChIP-seq signal in the promoter region in the KO tissues were filtered out, as these genes were believed to have no signals in WT tissues neither.
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2 Counts Per Million (log2CPM) using the Voom function implemented in the Limma R package (Ritchie et al., 2015).
To construct the global metagene Pol II-binding profile, normalized read counts (Fragments Per Kilobase of transcript per Million Mapped reads (FPKM) of a full gene length plus 2,000-bp flanks (TSS - 2,000 bp to TES + 2,000 bp) were obtain from all the genes that passed the filtering. Both flanks were divided into 20 equal-sized bins of 100 bp each. The gene bodies were scaled to 60 bins for the full gene length. FPKM was calculated from BAM input files using ngs.plot (Shen et al., 2014) with the following parameters: -G mm10 -R genebody -D ensembl -FL 200 -BOX 0 -SE 1 -VLN 0 -LWD 2 -WD 9. These global metagene Pol II binding profiles were only for visualization of differences in  Pol II density, and customarily, and customarily, inferential statistics was not conducted for such profiling.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files contains the profile of ChIP-Seq. NSC_TSS_counts_data.csv, NSC_GENEBODY.counts_data.csv, NSC_TES.counts_data.csv contain the raw counts of RPB1 signal In evry detected gene. NSC_counts_data_tsv contains the raw counts of RPB1 signal in every gene. NSC.log2cpm_data.tsv contains log2CPM value of RPB1 signal in every gene.

source_name: Neural stem cells

growth_protocol: The brains from e13.5 mouse fetuses were separated at the cervical spinal cord level, and the ganglionic eminences were dissected and harvested. The harvested tissue pieces were collected in complete NSC medium (NeuroCult NSC Basal Medium and NeuroCult NSC Proliferation Supplements  at a 9:1 ratio; Stemcell Technologies) and dissociated thoroughly but gently by pressing the pipette tip to the bottom of the tube and pipetting five times to obtain a single-cell suspension. The cells were plated at the density of 2x105 cells/ml in complete NSC medium supplemented with 20 ng/ml epidermal growth factor  (Stemcell Technologies). Five to six days later, the neurospheres were treated with AccutaseTM (Stemcell Technologies) and cultured for additional 5-6 days. The neurospheres of the second passage were used for experiments.

extract_protocol:
The cells were crosslinked with 66.7 µl 16% formaldehyde (1% final) at room temperature for 15 minutes. They were quenched with 107 µl 1.25 M glycine (0.125 M final) at room temperature for another 10 minutes in rotating tubes. The samples were centrifuged, and the pellets were washed twice with ice-cold PBS. The crosslinked cells were suspended in 300 µl swelling buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and incubated on ice for 20 minutes to release nuclei. The nuclei were harvested by centrifugation, resuspended in 200 µl ChIP sonication buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.5% SDS), and incubated on ice for 20 minutes. The nuclei were sonicated with a probe-based sonicator (FB120, probe:CL-18, FISHER SCIENTIFIC) at a 20% amplitude setting. The sonication was conducted using 15-second pulses at 15-second intervals for a total of 3 minutes. The sonicated nuclei were harvested by centrifugation, and then diluted with 800 µl ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl) to reach the final SDS concentration of 0.1%. These samples represented sonicated chromatin ready for immunoprecipitation.  To quantify chromatin and assess the degree of its fragmentation, we treated 5% of the sonicated nuclei (50 µl/sample) with 10 µg of RNase A for 15 minutes at 37 ºC followed by 20 µg of proteinase K for 30 minutes at 65 ºC. They were de-crosslinked for 5 minutes at 95 ºC. DNA was extracted with the QIAquick PCR Purification Kit. DNA concentration was determined with a Nanodrop 1000 Fluorospectrometer. DNA fragment sizes were confirmed to be 200-800 bp in length, according to electrophoresis.  For immunoprecipitation, an equal amount of sonicated chromatin, based on their prior DNA measurements, of different samples was reacted with anti-RPB1 N-terminal domain Ab (D8L4Y) (1:100) at 4 ºC overnight, followed by 40-µl magnetic protein G beads (Bio-Rad) for another 2 hours at 4 ºC. The beads were rinsed with wash buffer (100 mM Tris (pH 8.0), 500 mM LiCl, 1% NP-40, 1% deoxycholic acid) for 5 times and then with TE buffer once. The chromatin was eluted with elution buffer (50 mM Tris (pH 8.0), 10 mM EDTA, 1% SDS) at 65 ºC for 10 minutes. The immunoprecipitated chromatins were de-crosslinked at 65 ºC overnight with NaCl adjusted to 200 mM. The chromatins were then treated with 10 ug RNase A/sample at 37 ºC for 1 hour, followed by 200 ug proteinase K/sample for 2 hours at 45 ºC. DNA of the samples was purified with QIAquick PCR Purification kit and quantified by the Bioanalyzer (Agilient).
Libraries were prepared robotically with 0.2 to 2 ng of fragmented DNA ranging 100-300 bp in length, using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies . Size selection was carried out using SparQ beads (Qiagen) prior to PCR amplification (12 cycles). Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled, and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 225 pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2 x 100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Each library was sequenced at 25 million reads.

value: Neural stem cells

value: 129 sv X CD1

tag: developmental stage


title: spleen, HSC, Control, biological replicate 2


title: plasma, subject 45c43e5aT1

value: Female

value: Positive


title: ARMC5_KO_NSC 1


title: plasma, subject 44fc8c3bT12


title: ARMC5_KO_NSC 3


title: metagenomic sample obtained from skin of Pat8, Stage: nonlesional (sample43)

value: Skin

tag: condition

value: nonlesional


title: spleen, HSC, day 8 post 5-FU, biological replicate 3

value: 5-fluorouracil treated


title: plasma, subject 44fc8c3bT1


title: metagenomic sample obtained from skin of Pat7, Stage: nonlesional (sample40)

tag: individual


title: control-3

value: wild type

value: 12 months

value: cochlea

value: normal drinking water


title: control-2


title: ARMC5_WT_NSC 3

value: WT


title: metagenomic sample obtained from skin of Pat7, Stage: Plaque (sample39)

value: Plaque


title: plasma, subject 44ddfe84T8

tag: days since first sample

value: Yes


title: long bone, HSC, day 14 post 5-FU, biological replicate 3

source_name: bone marrow

tag: tissue

value: bone marrow

value: hematopoietic stem cell

value: wild-type C57BL/6


title: ARMC5_WT_NSC 2

value: Neural stem cells

tag: genotype


title: long bone, HSC, day 14 post 5-FU, biological replicate 4


title: metagenomic sample obtained from skin of Pat7, Stage: nonlesional (sample38)


title: plasma, subject 44ddfe84T1

tag: patient classification at first sample

value: No

value: Somascan discovery platform v4


title: long bone, HSC, day 14 post 5-FU, biological replicate 2


title: metagenomic sample obtained from skin of Pat7, Stage: Patch (sample37)

value: Patch


title: plasma, subject 44da5870T4

value: Male

tag: covid-19 status

value: Positive


title: long bone, HSC, day 14 post 5-FU, biological replicate 1

value: 5-fluorouracil treated


title: metagenomic sample obtained from skin of Pat8, Stage: Plaque (sample42)

value: Skin


title: ARMC5_KO_NSC_3

data_processing:
Reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads, and all reads were required to have a length of at least 32 bp. Trimming and clipping were performed using Trimmomatic.
Upstream processing of FastQ files was performed as described previously (Bourgey et al., 2019), using the ENSEMBL GRCm38 (Mus musculus) release 97 mouse reference genome sequence and annotations. Each readset was aligned using STAR (Dobin et al., 2013), which creates a Binary Alignment Map file (.bam). Then, all readset BAM files from the same sample were merged into a single global BAM file using Picard.
The pairwise Pearson’s correlation values of samples were calculated. The correlation controlled the general transcripts expression consistency between samples. It could check sample mix-up or error in name assignment. Thus, samples belonging to the same design group/condition were expected to show a higher level of correlation.
Gene expression levels were quantified using StringTie. Specifically, the count matrix was extracted from StringTie output using the auxiliary script prepDE.py as provided on the StringTie website. A gene here could be a novel gene with no overlap with a known gene. This resulted in count data for StringTie-assembled gene models.
It is generally beneficial to filter out lowly expressed genes before exploratory data analysis, but importantly prior to differential expression analysis (to reduce the multiple testing burden). For this data set, we filtered out genes that do not exceed 1 CPM in at least three samples. Out of the original genes, 17,711 genes are left after filtering.  Each gene was tested for differential expression between WT and Armc5 KO adrenal glands with EdgeR Likely Ratio Tests. Due to the concern that the augmented Pol II pool caused by Armc5 deletion might generally affect the transcription of all the gene in the KO adrenal glands, we set normalization factors for each sample as the ratio between the log2CPM value of Rn7sk of the sample to the average of all log2CPM values of Rn7sk across all samples. Rn7sk was transcribed by Pol III and was thus independent of the putative influence of the Pol II pool size.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files are ready to be viewed in Genome Viewer (UCSC).
Supplementary_files_format_and_content: Matrix csv file contains raw counts, log2CPM, 7sk RNA calibrated log2CPM of every gene and every sample

extract_protocol:
the total RNA was extracted by RNeasy kit (Qiagen).
The total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.), and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies). rRNA was depleted from 250 ng of total RNA using QIAseq FastSelect (Human 96rxns). cDNA synthesis was achieved with the NEBNext RNA First-Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), according to the manufacturer's instructions. Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). The average fragment size was determined using a LabChip GX (PerkinElmer). The libraries were normalized and pooled and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 225 pM on an Illumina NovaSeq S2 lane using the Xp protocol as per the manufacturer’s recommendations. The run was performed for 2 x 100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at a 1% level. Base-calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.

tag: strain

value: 129 sv X CD1


title: metagenomic sample obtained from skin of Pat6, Stage: nonlesional (sample35)

value: nonlesional


title: spleen, HSC, Control, biological replicate 1

value: spleen

value: untreated


title: ARMC5_KO_NSC_2


title: metagenomic sample obtained from skin of Pat6, Stage: Patch (sample34)


title: plasma, subject 449c6103T8

tag: subject id


title: ARMC5_WT_NSC 1

value: WT


title: plasma, subject 44da5870T1

value: Yes


title: long bone, HSC, day 8 post 5-FU, biological replicate 4

value: bone marrow


title: plasma, subject 449c6103T4


title: long bone, HSC, day 8 post 5-FU, biological replicate 2

value: hematopoietic stem cell


title: ARMC5_KO_NSC_1


title: metagenomic sample obtained from skin of Pat5, Stage: Patch (sample29)


title: long bone, HSC, day 8 post 5-FU, biological replicate 1

value: wild-type C57BL/6


title: ARMC5_WT_NSC_2

value: Neural stem cells


title: plasma, subject 44ddfe84T4

value: Female

value: No


title: plasma, subject 449c6103T12

value: Somascan discovery platform v4


title: metagenomic sample obtained from skin of Pat5, Stage: nonlesional (sample28)


title: long bone, HSC, Control, biological replicate 4


title: plasma, subject 449c6103T1

value: Male


title: ARMC5_WT_NSC_1


title: metagenomic sample obtained from skin of Pat5, Stage: Patch (sample27)

value: Patch


title: long bone, HSC, Control, biological replicate 3


title: T-3

city: jinan

first: xiao

last: ning

address: changqing

department: School of Bioengineering

institute: Qilu University of Technology (Shandong Academy of Sciences)

description: KN5585 maize inbred line

data_processing:
Primary sequencing data (raw reads) were generated by the Illumina HiSeq™ 2000.
After QC, the raw reads are filtered into clean reads, which are aligned to the reference sequence. The alignment data was used to calculate the distribution and alignment rate of reads on the reference gene.
In order to avoid the influence of gene length and sequencing depth on expression level, the method of RPKM (Reads per kilobases per million mapped reads) was used to normalize the sequencing data
Differentially expressed genes (DEGs) were determined using DEseq2.
Further, we also can perform deep analysis based on DEGs (We use 'FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' as the threshold to judge the significance of gene expression difference), including Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Takara). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: leaf

tag: time point

value: 3 days after drought

value: transgenic


title: plasma, subject 4499d594T4

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

source_name: serum

value: Positive


title: metagenomic sample obtained from skin of Pat4, Stage: nonlesional (sample25)

value: Skin

value: nonlesional


title: long bone, HSC, Control, biological replicate 2

tag: cell type

value: untreated


title: plasma, subject 4499d594T1

value: Yes


title: T-2

description: KN5585 maize inbred line

tag: treatment


title: metagenomic sample obtained from skin of Pat5, Stage: nonlesional (sample30)


title: long bone, HSC, day 8 post 5-FU, biological replicate 3

value: bone marrow

value: 5-fluorouracil treated


title: long bone, HSC, Control, biological replicate 1

value: hematopoietic stem cell

value: wild-type C57BL/6


title: plasma, subject 43a53f1fT4

tag: blood sample id

value: Female

value: Negative


title: T-1

description: KN5585 maize inbred line


title: metagenomic sample obtained from skin of Pat4, Stage: nonlesional (sample23)


title: CK-3

description: KN5585 maize inbred line

value: normal


title: ARMC5_WT_NSC_3

value: 129 sv X CD1

value: Neural stem cells

value: WT


title: metagenomic sample obtained from skin of Pat4, Stage: Plaque (sample24)

value: Plaque


title: H3K36M 4NQO

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania

data_processing:
10x Visium SpaceRanger mkfastq
Spot selection and cloupe file generation
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: 10x Visium SpaceRanger and Loupe Browser

source_name: tongue

extract_protocol:
Frozen sections of tongue were fixed, permeabilized, underwent cDNA synthesis
10x dual index kit TT Set A (PN-1000215)
150bp paired-end reads

value: tongue

value: Krt14-Cre(+); LSL-H3K36M


title: metagenomic sample obtained from skin of Pat4, Stage: Plaque (sample22)

value: Skin


title: plasma, subject 43a53f1fT1

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: Sex

value: No

value: Somascan discovery platform v4


title: CK-2

description: KN5585 maize inbred line

value: leaf

value: 3 days after drought


title: WT 4NQO

value: Krt14-Cre(-); LSL-H3K36M


title: plasma, subject 43a02363T8

tag: age

value: Positive

value: Yes


title: metagenomic sample obtained from skin of Pat3, Stage: nonlesional (sample20)

value: nonlesional


title: H633

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: DESeq2 output

source_name: tongue epithelia

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina
75bp single end reads

value: tongue epithelia


title: CK-1

description: KN5585 maize inbred line

value: normal


title: plasma, subject 43a02363T4

value: Female

tag: instrument model


title: metagenomic sample obtained from skin of Pat3, Stage: Patch (sample19)

value: Patch


title: plasma, subject 43a02363T12


title: metagenomic sample obtained from skin of Pat2, Stage: nonlesional (sample15)


title: H102


title: plasma, subject 43a02363T1


title: metagenomic sample obtained from skin of Pat2, Stage: Plaque (sample14)


title: H655


title: LRS5_SS2_bioRep3

city: Edinburgh

first: Behnaz

last: Nowrouzi

address: Mary Bruck Building, Colin Maclaurin Road

department: School of Engineering

country: United Kingdom

institute: The University of Edinburgh

description: Steady State 2, Biological Replicate 3

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files, followed by demultiplexing using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
RNA-seq data was processed using nf-core RNA-seq pipeline version 3.7 (https://nf-co.re/rnaseq).
Assembly: Ensembl yeast R64-1-1 genome
Following transcript abundance quantification with Salmon, tximport R package was used to aggregate the transcript-level estimates into gene level abundances.
Supplementary files format and content: tab-delimited text files include vst-normalised counts from DESeq2 for each sample

organism: Saccharomyces cerevisiae

source_name: Taxadiene-producing parent yeast cell, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 3

growth_protocol: Both parent (LRS5) and evolved (E_LRS5) taxadiene-producing yeast strains were inoculated in 100 mL of buffered SDG medium (pH=6, 20 g/L galactose, 6.7 g/L yeast nitrogen base with ammonium sulphate and without amino acids, 0.79 g/L complete synthetic mixture) in a 500 mL baffled shake flask. The precultures were then inoculated in triplicates in 1L Biostat Qplus bioreactors (Sartorius Stedim Biotech) at OD600=0.1. The chemostat experiments for both steady states were performed at dilution rates of 0.1 h-1, in 500 mL of SDG medium with 10 g/L galactose, while being controlled for pH six using 2 M of NaOH and H2SO4, agitation rate (600 rpm) and airflow (0.5 SPLM).

extract_protocol:
The withdrawn cell cuture broths were immediately poured in -20 °C-prechilled tubes on ice and centrifuged for two minutes at 19,341 ×g  in pre-chilled centrifuge. After the removal of the supernatants, the samples were flash frozen in liquid nitrogen and stored at -80 °C. The total RNAs were extracted using Qiagen RNeasy Plus mini kit following the manufacturer’s instructions (Qiagen).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB).

treatment_protocol: The gene expression profiles were studied during two steady states for both strains, upon completion of five residence time for each steady state. The steady state II (SSII) had the same condition (medium formulation and bioreactor parameters) as in steady state I (SSI), except that its feeding medium also contained H2O2 at a final concentration of 0.5 mM.

tag: cell line

value: Taxadiene-producing parent cell (LRS5)

tag: growth condition

value: galactose-containing defined medium supplemented with 0.5 mM H2O2, dilution rate:0.1 h-1 (steady state II)


title: metagenomic sample obtained from skin of Pat2, Stage: nonlesional (sample13)

tag: condition

tag: individual


title: plasma, subject 42cde147T1

first: Pushkala

last: Jayaraman

value: Male

tag: days since first sample

value: Negative


title: H570

tag: genotype

value: Krt14-Cre(+); LSL-H3K36M


title: LRS5_SS2_bioRep1

description: Steady State 2, Biological Replicate 1

source_name: Taxadiene-producing parent yeast cell, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 1


title: H945


title: plasma, subject 41663b51T1

tag: patient classification at first sample


title: metagenomic sample obtained from skin of Pat2, Stage: Plaque (sample12)

tag: tissue

value: Skin

value: Plaque


title: plasma, subject 416ded86T1

tag: covid-19 status

value: No

value: Somascan discovery platform v4


title: metagenomic sample obtained from skin of Pat1, Stage: nonlesional (sample10)


title: LRS5_SS1_bioRep3

description: Steady State 1, Biological Replicate 3

source_name: Taxadiene-producing parent yeast cell, steady state I of galactose-limited chemostat 3

tag: strain

value: galactose-containing defined medium, dilution rate:0.1 h-1 (steady state I)


title: plasma, subject 40dfb797T1

tag: subject id

value: Positive


title: H569

tag: cell type

value: Krt14-Cre(-); LSL-H3K36M


title: plasma, subject 406b17b7T1

value: Yes


title: LRS5_SS1_bioRep2

description: Steady State 1, Biological Replicate 2

source_name: Taxadiene-producing parent yeast cell, steady state I of galactose-limited chemostat 2


title: H943

value: tongue epithelia


title: metagenomic sample obtained from skin of Pat1, Stage: Plaque (sample8)

source_name: Skin


title: H711


title: plasma, subject 40604ef2T1


title: LRS5_SS1_bioRep1

description: Steady State 1, Biological Replicate 1

source_name: Taxadiene-producing parent yeast cell, steady state I of galactose-limited chemostat 1


title: RNAseq from Pat14, skin, Stage: nonlesional

data_processing:
After quality check with Fastqc version 0.11.9, raw reads were aligned against the human reference genome Ensembl built GRCh38.p13 using STAR 2.7.9a in –quantMode GeneCounts. The data was loaded into DESeq2 version 1.36.0, filtered for genes with a minimum of ten cumulative counts over all samples, and normalized using the internal DESeq2 method. Subsequently, a differential expression analysis using the Wald test was carried out adjusted for influences from individual patients introduced by the paired-sample design. Genes with <0.05 adjusted p-value (padj) were considered significant.
Pathway analyzes were performed using the R package pathfindeR. The table from DESeq2 reporting significant gene log2 fold-changes was used as input. The Reactome database was chosen to find enriched pathways.
Multiomics data integration: Two data modalities, the microbiome and the transcriptome, were integratively analyzed using MOFA2 version 1.6.0 (X). The microbiome dataset was originally created in our previous stand-alone analysis of the microbiome using MetaPhlAn 3.0.2. The MOFA2 model was trained with a single group, the option scale_views turned true, convergence_mode slow, and eight factors. Gene set enrichment analysis was performed with the MOFA2 function run_enrichment()
Virus Profiling: the pipeline VIRTUS was applied. Briefly, after mapping RNAseq reads to the human reference human reference genome Ensembl built GRCh38.p13, unmapped reads were aligned against 762 viral genomes to quantify the number of viral transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include unnormalized gene expression values for each Sample
Supplementary files format and content: DESeq2_log2fc_XXX_vs_nonlesional.tsv: tab-delimited file showing gene expression changes of plaque stage or patch stage vs nonlesional skin. Produced with DESeq2
Supplementary files format and content: gsea_XXX_enriched_terms.html: Gene set enrichment analysis of patch/plaque stage. Reactome database as background
Supplementary files format and content: Virus: tab-demilited file summarizing viruses found in RNAseq reads (mapping rate virus /mapping rate human)

extract_protocol:
Blood: Peripheral blood mononuclear cells (PBMCs) were isolated and the T cell fraction was enriched using the Pan T Cell Isolation Kit human (Miltenyi Biotec, Germany) . Total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen, Germany) . Skin: RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (74704, Qiagen, Germany) along with the TissueLyser II (85300, Qiagen, Germany)
400 ng RNA were used as input for NEBNext Ultra RNA Library Prep Kit (New England Biolabs, USA)

value: nonlesional


title: metagenomic sample obtained from skin of Pat1, Stage: Patch (sample9)


title: H165


title: H166


title: E_LRS5_SS2_bioRep1

description: Steady State 2, Biological Replicate 1

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 3

value: Taxadiene-producing cell evolved on H2O2 and galactose-containing defined medium while producing taxadiene (E_LRS5)


title: plasma, subject 3fb3ab81T8

value: Female


title: LRS5_SS2_bioRep2

description: Steady State 2, Biological Replicate 2

source_name: Taxadiene-producing parent yeast cell, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 2

value: Taxadiene-producing parent cell (LRS5)


title: E_LRS5_SS2_bioRep3

description: Steady State 2, Biological Replicate 3

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 2

value: galactose-containing defined medium supplemented with 0.5 mM H2O2, dilution rate:0.1 h-1 (steady state II)


title: H893


title: plasma, subject 3fb3ab81T4


title: RNAseq from Pat13, skin, Stage: nonlesional


title: plasma, subject 3fb3ab81T12


title: H940


title: plasma, subject 3eafb97fT8

value: Male


title: E_LRS5_SS1_bioRep3

description: Steady State 1, Biological Replicate 3

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state I of galactose-limited chemostat 2


title: RNAseq from Pat13, skin, Stage: Patch

value: Patch


title: plasma, subject 3eafb97fT1


title: E_LRS5_SS2_bioRep2

description: Steady State 2, Biological Replicate 2

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state II (+ 0.5 mM H2O2) of galactose-limited chemostat 1


title: H342 H3K27me3

data_processing:
Aligned using bowtie2
Differential enrichment called via DiffBind with DESeq2 and SICER2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: DiffBind with DESeq2 and SICER2

source_name: murine epidermis

extract_protocol:
Mouse epidermis single cell suspension
Cell Signaling CUT&RUN kit (#86652S) followed by NEBNext Ultra library preparation
37bp paired-end reads

value: murine epidermis

value: Krt14-Cre(+); LSL-H3K36M


title: E_LRS5_SS1_bioRep1

description: Steady State 1, Biological Replicate 1

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state I of galactose-limited chemostat 3


title: Liver_Organic group_L5

city: Mueang Nakhon Ratchasima

first: Panpradub

last: Sinpru

state: Nakhon Ratchasima

address: Maha Witthayalai Rd

department: School of Animal Technology and Innovation

country: Thailand

institute: Suranaree University of Technology

description: gene_count_FPKM.xlsx sample column: OR_L5

data_processing:
High-quality clean reads from the samples were mapped to the chicken reference genome using the HISAT2 version 2.0.5 software.
Differential gene expression analysis between high- and low-FCR samples was performed using DESeq2 version 1.20.0 package in R.
Assembly: GRCg6a
Supplementary files format and content: Column 1, gene_id: gene number; Column 2-21, Sample count: raw read count values of each sample; Column 22-41, Sample FPKM: FPKM of each gene for each sample; Column 42, gene_name: gene name; Column 43-46, gene_chr, gene_start, gene_end, gene_strand: gene location, including chromosome, starting position, end position, and strand; Column 47, gene_length: gene length, the sum of genes from the beginning to the end of all non-overlapping exon regions in chromosomes; Column 48, gene_description: gene description

organism: Gallus gallus

source_name: Liver

growth_protocol: A total of 250 one-day-old KRC (mixed-sex) were produced at the Poultry Research Unit of the University Farm. To compare transcriptomic profiles of KRC by rearing system, the chicks were randomly divided into two feeding trails: organic feeding by using only organic raw materials (OR, n = 125) and commercial feedstuff as a control group (CO, n = 125). The ingredient composition and calculated analysis of the feed used in the organic and conventional raising systems. The birds were housed in 5 indoor pens (25 birds/pen, 5 birds/m2) in each treatment group. At 21 days, the organic chickens only had access to an outdoor Ruzi pasture (4 birds/m2) up to slaughter age (91 days). All the chickens belonged to the same environmentally controlled poultry house and had access to feed and water ad libitum. Body weight and feed intake of chickens were collected every week for growth performance examination (body weight gain and feed conversion ratio; FCR).

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent.One μg of total RNA with RIN value ≥ 7.7  was used for the following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s instruction (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Chickens were raised under conventional system or organic system.

value: Liver

tag: treatment

value: Chicken raised under organic system


title: RNAseq from Pat14, skin, Stage: Plaque

value: Skin

value: Plaque


title: RNAseq from Pat10, skin, Stage: nonlesional


title: H347 H3K27me3


title: DNA methylation data PDX-derived tumor ICB984

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina HumanMethylation450 BeadChip or Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

source_name: Tumor from patient-derived xenograft ICB984

label_protocol: Standard Illumina Protocol

growth_protocol: For PDO and PDXO generation, fresh surgically resected tumor samples were disgregated within 24 hours of surgical resection and culured in PDO medium in a 37°C, 5% CO2 incubator (see Methods section for further details)

extract_protocol: Genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions; while PDOs/PDXOs were lysed in lysis buffer (20 mM EDTA, 10 mM Tris, 200 mM NaCl, 0.2% Triton X-100, 100 µg/ml Proteinase K, pH 8.0) for 1h at 37°C under agitation. Genomic DNA was extracted with phenol-chloroform and precipitated with isopropanol.

tag: sample type

value: fresh-frozen


title: RNAseq from Pat9, skin, Stage: nonlesional


title: RNAseq from Pat10, skin, Stage: Patch


title: H341 H3K27me3


title: H339 H3K27me3

value: Krt14-Cre(-); LSL-H3K36M


title: RNAseq from Pat9, skin, Stage: Plaque


title: plasma, subject 3eafb97fT4

city: New York

address: 1 Gustave Levy Pl

institute: Icahn School of Medicine at Mount Sinai

source_name: serum

tag: blood sample id

tag: Sex

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 3e99c9adT1

value: Female

tag: age

tag: instrument model


title: plasma, subject 3d6e228fT1


title: Liver_Organic group_L4

description: gene_count_FPKM.xlsx sample column: OR_L4


title: Liver_Organic group_L3

description: gene_count_FPKM.xlsx sample column: OR_L3


title: H193

source_name: tongue epithelia

value: tongue epithelia


title: plasma, subject 3d426f83T4


title: RNAseq from Pat8, skin, Stage: nonlesional

value: nonlesional


title: RNAseq from Pat8, skin, Stage: Patch


title: E_LRS5_SS1_bioRep2

description: Steady State 1, Biological Replicate 2

source_name: Taxadiene-producing yeast cell evolved on H2O2- and galactose-containing defined medium to induce taxadiene production, steady state I of galactose-limited chemostat 1

tag: cell line

value: Taxadiene-producing cell evolved on H2O2 and galactose-containing defined medium while producing taxadiene (E_LRS5)

tag: growth condition

value: galactose-containing defined medium, dilution rate:0.1 h-1 (steady state I)


title: DNA methylation data PDX-derived tumor HT028pGF1

source_name: Tumor from patient-derived xenograft HT028pGF1


title: Liver_Organic group_L2

description: gene_count_FPKM.xlsx sample column: OR_L2


title: H346 H3K27me3

value: murine epidermis


title: H343 H3K27me3


title: RNAseq from Pat7, skin, Stage: nonlesional

tag: condition

tag: individual


title: plasma, subject 3d426f83T1

value: Male

tag: days since first sample


title: plasma, subject 3d2f9980T1

tag: patient classification at first sample


title: RNAseq from Pat7, skin, Stage: Plaque

tag: tissue


title: H347 H3K36me2

tag: genotype

value: Krt14-Cre(+); LSL-H3K36M


title: Liver_Organic group_L1

description: gene_count_FPKM.xlsx sample column: OR_L1

value: Liver

value: Chicken raised under organic system


title: Liver_Control group_L5

description: gene_count_FPKM.xlsx sample column: CO_L5

value: Chicken raised under conventional system


title: H342 H3K36me2


title: plasma, subject 3c2b7e4fT1

tag: covid-19 status

value: Negative


title: RNAseq from Pat5, skin, Stage: nonlesional

value: Skin


title: plasma, subject 3c08d358T1

tag: subject id

value: Positive


title: RNAseq from Pat5, skin, Stage: Patch

value: Patch


title: plasma, subject 3b625ef6T1

value: Yes


title: H339 H3K36me2

tag: cell type

value: Krt14-Cre(-); LSL-H3K36M


title: H341 H3K36me2


title: Liver_Control group_L3

description: gene_count_FPKM.xlsx sample column: CO_L3

tag: treatment


title: Liver_Control group_L4

description: gene_count_FPKM.xlsx sample column: CO_L4


title: plasma, subject 399596aaT4

value: Female

value: Somascan discovery platform v4


title: H343 H3K36me2


title: Liver_Control group_L2

description: gene_count_FPKM.xlsx sample column: CO_L2


title: RNAseq from Pat4, skin, Stage: Plaque

value: Plaque


title: H346 H3K36me2


title: RNAseq from Pat4, skin, Stage: nonlesional

value: nonlesional


title: plasma, subject 399596aaT1

value: No


title: RNAseq from Pat3, skin, Stage: nonlesional


title: Liver_Control group_L1

description: gene_count_FPKM.xlsx sample column: CO_L1


title: RNAseq from Pat3, skin, Stage: Patch


title: plasma, subject 38a81b25T8


title: H347 IgG

value: murine epidermis


title: Pectoralis major muscle (Breast muscle)_Organic group_B5

description: gene_count_FPKM.xlsx sample column: OR_B5

source_name: Pectoralis major muscle (Breast muscle)

value: Pectoralis major muscle (Breast muscle)


title: RNAseq from Pat1, skin, Stage: nonlesional


title: plasma, subject 38a81b25T4

value: Male


title: H341 IgG

value: Krt14-Cre(+); LSL-H3K36M


title: Pectoralis major muscle (Breast muscle)_Organic group_B3

description: gene_count_FPKM.xlsx sample column: OR_B3

value: Chicken raised under organic system


title: plasma, subject 38a81b25T13


title: RNAseq from Pat1, skin, Stage: Plaque


title: Pectoralis major muscle (Breast muscle)_Organic group_B2

description: gene_count_FPKM.xlsx sample column: OR_B2


title: plasma, subject 38a81b25T12


title: H339 IgG


title: RNAseq from Pat8, blood --> PBMC --> T cell enriched

source_name: Blood

value: Blood

value: PBMC (T cell enriched)

value: Mycosis fungoides, blood


title: Pectoralis major muscle (Breast muscle)_Organic group_B1

description: gene_count_FPKM.xlsx sample column: OR_B1


title: H343 IgG


title: Pectoralis major muscle (Breast muscle)_Control group_B5

description: gene_count_FPKM.xlsx sample column: CO_B5

value: Chicken raised under conventional system


title: plasma, subject 388ec55eT1

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

value: Positive


title: RNAseq from Pat7, blood --> PBMC --> T cell enriched


title: plasma, subject 38a81b25T1

value: Yes


title: H346 IgG

value: Krt14-Cre(-); LSL-H3K36M


title: Pectoralis major muscle (Breast muscle)_Control group_B4

description: gene_count_FPKM.xlsx sample column: CO_B4


title: RNAseq from Pat4, blood --> PBMC --> T cell enriched


title: plasma, subject 3716fae4T1


title: Pectoralis major muscle (Breast muscle)_Control group_B3

description: gene_count_FPKM.xlsx sample column: CO_B3


title: RNAseq from Pat1, blood --> PBMC --> T cell enriched


title: Pectoralis major muscle (Breast muscle)_Organic group_B4

description: gene_count_FPKM.xlsx sample column: OR_B4


title: Pancreatic Tumor Tissue, vehicle, 2 days, KA009

city: New York City

first: Lukas

last: Vlahos

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic Tumor Tissue

growth_protocol: Tumor tissue was collected following humane euthanasia and trimmed of healthy pancreas tissue in a sterile petri dish. The tumor pieces were dissociated using a modified protocol based on Miltenyi (mouse) Tumor Dissociation Kit (Miltenyi Biotec, 130-096-730)

extract_protocol:
Tumor tissue was placed in a digestion buffer containing trypsin, DNase, and an enzymatic cocktail (Supplementary Table 7) and digested at 37°C for 42 minutes (37C_m_TDK_2 program) on a gentleMACS Octo Dissociator (Miltenyi Biotec, 130-096-427). Cell suspensions were then filtered through a 40 μm cell strainer (Corning, 431750) and red blood cells were removed by incubation with red cell lysis buffer (Millipore Sigma, 11814389001), before a final resuspension in 100 μL PBS + 0.01% BSA.
Single Cell 3' v3, 10x Genomics

treatment_protocol: Treatment with the vehicle hydroxypropyl-beta-cyclodextrin (HPBCD, Acros Organics; 5% w/w in water for injection (WFI)), or IPI-926 (kindly provided by PellePharm; 5 mg/ml) was performed daily via oral gavage at 40 mg/kg. Tumor tissue was collected 2 hours after final dose.

value: Pancreatic Tumor Tissue

value: vehicle, 2 days


title: Pancreatic Tumor Tissue, IPI-926, 2 days, KA008

description: 10x Genomics

value: IPI-926, 2 days


title: plasma, subject 36b52008T1

value: Female

value: Somascan discovery platform v4


title: H342 IgG

value: murine epidermis


title: HEC-1-A cells, RNAi-NCAPG3

city: Changsha

first: Chun

last: Fu

state: hunan

address: No.139 Renmin Road

department: Department of Obstetrics and Gynecology

institute: the Second Xiangya Hospital, Central South University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: hg38
Supplementary files format and content: All.HTSeq.counts

extract_protocol:
RNAi-Control or RNAi-NCAPG cells were collected and the RNA was extracted using Trizol (Thermo Fisher Scientific，15596018).
The sequencing library was conducted by NEBNext UltraTM RNA Library Prep Kit (NEB #E749), and purified by AMPure XP system, according to the standard Illumina protocols.

value: Human endometrial adenocarcinoma cells

value: NCAPG knockdown


title: Pectoralis major muscle (Breast muscle)_Control group_B2

description: gene_count_FPKM.xlsx sample column: CO_B2

value: Pectoralis major muscle (Breast muscle)


title: Pancreatic Tumor Tissue, vehicle, 2 days, KA007

description: 10x Genomics


title: HEC-1-A cells, RNAi-NCAPG2


title: Pectoralis major muscle (Breast muscle)_Control group_B1

description: gene_count_FPKM.xlsx sample column: CO_B1


title: HEC-1-A cells, RNAi-NCAPG1


title: Pancreatic Tumor Tissue, vehicle, 2 days, KA006

description: 10x Genomics


title: patient vtr144 on d56 treated with 20bcg, vaccination via po administration

city: Cleveland

first: Richard

last: Silver

state: OH

address: 10900 Euclid Ave

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center

description:
AAGTTTC_vtr144_d56_20bcg_po
vtr144_d56_20bcg_po

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM transformation added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts-per-million in tab-delimitted text format

source_name: Peripheral Blood

growth_protocol: Blood was drawn into CPT tubes and PBMC isolated, aliquoted and frozen.  Following thawing, CD4+ T cells were isolated using Miltenyi positive selection kits. Autologous monocyte-derived dendritic cells (MDDC) were prepared as described.

extract_protocol:
After overnight treatment with BCG/media, supernatants were harvested, frozen and stored for lysis and RNA extraction.
RiboZero v1

treatment_protocol: Autologuous CD4+ T cells cultured overnight with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio either in the presence of Danish BCG (Statens Serum Institut, Copenhagen, MOI 20:1), or medium alone.

value: Peripheral Blood

value: patient vtr144

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: Pancreatic Tumor Tissue, IPI-926, 2 days, KA005

description: 10x Genomics


title: HEC-1-A cells, RNAi-Control3

value: Control knockdown


title: plasma, subject 34518e80T1

tag: blood sample id

tag: Sex

value: Male

value: Positive


title: plasma, subject 33cf404aT1

tag: age

value: Yes

tag: instrument model


title: patient vtr56 on d56 treated with 20bcg, vaccination via po administration

description:
TATCCCT_vtr56_d56_20bcg_po
vtr56_d56_20bcg_po

value: patient vtr56


title: HEC-1-A cells, RNAi-Control2

tag: cell line


title: plasma, subject 338e187cT8


title: HEC-1-A cells, RNAi-Control1


title: RNASeq_DM_rep4

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic(v0.38)
Clean reads were aligned to the reference genome using STAR(v 2.7.0e)
The raw read counts of each gene were calculated using HTSeq(v 0.11.2)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

growth_protocol: The BM cells were harvested from the mice directly

extract_protocol:
Total RNA from individual mice was isolated with RNeasy Plus Mini Kit (QIAGEN)
The RNA libraries were prepared with the NEB Ultra RNA kit and followed by paired-end sequencing with a read length of 100 bp

treatment_protocol: The Lineage-cKit+Sca-1+ cells were purified from mouse bone marrow cells using beads sorting

value: Bone marrow

tag: strain

value: Lin-cKit+Sca-1+ bone marrow cells


title: plasma, subject 338e187cT4

value: No


title: plasma, subject 338e187cT21

value: Somascan discovery platform v4


title: plasma, subject 338e187cT20


title: Control (Pull down)

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

description: miRNA profiling by RNA sequencing

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Fastx.
Clean reads were compared with GRCh38.The analysis was performed by the Shanghai Biotechnology Corporation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files include TPM values  for each Sample

growth_protocol: BT549-SNHG15-MS2  Cells were cultured in  DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
the co-precipitated RNAs were extracted using mirVana™ miRNA Isolation Kit following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit.

treatment_protocol: Cell lysates were prepared and then incubated with Amylose resin coated with MBP-MCP (MS2 coat protein) or Amylose resin at 4°C for 5 h in the presence of RNasin (200 U/mL) and protease inhibitors. After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times in ice-cold lysis buffer.

value: breast cancer cells

value: SNHG15-MS2 overexpression

value: Amylose resin


title: patient vtr61 on d56 treated with 20bcg, vaccination via po administration

description:
CCCTTGG_vtr61_d56_20bcg_po
vtr61_d56_20bcg_po

value: patient vtr61


title: patient vtr98 on d56 treated with 20bcg, vaccination via po administration

description:
CACAGCA_vtr98_d56_20bcg_po
vtr98_d56_20bcg_po

value: Peripheral Blood

value: patient vtr98


title: RNASeq_DM_rep1


title: plasma, subject 3583469cT1

department: Charles Bronfman Institute of Personalized Medicine

value: Female


title: RNASeq_DM_rep3


title: RNASeq_DM_rep2


title: 1231A3-COL10A1KO-#20-day42-Ex3

city: Sakyoku, Kyoto

first: takeshi

last: kamakura

state: Kyoto

address: Shogoin Kawaharacho 53

institute: Kyoto University

data_processing:
long-rna-seq-pipeline v2.3.4 (ENCODE) with R v4.2.1 (The R Foundation)
the sequenced reads were mapped to the human reference genome GRCh38 v105 using STAR 2.5.1b with GENCODE v39 gene annotations
the expected gene counts and normalized gene expression values (TPM) were obtained using RSEM 1.2.23.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: hiPSCs were maintained on iMatrix511 silk coated dish in AK02N medium with P/S

extract_protocol:
RNA was isolatd using RNeasy micro kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold following manufacturer's protocols.

treatment_protocol:
Sclerotome cells were induced by bFGF, CHIR99021, Activin-A, SB431542, LDN193189, PD173074, XAV939, SAG in CDMi medium
Chondrogenic differentiation was induced by PDGF-BB, Dex, TGFβ3, BMP4, T3, β-GP in chondrogenic medium

value: hiPSC

value: chondrogenic differentiation

tag: time

value: day 42


title: plasma, subject 351bb4e8T1

tag: days since first sample

value: Negative


title: plasma, subject 338e187cT1

value: Male

tag: patient classification at first sample

value: Positive

value: Yes