title: colorectal cancer_IIA [HH Vb 023_257015613537_2_1]

description: miRNA expression


title: colorectal cancer_IV [HH Vb 053_257015613538_2_4]

status: Public on Jul 17 2021

type: RNA

city: Heidelberg

first: Andrea

middle: S

last: Bauer

address: Im Neuenheimer Feld 580

department: Functional Genome Analysis

country: Germany

institute: DKFZ

description: miRNA expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The *qnorm.txt.geo.GPL21576.txt files contain normalized signal intensity.

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer_IV_whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA including miRNA was isolated using the miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer´s instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: class

value: colorectal cancer

tag: uicc stage

value: IV

tag: tissue

value: whole blood


title: GD 70_Low_5001_Female

type: SRA

city: College Station

first: Michael

middle: Carey

last: Satterfield

state: TX

address: 2471 TAMUS

department: Animal Science

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Libraries were multiplexed and sequenced from both directions as 75 base pair paired-end reads on one lane on a NextSeq500 instrument
Raw sequences (FASTQ) were subjected to quality check by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The program fqtrim (https://ccb.jhu.edu/software/fqtrim/) was used to remove adapters, perform quality trimming (phred score >30) by a sliding window scan (6 nucleotides) and select read length of 30 nucleotides or longer after trimming.
The reads obtained from the quality control step were mapped to the sheep reference genome (Oar_v3.1) by using Hisat2 aligner. The program FeatureCounts was used to quantify read counts by using the sequences alignment files of each sample.
Genes with evidence of expression (counts per million; rowSum >5) were used for model-based differential expression analysis using the edgeR robust method.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: CSV file with genes by row and samples by column, raw counts
Supplementary_files_format_and_content: Matrix file with normalized CPM from edgeR for all samples

organism: Ovis aries

source_name: Placentome

extract_protocol:
Total RNA was extracted using Trizol reagent, treated with DNAse I, and purified using an RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control animals were fed 100% of their NRC nutritional requirements from Day 35 to Day 135 of pregnancy. Nutrient restricted animals were fed 50% of their NRC nutritional requirements for the same time period.

tag: treatment

value: Low

tag: day

tag: Sex

value: Female


title: colorectal cancer_III [HH Vb 057_257015613539_1_2]

description: miRNA expression

source_name: colorectal cancer_III_whole blood

value: III


title: GD 70_High_5210_Male

value: High

value: Male


title: colorectal cancer_IV [HH Vb 020_257015613537_1_4]

description: miRNA expression


title: GD 70_Low_5008_Female


title: GD 70_Low_5024_Male


title: colorectal cancer_IIA [HH Vb 012_257015613537_1_3]

description: miRNA expression

source_name: colorectal cancer_IIA_whole blood

value: IIA


title: GD 70_Low_5079_Male


title: Uncut caudal fin_scRNA

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene-barcodes matrices.
cellranger aggr v3.1.0 was used to combine the results of the two samples.
Genome_build: danRer11
Supplementary_files_format_and_content: MEX file format : the matrix.mtx file contains the filtered gene-barcode matrix (total UMI count per cell and gene combination) ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file.
In the file Aggregation_barcodes.tsv, barcodes appended with '-1' represent the sample 'Cut' and barcodes appended with '-2' represent the sample 'UnCut'.

organism: Danio rerio

source_name: caudal fin

extract_protocol:
Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine (MS222, Sigma) in zebrafish water. Approximately, 150 of regenerating caudal fin (cut) and intact caudal fin (uncut) samples were collected at 24 hours post amputation (hpA) and dissociated into a single-cell suspension. The concentration of freshly dissociated cells was adjusted to 700-800 cells/μl in PBS aiming to capture 4,000 cells by the 10X genomics device.
Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.

value: caudal fin

tag: developmental stage

value: larvae

value: uncut

tag: time

value: 24 hours post amputation


title: GD 70_Low_5041_Male


title: GD 70_Low_5137_Male


title: Cut caudal fin_scRNA

value: cut

value: 24 hours


title: DA and FL, E10.5

city: Kumamoto

first: Saori

last: Morino-Koga

state: Kumamoto

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

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

data_processing:
The cDNA libraries were sequenced by an Illumina HiSeqX.
The fastq files were aligned, filtered, and counted by the cellranger count (v5.0.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files and comma-separated value files

organism: Mus musculus

source_name: dorsal aorta, fetal liver

extract_protocol:
Tissues were dissociated using 1 mg/ml collagenase/dispase and then 0.25% trypsin-EDTA. Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
Library construction was performed by using 10X Chromium Single Cell 3' v3.1 kit.

tag: strain

tag: age

value: dorsal aorta, fetal liver


title: GD 70_High_5247_Female


title: DA and FL, E11.5


title: PC3 tw 4

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

data_processing:
Data were demultiplexed using Illumina's CASAVA 1.8.2 software
reads were aligned to the human genome using STAR: ultrafast universal RNA-seq aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx; differential gene expression

source_name: Prostate cancer cell line

growth_protocol: PC3 cells were cultured in DMEM with 10% FBS and ARCaP(M) cells were cultured in RPMI-1640 medium with 5% FBS. All media were supplemented with 25mM HEPES, and 100U/ml penicillin-streptomycin.

extract_protocol:
Tumor cells were trypsinized and collected into RLT Plus buffer.  RNA was extracted following the protocol in the RNeasy Plus Mini Kit
Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina) was utilized for building RNAseq libraries.  The barcoded libraries were multiplexed at equimolar concentrations and sequenced with 50 bp single reads on an Illumina HiSeq-2500 run in rapid mode.
The run was a standard load which means the libraries were flooded across both lanes.  There is L001 and L002 counts for the samples.

treatment_protocol: The mBMSC cells were embedded in Collagen I, plated in 6-well plates and differentiated into adipocytes according to our previously published protocols.  Briefly, collagen-embedded mBMSCs were grown to confluency for 48-72 hours and treated with adipogenic cocktail for 8-10 days. After mature adipocyte cultures were established (with minimum of 70% BMSCs differentiated into fat cells), tumor cells were seeded on top of a Transwell filter (0.2µm pore size) to allow sharing of soluble factors between the two cell types. After 48- to 72-hour co-culture, cells were washed with PBS and collected for RNA and protein analyses.

tag: cell type

value: prostate cancer metastatic cell line

value: bone

tag: cell line

value: Transwell Co-culture s with bone marrow adipocytes


title: PC3 tw 3


title: PC3 4

value: untreated


title: PC3 3


title: PC3 2


title: healthy [HH Vb 007_257015613537_1_1]

description: miRNA expression

source_name: healthy_whole blood

value: healthy

value: whole blood


title: PC3 tw 2


title: colorectal cancer_IIA [HH Vb 011_257015613537_1_2]

description: miRNA expression

value: colorectal cancer


title: GD 70_Low_5057_Male

value: Low


title: PC3 tw 1


title: PC3 1


title: ARCaP tw 3

value: ascites

value: ARCaP


title: ARCaP tw 4


title: ARCaP tw 2


title: ARCaP tw 1


title: TAM24_Sol_Exercised

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

description: Exercised SC- soleus 24hrs post 10X snRNA-seq

data_processing:
Sequenced reads were converted to fastq format after demultiplexed using the “cellranger mkfastq” function and aligned to the reference mouse genome using Cell Ranger (v4.0.0) developed and maintained by 10X Genomics.
The reference genome for the mouse was downloaded from Ensembl (GRCm38.p6, release 101, RefSeq accession GCA_000001635.8), which included the matching set of genome sequence (FASTA) and gene annotations (GTF). A custom transcriptome reference was created by appending the sequences and annotations of the transgenes of interest to the downloaded FASTA and GTF files, respectively. The sequence for rtTA (Tet-On 3G) was obtained from Cloning vector pDXTR (GenBank MN044710.1). The sequences for H2B-GFP, CreER(TM), and DTA were obtained from plasmid sequences for pBABE-H2BGFP (Addgene plasmid # 26790, 15028, 22677), respectively. In order to accommodate the high levels of unspliced transcripts in the nucleus, a “pre-mRNA” transcriptome reference was created through a two-step process. First, the previously generated custom GTF file was modified by converting gene labels from “transcript” to “exon” and appending the “_premrna” tag to the original “transcript_id”. Then, the modified GTF was used with the previously generated custom FASTA file with the added transgenes to generate the “pre-mRNA” reference using the “cellranger mkref” function. Reads from the Cell Ranger FASTQ files were aligned to the custom “pre-mRNA: reference using the “cellranger count” function.
Spliced and unspliced RNA reads were extracted from the Cell Ranger alignment results using the velocyto command line python tool with inputs being the custom FASTA and GTF files that included the transgenes. The “.loom” output of from velocyto was analyzed using scvelo, scanpy, and anndata python packages.
Genome_build: Mouse GRCm38.p6, release 101, RefSeq accession GCA_000001635.8
Supplementary_files_format_and_content: The .loom files are generated using velocyto by providing input Cell Ranger alignment and barcode/count matrices and the transcriptome annotations to quantify spliced and unspliced transcript counts.

molecule: nuclear RNA

source_name: Soleus muscle

growth_protocol: Mice housed in a humidity- and temperature-controlled facility, maintained on a 14:10 hour light-dark cycle with food and water ad libitum. A 6-month-old H2B-GFP mouse was administered doxycycline (0.5 mg/mL) in drinking water supplemented with 2% sucrose for 3 weeks. Soleus and plantaris muscles were collected after an overnight fast upon completion of doxycycline treatment and prepared immediately for snRNA-seq. Four Pax7-DTA mice were randomly assigned with two treated with vehicle (sunflower seed oil) and two treated with tamoxifen through daily intraperotoneal injections for 5 consecutive days. Vehicle treated mice (SC+) retains full complement of of satellite cells whereas the tamoxifen treatment (SC-) depletes satellite cells in skeletal muscles.

extract_protocol:
Hindlimb muscles were harvested following euthanasia and nuclei were isolated using the biochemical protocol developed by (Cutler et al., 2017). Briefly, muscles were minced with scissors in homogenization buffer (500 µl HEPES (1 M) 3 ml KCl (1 M) 250 µl spermidine (100 mM) 750 µl spermine tetrahydrochloride (10 mM) 10 ml EDTA (10 mM) 250 µl EGTA (100 mM) 2.5 ml MgCl (100 mM) 5.13 g sucrose, Dounce homogenized on ice in homogenization buffer and passed through a 40 µm filter into sorting buffer. For the Pax7-DTA soleus muscle samples, DAPI was added to label nuclei. Fluorescently labeled nuclei (DAPI+ or GFP+) were purified via Fluorescence-activated cell sorting (FACS) and collected in reverse transcription (RT) buffer.
Nuclei were loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v3 according to the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NextSeq 500 System at the University of Florida.

treatment_protocol: The mice were maintained in the same housing and food conditions without a wheel for the sedentary H2B-GFP mouse and with a wheel for each of the Pax7-DTA mice. After one week of acclimation to an unweighted wheel, the wheel is magnetically weighted with 2 g in week 1, 3 g in week 2, 4 g in week 3, and 5 g in week 4 for a total of four weeks training.

tag: exercise

value: exercised 24hrs post last bout

value: Pax7CreER/+ ; R26R-DTA

value: tamoxifen (SC-)

value: Skeletal Muscle


title: TAM4_Sol_Exercised

description: Exercised SC- soleus 4hrs post 10X snRNA-seq

value: exercised 4hrs post last bout


title: ARCaP 4


title: ARCaP 3


title: WT-ES-1

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

country: China

institute: Tongji University

description: Gene Abundance

data_processing:
RNA-seq raw reads were processed by BBDuk(version 38.34) to removed adapters and trim low-quality reads.  Reads( >35bp) were aligned to the mouse genome (mm9)  using STAR(version 0.6.0).
Refseq genes were quantified to FPKM using Stringtie.
Deseq2 was used to perform differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: controlES

extract_protocol:
The RNA samples were subjected to mRNA fragmentation, cDNA synthesis, and library preparation using a KAPA Stranded mRNA-Seq Kit Illumina platform (KK8440; Kapa, Wilmington, USA), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

tag: genotype

value: Wild type


title: VEH4_Sol_Exercised

description: Exercised SC+ soleus 4hrs post 10X snRNA-seq

value: vehicle (SC+)


title: OE-ES-1

description: Gene Abundance

source_name: overexpressionES

value: Dcaf11 overexpression


title: ARCaP 1

value: prostate cancer metastatic cell line


title: ARCaP 2

value: untreated


title: H2B_Pla_Sol_Sedentary

description:
myonuclear RNA
Sedentary plantaris and soleus purified myonuclei 10X snRNA-seq

source_name: Plantaris and Soleus muscles

value: sedentary

value: HSA-rtTA ; TRE-H2B-GFP

value: doxycycline


title: OE-ES-2

description: Gene Abundance


title: VEH24_Sol_Exercised

description: Exercised SC+ soleus 24hrs post 10X snRNA-seq


title: WT-ES-2

description: Gene Abundance


title: Anther 4_day_long-term_mild_heat rep3

city: Nijmegen

first: Ivo

last: Rieu

address: Heyendaalseweg 135

department: Radboud Institute for Biological and Environmental Sciences

country: Netherlands

institute: Radboud University

hyb_protocol: The hybridisation was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning) (P/N 701028, revision 5).

data_processing: The microarray signals were determined using MadMax microarray analysis software (hhtp://madmax.bioinformatics.nl). Robust Multiarray Averaging (RMA) was used for normalisation.

label: Biotin

organism: Solanum lycopersicum

source_name: Anther, long-term mild heat, 4 days

label_protocol: Total RNA (100 ng) was used for whole transcript cDNA synthesis using the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands), and subsequently labeled using the Affymetrix GeneChip WT Terminal Labeling Kit [catalog number 901524] (Affymetrix, Santa Clara, CA).

growth_protocol: Seeds were sown on commercial soil (Lentse Potgrond number 4, Horticoop B.V., Katwijk, The Netherlands) and covered with a thin layer of vermiculite. Two weeks later, seedlings were transplanted into the same soil supplemented with 4 g L-1 fertiliser (Osmocote exact standard 3-4 M, Everris International B.V., Geldermalsen, The Netherlands). During germination and the seedling growth period, plants were kept in cabinets under control condition (25°C/19°C day/night; 12h/12h photoperiod, ~200 µmol s-1 m-2 provided by Philips Green Power LED DR/B/FR 120 lamps; 60% relative humidity).

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, Thermo Fisher Scientific, Waltham, MA USA), followed by DNA digestion and purification with the RNeasy kit (Qiagen, Venlo, The Netherlands).

treatment_protocol: Upon flowering, approximately one month after sowing, plants were either maintained at control temperature (CT) or subjected to long-term mild heat (LTMH; 33°C/27°C, day/night). At three hours into the day after the end of the 1- or 4-day CT or LTMH treatment, anther cones from 3.6-3.7 mm flower buds (corresponding to early microspore stage, 9 days before anthesis) were collected.

tag: accession

value: Micro-Tom

value: Anther cone

value: Early microspore stage

value: long-term mild heat, 4 days


title: Anther 1_day_long-term_mild_heat rep3

source_name: Anther, long-term mild heat, 1 day

value: long-term mild heat, 1 day


title: Anther control_temperature rep4

source_name: Anther, control temperature

value: control temperature


title: Anther control_temperature rep3


title: Anther 1_day_long-term_mild_heat rep4


title: Anther 1_day_long-term_mild_heat rep1


title: Anther 4_day_long-term_mild_heat rep4


title: Anther 1_day_long-term_mild_heat rep2


title: Anther control_temperature rep2


title: Anther 4_day_long-term_mild_heat rep2


title: Anther 4_day_long-term_mild_heat rep1


title: Anther control_temperature rep1


title: N4P_Rep2

status: Public on Jul 16 2021

city: Hangzhou

first: Saisai

last: Wei

state: Zhejiang

address: 3 Qingchun East Road

institute: Sir Run Run Shaw Hospital, Zhejiang University

description:
processed data: processed data file  2.xls
S070_katimesbio-A_S18L0494_AHVMJCCCXY_S70_L005

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 fastp v0.20.0 with parameters -f 0 -F 0 -n 0 -l 50 -3 -W 4 -M 30 -q 25, then mapped to mm8 whole genome using HISAT2 v2.1.0 with parameters -dta -rna -strandness RF
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

molecule: polyA RNA

source_name: liver_4 h after nighttime PHx

extract_protocol:
8-week-old male mice were subjected to standard two-thirds liver resection from 8 am to 9 am or 8 pm to 9 pm and euthanized at the indicated times. Data at each timepoint were collected from 3 mice that underwent operation and 3 in the sham group.
Libraries were prepared using the SMART-RNAseq Library Prep Kit (KAITAI-BIO, AT4201) following the manufacturer’s protocol. Samples were then subjected to deep sequencing on an Illumina NovaSeq 6000 instrument.

tag: gender

value: male

value: PHx

value: 8 weeks

value: liver

tag: time point

value: 4 h after nighttime PHx


title: N24P_Rep1

description:
processed data: processed data file  2.xls
S065_katimesbio-A_S18L0489_AHVMJCCCXY_S65_L005

source_name: liver_24 h after nighttime PHx

value: 24 h after nighttime PHx


title: N24S_Rep3

description:
processed data: processed data file  2.xls
S076_katimesbio-A_S18L0500_AHVMJCCCXY_S76_L005

source_name: liver_24 h after nighttime sham operation

value: Sham

value: 24 h after nighttime sham operation


title: N24S_Rep2

description:
processed data: processed data file  2.xls
S062_katimesbio-A_S18L0486_AHVMJCCCXY_S62_L005


title: N4S_Rep3

description:
processed data: processed data file  2.xls
S19E0173

source_name: liver_4 h after nighttime sham operation

value: 4 h after nighttime sham operation


title: N24S_Rep1

description:
processed data: processed data file  2.xls
S061_katimesbio-A_S18L0485_AHVMJCCCXY_S61_L005


title: N24P_Rep2

description:
processed data: processed data file  2.xls
S066_katimesbio-A_S18L0490_AHVMJCCCXY_S66_L005


title: [15-scr](normalized)

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

description: The Human 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 45033 genes were collected from the authoritative data source including NCBI.

hyb_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation. Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.6) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.6) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes that have values greater than or equal to lower cut-off: 100.0 in 3 out of 4 samples (“All Targets Value”) were chosen for differentially expressed gene screening (All these genes can be found from the sheet “All Targets Value” in Gene Expression Profiling Data.xls file).

source_name: colorectal cancer cells

growth_protocol: The HCT15 human colon cancer cell lines were purchased from the Typical Culture Preservation Commission Cell Bank, Chinese Academy of Sciences. HCT15 was maintained on gelatinized 10cm-plate in RPMI-1640 Medium (Gibco) supplemented with 10% FBS (fetal bovin serum) (Gibco), 100 U penicillin/100 mg streptomycin (Gibco) at 37℃ and 5% CO2.

extract_protocol: Approximately 10000000 cells were collected and lysed with TRIzol® Reagent (Life Technologies) in the RNase-free Eppendorf tube. We then submitted the samples to KangChen-Biotech (Shanghai, China) for Microarray Analysis using the Human 12 × 135K Gene Expression Array (Roche NimbleGen). The experiment and data analysis for Microarray Analysis, including RNA isolation, microarray experiment, data processing, statistical analysis and gene ontology analysis, were done by KangChen-Biotech Corporation.

treatment_protocol: To build stable knockdown cells, the small hairpin RNAs (LYAR-shRNAs and Control-shRNA) were designed correspondingly according to the sense and antisense sequences of the two LYAR-specific siRNAs (The siRNA sequences against human LYAR and non-silencing were designed and chemically synthesized by Genepharma (Shanghai, China)). These chemically synthesized oligonucleotides were annealed to generate double-stranded oligonucleotides using the touch down program in the PCR instrument and inserted into the Xho I/Hpa I sites in the pLentiLox 3.7 vectors, which was subsequently confirmed by sequencing. Lentiviruses was packaged and produced in 293T cells. The supernatant of virus production was collected and filter-sterilized to infect the corresponding cells. The stably transfected cells were sorted and collected by flow cytometry using GFP fluorescence.

value: colorectal cancer cells

tag: sirna

value: Scramble-shRNA


title: N4S_Rep1

description:
processed data: processed data file  2.xls
S19E0168_S16_L002


title: N4S_Rep2

description:
processed data: processed data file  2.xls
S19E0169_S17_L002


title: 24P_Rep3

description:
processed data: processed data file 1.xls, processed data file  2.xls
S072_katimesbio-A_S18L0496_AHVMJCCCXY_S72_L005

source_name: liver_24 h after PHx

value: 24 h after PHx


title: 24S_Rep3

description:
processed data: processed data file 1.xls, processed data file  2.xls
S071_katimesbio-A_S18L0495_AHVMJCCCXY_S71_L005

source_name: liver_24 h after sham operation

value: 24 h after sham operation


title: 24S_Rep2

description:
processed data: processed data file 1.xls, processed data file  2.xls
S060_katimesbio-A_S18L0484_AHVMJCCCXY_S60_L005


title: N24P_Rep3

description:
processed data: processed data file  2.xls
S077_katimesbio-A_S18L0501_AHVMJCCCXY_S77_L005


title: 24P_Rep1

description:
processed data: processed data file 1.xls, processed data file  2.xls
S063_katimesbio-A_S18L0487_AHVMJCCCXY_S63_L005


title: N4P_Rep1

description:
processed data: processed data file  2.xls
S069_katimesbio-A_S18L0493_AHVMJCCCXY_S69_L005


title: 20S_Rep3

description:
processed data: processed data file 1.xls
20hS3

source_name: liver_20 h after sham operation

value: 20 h after sham operation


title: 16P_Rep3

description:
processed data: processed data file 1.xls
16h3

source_name: liver_16 h after PHx

value: 16 h after PHx


title: 20P_Rep2

description:
processed data: processed data file 1.xls
20h2

source_name: liver_20 h after PHx

value: 20 h after PHx


title: 16P_Rep1

description:
processed data: processed data file 1.xls
16h1


title: 16P_Rep2

description:
processed data: processed data file 1.xls
16h2


title: 16S_Rep3

description:
processed data: processed data file 1.xls
16hS3

source_name: liver_16 h after sham operation

value: 16 h after sham operation


title: 20P_Rep3

description:
processed data: processed data file 1.xls
20h3

value: male


title: 24P_Rep2

description:
processed data: processed data file 1.xls, processed data file  2.xls
S064_katimesbio-A_S18L0488_AHVMJCCCXY_S64_L005

value: PHx


title: 16S_Rep2

description:
processed data: processed data file 1.xls
16hS2

value: 8 weeks


title: 16S_Rep1

description:
processed data: processed data file 1.xls
16hS1

value: liver


title: 12S_Rep3

description:
processed data: processed data file 1.xls
12hS3

source_name: liver_12 h after sham operation

value: 12 h after sham operation


title: 12S_Rep2

description:
processed data: processed data file 1.xls
12hS2


title: 4P_Rep2

description:
processed data: processed data file 1.xls, processed data file  2.xls
S068_katimesbio-A_S18L0492_AHVMJCCCXY_S68_L005

source_name: liver_4 h after PHx

value: 4 h after PHx


title: 8P_Rep2

description:
processed data: processed data file 1.xls
8h2

source_name: liver_8 h after PHx

value: 8 h after PHx


title: 4P_Rep3

description:
processed data: processed data file 1.xls, processed data file  2.xls
S074_katimesbio-A_S18L0498_AHVMJCCCXY_S74_L005


title: 4P_Rep1

description:
processed data: processed data file 1.xls, processed data file  2.xls
S067_katimesbio-A_S18L0491_AHVMJCCCXY_S67_L005


title: 12S_Rep1

description:
processed data: processed data file 1.xls
12hS1

value: Sham


title: 8S_Rep2

description:
processed data: processed data file 1.xls
8hS2

source_name: liver_8 h after sham operation

value: 8 h after sham operation


title: 8P_Rep1

description:
processed data: processed data file 1.xls
8h1


title: 8S_Rep1

description:
processed data: processed data file 1.xls
8hS1


title: 8P_Rep3

description:
processed data: processed data file 1.xls
8h3


title: 8S_Rep3

description:
processed data: processed data file 1.xls
8hS3


title: 4S_Rep3

description:
processed data: processed data file 1.xls, processed data file  2.xls
S19E0172

source_name: liver_4 h after sham operation

value: 4 h after sham operation


title: 24S_Rep1

description:
processed data: processed data file 1.xls, processed data file  2.xls
S059_katimesbio-A_S18L0483_AHVMJCCCXY_S59_L005


title: 12P_Rep2

description:
processed data: processed data file 1.xls
12h2

source_name: liver_12 h after PHx

value: 12 h after PHx


title: 4S_Rep2

description:
processed data: processed data file 1.xls, processed data file  2.xls
S19E0171


title: 4S_Rep1

description:
processed data: processed data file 1.xls, processed data file  2.xls
S19E0170_S18_L002


title: 12P_Rep1

description:
processed data: processed data file 1.xls
12h1


title: 12P_Rep3

description:
processed data: processed data file 1.xls
12h3


title: [15-L2](normalized)

description: The Human 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 45033 genes were collected from the authoritative data source including NCBI.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation. Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

value: colorectal cancer cells

value: LYAR-shRNA


title: AH6886: Treated CD rep2

city: Barcelona

first: Victoria

last: Campuzano

state: Barcelona

address: Casanovas, 143

department: Biomedicina

country: Spain

institute: Universitat de Barcelona

data_processing:
Illumina Sequencing Analysis Viewer, Illumina run specifications, FastQC, and Quality control alignment INS-017
Mapping was performed with STAR/2.5.3a.
Correction by percentage of coefficient of variation (%CV<20)
Genome_build: Ensembl GRCm38 Mus musculus
Supplementary_files_format_and_content: norm counts txt

source_name: Cortical mRNA

growth_protocol: Cortex were fresh dissected from adult, 16 weeks old animals. Dissected tissues were directly frozen in liquid Nitrogen until RNA extraction

extract_protocol:
Total RNA extracted using RNAeasy Quiagen following manufacturer's instructions
Libraries were prepared according to Illumina's instructions

treatment_protocol: Treatment (Curcumin, 60 and Verapamil 10 mg/kg/day) was started at 8 weeks-old. All animals drank their treatments for 1 month until sacrifice a-16 weeks-old

value: Cortex

value: Treated


title: AH6885: Treated CD rep1


title: AH6884: Treated WT rep3


title: 20S_Rep1

description:
processed data: processed data file 1.xls
20hS1

value: 20 h after sham operation


title: AH6887: Treated CD rep3


title: AH6882: Treated WT rep1


title: 20P_Rep1

description:
processed data: processed data file 1.xls
20h1

value: 20 h after PHx


title: 20S_Rep2

description:
processed data: processed data file 1.xls
20hS2

value: male


title: AH6883: Treated WT rep2


title: AH6880: Untreated CD rep2

value: Untreated


title: AH6876: Untreated WT rep1


title: AH6877: Untreated WT rep2


title: AH6881: Untreated CD rep3


title: AH6879: Untreated CD rep1


title: AH6878: Untreated WT rep3


title: 16611_B

type: genomic

city: Houston

first: Andrew

last: DiNardo

state: Texas

address: 1102 Bates St

department: Global and Immigrant Health

institute: BCM

description: SAMPLE 18

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Minfi preprocessIllumina (R package) was used to process samples (for background subtraction and color correction). Average Beta (after minfi::preprocessIllumina in R).

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

value: TB disease

tag: timepoint

value: Baseline

value: Positive

value: F

value: peripheral blood mononuclear cells (PBMCs)


title: 117740_12m

description: SAMPLE 10

value: 12 month

value: Negative

value: M


title: 229310_B

description: SAMPLE 23

value: Healthy Control


title: 121610_12m

description: SAMPLE 14


title: 22804x_B

description: SAMPLE 31


title: 229210_B

description: SAMPLE 22


title: 120110_12m

description: SAMPLE 9


title: 111010_12m

description: SAMPLE 13


title: 110611_B

description: SAMPLE 15


title: 15411_B

description: SAMPLE 20


title: 229110_B

description: SAMPLE 24


title: 113110_12m

description: SAMPLE 8


title: 121110_12m

description: SAMPLE 11


title: 12911_B

description: SAMPLE 16


title: 122410_B

description: SAMPLE 4


title: 123411_B

description: SAMPLE 19


title: 14711

description: SAMPLE 32


title: IN381

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

data_processing: alignment to human genome (hg38 UCSC), feature counting to transcripts, compute reads per thousand bases of transcript per million total reads (RPKM)

source_name: Tempus RNA

extract_protocol:
Tempus Blood RNA Spin Isolation
DNAsed with TurboDNAse (Ambion)
polyA tailed captured polyT plate

treatment_protocol: Venipuncture blood stabilized and frozen in Tempus RNA preservative (ThermoFisher)

tag: cad status

value: CAD

tag: tissue

value: Whole blood


title: IN379


title: IN390


title: IN340


title: IN318


title: 14810_B

description: SAMPLE 3


title: IN353


title: 22802x_B

description: SAMPLE 30


title: 10111_B

description: SAMPLE 17


title: IN334


title: 111610_12m

description: SAMPLE 12


title: 228120_B

description: SAMPLE 27


title: IN319


title: IN317


title: 228220_B

description: SAMPLE 29


title: IN315


title: IN303


title: 13210_B

description: SAMPLE 6


title: IN335


title: IN343


title: IN301


title: IN384


title: IN344


title: IN389


title: IN385


title: 228030_B

description: SAMPLE 28


title: IN382


title: IN311


title: IN329


title: IN348


title: IN387


title: 123720_B

description: SAMPLE 5


title: IN386


title: IN342


title: IN388


title: IN377


title: IN369


title: IN339


title: IN333


title: IN323


title: IN330


title: IN313


title: IN349


title: IN322


title: IN357


title: IN368


title: IN393


title: IN351


title: IN312

value: LOW


title: IN356


title: IN395


title: IN360


title: IN307


title: IN328


title: IN324


title: IN358


title: IN338


title: IN345


title: IN391


title: IN394


title: IN376


title: IN383


title: IN378


title: IN341


title: IN373


title: IN372


title: IN392


title: IN374


title: 228010_B

description: SAMPLE 26


title: 229410_B

description: SAMPLE 25


title: IN370


title: 17211_B

description: SAMPLE 21


title: IN367


title: 118710_B

description: SAMPLE 2


title: IN366


title: 128210_B

description: SAMPLE 7


title: IN364


title: IN365


title: IN363


title: IN362


title: IN361


title: IN346


title: IN326


title: IN332


title: IN337


title: IN321


title: IN316


title: IN327


title: IN320


title: IN314


title: IN310


title: IN309


title: IN308


title: CDX113

data_processing: alignment to human genome (hg19, HG38), feature counting to transcripts, compute reads per thousand bases of transcript per million total reads (RPKM)

value: MID+

tag: normal

value: Abnorm

tag: abn-grade

value: E

tag: grade-num

tag: age yvo

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: H

tag: ethnicity

value: AA

tag: current smoker?

value: N

tag: htn

value: Y

tag: dyslipidemia

tag: diabetes

tag: insulin rx

value: U/F

tag: oral hypo-glycemic rx

tag: current medications

tag: depth

tag: deep group


title: CDX111

tag: cad status

tag: normal

tag: abn-grade

value: B

tag: grade-num

tag: gender

value: F

tag: age

value: HL

tag: tissue


title: CDX110

value: M

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

tag: ethnicity

value: C


title: CDX112

value: Norm

value: A

tag: current smoker?

tag: htn

tag: dyslipidemia

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications


title: CDX109

tag: cad status

value: LOW

tag: normal

tag: abn-grade

tag: grade-num

tag: gender

value: Toprol XL 100mg; Azor 10-40mg

tag: depth

tag: deep group

value: Whole blood


title: CDX107

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

value: Amlodipine 10mg; Benazepril 40mg; Tamsulosin 0.4mg

tag: tissue


title: CDX108

value: MID+

value: Abnorm

value: D

value: O

tag: bmi category

value: L

tag: ethnicity

tag: current smoker?

tag: htn

tag: dyslipidemia

tag: diabetes

tag: insulin rx

value: Lipitor 40mg; Lisinopril 40mg; HCTZ 25mg; Vitamin C; Vitamin E; Fish Oil; Biotin


title: CDX106

tag: cad status

tag: normal

tag: abn-grade

value: E

tag: grade-num

tag: gender

value: Y

value: H

value: AA

value: N

tag: oral hypo-glycemic rx

tag: current medications


title: CDX104

value: Norm

value: M

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

value: Metoprolol 50mg; Plaqaenil/hydroxychloroquine 200mg; Folic Acid 1mg; Calcium; Vit. D; Metformin 500mg;

tag: depth

tag: deep group


title: CDX105

value: F

tag: bmi

tag: bmi category

tag: ethnicity

tag: current smoker?

tag: htn

tag: dyslipidemia

value: Crestor 10mg; Bystolic 10mg; Benicar 20mg; Clonidine; Alendronat/ Tylenol PRN; Omega 3; Symbicort 160/45 2 puffs BID

tag: tissue


title: IN352

tag: cad status

value: CAD

tag: gender

value: Whole blood


title: CDX102

value: LOW

tag: normal

value: Abnorm

tag: abn-grade

value: B

tag: grade-num

value: C

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications

value: Toprol XL 50mg; Synthroid 88mg; Diovan/HCTZ 80/12.5mg; crestor 10mg; Amlodipine 5mg


title: CDX101

value: MID+

value: D

tag: age

tag: age yvo

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

value: Lipitor 40mg; Metoprolol 200mg; Digoxin 0.25mg; lantus 20 units; protonix 40mg; Coumadin 2mg; Synthroid 200mg

tag: depth

tag: deep group


title: CDX103

value: E

tag: bmi

tag: bmi category

value: L

tag: ethnicity

tag: current smoker?

value: N

tag: htn

value: Y

tag: dyslipidemia

value: Procardia XL 90mg;Lisinopril 40mg; HCTZ 25mg; Clonidine 0.4mg; Methadone; Glyburide

value: H

tag: tissue


title: CDX099

tag: cad status

tag: normal

tag: abn-grade

value: F

tag: grade-num

tag: gender

value: M

value: AA

tag: diabetes

tag: insulin rx

value: Bystolic 20mg; Simcor 500/20 mg; Actos/met 15/500 BID; Tribunzor 40/10/25mg


title: CDX096

value: LOW

value: Abnorm

value: B

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

tag: oral hypo-glycemic rx

tag: current medications

value: Whole blood


title: CDX094

value: MID+

tag: bmi

tag: bmi category

tag: ethnicity

value: C

tag: current smoker?

tag: htn

value: Pravastatin 80mg; Avapro 300mg; HCTZ 25mg PO

tag: depth

tag: deep group


title: CDX098

tag: cad status

tag: normal

tag: abn-grade

tag: grade-num

tag: gender

value: O

tag: dyslipidemia

tag: tissue


title: CDX093

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

value: L

value: HL

tag: diabetes

tag: insulin rx

value: Coumadin


title: CDX095

value: Norm

value: A

tag: bmi

tag: bmi category

tag: ethnicity

tag: current smoker?

value: N

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: Vitamin D; Plavix 75mg; Nexium 40


title: CDX097

tag: cad status

tag: normal

tag: abn-grade

tag: grade-num

tag: gender

value: M

value: Y

value: AA

value: Alegra D

tag: depth

tag: deep group


title: CDX100

value: LOW

value: F

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

value: H

tag: dyslipidemia

value: Lipitor 20mg; Atenolol 25mg; Norvasc 10mg; Zetia 10mg; Avapro 300mg; Aggrenox 25/200mg

tag: tissue


title: CDX092

value: Abnorm

value: B

tag: bmi

tag: bmi category

tag: ethnicity

value: C

tag: current smoker?

tag: htn

tag: diabetes

tag: insulin rx

value: Atenolol 25mg; Warfarin; Levoxyl 100 mg

value: Whole blood


title: CDX089

tag: cad status

value: MID+

tag: normal

tag: abn-grade

value: D

tag: grade-num

tag: gender

value: O

tag: oral hypo-glycemic rx

tag: current medications

value: Simvastatin 20mg; carvedilol 12.5 ; Benazepril 40; lasix 40mg; K-lor;


title: CDX088

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

value: L

value: N

value: Lisinopril 10mg; HCTZ 12.5mg

tag: depth

tag: deep group


title: CDX090

value: Norm

value: A

value: Y

tag: bmi

tag: bmi category

tag: ethnicity

tag: current smoker?

tag: htn

tag: dyslipidemia

tag: tissue


title: CDX087

tag: cad status

value: LOW

tag: normal

tag: abn-grade

tag: grade-num

tag: gender

value: F

value: AA

tag: diabetes

tag: insulin rx

value: Simvastatin 20mg QHS; Metoprolol 25mg; Amlodipine 10mg; Benazepril 40mg; HCTZ 37.5/25

value: H


title: CDX086

value: Abnorm

tag: age

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

value: C

tag: oral hypo-glycemic rx

tag: current medications

value: Lovastatin 10mg; Diovan 160mg; Plavix 75mg


title: CDX082

value: MID+

value: D

tag: bmi

tag: bmi category

tag: ethnicity

tag: current smoker?

tag: htn

value: Lovastatin 40mg; Metoprolol 25mg; Amlodipine 10mg;Diovan/HCTZ 160/25; Protonix 40; Lovenox 30

tag: depth

tag: deep group

value: Whole blood


title: CDX081

tag: cad status

tag: normal

tag: abn-grade

tag: grade-num

tag: gender

value: N

tag: dyslipidemia

value: pravastatin 40 ( started a month ago ); Metoprolol ( started 2 weeks ago ); Losartan 100mg; HCTZ 12.5mg;

tag: tissue


title: CDX084

value: B

value: M

tag: age

tag: age yvo

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

value: L

tag: diabetes

tag: insulin rx

value: Cozaar 50mg; Ibuprofen 800mg PRN; Maxide 37.5/25mg Qdaily


title: CDX080

value: LOW

value: F

value: Y

tag: bmi

tag: bmi category

tag: ethnicity

tag: current smoker?

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: Enalapril 2.5 mg; Zetia 10mg


title: CDX083

tag: cad status

tag: normal

value: Norm

tag: abn-grade

value: A

tag: grade-num

tag: gender

value: C

tag: depth

tag: deep group

value: H


title: Genomic DNA from lung adenocarcinoma_1940

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

hyb_protocol: The DNA is bisulfite-converted using the Zymo Bisulfite Conversion protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing:
minfi- R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues.
The processed_data.txt contain Average Beta and detection Pvalues
The signal_intensities.txt contains unmethylated and methylated signal intensities

source_name: Lung

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from fresh tissue specimens with the Maxwell® 16 Tissue DNA Purification Kit

value: Male

tag: age

tag: Stage

value: I

tag: tissue

value: Lung

tag: tissue type

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_1329S


title: Genomic DNA from lung adenocarcinoma_1932


title: CDX078

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: N

tag: dyslipidemia

tag: diabetes

tag: insulin rx

value: Lipitor 10mg; atenolol 100; Norvas 5; Lisinopril 40mg;

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1922

value: Female

value: II


title: CDX079

tag: cad status

value: LOW

tag: normal

tag: abn-grade

tag: grade-num

tag: ethnicity

value: AA

tag: current smoker?

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: Methylprednisone 4mg; Amoxicillin


title: Genomic DNA from lung adenocarcinoma_1920

tag: gender

tag: age

tag: Stage

tag: tissue

tag: tissue type


title: CDX091

value: F

tag: age yvo

value: Y

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

tag: dyslipidemia

value: Lipitor 80mg; Verspamil 240; Losartan 100mg; Metformin; Glipizide; HCTZ

tag: depth

tag: deep group


title: CDX077

tag: cad status

tag: normal

value: Abnorm

tag: abn-grade

value: B

tag: grade-num

value: M

value: O

tag: ethnicity

tag: current smoker?

tag: htn

tag: diabetes

tag: insulin rx

value: Simvastatin 10mg; taztia XT 360mg; Lisinopril 40mg; pradaxa 150mg; Avandamet 2/1000mg; Lyrica 100mg; Tramadol 100mg; Loratadine; HCTZ 25mg


title: Genomic DNA from lung adenocarcinoma_1915

tag: gender

value: Male

tag: age

tag: Stage

value: I

tag: tissue

value: Lung

tag: tissue type

value: tumor sample


title: CDX075

tag: age yvo

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: L

value: N

tag: dyslipidemia

tag: oral hypo-glycemic rx

tag: current medications

value: Janumet 50/500mg PO per day; Coumadin 7.5mg, held 5 days

value: Whole blood


title: CDX076

tag: cad status

value: LOW

tag: normal

value: Norm

tag: abn-grade

value: A

tag: grade-num

value: H

tag: ethnicity

value: AA

tag: current smoker?

tag: htn

tag: depth

tag: deep group


title: CDX085

value: MID+

value: Abnorm

value: F

tag: gender

tag: age

tag: age yvo

tag: asa

value: Y

tag: diabetes

tag: insulin rx

value: Simvastatin 40mg; Metoprolol 50mg Qdaily; Lisinopril 20mg; Gleeve 400mg Qdaily

tag: tissue


title: Genomic DNA from lung adenocarcinoma_1911

value: Female

tag: Stage

value: I

tag: tissue type


title: CDX073

tag: cad status

tag: normal

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

tag: dyslipidemia

tag: oral hypo-glycemic rx

tag: current medications


title: Genomic DNA from lung adenocarcinoma_1864

tag: gender

tag: age

value: III

value: Lung

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_1904

value: II


title: Genomic DNA from lung adenocarcinoma_1871


title: Genomic DNA from lung adenocarcinoma_1898

value: Male


title: CDX071

value: LOW

tag: abn-grade

value: B

tag: grade-num

tag: age yvo

value: O

tag: asa

tag: ethnicity

value: C

tag: current smoker?

value: N

tag: htn

value: Lipitor; metoprolol; Vorvasc; Losartan; Nexium; hydrochlorothiazide;Triamterene; Vitamin E; Sertaline

tag: depth

tag: deep group

value: L

value: Whole blood


title: CDX072

tag: cad status

tag: normal

value: Abnorm

value: M

value: Y

tag: height (in)

tag: weight (lbs)

tag: diabetes

tag: insulin rx

value: Simvastatin 80mg; Ibuprofen 800mg TID; Tramadol 50mg TID; Imdur 30mg started from 12/2/11

tag: tissue


title: Genomic DNA from lung adenocarcinoma_1854

tag: gender

value: Female

tag: age

tag: Stage

value: I

tag: tissue type


title: CDX069

value: MID+

tag: abn-grade

value: D

tag: grade-num

tag: age yvo

tag: asa

tag: bmi

tag: bmi category

tag: dyslipidemia

tag: oral hypo-glycemic rx

tag: current medications

value: H


title: CDX070

tag: cad status

tag: normal

value: E

tag: height (in)

tag: weight (lbs)

tag: ethnicity

value: AA

tag: current smoker?

tag: htn

value: Crestor 40mg daily; Bystolic 20mg daily; Nifedipine; Tekturna 300mg daily; Actos 15mg daily; Avapro 300mg; Plavix 75mg; Hydralazine 25mg BID; furosemide 40mg

tag: depth

tag: deep group


title: 120110_B

description: SAMPLE 1

value: TB disease

tag: timepoint

value: Baseline

value: Negative

tag: Sex

tag: age

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)


title: Genomic DNA from lung adenocarcinoma_1856

tag: gender

value: Male

tag: Stage

tag: tissue

value: Lung

tag: tissue type

value: tumor sample


title: CDX068

tag: cad status

value: Abnorm

tag: abn-grade

tag: grade-num

value: M

tag: age yvo

value: O

tag: asa

tag: bmi

tag: bmi category

value: L

value: C

value: N

tag: dyslipidemia

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications

value: Lisinopril 10mg PO; Calcium;

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1848

value: Female

tag: age

value: I


title: Genomic DNA from lung adenocarcinoma_1846

tag: gender

value: II


title: CDX067

value: LOW

tag: normal

value: B

value: F

tag: height (in)

tag: weight (lbs)

tag: ethnicity

value: AA

tag: current smoker?

tag: htn

value: Folic Acid, Calcium, Vit. D; methotrexate 16mg/wk.

tag: depth

tag: deep group

value: H


title: CDX066

tag: cad status

value: Abnorm

tag: abn-grade

tag: grade-num

tag: age yvo

value: Y

tag: asa

tag: bmi

value: Lipitor; Triamterne/HCTZ 37.5mg/25mg ; Trilipix 135mg; Citalopram 20mg; Losartan 100mg; Actos 30mg; Advain 250/50; Singular 10mg; metformin; recently started drugs:ASA 81mg x 3days; Byetta 250mg BID(10cc); calcium suppl.

tag: tissue


title: Genomic DNA from lung adenocarcinoma_1840

tag: age

tag: Stage

value: Lung

tag: tissue type

value: tumor sample


title: CDX074

value: MID+

tag: normal

value: E

tag: gender

value: M

tag: height (in)

tag: bmi category

value: L

value: C

value: N

tag: dyslipidemia

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications

value: Lipitor 20mg; GlucosamineYChondroitin; Niacin 500mg; Fishoil 2000mg


title: CDX065

tag: cad status

tag: abn-grade

value: D

tag: grade-num

value: O

tag: weight (lbs)

tag: ethnicity

tag: current smoker?

tag: htn

value: Vytorin 10/20mg; naprelan 750mg ( x 1wk )

tag: depth

tag: deep group

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1847

tag: gender

value: Female

tag: age

tag: Stage

value: I

tag: tissue

tag: tissue type


title: Genomic DNA from lung adenocarcinoma_1872

value: Male


title: CDX063

value: LOW

tag: normal

value: Norm

value: A

tag: age yvo

tag: asa

tag: height (in)

tag: bmi

tag: bmi category

value: H

value: AA

value: Y

tag: dyslipidemia

tag: diabetes

tag: insulin rx

value: Crestor 40mg; Atenolol 25; Amlodipine 10mg; Valsartan 320mg; HCTZ 50mg PO daily; Aldactone 25mg; Plavix 75mg for 4 days


title: Genomic DNA from lung adenocarcinoma_1839

value: Lung

value: tumor sample


title: CDX060

tag: cad status

value: MID+

value: Abnorm

tag: abn-grade

value: F

tag: grade-num

tag: weight (lbs)

value: L

tag: ethnicity

tag: current smoker?

value: N

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: Pravastatin 20; Atenolol 50; Lizinopril/ HCTZ  20/2.5


title: Genomic DNA from lung adenocarcinoma_1831

tag: gender

value: Female

tag: age

tag: Stage

value: II

tag: tissue

tag: tissue type


title: Genomic DNA from lung adenocarcinoma_1829

value: Male

value: I


title: CDX062

tag: normal

value: M

tag: age yvo

tag: asa

tag: height (in)

tag: bmi

tag: bmi category

tag: dyslipidemia

value: Crestor 20mg; Toprol 25mg; Losartan 50mg

tag: depth

tag: deep group

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1827

value: Unknown


title: Genomic DNA from lung adenocarcinoma_1826


title: CDX056

tag: cad status

tag: abn-grade

tag: grade-num

value: Y

tag: weight (lbs)

value: H

tag: ethnicity

value: AA

tag: current smoker?

tag: htn

tag: diabetes

tag: insulin rx

value: Lipitor 80mg; Metoprolol 50mg; Amlodipine 10mg; benazepril 20mg; Insulin 50 unit Nexium


title: CDX057

value: MID+

tag: normal

value: Abnorm

tag: gender

tag: age

tag: age yvo

value: O

value: C

tag: oral hypo-glycemic rx

tag: current medications

tag: tissue


title: CDX058

value: E

tag: asa

tag: height (in)

tag: bmi

tag: bmi category

value: N

tag: dyslipidemia

value: Lipitor 5mg; Carvedilol 37.5mg PO BID; Lisinopril; Janumet 50mg/1000mg. BID

tag: depth

tag: deep group


title: CDX054

tag: cad status

value: LOW

tag: abn-grade

value: B

tag: grade-num

value: F

tag: weight (lbs)

tag: ethnicity

tag: current smoker?

tag: htn

value: Metoprolol 25mg started 1 month ago; HCTZ 25mg; Losartan 50mg; Loratadine 10mg PO; Fluticasone; ASA 325 from 10/19/11;

value: L


title: Genomic DNA from lung adenocarcinoma_1807

tag: gender

value: Female

tag: age

tag: Stage

value: I

value: Lung

tag: tissue type

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_1808

tag: tissue


title: CDX053

tag: normal

value: M

tag: age yvo

tag: asa

tag: height (in)

tag: bmi

value: H

value: Y

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications

value: Coreg 125mg; Prinivil 40mg; Allopurinol 300mg Qday; Furasemide 40mg; Hytrin 2mg Qday;

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1822

value: Male


title: Genomic DNA from lung adenocarcinoma_1825


title: Genomic DNA from lung adenocarcinoma_1818


title: CDX055

tag: cad status

value: MID+

value: Abnorm

tag: abn-grade

tag: grade-num

value: O

tag: weight (lbs)

tag: bmi category

tag: ethnicity

value: C

value: N

tag: dyslipidemia

tag: depth

tag: deep group


title: Genomic DNA from lung adenocarcinoma_1844

tag: gender

tag: age

tag: Stage

tag: tissue

tag: tissue type


title: CDX052

tag: normal

value: F

tag: age yvo

tag: asa

tag: height (in)

tag: bmi

tag: current smoker?

tag: htn

tag: diabetes

tag: insulin rx

value: 81mg Aspirin; Lipitor 10mg; synthroid 15mg


title: Genomic DNA from lung adenocarcinoma_1795


title: Genomic DNA from lung adenocarcinoma_1787

value: Female


title: CDX050

tag: cad status

value: LOW

tag: abn-grade

value: B

tag: grade-num

tag: weight (lbs)

tag: bmi category

tag: ethnicity

value: AA

tag: dyslipidemia

tag: oral hypo-glycemic rx

tag: current medications

value: 81 mg Aspirin; Lisinopril 20mg; Glimepride 4mg;janumet 30/1000mg;ASA 325 start from 9/26/11


title: Genomic DNA from lung adenocarcinoma_1782

tag: gender

tag: age

tag: Stage

value: I

tag: tissue

value: Lung

tag: tissue type

value: tumor sample


title: CDX064

tag: normal

value: E

tag: age yvo

tag: asa

tag: height (in)

tag: bmi

value: L

tag: current smoker?

tag: htn

value: Y

value: Lipitor 10mg; HCTZ 12.5mg; Losartan 100mg; lipitor start 10 days ago

tag: depth

tag: deep group

value: Whole blood


title: CDX049

tag: cad status

value: Abnorm

tag: abn-grade

tag: grade-num

tag: weight (lbs)

tag: bmi category

tag: ethnicity

tag: dyslipidemia

tag: diabetes

tag: insulin rx

value: Lisinopril 5mg PO daily;HCTZ 25mg Q daily;Glipizide 5mg

value: H


title: CDX048

tag: normal

tag: gender

value: M

tag: age

tag: age yvo

value: O

value: N

value: U/F

tag: oral hypo-glycemic rx

tag: current medications

value: 81mg Aspirin;Simvastatin 40mg;Metoprolol 25mg daily;Norvasc 10mg daily;Losartan 50;HCTZ 25mg daily;Oxybutynin;Trazodone;Zyrtec;Terazosin; Simvastatin started from 9/6

tag: tissue


title: CDX059

value: MID+

value: D

tag: asa

tag: height (in)

tag: bmi

value: C

tag: current smoker?

tag: htn

value: 81mg Aspirin ; NSAIDS:PRN

tag: depth

tag: deep group


title: CDX043

tag: cad status

tag: abn-grade

value: F

tag: grade-num

tag: weight (lbs)

tag: bmi category

tag: ethnicity

tag: dyslipidemia


title: CDX042

value: LOW

tag: normal

value: Norm

value: A

tag: gender

tag: age

tag: age yvo

value: AA

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

value: Aspirin 325mg ; Lipitor;Lisinopril 40;  HZTZ 25; Omeprazol


title: Genomic DNA from lung adenocarcinoma_1769

value: Male

tag: Stage

value: I

tag: tissue

value: Lung

tag: tissue type

value: tumor sample


title: CDX041

tag: cad status

value: Abnorm

value: O

tag: asa

tag: height (in)

tag: bmi

value: H

tag: current smoker?

value: N

tag: htn

value: Y

tag: current medications

value: Simvastetin, Atenolol 50; Amlodipine 5 ; Benzapril 10 ; Chlorthalidone;Advair

tag: depth

tag: deep group

value: L

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1754

tag: gender

value: Female

tag: age


title: Genomic DNA from lung adenocarcinoma_1761


title: Genomic DNA from lung adenocarcinoma_1748


title: CDX040

value: MID+

tag: normal

tag: abn-grade

value: F

tag: grade-num

tag: age yvo

tag: weight (lbs)

tag: bmi category

tag: ethnicity

tag: dyslipidemia

tag: diabetes

value: 81 mg/day Aspirin;80 mg lipitor;50 mg Losartan;klor;20 mg methotrexate;25 mg/day Folic Acid;50 mg Butolic;75 mg plavix


title: CDX039

tag: cad status

value: D

value: M

tag: asa

tag: height (in)

tag: bmi

value: C

tag: insulin rx

tag: oral hypo-glycemic rx

value: 81 mg/day Aspirin;40 mg Lipitor;400 mg Acebutolol;10 Amlodipine;40 mg Benicar;100 mg Hydralaz;20 mg Potassium

tag: tissue


title: CDX035

tag: gender

tag: age

tag: current smoker?

tag: htn

tag: current medications

value: 81 mg/day Aspirin;50 mg/day Metoprolol;valsartan;esomeprazol 40;medication recently started; lipitor;325 mg ASA; 20 mg Famotidine

tag: depth

tag: deep group


title: Genomic DNA from lung adenocarcinoma_1806

tag: Stage

value: I

value: Lung

tag: tissue type

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_1491

value: Male


title: CDX032

tag: normal

value: Abnorm

tag: abn-grade

tag: grade-num

tag: age yvo

value: Y

tag: weight (lbs)

tag: bmi category

tag: ethnicity

value: N

tag: dyslipidemia

tag: diabetes

value: U/F

value: 81 mg/day Aspirin; Zocor 20 mg;  Paroxetine 40 mg/day; Metroprolol 50 mg (started 1-2 wks ago); ASA (started 1-2 weeks ago)


title: CDX037

tag: cad status

value: LOW

value: B

tag: gender

tag: age

tag: asa

tag: height (in)

tag: bmi

value: H

value: AA

tag: insulin rx

tag: oral hypo-glycemic rx

value: 81 mg/day Aspirin;80 mg provastatin;30 mg Labetalol;10 mg Amlodipine;5 mg Lisinopril;5 mg  Glipizide;100 mg Januvia

tag: tissue

value: Whole blood


title: CDX045

value: MID+

tag: normal

tag: abn-grade

value: D

value: M

value: L

value: C

tag: current smoker?

tag: htn

tag: current medications

value: 81 mg Aspirin;Lipitor 10mg;Toprol XL 25; Cardizem 180mg;Prilosee 20mg;Coenzime QID

tag: depth

tag: deep group


title: CDX030

value: Norm

value: A

tag: grade-num

tag: age yvo

tag: weight (lbs)

tag: bmi category

tag: ethnicity

value: O

tag: dyslipidemia

tag: diabetes


title: CDX028

tag: cad status

tag: gender

value: F

tag: age

value: Y

tag: asa

tag: height (in)

tag: bmi

value: N

tag: insulin rx

value: 81 mg/day Aspirin, 50 Toprol XL, 24 Cozaar


title: CDX029

value: LOW

tag: normal

value: Abnorm

tag: abn-grade

value: B

tag: current smoker?

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: Lipitor; Atenolol; 10 mg Atarax; 30 Lansoprazole; 20 Lasix; Iron

value: H

tag: tissue


title: Genomic DNA from lung adenocarcinoma_1767

value: Female

tag: Stage

value: I

value: Lung

tag: tissue type

value: tumor sample


title: CDX027

value: MID+

tag: grade-num

value: M

tag: age yvo

tag: weight (lbs)

tag: bmi category

value: L

tag: ethnicity

value: C

tag: dyslipidemia

tag: diabetes

value: (none)

tag: depth

tag: deep group

value: Whole blood


title: CDX025

tag: cad status

tag: normal

tag: abn-grade

tag: gender

tag: age

value: O

tag: asa

tag: height (in)

tag: bmi

value: AA

value: N

value: Y

tag: insulin rx

value: 81 mg/day Aspirin; 20 Lisinopril; 20 Lasix; 40 Prednisone; 25 mg HCTZ; Tetracycline (for 7 days)


title: Genomic DNA from lung adenocarcinoma_1322

tag: Stage

value: II

tag: tissue

tag: tissue type


title: Genomic DNA from lung adenocarcinoma_1274

value: Male


title: Genomic DNA from lung adenocarcinoma_1383


title: Genomic DNA from lung adenocarcinoma_1295

value: Female


title: Genomic DNA from lung adenocarcinoma_1294

value: III


title: Genomic DNA from lung adenocarcinoma_1414

value: Lung


title: Genomic DNA from lung adenocarcinoma_1273

value: I

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_1404


title: Genomic DNA from lung adenocarcinoma_1476


title: Genomic DNA from lung adenocarcinoma_1448


title: CDX024

value: MID+

value: Abnorm

value: E

tag: grade-num

value: M

tag: age yvo

tag: weight (lbs)

tag: bmi category

tag: ethnicity

tag: current smoker?

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: 20 mg Lisinopril; 20 mg Prilosec; 600/300 mg Epizicom; 2 mg Doxazosin; 200/50 BID Kaletra

value: H


title: CDX023

tag: cad status

tag: normal

tag: abn-grade

value: D

tag: gender

tag: age

value: L

value: AA

tag: dyslipidemia

tag: diabetes

value: 20 mg Simvastatin; 5 mg Bystolic; Nitro SL PRN

tag: depth

tag: deep group

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1266

value: Male

tag: Stage

tag: tissue

tag: tissue type


title: Genomic DNA from lung adenocarcinoma_1135


title: CDX022

tag: grade-num

value: F

tag: age yvo

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

tag: ethnicity

value: C

value: N

value: Y

tag: insulin rx

value: 80/4.5 Symbicort; 300 mg qday Tekturn; 10 mg Ambien; 180 mg Allegra; 25 HCTZ; 320 mg Diovan; 40 mg PO BID Lasix; 500 qday Valacyclovir; 400 mg Avelox (started recently); 60 mg Prednisone (started recently); Lipitor (started recently)


title: CDX034

tag: cad status

value: MID+

tag: normal

value: Abnorm

tag: abn-grade

tag: gender

tag: age

value: HL

tag: current smoker?

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: 81mg/day Aspirin;50mg metoprolol


title: CDX036

tag: grade-num

value: M

tag: age yvo

value: H

tag: dyslipidemia

tag: diabetes

value: 325 mg/day Aspirin; 40 mg Lipitor;250 mg metoprolol

tag: depth

tag: deep group

tag: tissue


title: CDX021

value: LOW

value: B

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

tag: ethnicity

tag: insulin rx

value: 81 mg/day Aspirin; 40 mg Pravastatin; 40 mg Micardis; 12.5 HCTZ


title: Genomic DNA from lung adenocarcinoma_1109

tag: gender

value: Male

tag: age

tag: Stage

value: I

value: Lung

tag: tissue type

value: tumor sample


title: CDX020

tag: cad status

tag: normal

value: Norm

tag: abn-grade

value: A

tag: grade-num

tag: age yvo

value: O

value: AA

tag: current smoker?

value: N

tag: htn

tag: oral hypo-glycemic rx

tag: current medications

value: 80 mg Simvastatin; 10 Lisinopril; 12/5 HCTZ; Prilosec; Claritin; Plavix 75 mg (new-started last week)

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_1097

tag: tissue


title: Genomic DNA from lung adenocarcinoma_1075

value: Female

value: IV


title: CDX019

value: MID+

value: Abnorm

value: D

value: M

value: Y

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: L

value: C

tag: dyslipidemia

tag: diabetes

value: 12.5 bid metoprolol; amiodarone 200 mg; acidophilus; famotidine

tag: depth

tag: deep group


title: Genomic DNA from lung adenocarcinoma_1023

tag: gender

tag: age

tag: Stage

value: III

value: Lung

tag: tissue type

value: tumor sample


title: CDX018

tag: cad status

tag: normal

tag: abn-grade

value: F

tag: grade-num

tag: age yvo

value: O

value: H

tag: ethnicity

tag: current smoker?

tag: htn

tag: insulin rx

value: 81 mg/day Aspirin 20 mg Lisinopril; 50/500 Janumet BID; Vitamin D; HCTZ-Triamterene; Glimepiride 2 mg (started recently); Folic Acid (started recently)


title: CDX017

value: LOW

value: Norm

value: A

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: As

value: N

tag: dyslipidemia

tag: oral hypo-glycemic rx

tag: current medications

value: 81 mg/day Aspirin; 135 mg Triplex; 5 mg Crestor; Glimepride 10 mg BFD; Diovan (started last wk); Prednisone 20 mg (yesterday Y today); 850 TID metformin; 100 mg Januvia; 30 mg Prevacid; Zantac (started today); 4 mg Actos (started today)

tag: tissue

value: Whole blood


title: Genomic DNA from lung adenocarcinoma_985

tag: gender

value: Female

tag: age

tag: Stage

value: II

tag: tissue type


title: CDX016

tag: cad status

tag: normal

tag: abn-grade

tag: grade-num

tag: age yvo

value: Y

value: L

tag: ethnicity

value: AA

tag: diabetes

value: MVI

tag: depth

tag: deep group


title: Genomic DNA from lung adenocarcinoma_1272

value: I

value: Lung

value: tumor sample


title: Genomic DNA from lung adenocarcinoma_902


title: Genomic DNA from lung adenocarcinoma_932


title: CDX015

value: F

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: C

tag: current smoker?

tag: htn

tag: dyslipidemia

tag: insulin rx

value: 20 Lisinopril; HCTZ 12.5

value: H


title: CDX005

tag: cad status

value: MID+

tag: normal

value: Abnorm

tag: gender

tag: age

value: N

tag: oral hypo-glycemic rx

tag: current medications

value: 325mg Aspirin; Simvastatin 40; Atenolol 50; Lasix 40; 7.5mg metolazone; asapro 300; januvia 1000; glumetza 1000 RID

tag: tissue


title: CDX013

value: LOW

value: Norm

tag: abn-grade

value: A

tag: grade-num

tag: age yvo

tag: ethnicity

tag: diabetes

value: 325 mg/day Aspirin; 10 mg Lipitor; 40/12.5 Benicar HCl; 100 mg Synthroid; 300 mg Qday CoQ10

tag: depth

tag: deep group

value: Whole blood


title: CDX014

value: D

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: L

tag: current smoker?

tag: htn

value: 81 mg/day Aspirin; Lactulose PRN; 5 mg Ambien; 150 mg Lithium; 25 mg Toprol XL; Mucomyst


title: CDX010

tag: cad status

tag: normal

tag: gender

value: M

tag: age

value: AA

value: Y

tag: dyslipidemia

tag: insulin rx

tag: oral hypo-glycemic rx

value: 5mg Bystolic; 10-160mg Exforge; 4mg glimepiride; 50mg Janumet; 20mg Lipitor


title: CDX009

tag: abn-grade

tag: grade-num

value: F

tag: age yvo

tag: ethnicity

tag: diabetes

tag: current medications

value: 20 mg Lipitor; 400 mg Lalbetalol BRD; Lisinopril; 37.5/25 Maxzide; 0.1 mg Clonidine; 5/40 Azor

value: H

tag: tissue


title: heart_HL7W-40

city: beijing

first: zhang

middle: yun

last: long

state: beijing

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology,

institute: School of Basic Medical Sciences, Capital Medical University

data_processing:
RNA samples with RNA Integrity Number (RIN) above 7 were depleted for ribosomal RNA and converted into cDNA library using NEBNext UltraTM RNA Library Prep Kit for Illumina®.
cDNA library were then sequenced at 10pM on the Illumina NovaSeq to generate 150 bp pair-end reads.
After adaptor-removing and quality control filtering, the clean reads were mapped to the mouse genome (Mm10) using hisat2(v2.0.0).
Stringtie (v1.2.4) was run with a reference annotation to generate FPKM values and Limma packages (v3.3.5) were used to identify differentially expressed genes (DEGs) between genotypes.
The differential expression genes were considered to be up or down regulated with at least p < 0.05 and FC>1.5.
Genome_build: hg38
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: heart tissue

extract_protocol:
The mice were euthanized by intraperitoneal injection of pentobarbital at 5th and 7th week post the dual intervention. Heart tissues were then removed and frozen in liquid nitrogen.Total RNA of mouse heart tissues was extracted using Trizol, according to manufacturer’s procedure, quantified and quality controlled using a 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina® .

treatment_protocol: Wide-type male C57BL/6J were treated with a combination of high fat diet and N[w]-nitro-l-arginine methyl ester (L-NAME, 0.5g/L solubled in saline) for 5 and 7 weeks to construct a HFpEF mouse model.

tag: strain

tag: Sex

value: male

value: heart tissue

tag: genotype

value: HFpEF model for 7 weeks


title: heart_HL7W-34


title: heart_HL7W-32


title: CIS2

city: Omaha

first: Marisa

last: Zallocchi

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

data_processing:
Base calling: Raw data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition.
Read quality: The Sequenced Reads/ raw reads often contain low quality reads or reads with adaptors. As we can see in Fig 1.3, which will affect the further analysis results. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); and, (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely, as shown below.
Gene Expression: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Reads count is proportional to be 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. (Mortazavi et al. 2008)
Genome_build: Mus_musculus_mm10
Supplementary_files_format_and_content: FPKM values for each sample in searchable Excel spreadsheet

growth_protocol: HEI-OC1 cells were maintained in high-glucose Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum (Life Technologies, USA) at 33 deg C and 10% CO2.

extract_protocol:
Total RNA from cisplatin exposed (n=2) and non-treated controls (n=2) HEI-OC1 cells was extracted using TRIzol (Thermo Fisher Scientific, USA), and purified by column using RNeasy Mini kit (QIAGEN). Samples (1 µg total RNA per sample) were shipped to Novogene (California, USA) for RNA sequencing.
The mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. First strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is enriched by PCR amplification and purification of PCR products by AMPure XP beads. Library quality construction: After library construction, diluting library to 1.5 ng/ul with the preliminary quantitative result by Qubit2.0 and detecting the insert size by Agilent 2100. Q-PCR is used to accurately quantify the library effective concentration (> 2nM), in order to ensure the library quality.
Libraries are fed into Illumina machines after pooling according to activity and expected data volume if library quality is up to standard.

treatment_protocol: Drug treated cells were exposed to 70 µM cisplatin for 15 hours.

tag: agent

value: cisplatin

tag: cell type

value: HEI-OCI_Cochlear hair cell like cells

tag: passages

tag: sample size

value: ~6,000,000 cultured cells


title: CTL2


title: CIS1


title: CD4+ T cells, Replicating (low Green) 2

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

description:
STAR_Gene_Counts.csv
AH6_2

data_processing:
Illumina Bcl2fastq v2.18
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Genome_build: hg19
Supplementary_files_format_and_content: STAR_Gene_Counts.csv

source_name: ZsGreen-Crimson+ 2

growth_protocol: Describe in Rantapriya et al. Cell Reports 2021 (Accepted)

extract_protocol: cDNA was synthesized using Takara SmartSeq v4 reagents from 1ng of total RNA. cDNA was fragmented by Covaris AFA to ~150bp and adapters ligated using Swift 2S library prep kit from 2ng of cDNA according to manufacturer's protocol.

value: human CD4+ T cells isolated from PBMC from a single donor

tag: infection

value: Infected with 20ng of p24 of HI.fate.SFFV (KB9 Env)

tag: viral state

value: Active transcription


title: CD4+ T cells, Replicating (low Green) 1

description:
STAR_Gene_Counts.csv
AH5_1

source_name: ZsGreen-Crimson+ 1

treatment_protocol: Describe in Rantapriya et al. Cell Reports 2021 (Accepted)


title: CD4+ T cells, Replicating 1

description:
STAR_Gene_Counts.csv
AH7_1

source_name: ZsGreen+Crimson+ 1


title: Genomic DNA from lung adenocarcinoma_956

tag: gender

value: Female

tag: age

tag: Stage

value: I

value: Lung

tag: tissue type

value: tumor sample


title: heart_HL7W-31


title: heart_HL5W-30

value: HFpEF model for 5 weeks


title: CD4+ T cells, Latent_1

description:
STAR_Gene_Counts.csv
AH3_1

source_name: ZsGreen+ 1

value: Latency


title: CTL1


title: Genomic DNA from lung adenocarcinoma_771


title: CD4+ T cells, Control

description:
STAR_Gene_Counts.csv
AH_Neg_2

source_name: Uninfected

value: Uninfected


title: heart_HL5W-29


title: PAPERCLIP for LN229 cells, Doxorubicin treated, replicate 2

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

data_processing:
library strategy: PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3′ End Retrieval by CrossLinking ImmunoPrecipitation)
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011). Trimmed reads that are at least 25-nt in length are retained for mapping to reference genome (hg19).
Mapping was performed using Novoalign without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster. The clusters were filtered by PH before downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the accompanying publication for further information.
Note: The submitted raw files are de-multiplexed and quality-filtered without further processing.
Genome_build: hg19
Supplementary_files_format_and_content: txt files for unique read counts at gene level (RefSeq)

extract_protocol:
Sample preparation, immunoprecipitation, SDS-PAGE and RNA extraction were performed using the PAPERCLIP protocol (Hwang et al. Cell Rep. 2016).
The sequencing library was constructed using the PAPERCLIP method (Hwang et al. Cell Rep. 2016).  The library contains a 11-nt degenerate linker sequence at the 5′ end (3-nt degenerate sequence, 4-nt sample multiplexing index and 7-nt random barcode) as described in (Hwang et al. Neuron 2017).

tag: cell line

tag: treatment

value: none (untreated)

tag: index

value: Index 6:GACT


title: heart_HL5W-28

value: male

tag: tissue

value: heart tissue


title: PAPERCLIP for LN229 cells, Doxorubicin treated, replicate 1

value: Index 4:TAGC


title: PAPERCLIP for LN229 cells, Untreated, replicate 2

value: Doxorubicin

value: Index 5:AGTC


title: heart_con-10

tag: strain

value: Normal


title: heart_HL7W-39

tag: Sex

value: HFpEF model for 7 weeks


title: PAPERCLIP for LN229 cells, Untreated, replicate 1

value: Index 3:CGAT


title: PAPERCLIP for HeLa cells, Untreated, replicate 2

value: HeLa


title: heart_con-7

tag: genotype


title: CD4+ T cells, Latent_2

description:
STAR_Gene_Counts.csv
AH3_2

source_name: ZsGreen+ 2

value: human CD4+ T cells isolated from PBMC from a single donor

value: Infected with 20ng of p24 of HI.fate.SFFV (KB9 Env)


title: PAPERCLIP for HeLa cells, Doxorubicin treated, replicate 2


title: heart_con-5


title: CD4+ T cells, Replicating 2

description:
STAR_Gene_Counts.csv
AH8_2

source_name: ZsGreen+Crimson+ 2

value: Active transcription


title: CDX003

tag: cad status

value: MID+

tag: normal

value: Abnorm

tag: abn-grade

value: F

tag: grade-num

value: M

tag: age yvo

value: O

tag: asa

tag: height (in)

tag: weight (lbs)

tag: bmi

tag: bmi category

value: L

tag: ethnicity

tag: current smoker?

value: N

tag: htn

value: Y

tag: dyslipidemia

tag: diabetes

tag: insulin rx

tag: oral hypo-glycemic rx

tag: current medications

value: 325mg aspirin; Lipitor10; metoprolol; ASA and Toprol XL (recent) since 3/31/11

tag: depth

tag: deep group

value: H

value: Whole blood


title: PAPERCLIP for HeLa cells, Untreated, replicate 1

tag: cell line

tag: treatment

value: none (untreated)

tag: index

value: Index 4:TAGC


title: N4P_Rep3

description:
processed data: processed data file  2.xls
S310_katimesbio-A_S18L0503_AHYGCWCCXY_S11_L005

source_name: liver_4 h after nighttime PHx

tag: strain

tag: gender

value: male

value: PHx

tag: age

value: 8 weeks

tag: tissue

value: liver

tag: time point

value: 4 h after nighttime PHx


title: PAPERCLIP for HeLa cells, Doxorubicin treated, replicate 1

value: HeLa

value: Doxorubicin

value: Index 3:CGAT


title: 32P_Rep2

description:
processed data: processed data file 1.xls
S20C0143-rep1-1-mRNA_L4_Y0001612E59

source_name: liver_32 h after PHx

value: 32 h after PHx


title: EXO_8

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

description:
Isolation of poly A+ RNA from total RNA
Unstranded RNA-seq

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM values calculated with Cuffnorm

source_name: Treatment  with SK-MEL-147 exosomes for 48h

growth_protocol: Cell were growing on gelatin-coated  6-well plates for 24h in 1 mL of EGM-2MV medium before treatments were added. Fresh medium was added when treatments started

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen). After the recovery of the aqueous phase using chlorophorm, a DNAse treatment was performed using the Mini RNeasy kit (Qiagen) following manufacturer instructions.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit, and sequenced on a Illumina HiSeq1500 sequencer.
Unstranded RNA-seq

treatment_protocol: 5 μg/mL of freshly purified exosomes were added in a volumen of 20 μL to the cells. For conditioned medium treatment 500 μL of exosome-depleted supernantants of SK-MEL-147 cells growing in DMEM were added to 500μL of EGM-2MV in each well

value: human lympahtic endothelial cells HMVECs (Lonza)

value: SK-MEL-147 exosomes for 48h


title: 32P_Rep1

description:
processed data: processed data file 1.xls
S20C0142-rep1-1-mRNA_L4_U85E59


title: heart_HL5W-23

tag: Sex

value: heart tissue

tag: genotype

value: HFpEF model for 5 weeks


title: 32P_Rep3

description:
processed data: processed data file 1.xls
S20C0144-rep1-1-mRNA_L4_R76E59


title: heart_con-1

value: Normal


title: heart_HL5W-21


title: EXO_6

source_name: Treatment  with SK-MEL-147 exosomes for 24h

value: SK-MEL-147 exosomes for 24h


title: 32S_Rep3

description:
processed data: processed data file 1.xls
S20C0147-rep1-1-mRNA_L4_Y0001615E59

source_name: liver_32 h after sham operation

value: Sham

value: 32 h after sham operation


title: EXO_5


title: 32S_Rep2

description:
processed data: processed data file 1.xls
S20C0146-rep1-1-mRNA_L4_Y0001614E59

value: male


title: EXO_7


title: EXO_3

source_name: Control

value: only volumen of PBS corresponding to volumen of exosomes


title: EXO_2


title: 28P_Rep3

description:
processed data: processed data file 1.xls
S20C0138-rep1-1-mRNA_L4_Y0001640E59

source_name: liver_28 h after PHx

value: PHx

value: 8 weeks

value: 28 h after PHx


title: 32S_Rep1

description:
processed data: processed data file 1.xls
S20C0145-rep1-1-mRNA_L4_Y0001613E59

value: liver


title: EXO_1


title: 28P_Rep2

description:
processed data: processed data file 1.xls
S20C0137-rep1-1-mRNA_L4_Y0001639E59


title: EXO_4


title: EXO_15

source_name: Exosome-depleted conditioned medium  for 24h

value: DMEM+secreted factors from SK-MEL-147 cells growing for 72h  (conditioned medium). Medium was depleted of exosomes by ultracentrifugation


title: 28P_Rep1

description:
processed data: processed data file 1.xls
S20C0136-rep1-1-mRNA_L4_Y0001638E59


title: heart_con-4


title: EXO_9


title: EXO_14


title: 28S_Rep3

description:
processed data: processed data file 1.xls
S20C0141-rep1-1-mRNA_L4_U84E59

source_name: liver_28 h after sham operation

value: 28 h after sham operation


title: EXO_13


title: 28S_Rep1

description:
processed data: processed data file 1.xls
S20C0139-rep1-1-mRNA_L4_U83E59


title: 28S_Rep2

description:
processed data: processed data file 1.xls
S20C0140-rep1-1-mRNA_L4_Y0001641E59


title: EXO_12

source_name: Control medium for 24h

value: DMEM (same amount as conditioned medium)


title: EXO_10

value: human lympahtic endothelial cells HMVECs (Lonza)


title: TLR7

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

description: CD45+ cells sorted from B16 tumor after treated with IL15 superagonist and anti-PD1 combination

data_processing:
Data were processed using the Cell Ranger v2.1.1 (10x Genomics) to generate count-level cell by gene matrix for further analysis.
Genome_build: mm10

source_name: CD45+ cells sorted from B16 tumor

growth_protocol: 5x10^5 B16-F10 tumor cells were implanted s.c into mice and  tumor resected 11 days post s.c. implantation.

extract_protocol:
TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 106 cells were stained using fluorescently labeled mouse CD45 antibody (clone 30F11) and Fixable Viability Dye eFluor 506 (Thermo Fisher Scientific; Waltham, MA) to sort for live CD45+ and CD45− cells using the FACSAria II cell sorter.
approximately 1.6x10^4 cells were onto Chromium Single Cell A chips and library construction performed using the Chromium Single Cell 5’ Library and Gel Bead Kit protocol (10x Genomics)
Libraries were sequenced using the NovoSeq 6000 platform (Illumina; San Diego, CA)

treatment_protocol: Following resection mice were treated with four different treatments.

tag: cell type

value: CD45+ cells sorted from B16 tumor

value: B16-F10 tumor bearing mice

value: Tlr7/8 agonist


title: TLR9C

description: CD45+ cells sorted from B16 tumor after treated with IL15 superagonist


title: siTET3

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

library_source: genomic

data_processing:
BaseCalling performed using BCL2Fastq version 1.8.4
Using Bismarck v0.11.1 to align reads against human hg19 reference genome
Methylation calling performed by Zymo Research proprietary pipeline
Genome_build: human hg19
Supplementary_files_format_and_content: bed file

source_name: Human UtLM (Coriell Cell Repositories)

growth_protocol: Human UtLM was maintained in growth medium (GM) (MEM, Sigma, #M3024, supplemented with 20% fetal bovine serum, 1X MEM Vitamins Solution , Invitrogen, #11120-052; 1X MEM Amino Acids Solution, Invitrogen, #11130-051; 1X  MEM Non-Essential Amino Acids, Invitrogen, #11140-050). To prepare for transfection, cells were seeded at a density of 6× 104 cells/well in GM in 12-well plates, respectively.

extract_protocol:
Genomic DNA was extracted by using Quick-gDNA MicroPrep kit from Zymo Research company according to the protocol
Libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.

treatment_protocol: Human UtLM was transfected with either control siRNA or siH19 or siTET3. 48h after transfection, cells were harvested and genomic DNA was extracted.

value: Telomerase immortalized cell line

tag: sirna


title: TLR3

description: CD45+ cells sorted from B16 tumor after treated with anti-PD1

value: Poly I:C


title: siH19


title: input_nHSC_None_6

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina NovaSeq Control Software" version 1.7.0 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real Time Analysis (RTA) version v3.4.4
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
BAM to fastQ conversion with bedtools2 (v.2.19.1) bamToFastQ
Read trimming and QC with Trim Galore! (v.0.3.3 with cutadapt v.1.8 and fastqc v0.11.3) using default parameters
Reads aligned to GRCm38/mm10 with bowtie2 (v.2.2.6) with --sensitive-local
Peak finding with MACS2 callpeak (v.2.2.7.1) for each ChIP vs matched input control
Reads were deduplicated with Picard Tools (v2.18.14-SNAPSHOT) MarkDuplicates
For profiles plots  replicate samples were merged with Picard MergeSamFiles
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: narrowPeak (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)

source_name: Haematopoietic stem cells

growth_protocol: Bone marrow derived macrophages (BMDM) were generated by flushing bone marrow from murine femurs and tibias and plating on non-tissue culture treated petri-dishes in complete 5 mmol/L glucose DMEM media (supplemented with 10% FBS, 2% penicillin -  streptomycin and 2 mmol/L glutamine) plus 20% L929 cell conditioned media for differentiation. After differentiation for 7 days, BMDM positively selected and plated at a density of 2 x105 cells/mL. HSCs were isolated using MagniSort Mouse Hematopoietic Lineage Depletion Kit (ThermoFisher Scientific, UK) by flushing bone marrow from murine femurs and tibias and incubating with markers to remove lineage committed cells (CD3, CD4, B220, Ter119 and Gr1) and enrich for HSCs.

extract_protocol:
1 x 10^6 cells/mL were fixed with 1% formaldehyde at room temperature for 10 minutes, washed with PBS and stored at -80oC. Cells were sheared using the Chromatin EasyShear Kit – Low SDS (Diagenode, Belgium) and sonicated using a Bioruptor® Pico sonication device (Cat# B01080010) (Diagenode, Belgium) according to the manufacture’s recommendations.
ChIP-seq libraries were prepared with the NEBNext Ultra II kit (New England Biolabs). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

treatment_protocol: BMDMs were stimulated in  5 mmol/L glucose DMEM media with either 10 ng/mL recombinant murine interferon-ɣ plus 100 ng/mL lipopolysaccharide or media only control for 16 hours.

value: Haematopoietic stem cells

tag: chip antibody

value: Unstimulated

tag: disease state

value: Control


title: input_nHSC_None_5


title: input_nHSC_None_4


title: input_nHSC_None_3


title: Isotype

description: CD45+ cells sorted from B16 tumor after treated with PBS

value: PBS


title: input_nHSC_None_2


title: input_nHSC_None_1


title: input_nBMDM_ctrl_6

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages


title: input_nBMDM_ctrl_5


title: input_nBMDM_ctrl_4


title: EXO_11


title: siCon

value: siControl


title: input_nBMDM_ctrl_3


title: GX_0.50_dFnrG_0_1

city: Hanada-shi

first: Seiji

last: Watanabe

address: Nakamura-cho

department: Central Research Institute

institute: Mizkan Group Co. Ltd

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Komagataeibacter medellinensis NBRC 3288

label_protocol: Labeling was performed by Roche NimbleGen, Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Gluconacetobacter xylinus NBRC 3288 delta-fnrG was grown to early-log phase (O.D.660nm 0.25) and mid-log phase (O.D.660nm 0.5) arobically shaking at 30°C in YPG media containing 1% (v/v) acetic acid and 3% (v/v) ethanol (Iida et al. J. Bacteriol. 190(7):2546). Cluture was statically incubated for 0 h and 3 h at 30°C.

extract_protocol: Total RNA was prepared by hot phenol method (Aiba et al. J. Biol. Chem. 256:11905). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at Roche Diagnostics Japan.

value: disruptant mutant fnrG::Cat

tag: growth phase

value: mid-log phase (O.D.660nm 0.5)

tag: time

value: 0 hr


title: GX_0.25_dFnrG_3_2

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. Total RNA was prepared from the same culture of SAMPLE 10.

value: early-log phase (O.D.660nm 0.25)

value: 3 hr


title: GX_0.50_dFnrG_3_2

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. Total RNA was prepared from the same culture of SAMPLE 14.


title: input_nBMDM_ctrl_1


title: GX_0.50_dFnrG_0_2

description: This sample is of Gluconacetobacter xylinus NBRC 3288 delta-fnrG harboring pTW201. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.


title: input_nBMDM_ctrl_2