title: ATAC-seq_CHD8-Control_CR3

status: Public on Nov 27 2019

city: STANFORD

first: BAHAREH

last: HADDADDERAFSHI

state: CA

address: 736 ESCONDIDO RD, APT 204

institute: Ms.

description:
Biological replicate#2 called: CR3 neurons, differentiated from sub clone 3, which is an iPS line.
processed data file: ATAC-seq-peaks.xlsx

data_processing:
Data analysis for ChIP-seq, RNA-seq and ATAC-seq is according to "method" section in the manuscript.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq-peaks.xlsx: Excel spreadsheet; Peaks overlapping both replicates and annotation of the genes close to the peaks.
Supplementary_files_format_and_content: Counts-RNA-seq-samples.txt: Tab-delimited text file; The count of the genes in RNA-seq experiment.
Supplementary_files_format_and_content: RNA-seq-DEGs.xlsx: Excel spreadsheet; The list of differentially expressed genes (DEGs).
Supplementary_files_format_and_content: ATAC-seq-peaks.xlsx: Excel spreadsheet; Opening and closing peaks and the annotation of the genes close to peaks.

source_name: Neurons

growth_protocol: CHD8-KO human ES cells generated from human embryonic stem cells (ESCs) line H9 (passage 50, WA01 WiCell Research Institute, Inc.) and an iPSC line from a male individual (karyotype is in Figure S2-1). Only cells with normal karyotype used for generating conditional knockout cells and downstream analysis. Pluripotent stem cells maintained in mTeSRTM 1 (STEMCELL Technologies) and small-molecule Thiazovivin (5uM) (STEMCELL Technologies) applied to the medium before single passaging during conversion to neurons. After that, the conversion of PSC to induced neurons was according to our previously published protocol.

extract_protocol:
Extract protocol for ChIP-seq, RNA-seq and ATAC-seq are according to "method" section in the manuscript.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols. ATAC : we followed the cited protocol in the method section: Chen, X. et al. Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. Nature communications 9, 4590, doi:10.1038/s41467-018-07115-y (2018).

treatment_protocol: Treatment of cells for ChIP-seq, RNA-seq and ATAC-seq are according to "method" section in the manuscript.

value: iPSC-derived neuron

tag: differentiation time

value: 3 weeks

tag: genotype/variation

value: Control (CHD8+/-)

tag: sample type

value: Bulk


title: DSS day 0_Csf1r-EP4-/- intestinal macrophage-3

status: Public on Nov 28 2019

type: SRA

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: colon

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: mice were orally administered 2.5% dextran sodium sulphate (DSS) in drinking water for 5 days

tag: strain

tag: tissue

value: colon

tag: marker


title: DSS day 0_Csf1r-EP4-/- intestinal macrophage-2


title: DSS day 0_WT intestinal macrophage-2

value: WT


title: DSS day 0_Csf1r-EP4-/- intestinal macrophage-1


title: CHD8_ChIPSeq_rep1

country: USA

description: processed data file: ChIP-seq-peaks.xlsx

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: ES-derived neuron

tag: chip-antibody

value: Anti HA:Rabbit-Sigma-H6908


title: ATAC-seq_CHD8-Control_CR1

description:
Biological replicate#1 called: CR1 neurons, differentiated from sub clone 1, which is an ES line.
processed data file: ATAC-seq-peaks.xlsx


title: RNA-seq_CHD8-Control_CR3

description:
Biological replicate#2 called: CR3 neurons, differentiated from sub clone 3, which is an iPS line.
PolyA mRNA
processed data file: Counts-RNA-seq-samples.txt
processed data file: RNA-seq-DEGs.xlsx


title: Input (is same for both ChIP experiments)


title: ATAC-seq_CHD8-Homozygous_KO_CR1


title: RNA-seq_CHD8-Homozygous_KO_CR3


title: RNA-seq_CHD8-Homozygous_KO_CR1

description:
Biological replicate#1 called: CR1 neurons, differentiated from sub clone 1, which is an ES line.
PolyA mRNA
processed data file: Counts-RNA-seq-samples.txt
processed data file: RNA-seq-DEGs.xlsx


title: RNA-seq_CHD8-Control_CR1


title: ATAC-seq_CHD8-Homozygous_KO_CR3


title: 2384

city: Durham

first: Alison

last: Harrill

state: NC

address: P.O. Box 12233, Mail Drop K2-17

institute: National Institute of Environmental Health Sciencees

data_processing:
Sequenced using Illumina HiSeq 2000
Samples with a read count lower than 1.5 million were excluded from further analyses. Output files in fastq format were uploaded to Partek Flow (Partek, St. Louis, MO) and underwent pre-alignment quality control.
The reads were trimmed and aligned using the STAR method.
DESeq2 differential gene expression analysis was performed on the raw gene counts in Partek Flow (Partek).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw and DESeq2 normalized gene counts for each sample

source_name: Zileuton_liver tissue

growth_protocol: Female Diversity Outbred (J:DO) mice at 6-20 weeks of age were kept in a specific pathogen free status standard barrier animal room and monitored monthly using in-room sentinel animals. Animals were acclimated on arrival for a minimum of two weeks; during this time, animals were weighed and randomized into test groups.

extract_protocol:
RNA was isolated from 25 mg of liver using the RNEasy Mini Kit  according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA purity and quality were assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) and RNA concentration was quantified using a Cytation 3 spectophotomerter (Biotek, Winooski, VT). Samples with an RNA Integrity Number (RIN) < 8 or 260/280 < 1.8 were excluded from further processing.
Extracted total RNA was used to prepare RNA-seq libraries using the TruSeq RNA Library Preparation kit v2 according to the manufacturer’s protocol and then sequenced using the Illumina HiSeq 2000

treatment_protocol: DO Mice received oral instillations of vehicle (sterile distilled water) or zileuton (300mg/kg) once daily for seven consecutive days.

value: Diversity Outbred (J:DO) mice

tag: animal id

tag: Sex

value: Female

tag: coat color

value: agouti

tag: exposure

value: Zileuton

tag: zileuton dose (mg/kg)

value: liver


title: 2377


title: 2379

value: white


title: 2348


title: 2397


title: CHD8_ChIPSeq_rep2

value: Anti CHD8 :Rabbit-Bethyl lab-A301-224A


title: 2238


title: 2289


title: 2350


title: 2393


title: 2300


title: 2194


title: 2293

value: black


title: 2279


title: 2236


title: 2333


title: 2199


title: 2389


title: 2192


title: 24-month_APP23_3

city: Hefei

first: Yong

last: Shen

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

country: China

data_processing:
Quality control: Illumina CASAVA version 1.8 was used for base calling.
Alignment: Sequencing read pairs were split into single nucleus RNA-seq read pairs based on the cell barcode in read2. Unique Molecular Identifiers (UMIs) were added in order to correctly identify PCR duplicates. Template switch oligo (TSO) sequence and ployA tail sequence in read1 were trimmed. After removing adapter contaminants and low-quality bases (N > 10%), we performed single-end alignment of read1 to mm10 mouse reference genome from UCSC using TopHat (version 2.0.12). Finally, Uniquely mapped reads were counted using the htseq-count script developed with HTSeq (version 0.6.0) .
genome build: mm10
processed data files format and content: mtx

molecule: polyA RNA

growth_protocol: Wild type (C57BL/6J) and APP23 transgenic mice (B6. Cg-Tg (Thy1-APP)3Somm/J) were fed ad libitum and maintained a regular light-dark cycle of 12 hours.

extract_protocol:
The hippocampus was first lysed and homogenized in EZ lysis buffer(Sigma, NUC101). with 0.4 U/μL RNasin Plus Ribonuclease inhibitor (Promega, N2615) and 0.2 U/μL SUPERase In RNase inhibitor (Life Technologies, AM2696) in a 7 mL Dounce tissue grinder to release the nuclei. The homogenized tissue was then filtered through a 40 μm cell strainer, washed and blocked with staining buffer (PBS containing 0.5% BSA and 0.2 U/μL RNasin Plus Ribonuclease inhibitor (Promega, N2615)) then stained using Rabbit recombinant monoclonal NeuN antibody (Abcam, EPR12763, 1:2000) and DAPI (Life Technologies) for neuronal nuclei and all nuclei, respectively. Both NeuN antibody and DAPI were diluted in staining buffer. The nuclei were then washed with staining buffer, re-suspended in 1 ml staining buffer, and proceeded directly to FACS sorting.
Single nuclei were vortexed for 90 s and incubated at 72℃ for 3 min to release all RNAs. The mRNAs were captured with barcoded reverse transcription primers with oligo-dT and UMIs and reverse-transcribed into first-strand cDNAs. The cDNAs were amplified using PCR, and products with different barcodes were pooled together. The index sequence with biotin was added to the 3’ ends of the pooled cDNA using PCR amplification. Following cDNA fragmentation using Covaris S220 Focused-ultrasonicator, Dynabeads MyOne Streptavidin C1 (Invitrogen, 65002) was used to capture the 3’ cDNAs and the sequencing libraries were constructed with Kapa Hyper Prep Kit (Kapa Biosystems, KK8505).

treatment_protocol: Mice were anesthetized with 2% pentobarbital sodium solution. Brain was removed from the skull after perfusion, the left hemisphere immediately placed on dry ice, and the right hemisphere immediately dissected for the hippocampus.

tag: genotype

tag: age

value: hippocampus

value: neuron


title: 2189


title: 2347


title: 2188


title: 24-month_APP23_2

institute: University of Science and Technology of China


title: 24-month_WT_2

value: wild type


title: 2186


title: 2200


title: 24-month_WT_1


title: 2187


title: 2180


title: 2177


title: 6-month_APP23_3


title: 2146


title: 2136


title: 6-month_APP23_2


title: 2131


title: 2130


title: 6-month_APP23_1


title: 2137


title: 6-month_WT_3


title: 2181


title: 2093


title: 2128


title: 2126


title: 6-month_WT_2


title: 6-month_WT_1


title: 24-month_APP23_1


title: 2183


title: 2089


title: 2083


title: 2082


title: 2075


title: 2047


title: 2046


title: 2043


title: 2045


title: 2025


title: 2037


title: 2367

source_name: Vehicle_liver tissue

value: Vehicle


title: 2368


title: 2365


title: 2318


title: 2270


title: 2366


title: 2129


title: 2317


title: 2319


title: 2098


title: 2266


title: 2217


title: 2269


title: 2264


title: 2216


title: 2090


title: 2166


title: 2218


title: 2215


title: 2214


title: 2213


title: 2364


title: 2164


title: 2116


title: 2163


title: 2118


title: 2117


title: 2115


title: 2167


title: 2068


title: 2113


title: 2066


title: 2067


title: 2065


title: 2267


title: 2064


title: 2019


title: 2063


title: 2018


title: 2017


title: 2013


title: 2014


title: 2165


title: shRASSF2-2_rep3

city: La Jolla

first: Sam

last: Stoner

address: 3855 Health Sciences Dr 0815

institute: University of California, San Diego

data_processing:
1) Paired-end reads were aligned to indexed hg38 reference genome using HISAT2 (v2.1.0).
2) For each sample, lane 1 and lane 2 BAM files were merged using Picard tools to produce one aligned BAM file per sample.
3) Gene-level counts for each sample were generated using featureCounts (v1.6.2).
4) Differential expression analysis was performed on Counts files (6 RASSF2-KD samples vs. 3 CTRL samples) using DESeq2 (v1.18.1).
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file is one excel sheet containing output of DESeq2 differential gene expression analysis in log2 fold-change (RASSF2-KD vs CTRL) ranked by adjusted p-values; normalized counts for all samples are also included.

source_name: THP-1 AML_shRASSF2-2

growth_protocol: THP-1 AML cells were maintained in RPMI supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to manufacturer's protocol, from 2.0 x 10^6 viable cells per condition, and resuspended in 30 ul RNAse-free sterile H20.
Library preparation and sequencing were performed by Novogene (Sacramento, CA). Post-QC, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Cells were selected in 1 ug/mL puromycin for 96 hours, following lentiviral transduction with indicated shRNA constructs.

tag: cell line

value: THP-1 AML

tag: trc shrna clone id


title: shRASSF2-2_rep1


title: shRASSF2-2_rep2


title: shRASSF2-1_rep3

source_name: THP-1 AML_shRASSF2-1


title: shCTRL_rep3

source_name: THP-1 AML_shCTRL

value: shCTRL


title: shRASSF2-1_rep2


title: WT Total Histone Mnase

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
SOLiD reads were mapped to sacCer3 using bfast-0.7.0a
Read counts per nucleotide were calculated using bamutils from NGSUtils
Average gene analysis were generated using ngs.plot
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited excel files includes averaged and normalized read counts across 100 points within a gene range of 500 bp upstream of the TSS and 1000bp downstream of the TSS and another file from 200bp upstream and 200bp dowstream of the termination end site

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: All cells were grown to an OD600 of 0.8

extract_protocol:
Mnase-seq
Mnase-seq protocol


title: shRASSF2-1_rep1


title: shCTRL_rep1


title: shCTRL_rep2


title: 2015


title: FHP

city: Duarte

first: Teresa

last: Ku

address: 1500 E Duarte Rd

department: Translational Research and Cellular Therapeutics

institute: City of Hope - Beckman Research Institute

description: CSC_PIN41_1_UN_Whole_C1_XCSCR_L24937_HGW73DSXX_S9_L001

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-hg19-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values file

source_name: Fetal pancreatic tissue

extract_protocol:
Single cell suspension was obtained from fresh human fetal pancreas by collagenase P digestion. 9,000 single cells were captured on a 10xGenomics Chromium controller using a Chromium single cell 3' library & Gel Bead kit V3 kit
Reverse transcription was performed in emulsion droplet with 10xGEM beads, full length of cDNA was amplified and 3' expression library was constructed with Tn5 transposase based method (with 10xGenomics chromium single cell 3' Library Constraction Kit V3).

tag: developmental stage

value: 15.4 weeks post conception

value: Pancreas


title: HrrA binding 0.5h after heme addition

city: Juelich

first: Andrei

last: Filipchyk

address: Wilhelm-Johnen-Straße

country: Germany

institute: FZ-Juelich

data_processing:
Data analysis and base calling were accomplished with the Illumina (MiSeq) instrument software and stored as fastq output files
The sequencing data obtained for each sample were imported into CLC Genomics Workbench (Version 9, Qiagen Aarhus A/S) for trimming and base quality filtering
The output was mapped to accession NC_003450.3 as C. glutamicum reference genome
Genomic coverage was convoluted with second order Gaussian kernel
The convolution profile was scanned in order to find points were first derivative changes its sign from positive to negative. This Points were considered as peaks and a score for each peak was set to the convolution value at he corressponding point
We fit the Gaussian curve to the distribution of peak scores (via optimize.fit function from SciPy packageand set a scopeak re thresholds equal mean + 4 sigmas of the fitted distribution
Genome_build: NC_003450.3
Supplementary_files_format_and_content: Processed data are in standard  bed format (6 fields) format representing genomic positions of the peaks. Please note, that reported peaks are unstranded, even though strand is set to ‘+’ for the reported peaks

organism: Corynebacterium glutamicum

source_name: precultures

growth_protocol: A preculture (C. glutamicum::hrrA-C-twinstrep) was inoculated in liquid BHI medium from a fresh BHI agar plate and incubated for 8-10 h at 30°C in a rotary shaker. After that, cells were transferred into a second preculture in CGXII medium containing 2 % (w/v) glucose and 0 µM FeSO4 to starve the cells from iron protocatechuic acid (PCA), which was added to the medium, allowed the uptake of trace amounts of iron. From an overnight culture, the main cultures were inoculated (CGXII medium containing 4µM heme) and harvested 0h, 0.5h, 2h, 4h, 9h or 24h after inoculation.

extract_protocol:
For cell disruption, the pellet was resuspended buffer A containing “cOmplete” protease inhibitor cocktail (Roche, Germany) and passed through a French pressure cell (SLM Ainco, Spectronic Instruments, Rochester, NY) five times at 172 MPa. The DNA was fragmented to ~500 bp by sonication (Branson Sonifier 250, Branson Ultrasonics Corporation, Connecticut, USA) and the supernatant was collected after ultra-centrifugation (150.000 x g, 4 °C, 1 h). The DNA-bound by the twin-Strep tagged HrrA protein was purified using Strep-Tactin XT Superflow column material (IBA Lifesciences, Göttingen, Germany) according to the supplier’s manual (applying the gravity flow protocol, 1.5 ml column volume). Washing of the column was performed with buffer W (100 mM Tris-HCl, 1 mM EDTA, 250 mM NaCl, pH 8,0) and the tagged protein was eluted with buffer E (100 mM Tris-HCl, 1 mM EDTA, 250 mM NaCl, pH 8.0, added 50 mM D-Biotin). After purification, 1 % (w/v) SDS was added to the elution fractions and the samples were incubated overnight at 65°C. For the digestion of protein, 400 µg/ml Proteinase K (AppliChem GmbH, Darmstadt, Germany) was added and incubated for 3 h at 55 °C. Subsequently, the DNA was purified as following: Roti-Phenol/Chloroform/Isoamyl alcohol (Carl Roth GmbH, Karlsruhe, Germany) was added to the samples in a 1:1 ratio and the organic phase was separated using Phase Lock Gel (PLG) tubes (VWR International GmbH, Darmstadt, Germany) according to the supplier’s manual. Afterwards, the DNA was precipitated by adding ice cold ethanol (to a conc. of 70 %) and centrifugation at 16.000 x g, 4 °C for 10 min. The DNA was washed with ice cold 70 % ethanol, then dried for 3 h at 50 °C and eluted in dH2O.
The resulting DNA was used for library preparation and indexing using the TruSeq DNA PCR-free sample preparation kit (Illumina, California, USA) according to the manufacturer’s instructions, only skipping fragmentation of the DNA. The resulting libraries were quantified using the KAPA library quant kit (Peqlab, Bonn, Germany) and normalized for pooling.

treatment_protocol: After 0 h, 0.5 h, 4 h, 9 h and 24 h, cells corresponding to an OD600 of 3.5 in 1 l were harvested by centrifugation at 4 °C, 5000 x g and washed once in 20 ml CGXII (without MOPS). Subsequently, the cell pellet was resuspended in 20 ml CGXII (without MOPS) containing 1 % (v/v) formaldehyde to crosslink the regulator protein to the DNA. After incubation for 20 min at RT, the cross linking was stopped by addition of glycine (125 mM), followed by an additional 5 minutes of incubation. After that, the cells were washed three times in buffer A (100 mM Tris-HCl, 1 mM EDTA, pH=8.0) and the pellets stored overnight at -80 °C.

tag: time point

tag: medium

value: CGXII

tag: heme concentration


title: Morphine rep5

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 12
MOR5

data_processing:
Reads were trimmed for quality using Trimmomatic (PMID:24695404)
The trimmed reads were then aligned to the mm10 mouse reference genome (obtained from Ensembl) to generate BAM formatted alignment files using STAR (PMID:23104886).
Subread featureCounts (PMID:24227677) was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl.
Counts per millions were calculated. Differential gene expressionanalysis was performed in R using limma (PMID:25605792)and edgeR (PMID:19910308) based on the gene counts output from Subread.
Genome_build: mm10
Supplementary_files_format_and_content: The file "NOWsCount.txt" a matrix table containing the raw count for each gene for each of the 12 samples.

source_name: brain

extract_protocol:
The spinal cords were removed and stored in RNA-later for RNA-extraction uisng Trizol reagent. 1 ug of total RNA was used for contruction of the sequecing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed on an Illumina NovaSEQ6000, using a NovaSEQ SP-100bp flowcell / reagent cassette. A pool of 12 samples  was sequenced on one lane of the flowcell.

tag: strain

value: CFW

tag: tissue

value: brainstem

value: Male

tag: agent

value: Morphine


title: HrrA binding 4h after heme addition


title: Morphine rep2

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 9
MOR2

value: Female


title: Saline rep6

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 7
SAL6

value: Saline


title: Morphine rep6

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 13
MOR6


title: Morphine rep4

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 11
MOR4


title: HrrA binding 2h after heme addition


title: Morphine rep1

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 8
MOR1


title: Saline rep5

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 6
SAL5


title: HrrA binding 9h after heme addition


title: Morphine rep3

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 10
MOR3


title: Saline rep3

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 4
SAL3


title: Saline rep2

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 3
SAL2


title: Saline rep1

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 2
SAL1


title: HrrA binding before heme addition


title: C1 strain AWRI R2 was cultivated  with 1.0 g/L PAs

city: Qingdao

first: Hongwei

last: Zhao

address: No.53 Zhengzhou Rd., Qingdao, China

institute: Qingdao University of Science and Technology

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
Trimmomatic (v0.30) was used for remove of technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20  to generate high quality clean data. For mapping stage,  reference genome sequences and gene model annotation files of S. cerevisiae S288C were downloaded from genome website and then Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05.We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Genome_build: Saccharomyces cerevisiae S288C   https://www.ncbi.nlm.nih.gov/genome/15?genome_assembly_id=22535
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

source_name: yeast cells

growth_protocol: Saccharomyces cerevisiae strain AWRI R2 was cultivated in model synthetic medium (MSM) supplemented with 0 g/L, 0.1g/L, 1.0 g/L PAs, respectively at 28°C for 72 h.

extract_protocol:
Yeast cells were grinded in liquid nitrogen. Total RNA of each sample was extracted using RNeasy Mini Kit (Qiagen).
One microgram of total RNA passing the quality test was used for library preparation based on the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).
After quantity and quality evaluation, Illumina HiSeq sequencing platform was employed for the library sequencing at GENEWIZ (Suzhou, China).

treatment_protocol: Ten milliliter of the fermentation broth was centrifuged at 6000 r/min for 5 min to collect the yeast cell pellets. The obtained yeast cells were washed 3 times with 0.9 % sodium chloride solution and rapidly frozen in liquid nitrogen before stored at -80°C for the following experiments.

value: AWRI R2

tag: treatment

value: 1.0 g/L PAs


title: B3 strain AWRI R2 was cultivated  with 0.1 g/L Pas

value: 0.1 g/L PAs


title: C3 strain AWRI R2 was cultivated  with 1.0 g/L PAs


title: C2 strain AWRI R2 was cultivated  with 1.0 g/L PAs


title: B2 strain AWRI R2 was cultivated  with 0.1 g/L Pas


title: B1 strain AWRI R2 was cultivated  with 0.1 g/L Pas


title: A3 strain AWRI R2 was cultivated  with 0 g/L PAs

value: 0 g/L PAs


title: HrrA binding 24h after heme addition


title: A2 strain AWRI R2 was cultivated  with 0 g/L PAs


title: A1 strain AWRI R2 was cultivated  with 0 g/L PAs


title: Saline rep4

description:
The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.
NOWScunts.txt_column 5
SAL4


title: Hippuristanol / DMS(+) replicate 2

status: Public on Nov 26 2019

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

country: United Kingdom

institute: Beatson Institute for Cancer Research

data_processing:
Library strategy: Structure-seq 2
The fastq_trimmer.py script from the StructureFold2 pipeline was used to remove 5’ and 3’ adapters, to trim bases from the 3’ end with a NextSeq quality score below 30  and to remove any reads that were less than 20nt after trimming. This script uses cutadapt.
Trimmed and filtered reads were mapped to the MCF7 specific transcriptome using bowtie2
sam_filter.py from the StructureFold2 pipeline was used to filter any mapped reads that contain more than 4 mismatches or that have a mismatch at position 1, which could have resulted from the addition of a random nt to the 3’ end of the cDNA prior to ligation. This script uses samtools.
The sam_to_rtsc.py script from the StructureFold2 pipeline was used to generate <.rtsc> files from each filtered <.sam> file generated in the previous step. Each <.rtsc> file contains the number of reverse transcriptase stops at each position of every transcript
The rtsc_to_react.py script from the StructureFold2 pipeline was used to generate <.react> files for each sample. The script uses a DMS(-) and DMS(+) <.rtsc> file to generate a <.react> file which contains the normalised reactivity for every adenine and cytosine within every transcript. The scale file generated from sample control_1 was used to scale all remaining samples
Genome_build: An MCF7 specific transcriptome was downloaded from http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/list.html
Supplementary_files_format_and_content: <.rtsc> files are flat text files containing reverse transcriptase stop counts, with three lines for every transcript. The first line contains the transcript ID. The second line contains tab seperated values indicating the number of reverse transcriptase stops at every position within the transcript. The third line is blank.
Supplementary_files_format_and_content: <.react> files are flat text files containing normalised reactivity values, with two lines for every transcript. The first line contains the transcript ID. The second line contains tab seperated values indicating the normalised reactivity for every adenine and cytosine in the transcript. Guanines and uracils are represented with "NA".

source_name: Adherent breast cancer cell line

growth_protocol: MCF7 cells grown in DMEM, high glucose, GlutaMAX Supplement, pyruvate (ThermoFisher 31966-021), supplemented with 10% FCS

extract_protocol:
RNA was extracted with TRIzol (ThermoFisher 15596026) as per manufacturer's instructions followed by isopropanol precipitation
120 µg total RNA per sample was subjected to two rounds of poly(A) selection with the Poly(A)Purist MAG Kit (AM1922), as per manufacturer's instructions. Poly(A) RNA was dissolved in 17 µl TE (10mM Tris-HCl pH7.5, 1mM EDTA). 1 µl was used to run on Bioanalyzer with the mRNA Nano assay to confirm removal of rRNA and 1 µl was used to determine RNA concentration with a nanodrop. The remaining 15 µl (typically slightly more than 1µg) was used in the following reverse transcription step. For each sample, 1 µg of poly(A) RNA was diluted to 15 µl and mixed with 2 µl of the N6 linker oligo: 5’CAGACGTGTGCTCTTCCGATCNNNNNN3’ (100 µM) and 3 µl KCl (1M) and split between 2 x 10 µl. RNA was denatured in a thermal cycler at 90°C for 1 min before rapidly cooling to 4°C and held for 1 min. Temperature was increased to 25°C and 4 µl 5X buffer (100mM Tris-HCl pH 8.4, 25mM MgCl2, 25mM DTT, 2.5mM dNTPs), 5 µl nuclease free water and 1 µl SuperScript III (200U/µl) (Thermo Fisher 18080085) was added to each 10 µl sample. Samples were incubated for 5 min at 25°C to promote annealing and to allow slight extension of RT primers, followed by 5 min at 42°C for further extension and finally 55°C for 50 min for full extension. Samples were then heated at 85°C for 5 min to denature the enzyme, followed by addition of 2 µl NaOH (1M) and incubation at 95°C for 10 min to hydrolyse the RNA. Samples were purified by gel extraction with an 8% polyacrylamide, 1mm thick denaturing gel. To ensure maximal removal of the N6 linker, which can form an unwanted byproduct if not removed, cDNA running above an N78 ssDNA oligo was purified, which should run 50nt higher than the N6 linker. cDNA was dissolved in 5.5 µl Tris-HCl (pH 8.0). To the 5.5 µl cDNA was added 0.5 µl hairpin donor oligo /5Phos/TGAAGAGCCTAGTCGCTGTTCANNNNNNCTGCCCATAGAG/3SpC3/ (400 µM), 2 µl betaine (5M) and 8 µl 50% PEG 8000 (added last and at room temperature to avoid precipitating DNA). Samples were heated at 95°C for 90sec and allowed to cool slowly to room temperature. 2 µl 10X T4 DNA ligase buffer and 2 µl T4 DNA ligase (400U/µl) (NEB M0202S) were added and the samples were incubated at 16°C for 6h followed by 30°C for 6h and then 65°C for 10 min to denature the enzyme. Samples were purified by gel extraction with a 6% polyacrylamide, 1mm thick denaturing gel and cDNA running above an N118 ssDNA oligo was purified; this oligo should run 50nt above any ligated N6 linker. Ligated cDNA was dissolved in 18 µl Tris-HCl (pH 8.0). To determine the number of PCR cycles required, 25 µl reactions were set up with 5 µl taken from the samples at cycles 11, 14, 17, 20 and 23 and the amplified DNA was run on a 5% polyacrylamide denaturing gel. Reactions were set up with 5 µl 1X Q5 buffer, 5 µl GC rich enhancer buffer, 0.5 µl dNTPs (10mM each), 0.25 µl Q5 Hot Start High-Fidelity DNA Polymerase (2000U/ml) (NEB M0493L), 1 µl Truseq forward primer: 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTGAACAGCGACTAGGCTCTTCA3’ (10 µM), 1 µl relevant Truseq reverse primer: 5’CAAGCAGAAGACGGCATACGAGATBARCODEGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC3’ (10 µM), 4.5 µl ligated cDNA and 7.75 water. Reactions were activated at 98°C for 30sec followed by cycling between 98°C for 10sec and 72°C for 45sec. It was determined that 17 cycles was optimal, as this was the first cycle where the product was visible on the gel. The remaining samples were amplified in 3 x 25 µl reactions as above, for 17 cycles plus a final extension time of 5 mins at 72°C and then combined and gel purified on a 5% polyacrylamide, 1.5mm thick denaturing gel. Resultant PCR products running between ~200-600nt, as determined with ss50 ladder (Simplex Sciences) were purified and dissolved in 20 µl Tris-HCl (pH 8.0). Samples were run on the Bioanalyzer with the high sensitivity DNA assay to ensure the size of the libraries was as expected with minimal byproduct contamination.

treatment_protocol: Cells were treated for 1h with 150nM hippuristanol or an equal volume of DMSO (0.07%) by replenishment of the growth media. Following 1h incubation, media was replaced with PBS with or without  50mM dimethyl sulphate (DMS) for 10min. PBS was then replaced with PBS containing 250mM DTT to quench the DMS, followed by extraction of the RNA with TRIzol

tag: dms

value: yes

tag: hippuristanol treatment


title: Hippuristanol / DMS(+) replicate 3


title: Hippuristanol / DMS(+) replicate 1


title: Line 1, Flight rep1 [FB1]

status: Public on Nov 07 2019

city: Stanford

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
Raw reads were aligned by HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml)(Kim et al., 2015) to human genome (hg38).
Aligned reads were quantitated by FeatureCounts (http://bioinf.wehi.edu.au/featureCounts/) with the annotation of ENSEMBL 85.
Normalization and differentially expressed genes test were implemented by DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) (Liao et al., 2014; Love et al., 2014).
Supplementary_files_format_and_content: table of normalized log2 transformed expression.

source_name: hiPSC-CM_4.5 weeks microgravity exposure

growth_protocol: Three hiPSC lines were generated using a previously published Sendai virus reprogramming protocol on peripheral blood mononuclear cells from three healthy individuals (Churko et al., 2013). These hiPSC lines were differentiated into hiPSC-CMs using a 2D monolayer differentiation protocol and were maintained in a 5% CO2/air environment as previously described (Lian et al., 2012; Sun et al., 2012)

extract_protocol:
RNALater (Thermo Fisher) was used to preserve flight samples designated for downstream RNA-sequencing analysis. Samples preserved in RNALater were stored at 4°C until return to our laboratory, when RNA was isolated from preserved wells in the BioCells using RNeasy kit (Qiagen) following the manufacturer’s protocol. DNase treatment was performed using RNase-free DNase kit (Qiagen). All RNA samples had RNA integrity number ≥ 8.9 and concentration ≥ 48 ng/µL (Agilent 2100 Bioanalyzer).
Library prep and sequencing were performed by BGI with 30-40 million paired-end 100bp reads per sample on the Illumina HiSeq platform.

tag: cell line source

value: hiPSC line1

tag: cell type

value: hiPSC-derived cardiomyocytes

value: 4.5 weeks microgravity exposure


title: HNSCC_14_PBMC

status: Public on Nov 13 2019

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Demultiplexing using CellRanger mkfastq
Alignment and generation of gene/barcode matrices using CellRanger count
Genome_build: GRCh38
Supplementary_files_format_and_content: files containing gene/barcode matrices

source_name: peripheral blood

extract_protocol: 10x 3' v2 scRNAseq

treatment_protocol: Ficoll density gradient centrifugation to isolate peripheral blood mononuclear cells from whole blood; mechanical distruption of tissues; live CD45+ single cells were sorted from all samples using a Beckman Coulter MoFlo Astrios.

value: peripheral blood

tag: disease state

value: Head and neck squamous cell carcinoma (HNSCC)


title: Hippuristanol / DMS(-) replicate 2

value: no


title: Hippuristanol / DMS(-) replicate 1


title: Control / DMS(-) replicate 1


title: Control / DMS(-) replicate 2


title: Control / DMS(-) replicate 3


title: Control / DMS(+) replicate 2


title: HNSCC_15_TIL

source_name: tumor tissue

value: tumor tissue


title: Control / DMS(+) replicate 1


title: Hippuristanol / DMS(-) replicate 3


title: Control / DMS(+) replicate 3


title: CSF_HC15

status: Public on Nov 04 2019

first: Olivia

last: Leventhal

state: California (CA)

address: 1201 Welch Road, rm p220

department: Neurology

institute: Stanford University

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped alligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples  were merged into one Seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: tar archive for each sample containing expression matrix, cellbarcodes, and genes

source_name: cerebrospinal fluid derived cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' Expression library kit.

value: cerebrospinal fluid

value: immune cells

tag: diagnosis

value: HC


title: CSF_HC14


title: HNSCC_15_PBMC


title: CSF_HC13


title: CSF_HC16


title: CSF_HC17


title: CSF_HC12


title: CSF_HC10


title: CSF_HC9


title: CSF_HC11


title: DNase-seq from breast epithelium (ENCLB231MGC)

status: Public on Nov 01 2019

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR600KUR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR600KUR
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2018-01-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB231MGC
instrument models: Illumina NextSeq 500,Illumina HiSeq 4000

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens female adult (51 year) breast epithelium tissue

value: breast epithelium

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 51 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Kristin Ardlie

tag: link

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS608BDX at ENCODE; https://www.encodeproject.org/ENCBS608BDX/


title: Histone ChIP-seq from right atrium auricular region (ENCLB420NQD)

description:
https://www.encodeproject.org/experiments/ENCSR954TSY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR954TSY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB420NQD
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) right atrium auricular region tissue

tag: antibody

value: right atrium auricular region

tag: description

value: EnTEX:Heart - Atrial Appendage

value: Bradley Bernstein, Broad

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Histone ChIP-seq from right atrium auricular region (ENCLB375ZSE)

description:
https://www.encodeproject.org/experiments/ENCSR668EVA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR668EVA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375ZSE
fragmentation methods: sonication (generic)
size range: 200-600


title: HNSCC_14_TIL

tag: tissue

value: tumor tissue

value: Head and neck squamous cell carcinoma (HNSCC)


title: ATAC-seq from sigmoid colon (ENCLB070YZI)

description:
https://www.encodeproject.org/experiments/ENCSR548QCP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human sigmoid colon
experiment encode accession: ENCSR548QCP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB070YZI
size range: 150-250

source_name: Homo sapiens sigmoid colon tissue male adult (37 years)

value: sigmoid colon

value: male

value: Michael Snyder, Stanford

value: 37 year

value: ENCBS919RQL at ENCODE; https://www.encodeproject.org/ENCBS919RQL/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: DNase-seq from prostate gland (ENCLB989JVY)

description:
https://www.encodeproject.org/experiments/ENCSR958QXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR958QXU
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB989JVY

source_name: Homo sapiens male adult (37 years) prostate gland tissue

value: prostate gland

value: tissue

value: adult

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS195BWE at ENCODE; https://www.encodeproject.org/ENCBS195BWE/


title: Histone ChIP-seq from right atrium auricular region (ENCLB211HPE)

description:
https://www.encodeproject.org/experiments/ENCSR668EVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR668EVA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB211HPE
fragmentation methods: none
size range: 200-600

value: right atrium auricular region

value: female

value: 51 year

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS088JMY at ENCODE; https://www.encodeproject.org/ENCBS088JMY/


title: ATAC-seq from breast epithelium (ENCLB095HXE)

description:
https://www.encodeproject.org/experiments/ENCSR846ZBX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human breast epithelium
experiment encode accession: ENCSR846ZBX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB095HXE
size range: 150-250

source_name: Homo sapiens breast epithelium tissue female adult (51 year)

value: breast epithelium

value: ENCBS824TRN at ENCODE; https://www.encodeproject.org/ENCBS824TRN/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ATAC-seq from right atrium auricular region (ENCLB165YSS)

description:
https://www.encodeproject.org/experiments/ENCSR062SVK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right atrium auricular region
experiment encode accession: ENCSR062SVK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-06-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB165YSS
size range: 150-250

value: Michael Snyder, Stanford

value: ENCBS900DWT at ENCODE; https://www.encodeproject.org/ENCBS900DWT/


title: DNase-seq from upper lobe of left lung (ENCLB048EBD)

description:
https://www.encodeproject.org/experiments/ENCSR164WOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR164WOF
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB048EBD

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: male

value: 37 year

value: John Stamatoyannopoulos, UW

value: ENCBS974IWX at ENCODE; https://www.encodeproject.org/ENCBS974IWX/


title: DNase-seq from tibial artery (ENCLB186SIN)

description:
https://www.encodeproject.org/experiments/ENCSR332MRT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332MRT
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB186SIN

source_name: Homo sapiens male adult (37 years) tibial artery tissue

value: tibial artery

value: tissue

value: adult

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS123ZWB at ENCODE; https://www.encodeproject.org/ENCBS123ZWB/


title: DNase-seq from tibial nerve (ENCLB321BCS)

description:
https://www.encodeproject.org/experiments/ENCSR754WNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR754WNA
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB321BCS

source_name: Homo sapiens male adult (37 years) tibial nerve tissue

value: tibial nerve

value: Kristin Ardlie

value: ENCBS127DSW at ENCODE; https://www.encodeproject.org/ENCBS127DSW/


title: DNase-seq from Peyer's patch (ENCLB574TGJ)

description:
https://www.encodeproject.org/experiments/ENCSR954AJK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954AJK
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB574TGJ
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens male adult (37 years) Peyer's patch tissue

value: Peyer's patch

value: ENCBS473KRY at ENCODE; https://www.encodeproject.org/ENCBS473KRY/


title: DNase-seq from esophagus muscularis mucosa (ENCLB226AJD)

description:
https://www.encodeproject.org/experiments/ENCSR944JCE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR944JCE
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB226AJD

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: ENCBS721REO at ENCODE; https://www.encodeproject.org/ENCBS721REO/


title: PBMC_Control_OW_95

type: RNA

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

hyb_protocol: Nanostring GX protocol

scan_protocol: Nanostring nCounter platform

data_processing: nSolver QC algorithm

source_name: PBMC

label_protocol: Nanostring GX protocol

extract_protocol: miRvana - total RNA

treatment_protocol: PBMC samples obtained under the “Brain‐Gut Interactions in Overweight and Normal Weight Patients with Chronic Abdominal Pain” clinical cohort natural history protocol (09-NR-0064)

tag: ibs subtype

value: Control

tag: weight

value: Overweight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

value: M

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_90

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

value: F


title: PBMC_IBSD_OW_96

value: IBS-D

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_98

tag: ibs subtype

tag: weight

value: Normal

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSC_NW_99

value: IBS-C

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_22

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: DNase-seq from esophagus squamous epithelium (ENCLB661JJQ)

description:
https://www.encodeproject.org/experiments/ENCSR783OCW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR783OCW
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB661JJQ
instrument models: Illumina NextSeq 500,Illumina HiSeq 4000

source_name: Homo sapiens male adult (37 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: tissue

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 37 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

tag: link

value: ENCBS387LKB at ENCODE; https://www.encodeproject.org/ENCBS387LKB/


title: PBMC_Control_OW_86

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSC_OW_84

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_87

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_21

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_92

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_17

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_11

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_82

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_83

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: DNase-seq from right atrium auricular region (ENCLB697VHV)

description:
https://www.encodeproject.org/experiments/ENCSR278SKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR278SKG
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB697VHV
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500

value: right atrium auricular region

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

tag: age

value: 51 year

tag: lab

tag: source

value: Kristin Ardlie

tag: link

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS251FWW at ENCODE; https://www.encodeproject.org/ENCBS251FWW/


title: PBMC_Control_NW_120

tag: ibs subtype

value: Control

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

value: F

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_81

tag: ibs subtype

tag: weight

value: Overweight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_80

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)

value: M


title: PBMC_Control_NW_88

tag: ibs subtype

tag: weight

value: Normal

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_24

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_NW_118

tag: ibs subtype

value: IBS-C

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_78

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_63

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_77

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSD_OW_61

tag: ibs subtype

value: IBS-D

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_126

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSD_OW_45

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_124

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_121

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_OW_44

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_122

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_115

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_34

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_36

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_31

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_56

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_13

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSD_OW_38

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_37

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSC_OW_112

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_76

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_26

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_33

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_29

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_NW_69

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSC_NW_27

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_28

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_NW_32

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSC_OW_71

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_127

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_68

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_67

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSD_NW_65

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_OW_66

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_52

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSC_OW_64

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_109

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSC_NW_59

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_106

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_79

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSD_NW_42

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSC_NW_102

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSD_OW_74

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSD_OW_41

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_85

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_NW_58

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSD_NW_55

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_54

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_5

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSD_NW_46

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_7

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_4

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_6

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSC_OW_101

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_OW_73

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_39

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_70

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_40

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_108

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_25

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSD_OW_47

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_18

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_49

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_14

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_12

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_103

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_OW_9

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_NW_8

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_IBSD_NW_53

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_IBSC_NW_111

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_IBSC_NW_110

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_NW_57

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_51

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: PBMC_Control_OW_72

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: PBMC_Control_OW_116

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)


title: PBMC_Control_NW_19

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: lipopolysaccharide binding protein (lbp) (pg/ml)

tag: soluble cd14 (scd14) (ng/l)

tag: serum il10

tag: hematocrit (%)

tag: mean corpuscular hemoglobin (mch)(picograms hemoglobin/red blood cell)

tag: lymphocytes (x10^9 cells/l)

tag: neutrophil_pct (%)

tag: neutrophils (x10^9 cells/l)

tag: platelets (x10^9/l)


title: GHE2098 [CNV]

status: Public on Oct 24 2019

type: genomic

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

country: France

institute: Hospices Civils de Lyon

description:
Characteristics definitions:
ID: sample ID
AGE: age at diagnosis
SEX: male (M) or female (F)
TREATMENT: treatment line used
IPI: calculated IPI
Age_Adjusted_IPI: calculated age-adjusted IPI
PFS_TIME: duration of progression free survival (PFS) in months
CENS_PFS: coded as 0 if PFS event, 1 if not
OS_TIME: duration of overall survival (OS) in months
CENS_OS: coded as 0 if OS event, 1 if not
COO: cell of origin according to Affymetrix GeneChip arrays as described in methods

hyb_protocol: Hybridization was performed according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505C, with FeatureExtraction version 10.5.1.1 (59 arrays), 10.7.1.1 (50 arrays) or 10.7.3.1 (110 arrays, please refer to the provided raw files for details).

data_processing: Agilent FeatureExtraction files were parsed and processed using the standard cghRA 1.6.0 protocol (GRCh37 probe remapping, fresh log2-ratio computation from « processedSignal » columns, flagged probe masking, summarization of replicated probes by their medians and WACA correction of wave artifacts). No normalization nor background-correction was applied to log-ratios provided in the data matrix.

source_name: DLBCL tumor biopsy, patient GHE-2098

label_protocol: 2µg of Whole-Genome Amplified (WGA) DNA were labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (pooled normal male DNA; Promega, Madison, WI) was labeled with cyanine-3 (Cy3).

extract_protocol: Genomic DNA was extracted from frozen tissues using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by spectrometry and agarose gel electrophoresis.

tag: ID

tag: tissue

value: DLBCL tumor biopsy

tag: age

tag: Sex

value: FEMALE

tag: treatment

value: R-ACVBP+Conso

tag: ipi

tag: coo

value: Other

source_name: PROMEGA reference DNA pool (male)

value: male


title: PBMC_IBSC_NW_43

tag: ibs subtype

tag: weight

tag: serum cortisol (ug/dl)

tag: plasma corticotrophin (acth) (pg/ml)

tag: c-reactive protein (crp) (mg/ml)

tag: erythrocyte sedimentation rate (esr)

tag: mean platelet volume (mpv)

tag: ldh

tag: monocytes (x10^9 cells/l)

tag: monocytes_pct (%)

tag: basophil_pct (%)

tag: basophils (x10^9 cells/l)

tag: eosinophil_pct (%)

tag: eosinophils (x10^9 cells/l)

tag: lymphocytes_pct (%)

tag: red blood cells (rbc) (trillion cells/l)

tag: white blood cells (wbc) (x10^9 cells/l)

tag: gender

tag: body mass index (bmi) (kg/m^2)


title: GHE2132 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2132

tag: ID

tag: tissue

tag: age

tag: Sex

value: MALE

tag: treatment

tag: ipi

tag: coo


title: GHE2026 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2026

value: ABC


title: GHE2023 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2023

value: GC


title: GHE2017 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2017


title: GHE2109 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2109


title: GHE2037 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2037


title: GHE2100 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2100


title: GHE2119 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2119


title: GHE2012 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2012


title: GHE2121 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2121


title: GHE2096 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2096


title: GHE2019 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2019


title: GHE2030 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2030


title: GHE2106 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2106


title: GHE2003 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2003


title: GHE2084 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2084


title: GHE1501 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1501

source_name: PROMEGA reference DNA pool (male)


title: GHE2005 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2005


title: GHE1450 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1450


title: GHE2002 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2002


title: GHE1554 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1554


title: GHE1498 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1498


title: GHE1440 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1440


title: GHE1537 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1537


title: GHE1553 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1553


title: GHE1521 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1521


title: GHE2127 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2127


title: GHE2036 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-2036


title: GHE1560 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1560


title: GHE1438 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1438


title: GHE1437 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1437


title: GHE1424 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1424


title: GHE1374 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1374

value: ACVBP


title: GHE1393 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1393

source_name: PROMEGA reference DNA pool (male)


title: GHE1390 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1390

value: PMBL


title: GHE1409 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1409


title: GHE1348 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1348


title: GHE1385 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1385


title: GHE1376 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1376


title: GHE1373 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1373


title: GHE1369 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1369


title: GHE1360 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1360


title: GHE1353 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1353


title: GHE1287 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1287


title: GHE1352 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1352


title: GHE1225 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1225


title: GHE1222 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1222


title: GHE1209 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1209


title: GHE1379 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1379


title: GHE1302 [CNV]

source_name: DLBCL tumor biopsy, patient GHE-1302