title: Huvecs, TBHP group,  rep2

city: Wenzhou

first: Weiyang

last: Gao

address: West Xueyuan Road, Wenzhou

institute: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University

data_processing:
mRNA was isolated by Oligo(dT)-attached magnetic beads
mRNA was then randomly fragmented in fragmentation buffer.
First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.
Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.
cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.
Assembly: PRKN, PINK1,TFEB, BAK, CYC
Supplementary files format and content: xls file represent for gene expression level (FPKM) matrix file
Supplementary files format and content: fpkm_density file represent for comparison diagram of FPKM density distribution, the peak value of distribution curve represents the region with the highest concentration of gene expression in the whole sample.

source_name: umbilical vein endothelium

growth_protocol: HUVEC were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HUVECs were grown to 70-80% confluence and divided into three groups: Control, TBHP, and TBHP + ML groups. The cells received the corresponding treatment, and then the TRIzol reagent (Invitrogen, 15596018) was used to extract the total RNA
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells in TBHP group received Tert-Butyl hydroperoxide（100 μM）to induce oxidative stress. Cells in TBHP + ML group received Tert-Butyl hydroperoxide（100 μM）and melatonin (100 μM).

value: umbilical vein endothelium

value: HUVECs

value: WT

value: treated with TBHP


title: Huvecs, TBHP group,  rep1

status: Public on Jun 29 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Huvecs, Control group,  rep3

value: control


title: GF_Cohort2_Mouse17

city: Nashville

first: Ryan

middle: M

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt University Medical Center

description: Demultiplexed, adapter and degenerate base-trimmed fastq files

data_processing:
After de-multiplexing, FastQC software was used for QC. www.bioinformatics.babraham.ac.uk/projects/fastqc
Cutadapt was used to trim 3' adapters and degenerate bases. Data provided is after this step.
Bowtie was used to map reads, as described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095027/
Assembly: mm9
Supplementary files format and content: algae_group5_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: bacteria_group1_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: bacteria_group2_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: fungus_group4_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.miRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.other.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.rRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.snoRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.snRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.tRNA.count.RPM.txt
Supplementary files format and content: RA_97_93.All.TaskReads.csv
Supplementary files format and content: RA_97_93.NonParallel.TaskReads.csv

organism: Mus musculus

source_name: Lipoprotein (HDL)

extract_protocol:
https://pubmed.ncbi.nlm.nih.gov/30128086/
NextFlex V3 Small RNA Seq (Perkin Elmer)

treatment_protocol: Age- and facility-matched mice

value: Lipoprotein (HDL)

value: GF


title: M030_BMK_LAIV_1D

type: RNA

city: Los Angeles

first: Pia

middle: S

last: Pannaraj

state: California

address: 4650 Sunset Blvd, MS#51

department: Infectious Diseases

institute: Children's Hospital of Los Angeles

description: Breast milk RNA 1 day after LAIV vaccination

hyb_protocol: Samples were hybridized to Human Exon 1.0 ST arrays (Thermo Fisher) using reagents from the GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher) and following vendor protocols.  Arrays were hybridized for 20 hours at 45° at 60rpm and washed on the GeneChip Fluidics Station 450 using protocol FS450_0001.

scan_protocol: Arrays were scanned using Thermo Fisher’s GeneChip Scanner 3000 7G driven by the GeneChip Operating Software (v. 1.1.1) and the Command Console Software (AGCC, v. 4.0).

data_processing:
Signal intensities for the probe selection regions (PSR) were quantile normalized by robust multichip averaging using affy R package (v. 3.14).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: breast milk, LAIV vaccine, 1D

label_protocol: Amplified cDNA was generated using the Ovation FFPE WTA System (NuGen Technologies).  Chemical and enzymatic fragmentation of amplified cDNA was followed by biotin labelling using the Encore Biotin Module (NuGen Technologies).

extract_protocol: RNA was extracted from whole blood and milk samples using Maxwell Simply RNA purification kit (Promega). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: fluid

tag: usbmk

tag: specimen

value: BMK

tag: timepoint

tag: run

tag: vaccine

value: LAIV

tag: flu season


title: M039_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

source_name: breast milk, IIV vaccine, 0D

value: IIV


title: Huvecs, TBHP + ML group,  rep2

value: treated with TBHP + ML


title: Huvecs, Control group,  rep2


title: ovule-3

city: Zhengzhou

first: Ji

last: Chengyan

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
Alignment   HISAT2    2.1.0    mapping reads to genome
Transcript Assembly     StringTie    1.3.2    sequence assembly
Gene Expression    Quantity HTSeq     0.6.0    estimating gene expression   level
Assembly: B. rapa genome v1.5 sequences, B. nigra genome v1.1 sequences and B.oleracea genome v1.0 sequences (http://brassicadb.cn)
Supplementary files format and content: tab-delimited text files include FPKM values for eachsample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica carinata x Brassica rapa

source_name: ovule

extract_protocol:
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02 following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: ovule

tag: developmental stage

value: meiosis to mature embryo sac formation

value: AABBCC

tag: sample type

value: Brassica allohexaploid (Brassica carinata male × Brassica rape female)


title: input_replicate2

city: Beijing

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

library_source: genomic

data_processing:
Reads from ChIP-seq experiments were aligned to the mm9 revision of the mouse reference genome using only annotated chromosomes 1-19, chrX, chrY, and chrM or to the hg19 revision of the human genome using only annotated chromosomes 1-22, chrX, chrY,  and chrM. Alignment was performed using bowtie (Langmead et al., 2009) with parameters –best –k 1 –m 1 –sam and –l set to read  length.
Regions with an exceptionally high coverage of ChIP-Seq reads (i.e., peaks) were identified using MACS with parameters –keepdup = auto –p1e-9 and with corresponding input control.
Genome_build: mm9
Supplementary_files_format_and_content: text files include ChIP-Seq reads for each Sample

molecule: genomic DNA

source_name: input replicate 2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27AC antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (VAHTS UniversalDNA Library Prep Kit for Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: iBMDM cells were infected with VSV or HSV-1 for 8 hours

tag: cell line

value: iBMDM

tag: strain

value: input

tag: antibody


title: anther-1

source_name: anther

value: anther

value: meiosis to pollen maturation


title: Huvecs, TBHP + ML group,  rep1

value: umbilical vein endothelium

value: HUVECs

value: WT


title: Huvecs, TBHP + ML group,  rep3


title: Huvecs, Control group,  rep1

value: control


title: H3K27AC_replicate2

source_name: ChIP with anti-H3K27ac antibody, replicate 2

value: no treatment

value: anti-H3K27ac antibody


title: sc_myc_pho4_nexus_2

city: Stanford

first: Amr

middle: Mohamed

last: Alexandari

state: CA

address: 240 Pasteur Dr

institute: Stanford University

data_processing:
ChIP-nexus libraries were sequenced in single-end mode (1 X 75 cycles) on a NextSeq 500 instrument. The adapters were trimmed using cutadapt (v 1.8.1) and reads were aligned to the Saccharomyces cerevisiae (sacCer3) genome using bowtie (v1.1.2). Reads were filtered using SAMtools (v1.3.1) to remove unmapped reads and PCR duplicates. Reads aligned to the same position with the same barcode, CIGAR string and the SAM flag were deduplicated using nimnexus dedup (v.0.1.1).
The final filtered BAM file was converted to tagAlign format (BED 3 + 3) using bedtools ‘bamtobed‘ (v.2.26). Cross-correlation scores were obtained for each file using phantompeakqualtools (v.1.2). BigWig tracks containing the strand-specific number of aligned 5′ read ends (pooled across all replicates) were generated using bedtools genomecov -5 -bg –strand <+/−>, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig v.4.
Peaks were called using MACS2 (v.2.1.1) by extending the 5’  ends of reads on each strand using a 150-bp window and then computing coverage of extended reads across both strands (shift = -75, extsize = 150). For each TF, peak calling was performed on filtered, aligned reads from each replicate using a relaxed threshold P=0.1.
Assembly: sacCer3
Supplementary files format and content: bigWig (positive and negative strands), narrowPeak
Library strategy: ChIP-nexus

organism: Saccharomyces cerevisiae

growth_protocol: The Myc-tagged Pho4 and Cbf1 Saccharomyces cerevisiae strains were cultured in 50 ml of yeast peptone dextrose (YPD) media at 25oC to OD600 ~ 0.8.

extract_protocol:
The yeast chromatin preparation was performed as previously described with minor modifications (Rossi, Lai, & Pugh, 2018). For each experiment, 50 ml of cells were cross-linked with 1% formaldehyde (Fisher Scientific) for 15 min at 25oC. The reaction was quenched by incubating with 125 mM glycine for 5 min. Cells were washed three times with cold wash buffer (10 mM Tris-HCl, pH 7.5, 100 mM NaCl) at 4oC. The pellet was snap frozen in liquid nitrogen after the last wash. The pellet was then resuspended in 700µl of FA lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% triton-X-100, 0.1% Sodium deoxycholate, supplemented with protease inhibitor) and transferred to 1.5 ml of Sarstedt micro tube. 1 ml of 0.5 mm zirconia/silica beads was added to the tube and cells were lysed in a Mini-BeadBeater 24 (BioSpec products) for three cycles (3 min ON/5 min OFF).Samples were kept on ice during the OFF cycles. Cell lysates were separated from silica beads and collected in a new 1.5 ml tube using a 23G 1” needle (BD Microlance) and centrifuged at maximum speed for 4 min at 4oC to pellet the chromatin. The supernatant was discarded and the pellet was resuspended in 750 µl of FA lysis buffer supplemented with 0.1% SDS. Samples were sonicated with a Bioruptor Pico (Diagenode) for 18 cycles of 30 s ON and 30 s OFF intervals. Chromatin extracts were centrifuged at 16,000 g for 10 min at 4oC and the supernatant was used for the ChIP reaction.
The ChIP-nexus was performed as previously described (He, Johnston, & Zeitlinger, 2015), with some modifications. Briefly, the chromatin was washed with Nexus wash buffers A to D (wash buffer A: 10 mM Tris-EDTA, 0.1% Triton X-100; wash buffer B: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS; wash buffer C: 250 mM NaCl, 5 mM Tris-HCl, pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA; wash buffer D: 250 mM LiCl, 0.5% IGEPAL CA-630, 10 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA) and 10 mM Tris, pH 7.5. End-repair and dA-tailing enzymatic reactions were performed using the NEBNext End Repair and NEBNext dA-tailing module. ChIP-nexus adapter mix containing four fixed barcodes (ACTG, CTGA, GACT and TGAC) were ligated with quick T4 DNA ligase. Following barcode extension, samples were treated with lambda exonuclease to generate high-resolution transcription factor binding footprints. Reverse crosslinking was performed at 65C for overnight, followed by ethanol precipitation of DNA. Purified DNA fragments were circularized, and directly subjected to PCR amplification. The libraries were gel purified before sequencing. For each factor, at least two biological replicates were prepared side-by-side from independent colonies.

treatment_protocol: Pho4 was induced by incubating cells for 2h at 25oCin phosphate-free media from Fisher Scientific (MP114027812), supplemented with 2% glucose and 0.1g/L sodium chloride.

tag: chip antibody

value: ab9E10 (abcam)


title: leaf-3

source_name: leaf

tag: tissue

value: leaf

value: young leave


title: leaf-2


title: visceral adipose tissue,  vis_196

city: Stockholm

first: Xiangyu

last: Li

address: Tomtebodavägen 23, Solna

department: Science for life laboratory

country: Sweden

institute: KTH-Royal Institute of Technology

data_processing:
Total million reads (or pairs) for a sample
Aggregated percentage of bases that have quality score more the Q30
Kallisto algorithm was used for quantification.
Assembly: Ensembl V102
Supplementary files format and content: tab-delimited text files include TPM and count values for each Sample

source_name: visceral adipose tissue

extract_protocol:
Total RNA from visceral AT was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen).
The RNA-seq libraries were prepared using the Illumina TruSeq RNA sample preparation kit following the manufacturer's instructions.

value: visceral adipose tissue

tag: cell type

value: visceral adipose cell

tag: diabetes

value: no

tag: gender

value: female

tag: age

tag: bmi (kg/m2)

tag: nafld/nash

value: NAFLD


title: Huvecs, TBHP group,  rep3

tag: genotype

tag: treatment

value: treated with TBHP


title: ovule-2

value: ovule

value: meiosis to mature embryo sac formation

value: AABBCC

value: Brassica allohexaploid (Brassica carinata male × Brassica rape female)


title: visceral adipose tissue,  vis_186

value: NASH


title: visceral adipose tissue,  vis_191


title: visceral adipose tissue,  vis_184


title: anther-3

value: anther

value: meiosis to pollen maturation


title: ovule-1


title: visceral adipose tissue,  vis_188


title: visceral adipose tissue,  vis_174


title: ZIL01132 visit 5

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing of ZIL01132 at visit 5.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray hugene10sthsentrezgcdf R package (version 23.0.0).

label: biotin

source_name: Brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: RNA was extracted using the QIAGEN miRNeasy Mini Kit according to the manufacturer's protocol.

treatment_protocol: Participants were randomized to combined treatment of aspirin (ASA, 81 mg QD) and zileuton (Zyflo CR) two 600 mg extended release tablets BID or placebo pills for 12 weeks.

tag: included in analysis

value: TRUE

tag: patient

tag: visit

value: visit 5

value: Aspirin+Zileuton

tag: site

value: UAZ Phoenix

tag: Sex

tag: smoking status

value: current smoker

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: visceral adipose tissue,  vis_181

tag: tissue

value: visceral adipose tissue

tag: cell type

value: visceral adipose cell

tag: diabetes

tag: gender

value: male

tag: age

tag: bmi (kg/m2)


title: anther-2

tag: developmental stage

tag: genotype

tag: sample type


title: visceral adipose tissue,  vis_172

value: no

tag: nafld/nash

value: NAFLD


title: visceral adipose tissue,  vis_173


title: leaf-1

value: leaf

value: young leave


title: ZIL01129 visit 6

description: Gene expression data from nasal brushing of ZIL01129 at visit 6.

tag: included in analysis

tag: patient

tag: visit

value: visit 6

tag: treatment

value: Placebo

tag: site

tag: Sex

value: female

tag: smoking status

tag: pack years


title: ZIL01125 visit 6

description: Gene expression data from nasal brushing of ZIL01125 at visit 6.

value: UAZ Tucson

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: ZIL01127 visit 5

description: Gene expression data from nasal brushing of ZIL01127 at visit 5.

tag: age


title: visceral adipose tissue,  vis_151

tag: tissue

tag: cell type

tag: diabetes

tag: gender

tag: bmi (kg/m2)


title: ZIL01132 visit 6

description: Gene expression data from nasal brushing of ZIL01132 at visit 6.

tag: included in analysis

tag: patient

tag: visit

tag: treatment


title: ZIL01129 visit 5

description: Gene expression data from nasal brushing of ZIL01129 at visit 5.

tag: site

tag: Sex

tag: smoking status

tag: pack years


title: ZIL01124 visit 5

description: Gene expression data from nasal brushing of ZIL01124 at visit 5.

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: ZIL01126 visit 5

description: Gene expression data from nasal brushing of ZIL01126 at visit 5.

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: ZIL01125 visit 5

description: Gene expression data from nasal brushing of ZIL01125 at visit 5.


title: visceral adipose tissue,  vis_150

tag: tissue

tag: cell type

tag: diabetes

tag: gender

tag: nafld/nash

value: NASH


title: ZIL01127 visit 2

description: Gene expression data from nasal brushing of ZIL01127 at visit 2.

tag: included in analysis

value: TRUE

tag: patient

tag: visit

value: visit 2

tag: treatment


title: ZIL01127 visit 6

description: Gene expression data from nasal brushing of ZIL01127 at visit 6.

value: Aspirin+Zileuton

tag: site

tag: Sex

tag: smoking status

tag: pack years


title: ZIL01125 visit 2

description: Gene expression data from nasal brushing of ZIL01125 at visit 2.

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: ZIL01129 visit 2

description: Gene expression data from nasal brushing of ZIL01129 at visit 2.

value: UAZ Phoenix

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: ZIL01124 visit 6

description: Gene expression data from nasal brushing of ZIL01124 at visit 6.

value: current smoker


title: ZIL01132 visit 2

description: Gene expression data from nasal brushing of ZIL01132 at visit 2.


title: ZIL01123 visit 2

description: Gene expression data from nasal brushing of ZIL01123 at visit 2.


title: ZIL01118 visit 6

description: Gene expression data from nasal brushing of ZIL01118 at visit 6.


title: visceral adipose tissue,  vis_162

tag: tissue

value: visceral adipose tissue

tag: cell type

tag: diabetes

tag: gender

tag: bmi (kg/m2)


title: ZIL01126 visit 6

description: Gene expression data from nasal brushing of ZIL01126 at visit 6.

tag: included in analysis

tag: patient

tag: visit

tag: treatment


title: ZIL01123 visit 5

description: Gene expression data from nasal brushing of ZIL01123 at visit 5.

value: visit 5

tag: site

tag: Sex

tag: smoking status

tag: pack years


title: ZIL01118 visit 2

description: Gene expression data from nasal brushing of ZIL01118 at visit 2.

value: male

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: ZIL01123 visit 6

description: Gene expression data from nasal brushing of ZIL01123 at visit 6.

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: visceral adipose tissue,  vis_156

tag: tissue

tag: cell type

value: visceral adipose cell

tag: diabetes

value: no

tag: gender

tag: nafld/nash


title: visceral adipose tissue,  vis_142

tag: bmi (kg/m2)

value: NAFLD


title: ZIL01118 visit 5

description: Gene expression data from nasal brushing of ZIL01118 at visit 5.

tag: included in analysis

tag: patient

tag: visit

tag: treatment

tag: site


title: ZIL01124 visit 2

description: Gene expression data from nasal brushing of ZIL01124 at visit 2.

tag: Sex

tag: smoking status

tag: pack years

tag: urinary cotinine

tag: rin


title: ZIL01117 visit 6

description: Gene expression data from nasal brushing of ZIL01117 at visit 6.

tag: age

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: Tie1/2_deletion_2

city: Helsinki

first: Sawan

middle: KUMAR

last: Jha

state: Haartmaninkatu 8

address: Haartm

department: Research Program Unit

country: Finland

institute: University of Helsinki

data_processing:
Smart-Seq2: Illumina Casava1.8 software was used for basecalling
Smart-Seq2:The sequencing reads were mapped to the mouse reference genome GRCm38 (mm10) with TopHat (version 2.1.1)
Smart-Seq2:Filtering duplicated reads using samtools software (version 0.1.18)
Smart-Seq2:Summarizing gene counts using Subread package (featureCounts function, version 1.4.6-p5)
Smart-Seq2:Raw expression data were processed further in R (version 3.5.1 and version 4.0.3) using Seurat R package (v4.0.6).For QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018).
10X:The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3‚ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
10X:Reads were aligned to mouse reference genome mm10.
10X:Analyses shown in manuscript were performed with Seurat V4.0 (Hao et al., 2021)
10X:Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
10X:Analyses shown in manuscript were performed with Seurat V4.0 (Hao et al., 2021)
Assembly: GRCm38
Supplementary files format and content: Smart-Seq: Matrix table with raw gene counts for every sample/ cell (express_matrix) + gene length and gene title files organized in folders corresponding to the individual plates/samples. 10X: Aggregated matrix files (*matrix.mtx) containing cell counts and tab separated metadata files (*_genes.tsv and *_barcodes.tsv)

source_name: Ear Skin

extract_protocol:
For SMART SEQ experiment: Ear skins of euthanized mice were minced and dissociated by incubation  with 5 mg mL-1 collagenase II, 0.2 mg mL-1 DNase I and 0.2% FBS in PBS for 15 min at 37°C and 750  rpm. Digests were quenched by the addition of 2 mM EDTA f.c., subsequently filtered through a 40 μm  filter and washed for 5 min at 300 g and 4°C with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA). Fcreceptor  binding was blocked by incubation with rat anti-mouse CD16/CD32 (clone 93, 0.5 μg mL-1) for  10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390,  1.0 μg mL-1), anti-PDPN (clone 8.1.1 1 μg mL-1), anti-CD45 (clone 30-F11, 4 μg mL-1), anti-CD11b  (clone M1/70, 4 μg mL-1) and anti-TER-119 (clone TER-119, 4 μg mL-1) antibodies for 20 min on ice.  Prior to sorting of live CD31+ PDPN+ CD45- CD11b- Ter119- lymphatic endothelial cells on a BD FACS  Aria III, samples were filtered through a 40 μm filter and supplemented with 1 μM SytoxBlue to label  dead cells. For 10X experiment: Mouse ear skins minced and dissociated by incubation with 5 mg mL-1 collagenase II, 0.2 mg mL-1 DNase I and 0.2% FBS in PBS for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 70 µm filter and centrifuged at 300g for 5 min at +4C. Cells were resuspended in FACS buffer (PBS, 2% FBS, and 2 mM EDTA) and filtered through a 35 µm cell strainer. Fc-receptor binding was blocked by incubation with rat anti-mouse CD16/CD32 (BD Pharmingen 553142, clone 93, 0.5 µg mL-1) for 10 min on ice followed by incubation with fluorophore-conjugated anti-CD31 (BD Pharmingen 561814, clone MEC 13.3), anti-PDPN (BD 127411 clone 8.1.1 1 µg mL-1), anti-CD45 (BioLegend 103108 clone 30-F11, 4 µg mL-1) and anti-TER-119 (Invitrogen 11-5921-82 clone TER-119, 4 µg mL-1) antibodies on ice for 30 min. Prior to sorting samples were filtered through a 35 µm cell strainer and supplemented with DAPI to label dead cells (0.1 µg mL-1). Live CD31+ PDPN+ CD45- CD11b- Ter119- lymphatic endothelial cells and CD31+ PDPN- CD45- CD11b- Ter119- blood endothelial cells were sorted and pooled. Cell sorting was performed with BD Influx.
Smart-Seq2 library preparation according to Picelli S et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 2014;9(1):171–181. For 10X data, The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 2 chemistry

treatment_protocol: For induction of Cre mediated recombination in Prox1-CreERT2;Tie1fl/fl or Prox1-CreERT2;Tie1;Tie2fl/fl pups, 4-hydroxytamoxifen (4-OHT), dissolved in ethanol (25 mg/ml), was administered to postnatal pups by intragastric injections (2.5 μl, 62.5 μg) at P1-P5.For antibody treatment, Mice were treated with dose of 20 mg/kg of Ang2 blocking antibody (18E5, a gift from Eli Lily) or mouse IgG1 control antibody every three days from P16 to P21.

tag: strain

tag: genotype

value: Cre+

tag: gender

tag: tissue

value: skin

tag: cell type

value: FACs sorted LECs

tag: facs sorting

value: Podoplanin and CD31

tag: protocol

value: smart-seq

tag: plate id


title: visceral adipose tissue,  vis_138

tag: diabetes

value: female

tag: bmi (kg/m2)

tag: nafld/nash


title: visceral adipose tissue,  vis_133


title: visceral adipose tissue,  vis_130


title: Ctrl_3

value: Cre-

tag: treatment


title: visceral adipose tissue,  vis_122

tag: age


title: Tie1_deletion_1


title: visceral adipose tissue,  vis_137


title: visceral adipose tissue,  vis_124

value: NASH


title: Ctrl_2


title: ZIL01117 visit 2

description: Gene expression data from nasal brushing of ZIL01117 at visit 2.

tag: included in analysis

value: TRUE

tag: patient

tag: visit

value: visit 2

value: Placebo

tag: site

value: UAZ Tucson

tag: Sex

tag: smoking status

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin


title: visceral adipose tissue,  vis_57

tag: tissue

value: visceral adipose tissue

tag: cell type

tag: gender


title: visceral adipose tissue,  vis_127

tag: diabetes

value: male

tag: bmi (kg/m2)


title: Ctrl_4

tag: strain

tag: genotype

tag: treatment

tag: facs sorting

tag: protocol

tag: plate id


title: Ctrl_1

tag: age


title: ZIL01112 visit 2

description: Gene expression data from nasal brushing of ZIL01112 at visit 2.

tag: included in analysis

tag: patient

tag: visit

tag: site

tag: Sex

tag: smoking status

value: current smoker

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: Tie1/2_deletion_1

tag: gender

tag: tissue

tag: cell type


title: ZIL01116 visit 2

description: Gene expression data from nasal brushing of ZIL01116 at visit 2.

tag: treatment

value: Aspirin+Zileuton

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin


title: Tie1_deletion_2

tag: strain

tag: genotype

tag: age

tag: facs sorting

tag: protocol

tag: plate id


title: ZIL01116 visit 6

description: Gene expression data from nasal brushing of ZIL01116 at visit 6.

tag: included in analysis

tag: patient

tag: visit

value: visit 6

tag: site

tag: Sex

tag: smoking status

tag: batch


title: ZIL01112 visit 5

description: Gene expression data from nasal brushing of ZIL01112 at visit 5.

value: visit 5

tag: treatment

tag: pack years

tag: lte4 pg/ml

tag: pgem ng/ml


title: visceral adipose tissue,  vis_55

tag: tissue

tag: cell type

value: visceral adipose cell

tag: diabetes

tag: gender

tag: bmi (kg/m2)

tag: nafld/nash


title: ZIL01109 visit 5

description: Gene expression data from nasal brushing of ZIL01109 at visit 5.

tag: included in analysis

tag: age

tag: urinary cotinine

tag: rin

tag: mean rin


title: ZIL01116 visit 5

description: Gene expression data from nasal brushing of ZIL01116 at visit 5.

tag: patient

tag: visit

tag: site

tag: Sex

tag: smoking status

value: creatinine:BLQ (< 5 ng/nL)


title: visceral adipose tissue,  vis_58


title: ZIL01109 visit 2

description: Gene expression data from nasal brushing of ZIL01109 at visit 2.

tag: treatment

tag: pack years

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: visceral adipose tissue,  vis_50

tag: tissue

tag: cell type

tag: diabetes

tag: gender

tag: bmi (kg/m2)


title: ZIL01112 visit 6

description: Gene expression data from nasal brushing of ZIL01112 at visit 6.

tag: included in analysis

tag: age

tag: urinary cotinine

tag: rin


title: visceral adipose tissue,  vis_53

tag: nafld/nash


title: ASTRO-JAK2ca-2

city: EVRY

first: céline

last: DERBOIS

state: essonne

address: 2 rue Gaston crémieux

country: France

institute: CEA/CNRGH

description: replicate 2-astrocyte-test group

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: Astrocytes

label_protocol: RNA was amplified with the Ovation PicoSL VTA system V2 kit (NuGen technologies) and Biotinylated cDNA were prepared with The Encore biotiNL kit (NuGen technologies) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser (Pico chips).

value: Astrocytes

tag: gene transfer

tag: strain

tag: Sex

tag: Stage

value: adult

tag: organ

value: brain


title: visceral adipose tissue,  vis_47

value: female


title: ASTRO-JAK2ca-4

description: replicate 4-astrocyte-test group


title: ASTRO-JAK2ca-3

description: replicate 3-astrocyte-test group


title: visceral adipose tissue,  vis_46

value: NAFLD


title: visceral adipose tissue,  vis_39


title: visceral adipose tissue,  vis_35


title: visceral adipose tissue,  vis_34

value: NASH


title: visceral adipose tissue,  vis_25


title: ZIL01104 visit 6

description: Gene expression data from nasal brushing of ZIL01104 at visit 6.

value: TRUE

tag: patient

tag: visit

tag: treatment

tag: site

tag: smoking status

tag: pack years

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: ZIL01107 visit 5

description: Gene expression data from nasal brushing of ZIL01107 at visit 5.

tag: included in analysis

tag: age

tag: urinary cotinine

tag: pgem ng/ml


title: ZIL01107 visit 6

description: Gene expression data from nasal brushing of ZIL01107 at visit 6.

tag: rin


title: ZIL01104 visit 5

description: Gene expression data from nasal brushing of ZIL01104 at visit 5.

value: Placebo

tag: Sex


title: CDK5f/f [C1-L]

city: Nanjing

first: chen

last: xiang

address: chunhua street

institute: nanjing medical university

data_processing:
Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic， Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA)

tag: strain

value: untreated

tag: genotype

tag: tissue

value: Hippocampus


title: ZIL01104 visit 2

description: Gene expression data from nasal brushing of ZIL01104 at visit 2.

tag: patient

tag: visit

value: visit 2

value: UAZ Tucson


title: Cdh5-CreERT2;CDK5f/f [K1-L]

tag: treatment

value: Tamoxifen


title: ASTRO-GFP-4

description: replicate 4-astrocyte-control group

tag: cell type

tag: gene transfer

value: GFP

value: male

tag: Stage

tag: organ


title: QpcKO_79

first: Volker

middle: Hans

last: Haase

data_processing:
Novogene performed differential expression significant analysis of two conditions/groups by using the DESeq2 R package, while the significant criterion is padj<0.05.
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. We use STAR to accomplish the mapping.
Novogene uses the clusterProfiler software for enrichment analysis, including GO Enrichment, DO Enrichment, KEGG and Reactome database Enrichment.
we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.
The procedure of raw reads filtering is as follows:  (1) Remove reads containing adapters;  (2) Remove reads containing N > 0.1% (N represents base that could not be determined);  (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 20.
Genome_build: mm10

source_name: nephron progenitor cells

extract_protocol:
Total RNA was reverse-transcribed and amplified directly from FACS-sorted cells using TAKARA V4 ultra low input kit(cat:634888)
performed by Novogene,250~300 bp insert cDNA library, PolyA selected, non-strand specific

tag: mouse line

value: Six2-Qpc knockout mouse

value: embryonic day E18.5


title: ASTRO-GFP-2

description: replicate 2-astrocyte-control group

value: Astrocytes


title: visceral adipose tissue,  vis_22

value: visceral adipose tissue

value: visceral adipose cell

tag: diabetes

tag: gender

tag: bmi (kg/m2)

tag: nafld/nash


title: ASTRO-GFP-3

description: replicate 3-astrocyte-control group

value: adult

value: brain


title: visceral adipose tissue,  vis_23

tag: age

value: NAFLD


title: ASTRO-GFP-1

description: replicate 1-astrocyte-control group

tag: Sex


title: ZIL01107 visit 2

description: Gene expression data from nasal brushing of ZIL01107 at visit 2.

tag: included in analysis

value: TRUE

value: Aspirin+Zileuton

tag: site

value: female

tag: smoking status

value: current smoker

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: QpcKO_78

tag: mouse line


title: ZIL01103 visit 6

description: Gene expression data from nasal brushing of ZIL01103 at visit 6.

tag: patient

tag: visit

value: visit 6

tag: treatment


title: ZIL01103 visit 5

description: Gene expression data from nasal brushing of ZIL01103 at visit 5.

value: visit 5

value: UAZ Tucson


title: OTHER-GFP-1

description: replicate 1-other cells-control group

source_name: GFPnegative brain cells

tag: cell type

value: GFPnegative brain cells

tag: gene transfer

value: GFP

tag: strain

tag: Stage

tag: organ


title: ZIL01103 visit 2

description: Gene expression data from nasal brushing of ZIL01103 at visit 2.

tag: included in analysis

value: visit 2

tag: site

tag: Sex

tag: age

tag: smoking status


title: ASTRO-JAK2ca-1

description: replicate 1-astrocyte-test group

value: male


title: OTHER-GFP-2

description: replicate 2-other cells-control group


title: visceral adipose tissue,  vis_17

tag: tissue

tag: diabetes

tag: gender

tag: bmi (kg/m2)

tag: nafld/nash

value: NASH


title: ZIL01102 visit 6

description: Gene expression data from nasal brushing of ZIL01102 at visit 6.

tag: patient

tag: visit

value: Placebo

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: QpcKO_77

tag: mouse line

value: Six2-Qpc knockout mouse

value: embryonic day E18.5


title: QpcKO_75

tag: age


title: Health_K

city: Guangzhou

first: Yang

last: yanqi

address: YanjiangXi Road 107

institute: Sun Yat-Sen Memorial Hospital

description: 2x100 paired-end sequence reads

data_processing:
read alignment: ACGT101-miR (LC Sciences, Houston, Texas, USA)
read quantification and normalization: Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
Genome build: miRBase 22.0

source_name: plasma exosomes

extract_protocol: Total RNA was extracted by Total RNA Purification Kit（LC Sciences, Cat. TRK-1001）following the manufacturer's instructions.

tag: disease state

value: Healthy

value: plasma exosomes

value: F


title: Health_J

description: 2x100 paired-end sequence reads

tag: tissue


title: QpcKO_74


title: Health_H

description: 2x100 paired-end sequence reads

value: M


title: Cont_72

value: Six2-Qpc heterozygous mouse


title: Health_G

description: 2x100 paired-end sequence reads


title: Health_E

description: 2x100 paired-end sequence reads


title: Health_F

description: 2x100 paired-end sequence reads


title: Cont_71


title: Health_B

description: 2x100 paired-end sequence reads


title: ZIL01102 visit 5

description: Gene expression data from nasal brushing of ZIL01102 at visit 5.

tag: included in analysis

value: TRUE

tag: treatment

tag: site

tag: Sex

value: female

tag: smoking status

value: current smoker


title: Health_D

description: 2x100 paired-end sequence reads

tag: gender


title: Health_C

description: 2x100 paired-end sequence reads


title: Health_I

description: 2x100 paired-end sequence reads


title: ZIL01102 visit 2

description: Gene expression data from nasal brushing of ZIL01102 at visit 2.

tag: patient

tag: visit

value: UAZ Tucson

tag: pack years


title: ZIL01092 visit 6

description: Gene expression data from nasal brushing of ZIL01092 at visit 6.

value: visit 6

tag: urinary cotinine

tag: rin

tag: mean rin


title: Cont_76


title: ZIL01092 visit 5

description: Gene expression data from nasal brushing of ZIL01092 at visit 5.

value: visit 5

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: Cont_73

tag: mouse line

tag: age


title: ZIL01077 visit 6

description: Gene expression data from nasal brushing of ZIL01077 at visit 6.

tag: included in analysis

value: Aspirin+Zileuton

value: UAZ Phoenix


title: ZIL01092 visit 2

description: Gene expression data from nasal brushing of ZIL01092 at visit 2.

value: visit 2

tag: treatment


title: IHD_10

description: 2x100 paired-end sequence reads

tag: disease state

value: STEMI

tag: tissue


title: ZIL01077 visit 2

description: Gene expression data from nasal brushing of ZIL01077 at visit 2.

tag: site

tag: Sex

tag: smoking status


title: ZIL01074 visit 5

description: Gene expression data from nasal brushing of ZIL01074 at visit 5.

tag: patient

tag: visit


title: Health_A

description: 2x100 paired-end sequence reads

tag: gender


title: ZIL01077 visit 5

description: Gene expression data from nasal brushing of ZIL01077 at visit 5.

tag: pack years

tag: urinary cotinine

tag: rin


title: ZIL01074 visit 6

description: Gene expression data from nasal brushing of ZIL01074 at visit 6.

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: rep3_200N_Col-0

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia sinica

description: gene expression of 14d seedlings grown in 200 mM NaCl plates

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis V4 4*44K Microarray (Agilent Technologies,  USA) at 65°C for 17 h.

scan_protocol: The microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3. The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

data_processing: The CEL files were analyzed using GeneSpring (version 14.9.1, Agilent technology). The raw signal values employed a cutoff if the values in all samples were <100. Following the cutoff, Quantile normalization and baseline transformation to median of all samples were performed. The normalized genes were then statistically analyzed using two-way ANOVA and the p values were computing with multiple testing corrections of Benjamini-Hochberg False Discovery Rate (p value cutoff of 0.05). Three biological replicates were performed in this experiment. Gene expression passed 2-way ANOVA (p<0.05) were applied to fold change (FC) comparison.

organism: Arabidopsis thaliana

source_name: 14d seedlings, Col-0, 200 mM NaCl plate, replicate 3

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye,  Agilent Technologies, USA) during the in vitro transcription process. 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes.

growth_protocol: all seeds were sterilized and subjected to cold pretreatment at 4℃ for 3 days in dark before sowing in MS plates, which contains the following compositions: half strength of MS (Murashige and Skoog 1962), B5 organic compound (Gamborg et al. 1968), 1% sucrose, 0.05% MES [2-(N-morpholino)ethanesulfonic acid monohydrate]. After adjusting the pH to 5.7, 7 g/L phytoagar (Duchefa Biochemie) was added. The plants were grown under 16h/8h day/night photoperiod with a light intensity of approximately 50 µmol m-2s-1. 14-day-old seedlings were harvested in liquid N2.

extract_protocol: RNA was prepared using the Qiagen RNeasy Plant Mini Kit (Qiagen, Hilden, DE) following the manufacturer's recommendations. This protocol includes an on-column DNase digestion using the RNAse-Free DNase Set (Qiagen, Hilden, DE) to digest contaminating DNA in RNA solutionsd. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 0N: seeds were sow in MS plates containing no NaCl. 200N: seeds were sow in MS plates containing 200 mM NaCl.

value: whole seedling


title: rep3_0N_iU1-52

description: gene expression of 14d seedlings grown in MS plates

source_name: 14d seedlings, iU1-52, MS plate, replicate 3


title: rep3_200N_iU1-52

source_name: 14d seedlings, iU1-52, 200 mM NaCl plate, replicate 3


title: ZIL01074 visit 2

description: Gene expression data from nasal brushing of ZIL01074 at visit 2.

tag: age

tag: pgem ng/ml


title: rep2_200N_iU1-52

source_name: 14d seedlings, iU1-52, 200 mM NaCl plate, replicate 2


title: rep3_0N_Col-0

source_name: 14d seedlings, Col-0, MS plate, replicate 3


title: IHD_9

description: 2x100 paired-end sequence reads


title: IHD_5

description: 2x100 paired-end sequence reads


title: ZIL01071 visit 5

description: Gene expression data from nasal brushing of ZIL01071 at visit 5.

tag: included in analysis

tag: treatment

value: male


title: IHD_8

description: 2x100 paired-end sequence reads

tag: disease state

tag: tissue


title: IHD_6

description: 2x100 paired-end sequence reads


title: IHD_4

description: 2x100 paired-end sequence reads


title: IHD_3

description: 2x100 paired-end sequence reads


title: IHD_7

description: 2x100 paired-end sequence reads


title: ZIL01071 visit 2

description: Gene expression data from nasal brushing of ZIL01071 at visit 2.

tag: site

tag: Sex


title: rep2_0N_iU1-52

source_name: 14d seedlings, iU1-52, MS plate, replicate 2


title: ZIL01071 visit 6

description: Gene expression data from nasal brushing of ZIL01071 at visit 6.

tag: patient

tag: smoking status


title: rep2_200N_Col-0

source_name: 14d seedlings, Col-0, 200 mM NaCl plate, replicate 2


title: rep2_0N_Col-0

source_name: 14d seedlings, Col-0, MS plate, replicate 2


title: IHD_1

description: 2x100 paired-end sequence reads

tag: gender


title: ZIL01070 visit 6

description: Gene expression data from nasal brushing of ZIL01070 at visit 6.

tag: visit

value: Placebo

tag: pack years


title: ZIL01070 visit 5

description: Gene expression data from nasal brushing of ZIL01070 at visit 5.

tag: urinary cotinine

tag: rin


title: IHD_2

description: 2x100 paired-end sequence reads

value: plasma exosomes


title: rep1_200N_Col-0

source_name: 14d seedlings, Col-0, 200 mM NaCl plate, replicate 1


title: rep1_200N_iU1-52

source_name: 14d seedlings, iU1-52, 200 mM NaCl plate, replicate 1


title: ZIL01117 visit 5

description: Gene expression data from nasal brushing of ZIL01117 at visit 5.

source_name: Brushing of nasal epithelium

tag: mean rin

tag: batch


title: ZIL01068 visit 5

description: Gene expression data from nasal brushing of ZIL01068 at visit 5.

tag: age

tag: lte4 pg/ml


title: ZIL01070 visit 2

description: Gene expression data from nasal brushing of ZIL01070 at visit 2.

tag: included in analysis

tag: pgem ng/ml


title: ZIL01063 visit 2

description: Gene expression data from nasal brushing of ZIL01063 at visit 2.

tag: treatment


title: ZIL01063 visit 6

description: Gene expression data from nasal brushing of ZIL01063 at visit 6.


title: rep1_0N_iU1-52

source_name: 14d seedlings, iU1-52, MS plate, replicate 1

tag: tissue


title: ZIL01063 visit 5

description: Gene expression data from nasal brushing of ZIL01063 at visit 5.

tag: site


title: ZIL01068 visit 2

description: Gene expression data from nasal brushing of ZIL01068 at visit 2.

tag: Sex


title: rep1_0N_Col-0

source_name: 14d seedlings, Col-0, MS plate, replicate 1


title: AM3, primordia at the In2–In3 stages, rep3

city: Shanghai

first: Yan-Jie

last: Zhang

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

description: Gene expression of panicle primordia in OsGATA6-AM line

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent rice Gene Expression（4*44K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C), using one color scan setting and profile AgilentHD_GX_1Color for 4x44K microarrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Oryza sativa

source_name: panilce primordia at the In2–In3 stages,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the LowInput Quick-Amp Labeling Kit，one-color(24×) (Agilent,5190-2305) according to the manufacturer's instructions, followed by RNeasy® Mini Kit (QIAGEN, 74106). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: All the plants grown in a paddy field in Shanghai (June–October), China.

extract_protocol: RNA was extracted by RNA QUEOUS KIT(Ambion-1912) following the manufacturer's instructions.

treatment_protocol: There is no treatment.

value: panicle primordia

tag: Stage

value: In2–In3 stages

tag: line


title: Bacteriota of colon biopsy from patient CH47

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 5 --p-trim-left-r 0 --p-trunc-len-f 227 --p-trunc-len-r 220 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 12
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 232 --p-trunc-len-r 211 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza
qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 12 --o-classification assigned_taxa.qza –verbose
Library strategy: amplicon sequencing

source_name: Biopsy

growth_protocol: Sample were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: condition

value: EGPA

value: M

tag: anca

tag: immunosuppression


title: Set-2_shTP53-RB1-Enz-2

city: Dallas

first: Tao

last: Wang

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

description: processed data file: Set-2_deseq2_vst_counts.csv

data_processing:
Bulk RNAseq:
Adapter trimming and quality trimming was performed with trimgalore (v0.5.0), and ribosomal RNA was removed using SortMeRNA (v4.1.0), using the original FASTQ files.
Trimmed and filtered reads were aligned to reference (GRCh37) with STAR (vSTAR2.6.1d). FeatureCounts (v1.6.4) was used for gene counts, biotype counts, and rRNA estimation.
Reads counts.csv files for genes and transcripts were generated by StringTie (v1.3.5), and RSeQC (v3.0.0) was used for generating RNA quality control metrics.
Reads counts from all samples were normalized using the R package DESeq2 1.26. The vst command in DESeq2 were also used to perform the variance stabilizing transformation.
scRNAseq:
10X scRNA-seq data was preprocessed using the Cellranger v5.0 software. All parameters were set to default.
Used the count command to process the 10x single-cell RNA-seq output into cells by gene expression count matrix
Used the aggr command to pool sequencing runs from 6 samples.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample; HDF5 Feature Barcode Matrix Format

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol:
For RNAseq samples: LNCaP/AR cells transduced with different CRISPR constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol. For scRNAseq samples: Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 900-1100 cells/μl. Cells were loaded between 10,000 and 17,000 cells/chip position using the Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1 barcoding chemistry).
For RNAseq samples: RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA. For scRNAseq samples: Single-cell gene expression libraries were generated according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols.
For RNAseq samples: RNA-Seq. For scRNAseq samples: Single-cell RNA-seq were performed by the 10x Genomic single cell 5’library platform.

treatment_protocol: For RNAseq samples: When treated with 10 µM enzalutamide and/or 5 µM filgotinib, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 6 days.

tag: cell line

value: LNCaP/AR

tag: cell type

value: prostate cancer cells

tag: genotype/variation

value: enzalutamide 10µM


title: Set-2_shTP53-RB1-Veh-3

source_name: LNCaP/AR_shTP53-RB1_Vehicle DMSO

value: Vehicle DMSO


title: Set-2_shTP53-RB1-Veh-1


title: Set-2_shTP53-RB1-Veh-2


title: Set-2_shTP53-RB1-Enz-3


title: ZIL01061 visit 5

description: Gene expression data from nasal brushing of ZIL01061 at visit 5.

value: TRUE

tag: patient

tag: visit

value: visit 5

value: female

tag: smoking status

value: current smoker

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: ZIL01061 visit 6

description: Gene expression data from nasal brushing of ZIL01061 at visit 6.

tag: included in analysis

value: visit 6

tag: treatment

tag: site

value: UAZ Phoenix

tag: Sex

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: ZIL01058 visit 2

description: Gene expression data from nasal brushing of ZIL01058 at visit 2.

value: visit 2


title: ZH11, primordia at the In2–In3 stages, rep2

description: Gene expression of panicle primordia in wild type ZH11

source_name: panilce primordia at the In2–In3 stages,replicate 2

tag: tissue

tag: Stage

tag: line

value: wild type ZH11


title: ZH11, primordia at the In2–In3 stages, rep1

source_name: panilce primordia at the In2–In3 stages,replicate 1


title: Bacteriota of colon biopsy from patient CH45

tag: condition

value: Unknown

tag: anca

tag: immunosuppression


title: Set-2_shNT-Veh-1

source_name: LNCaP/AR_shNT_Vehicle DMSO

tag: cell line

tag: cell type

tag: genotype/variation

value: shNT


title: AM3, primordia at the In2–In3 stages, rep2

value: panicle primordia

value: In2–In3 stages


title: ZIL01061 visit 2

description: Gene expression data from nasal brushing of ZIL01061 at visit 2.

tag: patient

tag: visit

value: Placebo

tag: smoking status

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: Bacteriota of colon biopsy from patient CH22

value: EGPA

tag: Sex

value: M


title: ZIL01058 visit 5

description: Gene expression data from nasal brushing of ZIL01058 at visit 5.

tag: included in analysis

tag: treatment

tag: site

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: AM3, primordia at the In2–In3 stages, rep1

tag: tissue

tag: Stage

tag: line


title: ZIL01055 visit 5

description: Gene expression data from nasal brushing of ZIL01055 at visit 5.

tag: patient

tag: visit

value: Aspirin+Zileuton

value: male


title: ZIL01055 visit 2

description: Gene expression data from nasal brushing of ZIL01055 at visit 2.

value: TRUE

tag: smoking status

tag: pack years


title: Bacteriota of colon biopsy from patient CH31

tag: condition

value: F

tag: anca

tag: immunosuppression


title: ZIL01055 visit 6

description: Gene expression data from nasal brushing of ZIL01055 at visit 6.

tag: Sex

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: Set-2_shTP53-RB1-Enz-1

tag: cell line

value: LNCaP/AR

tag: cell type

value: prostate cancer cells

tag: genotype/variation

tag: treatment

value: enzalutamide 10µM


title: ZIL01045 visit 6

description: Gene expression data from nasal brushing of ZIL01045 at visit 6.

tag: included in analysis

value: visit 6

tag: site

value: UAZ Phoenix

value: female

tag: age

value: current smoker

tag: lte4 pg/ml

tag: pgem ng/ml


title: Set-2_shNT-Veh-3

value: shNT

value: Vehicle DMSO


title: Bacteriota of stool from patient CH59

source_name: Stool

tag: condition

value: Healthy

value: Unknown


title: Bacteriota of colon biopsy from patient CH28

value: EGPA

tag: anca


title: Set-2_shNT-Enz-2


title: Bacteriota of colon biopsy from patient CH175

value: M

tag: immunosuppression


title: Set-2_shNT-Veh-2


title: Set-1_SOX2-OE-3

description: processed data file: Set-1_deseq2_vst_counts.csv

source_name: LNCaP/AR_SOX2-OE_Vehicle DMSO


title: Set-2_shNT-Enz-3


title: ZIL01045 visit 2

description: Gene expression data from nasal brushing of ZIL01045 at visit 2.

tag: patient

tag: visit

value: visit 2

value: Placebo

tag: Sex

tag: smoking status

tag: pack years


title: Set-1_SOX2-OE-2

tag: cell line


title: Bacteriota of stool from patient CH32


title: Bacteriota of stool from patient CH55


title: Bacteriota of stool from patient CH52


title: ZIL01042 visit 6

description: Gene expression data from nasal brushing of ZIL01042 at visit 6.

value: TRUE

value: male

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: Set-2_shNT-Enz-1

value: LNCaP/AR

tag: cell type

tag: genotype/variation

tag: treatment


title: Set-1_shTP53-RB1-SOX2-3

source_name: LNCaP/AR_shTP53-RB1-SOX2_Vehicle DMSO

value: prostate cancer cells


title: Bacteriota of stool from patient CH53


title: ZIL01045 visit 5

description: Gene expression data from nasal brushing of ZIL01045 at visit 5.

tag: included in analysis

value: visit 5

tag: site

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: Bacteriota of stool from patient CH24

tag: condition

tag: anca

tag: immunosuppression


title: ZIL01043 visit 6

description: Gene expression data from nasal brushing of ZIL01043 at visit 6.

tag: patient

tag: visit

value: visit 6

value: Aspirin+Zileuton

tag: Sex

tag: smoking status

tag: pack years


title: Set-1_SOX2-OE-1

tag: cell line


title: Bacteriota of stool from patient CH26


title: ZIL01043 visit 5

description: Gene expression data from nasal brushing of ZIL01043 at visit 5.

value: UAZ Phoenix

value: female

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch


title: ZIL01042 visit 2

description: Gene expression data from nasal brushing of ZIL01042 at visit 2.

tag: included in analysis

tag: treatment

tag: site

value: current smoker


title: Set-1_shTP53-RB1-2

tag: cell type

tag: genotype/variation

value: Vehicle DMSO


title: Set-1_shTP53-RB1-SOX2-2


title: Set-1_shTP53-RB1-1


title: Set-1_shTP53-RB1-SOX2-1


title: ZIL01042 visit 5

description: Gene expression data from nasal brushing of ZIL01042 at visit 5.

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: Set-1_shNT-3

value: shNT


title: ZIL01038 visit 6

description: Gene expression data from nasal brushing of ZIL01038 at visit 6.

tag: patient

tag: visit


title: Bacteriota of stool from patient P6

tag: condition

tag: Sex

value: F

tag: anca

tag: immunosuppression


title: Bacteriota of stool from patient P7

value: EGPA


title: Set-1_shTP53-RB1-3

tag: cell line


title: ZIL01035 visit 6

description: Gene expression data from nasal brushing of ZIL01035 at visit 6.

tag: smoking status

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin


title: ZIL01035 visit 2

description: Gene expression data from nasal brushing of ZIL01035 at visit 2.

tag: included in analysis

tag: treatment

tag: site

tag: batch


title: Set-1_shNT-1

tag: cell type

tag: genotype/variation


title: Bacteriota of stool from patient CH23

value: Healthy

value: Unknown


title: Set-1_shNT-2


title: Bacteriota of stool from patient CH11


title: Bacteriota of stool from patient P5


title: ZIL01038 visit 5

description: Gene expression data from nasal brushing of ZIL01038 at visit 5.

tag: patient

tag: visit

tag: age

tag: lte4 pg/ml

tag: pgem ng/ml


title: Bacteriota of stool from patient P4

tag: condition

tag: Sex

value: M

tag: anca

tag: immunosuppression


title: DRG primary neurons GW Rep1

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Library strategy: RiboTag-Seq
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: raw counts

source_name: DRG primary neurons

growth_protocol: Primary neurons were cultures from DRG of juvinile mice and plated onto poly-l -lysine coated coverslips with media (DMEM/F12, suppplemented with 10% FBS) changes every two days till DIV 5.

extract_protocol:
Treated primary neuronal  cells were processed to immunoprecipitate HA-tagged ribosomes, followed by RNA isolation using Pico pure RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: replicates were treated either vehicle or LXR agonist GW3965 for 24hrs.

tag: strain

tag: tissue

value: dorsal root ganglia (DRG)

value: Neuronal cells

tag: genotype

value: WT


title: Bacteriota of stool from patient CH9


title: DRG primary neurons Vehicle Rep1

tag: treatment

value: Vehicle


title: Bacteriota of stool from patient CH31


title: ZIL01035 visit 5

description: Gene expression data from nasal brushing of ZIL01035 at visit 5.

tag: included in analysis

value: TRUE

value: visit 5

tag: site

value: male

tag: smoking status

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin


title: ZIL01038 visit 2

description: Gene expression data from nasal brushing of ZIL01038 at visit 2.

tag: patient

tag: visit

value: visit 2

value: Aspirin+Zileuton

value: UAZ Phoenix

tag: age

tag: batch

tag: lte4 pg/ml


title: DRG primary neurons GW Rep2

tag: cell type


title: ZIL01029 visit 2

description: Gene expression data from nasal brushing of ZIL01029 at visit 2.

value: UAZ Tucson

tag: Sex

value: current smoker

tag: pgem ng/ml


title: ZIL01028 visit 2

description: Gene expression data from nasal brushing of ZIL01028 at visit 2.

value: female


title: Ribonav NC Rep2

source_name: DRG

extract_protocol:
DRG were removed and processed to immunoprecipitate HA-tagged ribosomes, followed by RNA isolation using Pico pure RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were fed normal chow or western diet for 11 weeks

tag: strain

tag: tissue

value: 19 weeks age

tag: genotype

value: control


title: Bacteriota of stool from patient P1

tag: condition

value: EGPA

tag: anca

tag: immunosuppression


title: ZIL01029 visit 6

description: Gene expression data from nasal brushing of ZIL01029 at visit 6.

tag: included in analysis

value: visit 6

tag: treatment

tag: site

tag: smoking status

tag: pack years

tag: urinary cotinine


title: ZIL01029 visit 5

description: Gene expression data from nasal brushing of ZIL01029 at visit 5.

tag: patient

tag: visit

tag: age

tag: rin

tag: mean rin

tag: batch


title: Bacteriota of stool from patient P3

tag: Sex

value: F


title: Ribonav NC Rep1

tag: strain

tag: tissue

value: dorsal root ganglia (DRG)

tag: genotype


title: DRG primary neurons Vehicle Rep2

tag: cell type

value: Neuronal cells

value: WT


title: ZIL01028 visit 5

description: Gene expression data from nasal brushing of ZIL01028 at visit 5.

tag: included in analysis

value: TRUE

tag: lte4 pg/ml

tag: pgem ng/ml


title: Bacteriota of stool from patient P2

tag: condition

tag: anca

tag: immunosuppression


title: ZIL01028 visit 6

description: Gene expression data from nasal brushing of ZIL01028 at visit 6.

tag: patient

tag: treatment

tag: site

tag: smoking status

tag: pack years

tag: urinary cotinine


title: BCC1

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: BCC1 (LY31120)

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina).
Raw sequencing data provided as fastq files were processed using the count function of the Cell Ranger pipeline (v. 5.0.1, 10x Genomics).
The count function allowed us to demultiplex reads to individual cells, to align the reads to the human GRCh38 reference (v. GRCh38-2020-A), and to generate filtered matrices of gene counts by cell barcodes.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data files consist of the 3 files generated by Cell Ranger v5.0.1, containing only detected cellular barcodes (filtered_feature_bc_matrix). The file "matrix.mtx.gz" is a sparse matrix containing number of UMIs per gene (in rows) per single cell (in columns). The file "barcodes.tsv.gz" contains the list of detected cellular barcodes (i.e. single cell identities) corresponding to the columns in "matrix.mtx.gz", and the file "features.tsv.gz" contains the genes corresponding to the rows in "matrix.mtx.gz".

molecule: polyA RNA

source_name: Mohs specimen residual debulking piece of skin

extract_protocol:
Fresh tumor tissue was minced and enzymatically digested to obtain a single cell suspension. Single living cells were then FACS sorted. The cells were resuspended to reach a target final concentration of approximately 1,000 cells/μl.  ScRNA-seq was performed using the Chromium Next GEM single cell 3' reagent kit v3.1 (10xGenomics) following the manufacturer's protocol with a target number of captured cells of 10,000.
Sequencing libraries were prepared after GEM generation and barcoding using the Chromium Next GEM single cell 3'reagent kit v3.1 (10xGenomics) the following manufacturer's protocol.

tag: tumor type

value: infiltrative basal cell carcinoma

tag: location

value: left ear

value: skin biopsy


title: Bacteriota of colon biopsy from patient CH34

tag: Sex

value: M


title: BCC2

description: BCC2 (LY160221)

value: (nod and) infiltrative basal cell carcinoma

value: forehead

tag: tissue


title: HHP92Y

first: Qiang

last: Ma

address: Datun Road, #15

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta (release 95) pre-mRNA genome and GRCh38 pre-mRNA genome by Cell Ranger count (v3.0.2).
Alignment results of macaque data and human data were separately aggragated by Cell Ranger aggr (v3.0.2).
Aggragated data of macaque and human were separately read into scanpy.
Genome_build: macaca mulatta release 95
Genome_build: GRCh38
Supplementary_files_format_and_content: The file MHP_year4_11_23_raw.h5ad and HHP_year69_92_raw.h5ad are both formatted by h5ad (created by scanpy), contain the 3 macaque samples and 2 human samples, respectively.

source_name: human hippocampus

extract_protocol:
hippocampal formation samples were homogenized in nuclei lysis buffer, isolated nuclei were loaded on 10X Genomics system.
Chromium Single Cell 3' Reagent Kits v3

tag: age

value: 92 years old

value: hippocampus


title: Ribonav HFD Rep2

tag: strain

value: 19 weeks age

tag: genotype

value: high-fat diet (HFD)


title: ZIL01017 visit 6

description: Gene expression data from nasal brushing of ZIL01017 at visit 6.

tag: included in analysis

tag: visit

value: Placebo

value: UAZ Tucson

value: male

value: current smoker

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml

tag: pgem ng/ml


title: HHP67Y

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta (release 95) pre-mRNA genome and GRCh38 pre-mRNA genome by Cell Ranger count (v3.0.2).
Alignment results of macaque data and human data were separately aggragated by Cell Ranger aggr (v3.0.2).
Aggragated data of macaque and human were separately read into scanpy.
Genome_build: macaca mulatta release 95
Genome_build: GRCh38
Supplementary_files_format_and_content: The file MHP_year4_11_23_raw.h5ad and HHP_year6_92_raw.h5ad are both formatted by h5ad (created by scanpy), contain the 3 macaque samples and 2 human samples, respectively.

value: 67 years old


title: Ribonav HFD Rep1

value: dorsal root ganglia (DRG)

value: WT

tag: treatment


title: Bacteriota of stool from patient CH61

tag: condition

value: EGPA

value: F

tag: anca

tag: immunosuppression


title: ZIL01014 visit 6

description: Gene expression data from nasal brushing of ZIL01014 at visit 6.

value: TRUE

tag: patient

value: visit 6

tag: site

tag: smoking status

tag: pack years

tag: urinary cotinine


title: ZIL01014 visit 2

description: Gene expression data from nasal brushing of ZIL01014 at visit 2.

value: visit 2

tag: Sex

tag: age


title: Bacteriota of stool from patient CH43


title: Bacteriota of stool from patient CH47

value: M


title: ZIL01022 visit 5

description: Gene expression data from nasal brushing of ZIL01022 at visit 5.

tag: included in analysis

tag: visit

value: visit 5


title: Bacteriota of stool from patient CH41


title: 11008_C1D1 peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: peripheral CD3+ T-cells

data_processing:
Illumina Casava-1.8.2 software used for basecalling
Genome_build: hg19
Supplementary_files_format_and_content: Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark. CpG-context methylation call output files are in txt format and filtered for at least 10 covered cytosines per site.

source_name: DLBCL

extract_protocol: enhanced reduced representation bisulfite sequencing method (eRRBs) was followed as reported in Garrett-Bakelman et al 2015 10.3791/52246

tag: sample type

value: peripheral CD3+ T-cells, post CC486 treatment (C1D1)


title: ZIL01017 visit 5

description: Gene expression data from nasal brushing of ZIL01017 at visit 5.

source_name: Brushing of nasal epithelium

tag: rin

tag: mean rin

tag: batch


title: 11008_C1D-6 peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)

description: peripheral CD3+ T-cells

value: peripheral CD3+ T-cells, pre CC486 treatment (C1D-6)


title: ZIL01022 visit 6

description: Gene expression data from nasal brushing of ZIL01022 at visit 6.

tag: treatment

tag: lte4 pg/ml

tag: pgem ng/ml


title: ZIL01020 visit 5

description: Gene expression data from nasal brushing of ZIL01020 at visit 5.

value: Aspirin+Zileuton

value: female


title: Bacteriota of stool from patient CH34

tag: condition

tag: anca

tag: immunosuppression


title: Bacteriota of stool from patient CH39


title: Bacteriota of stool from patient CH20


title: ZIL01022 visit 2

description: Gene expression data from nasal brushing of ZIL01022 at visit 2.

tag: patient

value: Placebo

tag: site

value: UAZ Tucson

tag: smoking status


title: Bacteriota of stool from patient CH180

tag: Sex


title: Bacteriota of stool from patient CH27


title: Bacteriota of stool from patient CH18


title: Bacteriota of stool from patient CH15


title: Bacteriota of stool from patient CH10


title: 31018_C1D1 DLBCL tissue RNA-Seq

description: DLBCL tissue

data_processing:
Illumina Casava-1.8.2 software used for basecalling
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited csv file includes Salmon TPM values for genes for RNA-sequenced samples

extract_protocol: qiagen extraction and TruSeq RNA sample prep kit.

value: DLBCL tissue, post CC486 treatment (C1D1)


title: ZH11, primordia at the In2–In3 stages, rep3

description: Gene expression of panicle primordia in wild type ZH11

tag: tissue

value: panicle primordia

tag: Stage

value: In2–In3 stages

tag: line

value: wild type ZH11


title: ZIL01017 visit 2

description: Gene expression data from nasal brushing of ZIL01017 at visit 2.

tag: included in analysis

tag: visit

value: male

tag: age

value: current smoker

tag: pack years

tag: urinary cotinine


title: Bacteriota of stool from patient CH37

value: EGPA

value: F


title: ZIL01014 visit 5

description: Gene expression data from nasal brushing of ZIL01014 at visit 5.

value: TRUE

tag: treatment

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: ZIL01011 visit 6

description: Gene expression data from nasal brushing of ZIL01011 at visit 6.

tag: patient

value: visit 6

tag: pgem ng/ml


title: Bacteriota of stool from patient CH25

tag: condition

value: M

tag: anca

tag: immunosuppression


title: 31018_C1D-6 DLBCL tissue RNA-Seq

description: DLBCL tissue

tag: sample type

value: DLBCL tissue, pre CC486 treatment (C1D-6)


title: Bacteriota of stool from patient CH28

tag: Sex


title: Bacteriota of stool from patient CH1


title: ZIL01013 visit 5

description: Gene expression data from nasal brushing of ZIL01013 at visit 5.

tag: included in analysis

value: visit 5

tag: site

tag: smoking status


title: ZIL01013 visit 6

description: Gene expression data from nasal brushing of ZIL01013 at visit 6.

tag: visit

tag: age

tag: pack years


title: 31018_C1D-6 DLBCL tissue Bisulfite-Seq (reduced representation)

description: DLBCL tissue


title: 31016_C1D1 DLBCL tissue  Bisulfite-Seq (reduced representation)

description: DLBCL tissue

value: DLBCL tissue, post CC-486 treatment (C1D1)


title: Bacteriota of stool from patient CH22


title: ZIL01013 visit 2

description: Gene expression data from nasal brushing of ZIL01013 at visit 2.

value: visit 2

tag: treatment

value: female

tag: urinary cotinine

tag: rin


title: ZIL01058 visit 6

description: Gene expression data from nasal brushing of ZIL01058 at visit 6.

value: Placebo

value: UAZ Phoenix

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: Bacteriota of stool from patient CH175

tag: condition


title: 31016_C1D-6 DLBCL tissue  RNA-Seq

description: DLBCL tissue

value: DLBCL tissue, pre CC-486 treatment (C1D-6)


title: ZIL01011 visit 5

description: Gene expression data from nasal brushing of ZIL01011 at visit 5.

tag: patient

value: Aspirin+Zileuton

value: UAZ Tucson

tag: pgem ng/ml


title: 31016_C1D1 DLBCL tissue RNA-Seq

description: DLBCL tissue

tag: sample type

value: DLBCL tissue, post CC486 treatment (C1D1)


title: Bacteriota of stool from patient CH14

tag: Sex

tag: anca

tag: immunosuppression


title: ZIL01009 visit 6

description: Gene expression data from nasal brushing of ZIL01009 at visit 6.

tag: included in analysis

tag: site

value: male

tag: smoking status

value: current smoker

value: creatinine:BLQ (< 5 ng/nL)


title: 31008_C1D1 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)

value: DLBCL tissue and peripheral CD3+ T-cells, post CC-486 treatment (C1D1)


title: 31016_C1D-6 DLBCL tissue  Bisulfite-Seq (reduced representation)

description: DLBCL tissue


title: ZIL01011 visit 2

description: Gene expression data from nasal brushing of ZIL01011 at visit 2.

value: TRUE

tag: visit

tag: age

tag: pack years


title: ZIL01009 visit 5

description: Gene expression data from nasal brushing of ZIL01009 at visit 5.

tag: treatment

tag: urinary cotinine

tag: rin


title: 31008_C1D-6 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)

value: DLBCL tissue and peripheral CD3+ T-cells, pre CC-486 treatment (C1D-6)


title: 31008_C1D-6 DLBCL tissue RNA-Seq

description: DLBCL tissue


title: Bacteriota of stool from patient CH12

value: EGPA

value: M


title: 31005_C1D1 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)


title: 31005_C1D-6 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)


title: 31005_C1D1 DLBCL tissue RNA-Seq

description: DLBCL tissue

value: DLBCL tissue, post CC-486 treatment (C1D1)


title: WT3

first: Dulari

last: Jayawardena

state: Illinois

address: 820 S Damen Avenue, Rm 7221

institute: University of Illinois at Chicago

description: Distal Colonic RNA

hyb_protocol: none provided by the submitter

scan_protocol: none provided by the submitter

data_processing: none provided by the submitter

label: Nanostring

source_name: distal colonic mucosa

label_protocol: none provided by the submitter

extract_protocol: none provided by the submitter

treatment_protocol: Wild type and DRA KO  mice distal colonic mucosal was scaraped and RNA was harvested using Trizol reagent at 6-8 weeks of age

tag: tissue

value: colon


title: DRA KO3

description: Distal Colonic RNA


title: ZIL01008 visit 6

description: Gene expression data from nasal brushing of ZIL01008 at visit 6.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray hugene10sthsentrezgcdf R package (version 23.0.0).

extract_protocol: RNA was extracted using the QIAGEN miRNeasy Mini Kit according to the manufacturer's protocol.

value: visit 6

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: ZIL01009 visit 2

description: Gene expression data from nasal brushing of ZIL01009 at visit 2.

tag: patient

value: visit 2

value: Placebo

tag: pgem ng/ml


title: 31003_C1D1 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)

tag: sample type


title: ZIL01005 visit 5

description: Gene expression data from nasal brushing of ZIL01005 at visit 5.

value: visit 5

tag: Sex


title: ZIL01005 visit 6

description: Gene expression data from nasal brushing of ZIL01005 at visit 6.

tag: included in analysis


title: ZIL01001 visit 6

description: Gene expression data from nasal brushing of ZIL01001 at visit 6.

tag: site


title: 31003_C1D1 DLBCL tissue RNA-Seq

description: DLBCL tissue


title: WT2

description: Distal Colonic RNA


title: ZIL01005 visit 2

description: Gene expression data from nasal brushing of ZIL01005 at visit 2.

tag: smoking status


title: ZIL01008 visit 5

description: Gene expression data from nasal brushing of ZIL01008 at visit 5.

tag: visit

value: Aspirin+Zileuton


title: ZIL01001 visit 5

description: Gene expression data from nasal brushing of ZIL01001 at visit 5.

value: UAZ Tucson

tag: age


title: DRA KO2

description: Distal Colonic RNA


title: DRA KO1

description: Distal Colonic RNA


title: 31003_C1D-6 DLBCL tissue RNA-Seq

description: DLBCL tissue and peripheral CD3+ T-cells

data_processing:
Illumina Casava-1.8.2 software used for basecalling
Genome_build: hg19
Supplementary_files_format_and_content: Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark. CpG-context methylation call output files are in txt format and filtered for at least 10 covered cytosines per site. Tab-delimited csv file includes Salmon TPM values for genes for RNA-sequenced samples

value: DLBCL tissue, pre CC-486 treatment (C1D-6)


title: 31003_C1D-6 DLBCL tissue and peripheral CD3+ T-cells Bisulfite-Seq (reduced representation)


title: WT1

description: Distal Colonic RNA


title: 12hr Stiff Rd3 [DS3B220_S20]

city: Berkeley

first: Paola

middle: A

last: Lopez

address: Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

data_processing:
The reads were initially trimmed using BBDuk to remove Illumina adapters and to filter low quality reads.
The samples were then aligned to ratRibosomal genes using bbmap to remove ribosomal contaminated RNA. Any samples less than 21 bases were removed using BBduk.
Read quality analysis was performed using FastQC to assure there was a Phred score > 28.
The reads were aligned to the rattus norvegicus genome (rn6) using hisat2 v2.1.0.
the aligned reads were converted to counts using htseq.

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Phenol-free total RNA was extracted from the cell pellets using RNeasy Plus Micro Kit with gDNA eliminator columns (Quiagen) following the manufacturer’s protocol.
RNA-seq library preparation was carried out by the DNA Technologies and Expression Analysis Core at the University of California, Davis Genome Center using QuantSeq FWD

value: hippocampus

value: female

tag: developmental stage

value: adult

tag: cell type

value: neural stem cell

tag: genotype

value: WT

tag: time

value: mixed differentiation medium (DMEM-F12 with N2 supplemented with 1 uM of retinoic acid and 1% FBS)


title: 36hr Stiff Rd3 [DS3B424_S24]

tag: tissue

tag: treatment


title: H1650 2D exosomes-2R

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background and batch corrected using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) implemented in the Transcriptome Analysis Console software version 4.0 (TAC 4.0).

source_name: Exosomes from H1650 cell line grown in adherence conditions (2D) replicate 2

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 13 ngs total RNA (GeneChip Whole Transcript WT Expression Arrays, Affymetrix).

growth_protocol: Primary culture cells were maintained in Dulbecco's Modified Eagle Medium/F12™ supplemented with 1% L-glutamine (Gibco-BRL Life Technologies), 10% fetal bovine serum (Gibco-BRL Life Technologies) and 1% penicillin/streptomycin (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cell lines were maintained in RPMI-1640 medium supplemented with MEM Non-Essential Amino Acids (0.001%) (Gibco-BRL Life Technologies), 10% fetal bovine serum (Gibco-BRL Life Technologies) and 1% penicillin/streptomycin (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.
Exosomes were isolated using ultracentrifugation from cell cultures supernatant and the samples were characterized in size, morphology and specific surface markers determination.
Total RNA was extracted from exosomes using Total RNA Purification Kit (Norgen Biotek, Canada) according to the manufacturer's instructions.

tag: cell line

value: Lung cancer cell line

tag: histology

value: LUAD (lung adenocarcinoma)


title: 24hr Stiff Rd3 [DS3B322_S22]


title: 12hr Soft Rd3 [DS3A219_S19]


title: ZIL01001 visit 2

first: Adam

last: Gower

description: Gene expression data from nasal brushing of ZIL01001 at visit 2.

value: TRUE

tag: patient

value: male

value: current smoker

tag: pack years

tag: urinary cotinine

tag: rin

tag: mean rin

tag: batch

tag: lte4 pg/ml


title: 24hr Soft Rd3 [DS3A321_S21]

tag: Sex


title: 0hr Stiff Rd3 [DS3B118_S18]


title: 36hr Soft Rd3 [DS3A423_S23]


title: 36hr Stiff Rd2 [DS2B416_S16]


title: 24hr Stiff Rd2 [DS2B314_S14]


title: 0hr Soft Rd3 [DS3A117_S17]


title: 12hr Stiff Rd2 [DS2B212_S12]


title: H1650 3D exosomes-2R

source_name: Exosomes from H1650 cell line grown in tumorspheres formation (3D) replicate 2


title: H1650 2D exosomes-1R

source_name: Exosomes from H1650 cell line grown in adherence conditions (2D) replicate 1


title: 0hr Stiff Rd2 [DS2B110_S10]


title: ZIL01008 visit 2

description: Gene expression data from nasal brushing of ZIL01008 at visit 2.

tag: included in analysis

tag: visit

value: visit 2

tag: site

tag: age

tag: smoking status

tag: pgem ng/ml


title: 24hr Soft Rd2 [DS2A313_S13]

tag: tissue

tag: developmental stage

tag: cell type

tag: genotype

tag: time

tag: treatment


title: U87MG, radioresistant, bio_rep3, tech_rep3

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: U87MG GBM 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 harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: U87MG cells were subcutaneously or orthotopically implanted in BALB/c nude mice and repeatedly exposed to IR. We then obtained the radioresistant U87MG cells that survived IR (2 Gy each, 30 Gy in total).

tag: cell line

value: Glioblastoma cell

value: Luciferase expressing

value: Irradiated (total 30 Gy)


title: U87MG, radioresistant, bio_rep3, tech_rep2


title: 0hr Soft Rd2 [DS2A19_S9]


title: H1975 2D exosomes-2R

source_name: Exosomes from H1975 cell line grown in adherence conditions (2D) replicate 2

tag: histology


title: FIS 343 2D exosomes-2R

source_name: Exosomes from FIS 343 primary culture grown in adherence conditions (2D) replicate 2

value: FIS 343


title: H2228 3D exosomes-2R

source_name: Exosomes from H2228 cell line grown in tumorspheres formation (3D) replicate 2


title: FIS 343 3D exosomes-2R

source_name: Exosomes from FIS 343 primary culture grown in tumorspheres formation (3D) replicate 2


title: H2228 2D exosomes-1R

source_name: Exosomes from H2228 cell line grown in adherence conditions (2D) replicate 1


title: H1650 3D exosomes-1R

source_name: Exosomes from H1650 cell line grown in tumorspheres formation (3D) replicate 1


title: FIS 343 2D exosomes-1R

source_name: Exosomes from FIS 343 primary culture grown in adherence conditions (2D) replicate 1


title: 36hr Stiff Rd1 [DS1B48_S8]


title: H1975 2D exosomes-1R

source_name: Exosomes from H1975 cell line grown in adherence conditions (2D) replicate 1


title: 36hr Soft Rd2 [DS2A415_S15]


title: U87MG, radioresistant, bio_rep3, tech_rep1


title: 12hr Stiff Rd1 [DS1B24_S4]


title: U87MG, radioresistant, bio_rep2, tech_rep3


title: U87MG, radioresistant, bio_rep2, tech_rep2


title: H1975 3D exosomes-2R

source_name: Exosomes from H1975 cell line grown in tumorspheres formation (3D) replicate 2


title: SAMPLE1-CD4-TCR

first: Liang

last: Chen

address: 99 ShangDa Road

institute: Shanghai University

description: 10x Genomics

data_processing:
Cellranger VDJ (v 3.0.2)
vdjtools
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: VDJ-seq

source_name: peripheral blood

extract_protocol:
T cells obtained from PBMCs stimulated by DCs  for 30 d were sorted by FACS. CD3+CD4+ T cells were collected, and 1×106/ml T cells were used in further 10x Genomics Chromium™ Single Cell V(D)J immune repertoire profiling performed and analysed by Novogene.
Gel beads containing barcode information are mixed withsamples and enzymes and then combined with oil surfactants to form GEMs. The barcode sequence of the library built by V(D)J was connected to the switch oligo TSO sequence. The reverse transcription of mRNAs was reverse transcribed to the 5′ end by poly(T) primers, and CCC was added at the end to capture the cDNA. Transcription continued to add the barcode sequence to the 5′ end cDNA sequence. Nested PCR was performed using the universal primer of the 5′ adaptor and the continuous nested primers of the TCR constant region. This process was combined with the sequencing adaptor P5 to achieve the enrichment of the V(D)J region of the TCR. The enzymatic digestion method randomly interrupts the V(D)J cDNA. By controlling the interrupted sequences of different lengths, the entire V(D)J fragment cDNA sequence was covered, and the sequencing adapter P7 was added to perform PCR amplification. The main analysis content of single cell V(D)J included using Trimmomatic to trim the original data to obtain clean data and then using fastqc to evaluate the data quality of rawdata and cleandata. Then, TCR clone subtype analysis was performed by Novogene using the Cell Ranger software provided by 10x Genomics to perform each step of screening, contig stitching, and cloning type analysis and abundance analysis of samples, and VDJtools software was used to characterize V/J paired genes and CDR3 regions.

value: T cells

value: peripheral blood

value: uncollected


title: U87MG, radioresistant, bio_rep2, tech_rep1


title: 24hr Stiff Rd1 [DS1B36_S6]

value: hippocampus

value: female

value: adult


title: 0hr Stiff Rd1 [DS1B12_S2]

value: neural stem cell

value: WT

value: mixed differentiation medium (DMEM-F12 with N2 supplemented with 1 uM of retinoic acid and 1% FBS)


title: U87MG, radioresistant, bio_rep1, tech_rep3


title: H2228 2D exosomes-2R

source_name: Exosomes from H2228 cell line grown in adherence conditions (2D) replicate 2

value: Lung cancer cell line

value: LUAD (lung adenocarcinoma)


title: FIS 301 2D exosomes-2R

source_name: Exosomes from FIS 301 primary culture grown in adherence conditions (2D) replicate 2

value: FIS 301

value: LUSC (lung squamous cell carcinoma)


title: FIS 301 3D exosomes-2R

source_name: Exosomes from FIS 301 primary culture grown in tumorspheres formation (3D) replicate 2


title: H1975 3D exosomes-1R

source_name: Exosomes from H1975 cell line grown in tumorspheres formation (3D) replicate 1


title: SW900 2D exosomes-2R

source_name: Exosomes from SW900 cell line grown in adherence conditions (2D) replicate 2


title: 36hr Soft Rd1 [DS1A47_S7]

source_name: hippocampus


title: U87MG, radioresistant, bio_rep1, tech_rep1

value: Glioblastoma cell


title: FIS 301 3D exosomes-1R

source_name: Exosomes from FIS 301 primary culture grown in tumorspheres formation (3D) replicate 1


title: FIS 301 2D exosomes-1R

source_name: Exosomes from FIS 301 primary culture grown in adherence conditions (2D) replicate 1


title: U87MG, radioresistant, bio_rep1, tech_rep2

value: Luciferase expressing


title: 31018_C1D1 DLBCL tissue Bisulfite-Seq (reduced representation)

description: DLBCL tissue

source_name: DLBCL

tag: sample type

value: DLBCL tissue, post CC486 treatment (C1D1)


title: 24hr Soft Rd1 [DS1A35_S5]


title: U87MG, control, bio_rep3, tech_rep3

value: Non-irradiated


title: U87MG, control, bio_rep3, tech_rep2


title: U87MG, control, bio_rep3, tech_rep1