title: Participant ID and visit (v) # phchp248v5 Independent Discovery Cohort (n=36) (91 visits)


title: RNA-Seq CTL2

status: Public on Mar 15 2019

type: SRA

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

library_source: transcriptomic

data_processing:
For RRBS data, the adapter sequences and low quality base calls (< 30) were trimmed from the 3’ end using Trim_Galore program with –rrbs option.
The bisulfite converted sequencing reads were then aligned to the mouse reference genome (mm10) using Bismark program.
For mRNA-Seq data, adaptor and lower-quality bases were trimmed with Trim-galore.
Reads were aligned to the Gencode mouse genome (GRCm38) using STAR-2.4.1d.
Read counts for each sample was obtained using HTSeq-0.6.1 (htseq-count).
Genome_build: mm10
Supplementary_files_format_and_content: RRBS: Bismark coverage file, mRNA-Seq: HTSeq count file

molecule: total RNA

organism: Mus musculus

source_name: Six2+ cells from kidney

extract_protocol:
Genomic DNA was extracted from whole kidneys using Puregene Core Kit A (Qiagen). RNA was isolated using RNeasy mini kit (Qiagen).
Genome wide DNA methylome analysis was performed of using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode) following manufacturer’s instruction. 200ng total RNA was used to isolate poly A purified mRNA using the Illumina TruSeq RNA Preparation Kit.

tag: strain

tag: tissue

value: kidney

tag: age

tag: genotype

value: Dnmt1 f/f


title: RNA-Seq CTL3


title: YeO:8 (8081v) 25°C stationary growth phase, enriched 2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

description: enriched for primary transcripts

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: NC_008800.1 Yersinia enterocolitica subsp. enterocolitica 8081; CP030980/CP030981 Yersinia enterocolitica subsp. Y1
Supplementary_files_format_and_content: *.tab files: CSV format with raw read counts per gene; tar-Archive DESeq2_results.tar.gz with  DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

organism: Yersinia enterocolitica

source_name: in vitro culture

growth_protocol: bacteria were grown in LB medium

extract_protocol:
total RNA was isolated using hot phenol extraction
cDNA libraries were constructed using NEBNext Multiple Small RNA Library Prep Set (New England Biolabs)

treatment_protocol: Purification of mRNA was done using human/mouse/rat ScriptSeq complete kit (Illumina). Following the purification, the RNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).

tag: grwoth condition

value: 25C, exponential growth phase


title: YeO:8 (8081v) 25°C exponential growth phase, not enriched 2

description: not enriched for primary transcripts


title: Participant ID and visit (v) # phchp243v4 Independent Discovery Cohort (n=36) (91 visits)

type: RNA

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

country: USA

institute: Indiana University Medical School

description:
Discovery Cohort Blood Gene Expression
We used three independent cohorts: discovery (major psychiatric disorders with changes in state stress), validation (major psychiatric disorders with clinically severe trait and state stress), and testing (an independent major psychiatric disorders cohort for predicting state stress, and for predicting trait future hospitalization visits with stress as the primary reason)
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a self-report visual analog scale (1-100) for quantitatively assessing state stress at that particular moment in time (Simplified Stress Scale- SSS), which has 4-items (Life Stress, Financial Stress, Health Stress and Social Stress). We also administered the PTSD Checklist- Civilian Version (PCL-C) scale, which measures clinical severity of trait stress symptoms over the month preceding testing. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing

hyb_protocol: Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.

scan_protocol: Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values

data_processing: The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis.  We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and  statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.

label: Biotin

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Sample Labeling:  Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps:     1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.    2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA.    3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.    4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step.    5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol: Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

tag: gender-diagnosis

value: M-PTSD

tag: vas stress score (1-100)


title: RNA-Seq CTL1


title: RRBS Adult3

library_source: genomic

molecule: genomic DNA

value: 6 weeks

value: wild type


title: 1c_NKG2DLpos

city: Basel

first: Claudia

last: Lengerke

address: Hebelstr. 20

department: Department of Biomedicine

country: Switzerland

institute: University Hospital Basel and University of Basel

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression W ash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.6 (both Agilent Technologies), Excel 2010 (Microsoft) and the IMGM internal tool marfin v1.9 were used for quality control, statistical data analysis, filtering of differentially expressed transcript, RNA annotation and visualization.

source_name: CD34 expressing AML, sorted fraction: NKG2DLpos

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies). All steps were carried out according to manufacturer’s instructions. cRNA concentration (ng/μl), RNA absorbance ratio (A260nm/A280nm) and Cyanine-3 dye concentration (pmol/μl) were recorded for all cRNA samples using NanoDrop ND-1000 UV- VIS spectrophotometer. Yield and specific activity of each reaction were determined. The RNA 6000 Nano LabChip Kit (Agilent Technologies) was used on the 2100 Bioanalyzer to analyze the quality of labeled non-fragmented cRNA.

growth_protocol: Standard protocol for primary human tissue

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and RNA concentration and purity determined on the NanoDrop ND-1000 spectral photometer (peqlab). The 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano as well as the 6000 Pico LabChip Kit (Agilent Technologies) were used to analyze RNA integrity.

treatment_protocol: For simultaneous staining of all NKG2DL, a recombinant NKG2D-Fc chimera (fusion protein) and the corresponding isotype control were purchased from R&D (Minneapolis, MN, USA) and biotinylated with the One-step biotinylation kit (MACS Miltenyi) according to manufactures instructions. Prior to staining, cells were blocked with human IgG (Sigma-Aldrich) and washed. Then biotinylated fusion protein or control (10µg/ml each) were added followed by two washing steps. Afterwards streptavidin-PE (LifeTechnologies, Carlsbad, CA, USA) and selection antibodies were further added prior to sorting into NKG2DLpos and NKG2DLneg fractions

tag: origin

value: AML, peripheral blood, CD33+

tag: sorted fraction


title: 1a_NKG2DLpos


title: Participant ID and visit (v) # phchp243v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp258v1 Independent Discovery Cohort (n=36) (91 visits)

value: F-BP


title: YeO:3 (Y1) 37°C stationary growth phase, not enriched 2

description: not enriched for primary transcripts


title: YeO:8 (8081v) 25°C exponential growth phase, enriched 2

description: enriched for primary transcripts


title: Participant ID and visit (v) # phchp214v3 Independent Discovery Cohort (n=36) (91 visits)

value: F-PTSD


title: 1b_NKG2DLpos


title: RRBS Adult2


title: Participant ID and visit (v) # phchp226v3 Independent Discovery Cohort (n=36) (91 visits)

value: M-MDD


title: Participant ID and visit (v) # phchp248v2 Independent Discovery Cohort (n=36) (91 visits)

value: M-SZ


title: YeO:3 (Y1) 37°C stationary growth phase, enriched 2

description: enriched for primary transcripts


title: Participant ID and visit (v) # phchp226v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp243v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 37°C exponential growth phase, not enriched 2

description: not enriched for primary transcripts


title: RRBS Dnmt1 KO3

value: Six2Cre Dnmt1 f/f


title: YeO:3 (Y1) 25°C stationary growth phase, not enriched 2

description: not enriched for primary transcripts


title: Participant ID and visit (v) # phchp214v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp214v2 Independent Discovery Cohort (n=36) (91 visits)


title: RRBS Dnmt1 KO1


title: Participant ID and visit (v) # phchp226v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp213v3 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C stationary growth phase, enriched 2

description: enriched for primary transcripts


title: Participant ID and visit (v) # phchp209v3 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C exponential growth phase, not enriched 2

description: not enriched for primary transcripts


title: YeO:3 (Y1) 25°C exponential growth phase, enriched 2

description: enriched for primary transcripts


title: RRBS CTL3


title: Participant ID and visit (v) # phchp209v1 Independent Discovery Cohort (n=36) (91 visits)


title: RRBS CTL2


title: YeO:8 (8081v) 37°C stationary growth phase, enriched 1

description: enriched for primary transcripts


title: Isl 3 plus  (IFNa)

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were aligned to several human reference databases including hg19 human genome, exon, splicing-junction segments, and contamination database including ribosome and mitochondrial sequences using BWA alignment algorithm.
After filtering reads mapped to the contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 miss-matches for each transcript were then counted as expression level for the corresponding transcripts.
The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription levels across samples.
Genome_build: hg19
Supplementary_files_format_and_content: log2 normalized counts

source_name: pancreatic islets_plus  (IFNa)

growth_protocol: Deidentified anonymous human islets were obtained through the NIH-supported Integrated Islet Distribution Program (IIDP). Upon arrival islets were grown for 24h in RPMI (Gibco) supplemented with 5.5 mM glucose and 10% FBS at 37ºC in 5% CO2.

extract_protocol:
Total RNA from islets treated and untreated with IFNα was extracted using TRIzol (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24h of culture islet samples were stimulated with 2000 U/ml IFNα (Millipore) for 24h.

tag: subject status

value: non-diabetic donor

tag: tissue/cell type

value: pancreatic islets

tag: treatment

value: 2000 IU IFNα for 24hrs


title: YeO:3 (Y1) 37°C exponential growth phase, enriched 2

description: enriched for primary transcripts


title: Isl 2 plus  (IFNa)


title: YeO:8 (8081v) 37°C stationary growth phase, not enriched 1

description: not enriched for primary transcripts


title: Isl 3 minus (IFNa)

source_name: pancreatic islets_minus (IFNa)


title: RRBS Dnmt1 KO2


title: YeO:8 (8081v) 37°C exponential growth phase, enriched 1

description: enriched for primary transcripts


title: YeO:8 (8081v) 37°C exponential growth phase, not enriched 1

description: not enriched for primary transcripts


title: RRBS CTL1


title: Isl 2 minus (IFNa)


title: Isl 1 plus  (IFNa)


title: Participant ID and visit (v) # phchp204v3 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 25°C stationary growth phase, not enriched 1

description: not enriched for primary transcripts


title: YeO:8 (8081v) 25°C stationary growth phase, enriched 1

description: enriched for primary transcripts


title: Participant ID and visit (v) # phchp213v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp204v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp196v3 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp204v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp193v4 Independent Discovery Cohort (n=36) (91 visits)

value: M-BP


title: Participant ID and visit (v) # phchp196v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 25°C exponential growth phase, not enriched 1

description: not enriched for primary transcripts


title: Isl 1 minus (IFNa)


title: YeO:8 (8081v) 25°C exponential growth phase, enriched 1

description: enriched for primary transcripts


title: YeO:3 (Y1) 37°C stationary growth phase, not enriched 1

description: not enriched for primary transcripts


title: YeO:3 (Y1) 37°C stationary growth phase, enriched 1

description: enriched for primary transcripts


title: YeO:3 (Y1) 37°C exponential growth phase, not enriched 1

description: not enriched for primary transcripts


title: 34L-1 [miRNA]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: non-cancer liver organoids

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Total RNAs were extracted from tissues of organoids using miRVana isolation kit.

value: non-cancer liver organoids


title: 44T [miRNA]

source_name: neuroendocrine carcinoma organoids

value: neuroendocrine carcinoma organoids


title: 42L [miRNA]


title: 45L [miRNA]


title: YeO:3 (Y1) 37°C exponential growth phase, enriched 1

description: enriched for primary transcripts


title: YeO:3 (Y1) 25°C stationary growth phase, not enriched 1

description: not enriched for primary transcripts


title: 30T [miRNA]

source_name: organoids established using cancer tissue but failed in long culture


title: YeO:3 (Y1) 25°C stationary growth phase, enriched 1

description: enriched for primary transcripts


title: Participant ID and visit (v) # phchp193v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp176v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp173v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp166v2 Independent Discovery Cohort (n=36) (91 visits)


title: 27T [miRNA]

value: organoids established using cancer tissue but failed in long culture


title: Participant ID and visit (v) # phchp193v3 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp173v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp176v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C exponential growth phase, enriched 1

description: enriched for primary transcripts

value: 25C, exponential growth phase


title: YeO:8 (8081v) 37°C stationary growth phase 3

value: 37C, stationary growth phase


title: YeO:3 (Y1) 25°C exponential growth phase, not enriched 1

description: not enriched for primary transcripts


title: YeO:8 (8081v) 37°C stationary growth phase 2


title: 28N2 [miRNA]

source_name: non-cancer organoids

value: non-cancer organoids


title: 28N1 [miRNA]


title: 26T [miRNA]

source_name: cholangiocarcinoma organoids

value: cholangiocarcinoma organoids


title: 21T [miRNA]

source_name: gallbladder cancer organoids

value: gallbladder cancer organoids


title: 9T-TI [miRNA]

source_name: cholangiocarcinoma tissue

value: cholangiocarcinoma tissue


title: 9T [miRNA]


title: Participant ID and visit (v) # phchp164v2 Independent Discovery Cohort (n=36) (91 visits)

value: F-MDD


title: YeO:8 (8081v) 37°C stationary growth phase 1


title: Participant ID and visit (v) # phchp164v3 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp166v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp160v3 Independent Discovery Cohort (n=36) (91 visits)

value: F-SZA


title: Participant ID and visit (v) # phchp166v4 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp160v2 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 37°C exponential growth phase 3

value: 37C, exponential growth phase


title: 2T [miRNA]

source_name: pancreatic cancer organoids

value: pancreatic cancer organoids


title: Participant ID and visit (v) # phchp157v3 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp160v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 37°C exponential growth phase 1


title: 41N [miRNA]


title: YeO:8 (8081v) 25°C stationary growth phase 3

value: 25C, stationary growth phase


title: YeO:8 (8081v) 25°C stationary growth phase 2


title: 40N1 [miRNA]


title: Participant ID and visit (v) # phchp154v3 Independent Discovery Cohort (n=36) (91 visits)

value: M-PSYCH


title: Participant ID and visit (v) # phchp157v2 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 25°C stationary growth phase 1


title: 36T [miRNA]


title: 39T [miRNA]


title: Participant ID and visit (v) # phchp154v2 Independent Discovery Cohort (n=36) (91 visits)


title: 39N [miRNA]


title: YeO:8 (8081v) 37°C exponential growth phase 2


title: YeO:8 (8081v) 25°C exponential growth phase 3


title: 36N [miRNA]


title: YeO:8 (8081v) 25°C exponential growth phase 2


title: RRBS Adult1

value: kidney

value: 6 weeks

value: wild type


title: Participant ID and visit (v) # phchp154v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp153v4 Independent Discovery Cohort (n=36) (91 visits)

value: M-BP


title: Participant ID and visit (v) # phchp153v6 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp153v2 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 37°C stationary growth phase 1


title: YeO:3 (Y1) 37°C stationary growth phase 3


title: YeO:3 (Y1) 37°C stationary growth phase 2


title: YeO:3 (Y1) 37°C exponential growth phase 2


title: YeO:3 (Y1) 37°C exponential growth phase 1


title: YeO:3 (Y1) 37°C exponential growth phase 3


title: Jejunum_animal_75

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

description: Jejunum section without Peyers' patches

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to GPL19893 microarray (Agilent 8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 44601 spots out of 62976 were selected.  The mean signal of the 12 first samples, 8 next and 4 last ones were substracted to individuals signals to correct the batch effect of the 3 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44600 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Jejunum

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Six crossbred weanling piglets housed in floored indoor pens were used in this study. The piglets were weaned at the age of 28 days and transported to the animal facility of the INRA Research Center in Food Toxicology (Toxalim, Toulouse, France). Animals were kept until 10 weeks of age.

extract_protocol: Total RNA was extracted in lysing matrix D tubes (MP Biomedicals, Illkirch, France) containing guanidine thiocyanate-acid phenol (Eurobio, Courtaboeuf, France). Quality of these samples was assessed on Bioanalyzer 2100 (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA). All samples had a RIN over 7.5.

treatment_protocol: Animals had ad libitum access to water and feed for the duration of the trial. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. The liver, spleen, and two portions of the jejunum – one with and one without JPPs – were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.

value: Jejunum

tag: animal


title: Participant ID and visit (v) # phchp153v1 Independent Discovery Cohort (n=36) (91 visits)


title: Peyer_animal_73

description: Jejunum section with Peyer's patch

source_name: Peyer

value: Peyer


title: Participant ID and visit (v) # phchp151v2 Independent Discovery Cohort (n=36) (91 visits)

value: M-SZ


title: Participant ID and visit (v) # phchp151v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C stationary growth phase 3


title: Participant ID and visit (v) # phchp134v6 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C stationary growth phase 2


title: Jejunum_animal_71

description: Jejunum section without Peyers' patches


title: Jejunum_animal_73

description: Jejunum section without Peyers' patches


title: Participant ID and visit (v) # phchp132v6 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp134v2 Independent Discovery Cohort (n=36) (91 visits)


title: Jejunum_animal_70

description: Jejunum section without Peyers' patches


title: Participant ID and visit (v) # phchp134v4 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 25°C exponential growth phase 1

value: 25C, exponential growth phase


title: Peyer_animal_75

description: Jejunum section with Peyer's patch


title: Participant ID and visit (v) # phchp134v3 Independent Discovery Cohort (n=36) (91 visits)


title: Peyer_animal_71

description: Jejunum section with Peyer's patch


title: Peyer_animal_70

description: Jejunum section with Peyer's patch


title: Participant ID and visit (v) # phchp132v1 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C stationary growth phase 1


title: Jejunum_animal_69

description: Jejunum section without Peyers' patches


title: Participant ID and visit (v) # phchp124v2 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:3 (Y1) 25°C exponential growth phase 3


title: YeO:3 (Y1) 25°C exponential growth phase 1


title: YeO:3 (Y1) 25°C exponential growth phase 2


title: Peyer_animal_69

description: Jejunum section with Peyer's patch


title: Participant ID and visit (v) # phchp124v1 Independent Discovery Cohort (n=36) (91 visits)


title: notch-RNAi#3

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using STAR 2.5.2b with default parameters.
RPKM (reads per kilobase per million) was calculated for each gene.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Drosophila melanogaster

source_name: FACS sorted ISC

extract_protocol:
RNA and library was prepared by following the manufacturer’s instructions
Libraries were prepared for sequencing using standard Illumina protocols

value: intestine

value: adult stage 5-7 days old

value: notch RNAi


title: Spleen_animal_75

description: spleen section

source_name: Spleen

value: Spleen


title: w1118_1

city: Stanford

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

institute: Stanford University

data_processing:
fastx_trimmer was used to trim the 76th base from reads.
Reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations.
Read counts were obtained using featureCounts from the Subread package.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: Normalized gene expression profiles for each sample in tab-delimited columns with a header in the first line.

molecule: polyA RNA

source_name: head

growth_protocol: Heads were dissected from 3 day old male flies grown at 18C.

extract_protocol:
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), depleted of ribosomal RNA, and treated again using TURBO DNase.
Libraries produced using the KAPA RNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 75-bp cycles.

value: head

value: 3 day


title: w1118_2


title: Peyer_animal_68

description: Jejunum section with Peyer's patch


title: notch-RNAi#2


title: Participant ID and visit (v) # phchp109v2 Independent Discovery Cohort (n=36) (91 visits)

source_name: Whole Blood


title: Participant ID and visit (v) # phchp052v3 Independent Discovery Cohort (n=36) (91 visits)


title: Liver_animal_75

description: liver section

source_name: Liver

value: Liver


title: Participant ID and visit (v) # phchp052v2 Independent Discovery Cohort (n=36) (91 visits)


title: Jejunum_animal_68

description: Jejunum section without Peyers' patches


title: Liver_animal_71

description: liver section


title: notch-RNAi#1


title: Participant ID and visit (v) # phchp109v1 Independent Discovery Cohort (n=36) (91 visits)


title: Adar5G1_3

value: y, sc, Adar5G1


title: gro-RNAi#3

value: groucho RNAi


title: Spleen_animal_71

description: spleen section


title: Liver_animal_73

description: liver section


title: gro-RNAi#2


title: Adar5G1_2


title: PBMC genomic DNA GWI 8

type: genomic

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description:
PBMC genomic DNA from GWI subject 8
205G

hyb_protocol: bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.

label: Cy3, Cy5

source_name: GWI PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood & Tissue Kit according to manufacturer instructions

tag: gender

value: male

tag: subject id

value: GWI subject 8

tag: disease state

value: Gulf War Illness (GWI)

tag: cell type

value: peripheral blood mononuclear cells (PBMC)


title: gro-RNAi#1


title: Liver_animal_70

description: liver section


title: w1118_3

tag: strain


title: Dl-GFP#3

tag: tissue

value: Wild type


title: PBMC genomic DNA GWI 9

description:
PBMC genomic DNA from GWI subject 9
214G

value: GWI subject 9


title: Dl-GFP#2

tag: age


title: PBMC genomic DNA GWI 10

description:
PBMC genomic DNA from GWI subject 10
223G

value: GWI subject 10


title: Spleen_animal_69

description: spleen section


title: PBMC genomic DNA Healthy Control [HC] 9

description:
PBMC genomic DNA from HC subject 9
196H

source_name: HC PBMC

value: HC subject 9

value: Healthy Control [HC]


title: Dl-GFP#1

value: intestine

value: adult stage 5-7 days old

tag: genotype


title: PBMC genomic DNA GWI 4

description:
PBMC genomic DNA from GWI subject 4
127G

value: GWI subject 4


title: Spleen_animal_68

description: spleen section

value: Spleen


title: PBMC genomic DNA Healthy Control [HC] 10

description:
PBMC genomic DNA from HC subject 10
217H

value: HC subject 10


title: PBMC genomic DNA GWI 7

description:
PBMC genomic DNA from GWI subject 7
181G

value: GWI subject 7


title: PBMC genomic DNA Healthy Control [HC] 7

description:
PBMC genomic DNA from HC subject 7
106H

value: HC subject 7


title: PBMC genomic DNA GWI 6

description:
PBMC genomic DNA from GWI subject 6
163G

value: GWI subject 6


title: 12975_KG_S3_R1_001: Small RNAs from ovaries of KG02245 transgenic strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the raw counts of clipped read occurrences in each library.

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries


title: Liver_animal_68

description: liver section

value: Liver


title: Liver_animal_69

description: liver section


title: Skin_HumanSkinFibroblast_donor3

status: Public on Mar 14 2019

city: Milan

first: Mario

last: Barilani

address: Via F. Sforza 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
HSF_3

hyb_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples. ComBat method (Johnson WE, 2007; doi: 10.1093/biostatistics/kxj037)

source_name: steady state cells

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: alphaMEM + 20% fetal bovine serum

extract_protocol: Trizol extraction. Total RNA from each sample was quantified using the NanoDrop ND-1000. Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: steady state

tag: Sex

value: male

value: 45 years

value: Skin

value: fibroblast


title: PBMC genomic DNA GWI 3

description:
PBMC genomic DNA from GWI subject 3
103G

value: GWI subject 3

value: Gulf War Illness (GWI)

value: peripheral blood mononuclear cells (PBMC)


title: PBMC genomic DNA GWI 5

description:
PBMC genomic DNA from GWI subject 5
151G

value: GWI subject 5


title: PBMC genomic DNA Healthy Control [HC] 6

description:
PBMC genomic DNA from HC subject 6
94H

value: HC subject 6

value: Healthy Control [HC]


title: S05_Isl 3 plus  (IFNa)

description: human islets

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 450 Methyl Beadchip using standard Illumina protocol

data_processing: GenomeStudio (Illumina); Beta values were further log2 transformed and normalized by R package IMA.

label: Cy5 and Cy3

source_name: pancreatic islets_plus  (IFNa)

extract_protocol: DNA was extracted from islet samples treated or untreated with IFNα, and was subjected to methylation analysis using Illumina 450K methyl BeadChip

value: non-diabetic donor

value: pancreatic islets

value: 2000 IU IFNα for 24hrs


title: S06_Isl 3 minus (IFNa)

description: human islets

source_name: pancreatic islets_minus (IFNa)


title: S03_Isl 2 plus  (IFNa)

description: human islets


title: Spleen_animal_73

description: spleen section

value: Spleen


title: PBMC genomic DNA Healthy Control [HC] 8

description:
PBMC genomic DNA from HC subject 8
142H

value: HC subject 8


title: PBMC genomic DNA Healthy Control [HC] 5

description:
PBMC genomic DNA from HC subject 5
82H

value: HC subject 5


title: Adar5G1_1

value: y, sc, Adar5G1

value: head

value: 3 day


title: Spleen_animal_70

description: spleen section


title: CordBlood_HumanMesenchymalStemCell_donor3

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
CBMSC_3

value: male

value: 38-42 weeks (gestational age)

value: Cord blood

value: mesenchymal stem cell


title: CordBlood_HumanMesenchymalStemCell_donor2

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
CBMSC_2


title: BoneMarrow_HumanMesenchymalStemCell_donor2

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
BMMSC_2

value: 64 years

value: Bone marrow


title: S04_Isl 2 minus (IFNa)

description: human islets


title: Extrahepatic Cholangiocarcinoma and adjacent noncancerous tissues from patient 1

city: Harbin

first: Fu Min

state: Heilongjiang Province

address: Xuefu road no. 246 in nangang district

department: Department of Hepatopancreatobiliary Surgery

institute: Second Affiliated Hospital of Harbin Medical University

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: Cancer tissue from patient 1

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: Cancer tissue from patient 1

source_name: adjacent noncancerous tissue from patient 1


title: Extrahepatic Cholangiocarcinoma and adjacent noncancerous tissues from patient 3

source_name: Cancer tissue from patient 3

value: Cancer tissue from patient 3

source_name: adjacent noncancerous tissue from patient 3


title: S01_Isl 1 plus  (IFNa)

description: human islets

value: non-diabetic donor


title: Extrahepatic Cholangiocarcinoma and adjacent noncancerous tissues from patient 2

source_name: Cancer tissue from patient 2

value: Cancer tissue from patient 2

source_name: adjacent noncancerous tissue from patient 2


title: 12975_vf_S2_R1_001: Small RNAs from ovaries of KG02245 transgenic strain, carrying the Su(Hw) mutation

value: ovaries


title: SAUSA300_LAC_agr_KO

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from Ion Torrent Server using File Exporter
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform for analysis and adapters trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using "RNA-Seq Analysis" function with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization
Normalized expression values and fold change comparisons were exported in excel format
Genome_build: NC_007793.1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as normalized RPKM values

organism: Staphylococcus aureus

source_name: bacterial cells, pelleted

growth_protocol: Overnight S. aureus cultures were used to inoculate fresh tryptic soy broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. Test cultures were grown for 5 hours and 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies.

treatment_protocol: Samples were stored at -80°C prior to RNA extraction.

value: LAC

value: agr operon deletion strain

tag: growth medium

value: TSB

tag: growth conditions


title: SAUSA300_LAC_WT

value: Wildtype parental strain


title: ler_T2h_3, sRNA

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

institute: CNRS

description: small RNA

data_processing:
Trimmed and quality filtered reads were mapped with ShortStack v3.8.5 (Johnson et al 2016) using the following arguments :--mismatches 0, -bowtie_m all, --mmap u).
ShortStack v3.8.5 (Johnson et al 2016) was used to annotate each annotation gene and TE) as small RNA precursor and counts small RNA accumulation per size.
Genome_build: genome of Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: type:count file (txt); content:gene ID,nb single reads per size from 20nt to 25nt

organism: Arabidopsis thaliana

growth_protocol: Media = MS/10 +P (KH2PO4 500µM) hygrometry = 33% humidity Temperature = 24°C day/ 21°c night Light = 16 hours day / 8 hours night

extract_protocol:
Small RNAs were extracted using mirVana™ miRNA Isolation Kit (Ambion AM 1560, part IV/A. Isolation of Small RNAs from Total RNA Samples).
Small RNA libraries were construct from 50ng of miRNA using Ion Total RNA-Seq Kit v2 (Ion Torrent, Life Technologies) according to manufacturer instruction. Libraries were then sequenced on Ion PI™ Template OT2 200 Kit v3 on ION PI v2 chip. Adapter were removed

treatment_protocol: Name:MS/10-P media 2h - time course study - compound addition,phosphate:time 2hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.

tag: ecotype

value: Landsberg erecta

tag: time

value: 2 hours

value: wild type

tag: developmental stage

value: roots


title: genomic DNA from sample 449

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
Processed data in Series matrix table: Funnorm normalized

source_name: whole blood

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: education level

tag: history of myocardial infarction

value: F

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran

value: whole blood


title: Skin_HumanSkinFibroblast_donor1

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
HSF_1

value: male

tag: age

value: 39 years

tag: tissue

value: Skin

tag: cell type

value: fibroblast


title: CordBlood_HumanMesenchymalStemCell_donor1

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
CBMSC_1

tag: Sex

value: 38-42 weeks (gestational age)

value: Cord blood

value: mesenchymal stem cell


title: BoneMarrow_HumanMesenchymalStemCell_donor3

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
BMMSC_3

value: 35 years

value: Bone marrow


title: PBMC genomic DNA Healthy Control [HC] 4

description:
PBMC genomic DNA from HC subject 4
58H

tag: gender

tag: subject id

value: HC subject 4

tag: disease state

value: Disease state:Healthy Control [HC]

value: peripheral blood mononuclear cells (PBMC)


title: PBMC genomic DNA GWI 1

description:
PBMC genomic DNA from GWI subject 1
67G

value: GWI subject 1

value: Gulf War Illness (GWI)


title: genomic DNA from sample 305

description: whole blood case sample

value: case


title: genomic DNA from sample 250

description: whole blood control sample

value: control

value: M


title: S02_Isl 1 minus (IFNa)

description: human islets

tag: subject status

value: non-diabetic donor

tag: tissue/cell type

value: pancreatic islets


title: SAUSA300_LAC_1984_tn

tag: strain

value: LAC

tag: genotype

value: SAUSA300_1984 transposon mutant

tag: growth medium

value: TSB

tag: growth conditions


title: genomic DNA from sample 30

description: whole blood case sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

value: F

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

value: whole blood


title: genomic DNA from sample 33

description: whole blood case sample

tag: age

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran

tag: tissue


title: PBMC genomic DNA Healthy Control [HC] 3

description:
PBMC genomic DNA from HC subject 3
46H

tag: gender

value: male

tag: subject id

value: HC subject 3

tag: disease state

value: Healthy Control [HC]

tag: cell type


title: genomic DNA from sample 140

description: whole blood control sample

tag: Sex


title: PBMC genomic DNA Healthy Control [HC] 1

description:
PBMC genomic DNA from HC subject 1
10H

value: HC subject 1


title: Skin_HumanSkinFibroblast_donor2

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
HSF_2

value: 55 years

value: Skin

value: fibroblast


title: genomic DNA from sample 232

description: whole blood control sample


title: BoneMarrow_HumanMesenchymalStemCell_donor1

description:
circRNA expression in 70-90% confluence steady state condition 24 hours after medium change
BMMSC_1

value: 41 years

value: Bone marrow

value: mesenchymal stem cell


title: genomic DNA from sample 315

description: whole blood case sample

value: case

value: M


title: PBMC genomic DNA Healthy Control [HC] 2

description:
PBMC genomic DNA from HC subject 2
34H

value: HC subject 2

value: peripheral blood mononuclear cells (PBMC)


title: ler_T2h_1, sRNA

description: small RNA

tag: ecotype

value: Landsberg erecta

tag: time

value: 2 hours

tag: genotype

value: wild type

tag: developmental stage

value: roots


title: genomic DNA from sample 175

description: whole blood case sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: snp based principle component 1

value: whole blood


title: col_T2h_1, sRNA

description: small RNA

value: Columbia


title: ler_T2h_2, sRNA

description: small RNA


title: ler_T1h_3, sRNA

description: small RNA

treatment_protocol: Name:MS/10-P media 1h - time course study - compound addition,phosphate:time 1hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.

value: 1 hour


title: ler_T1h_2, sRNA

description: small RNA


title: genomic DNA from sample 460

description: whole blood control sample

value: control

tag: age

value: F

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell


title: ler_T0_3, sRNA

description: small RNA

treatment_protocol: no treatment

tag: tissue


title: ler_T1h_1, sRNA

description: small RNA


title: genomic DNA from sample 28

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 451

description: whole blood case sample


title: ler_T0_2, sRNA

description: small RNA


title: genomic DNA from sample 209

description: whole blood case sample


title: ler_T0_1, sRNA

description: small RNA


title: genomic DNA from sample 284

description: whole blood case sample


title: PBMC genomic DNA GWI 2

description:
PBMC genomic DNA from GWI subject 2
91G

tag: gender

value: male

tag: subject id

value: GWI subject 2

tag: disease state

value: Gulf War Illness (GWI)

tag: cell type


title: col_T2h_3, sRNA

description: small RNA

tag: ecotype

tag: time

tag: genotype


title: genomic DNA from sample 413

description: whole blood control sample

tag: diagnosis

tag: education level

tag: Sex


title: genomic DNA from sample 341

description: whole blood control sample

tag: history of myocardial infarction

tag: age

tag: snp based principle component 1


title: col_T1h_3, sRNA

description: small RNA

tag: developmental stage


title: genomic DNA from sample 299

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: tissue


title: KD NRDE2-MTR4 IP-2

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

description: MTR4 IP RNAs

data_processing:
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets.
To compare the expression of individual RNAs, we calculated the corrected reads per million (RPM) of each transcript. Fold changes were computed from the average normalized read coverage per million bases for ensemble gene.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text files include RPM values for each Sample

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS (Biochrom).

extract_protocol:
RNA was isolated from HeLa with TRIzol (Invitrogen).
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina)

treatment_protocol: For knockdown, siRNA were carried out with  Lipofectamine RNAimax(Invitrogen) for 72 hr.

tag: cell line

value: HeLa

value: uterine cervix

tag: genotype/variation

value: KD NRDE2


title: col_T1h_2, sRNA

description: small RNA


title: genomic DNA from sample 485

description: whole blood control sample

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 8

description: whole blood case sample

value: case

value: M


title: genomic DNA from sample 138

description: whole blood case sample


title: genomic DNA from sample 499

description: whole blood control sample


title: KD NRDE2-MTR4 IP-1

description: MTR4 IP RNAs


title: KD Cntl-MTR4 IP-3

description: MTR4 IP RNAs

value: KD control


title: col_T2h_2, sRNA

description: small RNA

tag: ecotype

tag: time

value: 2 hours


title: col_T1h_1, sRNA

description: small RNA

tag: genotype

value: wild type


title: KD Cntl-MTR4 IP-1

description: MTR4 IP RNAs


title: genomic DNA from sample 269

description: whole blood control sample

tag: diagnosis

tag: education level


title: genomic DNA from sample 234

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex


title: col_T0_3, sRNA

description: small RNA

value: roots


title: col_T0_2, sRNA

description: small RNA


title: KD Cntl-NE-1_nuclearRNA

description: rRNA-depleted nuclear RNAs

molecule: nuclear RNA

extract_protocol:
RNA was isolated from HeLa with TRIzol (Invitrogen). 1ug of nuclear RNA was depleted with rRNA and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina)

tag: rna fraction

value: nuclear


title: genomic DNA from sample 57

description: whole blood case sample

tag: age

tag: snp based principle component 1

value: whole blood


title: genomic DNA from sample 267

description: whole blood control sample

tag: snp based principle component 2

tag: cellcount-nk


title: KD NRDE2-MTR4 IP-3

description: MTR4 IP RNAs

tag: tissue


title: genomic DNA from sample 495

description: whole blood control sample

tag: cellcount-bcell


title: col_T0_1, sRNA

description: small RNA

value: Columbia

tag: developmental stage


title: KD Cntl-MTR4 IP-2

description: MTR4 IP RNAs

tag: cell line

tag: genotype/variation


title: KD NRDE2-NE-2_nuclearRNA

description: rRNA-depleted nuclear RNAs


title: genomic DNA from sample 86

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 123

description: whole blood case sample


title: KD NRDE2-Total 2

description: rRNA-depleted total RNAs

extract_protocol:
RNA was isolated from HeLa with TRIzol (Invitrogen). 1ug of total RNA was depleted with rRNA and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina)


title: KD Cntl-NE-2_nuclearRNA

description: rRNA-depleted nuclear RNAs


title: genomic DNA from sample 378

description: whole blood case sample


title: genomic DNA from sample 147

description: whole blood control sample

value: control


title: genomic DNA from sample 199

description: whole blood case sample

value: F


title: KD Cntl-Total 2

description: rRNA-depleted total RNAs


title: genomic DNA from sample 274

description: whole blood case sample


title: A395G-V2

city: Fajara

first: Karim

last: MANE

address: Atlantic Boulevard

department: Statistics and Bioinformatics

country: Gambia

institute: MRCG @ LSHTM

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
then reads in fastq were mapped to human Homo_sapiens.GRCh38.fasta using DART v1.3.3
Reads Per Kilobase of exon per Megabase of library size (RPKM), Transcripts Per Megabase of library size (TPM), Counts Per Megabase of library size (CPM), Reads Per Kilobase of library size (RPK)  were calculated using the Rsubread R package. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Homo_sapiens.GRCh38 (http://hgdownload.cse.ucsc.edu/goldenPath/hg38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM, TPM, CPM, RPK values for each Sample

source_name: Whole blood

growth_protocol: Whole blood collected into PAXgene tubes and stored at -70C within 4 hours of collection until the day of extraction

extract_protocol:
PAXgene blood miRNA extraction kit: https://www.qiagen.com/gb/shop/sample-technologies/rna/mirna/paxgene-blood-mirna-kit/?akamai-feo=off&clear=true#productdetails
Globin clear followed by Truseq RNA preparation methods

value: Whole blood

tag: vaccination timepoint

value: day 2


title: A399H-V0

value: day 0


title: A395G-V0


title: KD NRDE2-Total 1

description: rRNA-depleted total RNAs

value: HeLa


title: genomic DNA from sample 18

description: whole blood case sample

tag: diagnosis


title: genomic DNA from sample 92

description: whole blood case sample

tag: education level


title: genomic DNA from sample 130

description: whole blood case sample

tag: history of myocardial infarction


title: genomic DNA from sample 177

description: whole blood control sample

tag: Sex


title: genomic DNA from sample 452

description: whole blood case sample


title: genomic DNA from sample 81

description: whole blood case sample


title: genomic DNA from sample 251

description: whole blood control sample


title: A399H-V2


title: genomic DNA from sample 518

description: whole blood case sample


title: genomic DNA from sample 416

description: whole blood case sample


title: genomic DNA from sample 399

description: whole blood case sample


title: A381A-V0


title: KD Cntl-Total 1

description: rRNA-depleted total RNAs

value: uterine cervix


title: KD NRDE2-NE-1_nuclearRNA

description: rRNA-depleted nuclear RNAs

tag: rna fraction

value: KD NRDE2


title: A376J-V0


title: genomic DNA from sample 216

description: whole blood control sample

tag: age


title: A371D-V2


title: genomic DNA from sample 355

description: whole blood control sample

tag: snp based principle component 1


title: A391K-V2


title: A391K-V0


title: genomic DNA from sample 76

description: whole blood case sample

value: case

tag: snp based principle component 2


title: A349G-V0


title: A388G-V2


title: genomic DNA from sample 266

description: whole blood control sample

value: M

tag: cellcount-nk


title: A388G-V0

tag: tissue


title: A381A-V2


title: A384B-V2


title: genomic DNA from sample 462

description: whole blood control sample

tag: cellcount-bcell


title: genomic DNA from sample 481

description: whole blood case sample


title: genomic DNA from sample 157

description: whole blood control sample


title: A384B-V0


title: A329J-V0


title: genomic DNA from sample 357

description: whole blood case sample


title: genomic DNA from sample 60

description: whole blood case sample


title: A376J-V2


title: A371D-V0


title: genomic DNA from sample 501

description: whole blood control sample


title: genomic DNA from sample 133

description: whole blood case sample


title: A349G-V2


title: A082C-V2


title: genomic DNA from sample 282

description: whole blood case sample


title: A329J-V2


title: genomic DNA from sample 496

description: whole blood control sample


title: genomic DNA from sample 170

description: whole blood control sample


title: A086F-V0


title: A079E-V2


title: A321B-V0


title: genomic DNA from sample 503

description: whole blood control sample


title: genomic DNA from sample 448

description: whole blood case sample


title: genomic DNA from sample 223

description: whole blood case sample


title: A321B-V2


title: A075C-V2


title: A086F-V2


title: genomic DNA from sample 43

description: whole blood case sample


title: genomic DNA from sample 477

description: whole blood case sample


title: genomic DNA from sample 288

description: whole blood case sample


title: A059A-V2


title: A082C-V0


title: genomic DNA from sample 332

description: whole blood control sample


title: A059A-V0


title: A079E-V0


title: genomic DNA from sample 196

description: whole blood control sample


title: genomic DNA from sample 44

description: whole blood case sample


title: genomic DNA from sample 387

description: whole blood case sample


title: genomic DNA from sample 211

description: whole blood control sample


title: genomic DNA from sample 42

description: whole blood case sample


title: A056G-V0


title: genomic DNA from sample 65

description: whole blood case sample


title: genomic DNA from sample 432

description: whole blood control sample


title: A056G-V2


title: A075C-V0


title: genomic DNA from sample 408

description: whole blood case sample


title: A044C-V2


title: genomic DNA from sample 461

description: whole blood case sample


title: genomic DNA from sample 70

description: whole blood case sample


title: A044C-V0


title: genomic DNA from sample 246

description: whole blood control sample


title: A035G-V2


title: A038B-V2


title: A065B-V2


title: A038B-V0


title: A065B-V0


title: genomic DNA from sample 136

description: whole blood case sample


title: A035G-V0


title: A031K-V2


title: genomic DNA from sample 197

description: whole blood control sample


title: genomic DNA from sample 228

description: whole blood case sample


title: genomic DNA from sample 192

description: whole blood control sample


title: A030J-V2


title: genomic DNA from sample 115

description: whole blood case sample


title: A030J-V0


title: A026E-V2


title: genomic DNA from sample 381

description: whole blood case sample


title: genomic DNA from sample 489

description: whole blood case sample


title: A026E-V0


title: genomic DNA from sample 159

description: whole blood control sample


title: A017E-V2


title: genomic DNA from sample 23

description: whole blood case sample


title: A016D-V2


title: A016D-V0


title: genomic DNA from sample 458

description: whole blood case sample


title: genomic DNA from sample 328

description: whole blood control sample


title: genomic DNA from sample 362

description: whole blood case sample


title: A017E-V0


title: PMA 3_Input_ChIP-seq

city: La Jolla

first: Matthew

last: Denholtz

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

description: ChIP-seq

data_processing:
Raw fastq files were aligned to the human genome build hg38 using bowtie [Langmead/Salzberg, Genome Biology, 2009] with the following parameters: -m1 --best --strata.
Sequencing data was reorganized as a HOMER (Heinz et al Mol. Cell 2010)-formatted tag directory for each data set and multiple reads mapping to the same base pair were collapsed to a single hit using the makeTagDirectory command in HOMER with the following parameters: -tbp 1
ChIP peaks were called using the findPeaks command in HOMER with default parameters
Unique reads from individual high quality biological replicates were pooled and ChIP peaks were re-called on pooled data as above using pooled inputs, conclusions were drawn from pooled ChIPseq data
Genome_build: hg38
Supplementary_files_format_and_content: ChIP peaks from pooled ChIPseq experiments are included, as are HOMER-formated tsv files for pooled input data sets. Tsv file scores represent reads per base pair.

source_name: Peripheral blood neutrophils

growth_protocol: Human blood collected into heperinized syringes via venupuncture , granulocytes were purified from whole blood via density centrifugation with PolymorphPrep reagent (Accurate Chemical Scientific Corp., cat# AN1114683), purified granulocytes were cultured in HBSS +Ca +Mg -Phenol red (Life Technologies, cat# 14025092) + 0.5% endotoxin free BSA (Akron Biotech cat# Ak8917-0100) at 37degC, 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA end repair was performed using an Epicenter End-It kit (Lucigen ER0720), according to manufacturer’s instructions and column purified in a Zymo Minelute column (Zymo D4013). A-tails were added by incubating DNA in 1x NEB buffer 2 (New England Biolabs B7002S) with the addition of 200uM dATP and 7.5 units Klenow (exo-) (New England Biolabs M0212L) at 37 degrees for 45 minutes. NEB Next adaptors (New England Biolabs E7337A) were ligated using an NEB quick ligation kit (New England Biolabs M2200L) at benchtop temperature for 30 minutes followed by treatment with 2uL USER enzyme (New England Biolabs M5505L) for 15 minutes at 37°C. DNA was purified using a two-step SPRI bead protocol (from Rohland/Reich; Genome Research), resulting in purification of DNA fragments between 200-800 bp.

treatment_protocol: Human neutrophils were stimulated for three hours with either 25nM PMA (Promega, cat# V1171) or via co-culture with E. coli strain K1 at an MOI of 5 in culture conditions mirroring those in the growth protocol above

tag: chip antibody


title: genomic DNA from sample 324

description: whole blood control sample


title: PMA 1_Input_ChIP-seq

description: ChIP-seq


title: A031K-V0


title: genomic DNA from sample 187

description: whole blood control sample


title: Ecoli 2_RNAseq

description: RNAseq

data_processing:
Reads were aligned to human genome . Raw fastq files were aligned to the human genome build hg38 using tophat2 [Kim/Salzberg, GenomeBiology, 2013] with the following parameters: --library-type fr-firststrand -a 15
Duplicated reads were removed using Picard tools command MarkDuplicates REMOVE_DUPLICATES=T
Gene expression values were computed for each replicate across each condition using cuffdiff with an hg38 refflat file as reference with the following parameters: --library-type fr-firststrand
Genome_build: hg38
Supplementary_files_format_and_content: .txt file, computed gene expression values for every gene for each replicate and condition

source_name: Periferal blood neutrophils

extract_protocol:
Neutrophil were washed twice with PBS and lysed in Qiagen buffer RLT (from Qiagen kit 74106) + 10uL/mL beta-mercaptoethanol and run through a QiaShredder (Qiagen 79654)
Total RNA was purified via RNeasy mini kit (Qiagen 74106) according to the manufactures instructions, including the RNase-free DNase (Qiagen 79254) treatment step. RNA was eluted in H2O, Turbo DNase kit buffer (ThermoFisher/Ambion AM1907) was added to a 1x concentration and RNA was treated with 4 units of Turbo DNase at 37degrees for 30 minutes. Turbo DNase was then treated with inactivation reagent per manufacturer’s specifications. mRNA was purified from total RNA using a Dynabead mRNA purification kit (Life Technologies 61006). First strand synthesis was performed using SuperScript III first strand synthesis system (ThermoFisher 18080051) as follows: 100-500ng RNA; 0.5uL Oligo(dT) primer; 0.8uL random hexamer; 1uL 10mM dNTP, H2O to 9.5uL. Mixture was incubated to 70 degrees for 10 minutes then snap frozen. First strand synthesis mix composed of 2uL 10x RT buffer, 4uL 25mM MgCl2, 2uL 0.1M DTT, 0.uL of 120ng/uL ActinomycinD, 40U RNaseOUT, 200U SuperScriptIII was added to the mixture which was then incubated at 25 degrees for 10 minutes, 42 degrees for 45 minutes, 50 degrees for 25 minutes, and 75 degrees for 15 minutes. Unincorporated nucleotides were removed from the mixture using a ProbeQuant G-50 column (Sigma GE28-9034-08). First strand synthesis reaction as then brought to 51uL with H2O and cooled on ice. 24uL of second strand mixture composed of 1uL 10x RT buffer, 2uL 25mM MgCl2, 1uL 0.1M DTT, 2uL of 10mM dATP, dGTP, dCTP, dUTP mix, 15uL of 5x second strand synthesis buffer (New England Biolabs B6117S), 0.5uL E. coli ligase (NEB M0205S), 2uL DNA polymerase I (NEB M0209S), and 0.5uL RNaseH was added and mixture was incubated at 16 degrees for 2 hours. DNA was purified using a DNA clean and concentrator kit (Zymo D4013), and sonicated on a Covaris E220 with the following settings; Duty cycle 10%; Intensity 5; Cycle per burst 200; Time (seconds) 180. Sonicated DNA was purified using a DNA clean and concentrator kit. DNA was prepared for high throughput sequencing using the methodology described above for ChIP-seq, with the addition of 1uL UNG (ThermoFisher/Applied Biosystems N8080096) during USER enzyme treatment.

tag: treatment

value: E. coli


title: PMA 2_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 94

description: whole blood case sample


title: genomic DNA from sample 131

description: whole blood case sample


title: Ecoli 1_RNAseq

description: RNAseq


title: US 5_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 441

description: whole blood case sample


title: genomic DNA from sample 405

description: whole blood control sample


title: US 3_Input_ChIP-seq

description: ChIP-seq


title: PMA 2_RNAseq

description: RNAseq

value: PMA


title: genomic DNA from sample 40

description: whole blood case sample


title: genomic DNA from sample 339

description: whole blood NA sample


title: PMA 1_RNAseq

description: RNAseq


title: genomic DNA from sample 331

description: whole blood control sample


title: genomic DNA from sample 401

description: whole blood case sample


title: genomic DNA from sample 352

description: whole blood control sample


title: genomic DNA from sample 487

description: whole blood case sample


title: genomic DNA from sample 459

description: whole blood control sample


title: PMA 1_H3K4me3 _ChIP-seq

description: ChIP-seq


title: US 1_H3K4me3 _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 467

description: whole blood control sample


title: US 1_RNAseq

description: RNAseq

value: unstimulated


title: genomic DNA from sample 380

description: whole blood NA sample


title: genomic DNA from sample 110

description: whole blood case sample


title: Ecoli 2_HiC_R1

description: In situ HiC

data_processing:
HiC data was aligned, filtered, assembled into valid interaction pairs, normalized, and assembled into contact matrices using HiCPro v2.10.0 with default settings - Servant et al., Genome Biology, 2015
Genome_build: hg38
Supplementary_files_format_and_content: valid read pairs aligning to the hg38 genome build as defined by HiCPro v2.10.0 run with default settings

extract_protocol:
Nuclei isolation, chromatin digestion, nucleotide fill-in, ligation, and DNA purification were performed as detailed in Rao et al., Cell, 2014 - In situ HiC
Library construction was performed as detailed in Rao et al., Cell, 2014 - In situ HiC

tag: restriction enzyme

value: MboI


title: genomic DNA from sample 121

description: whole blood case sample

tag: cellcount-mono


title: genomic DNA from sample 172

description: whole blood control sample

tag: cellcount-gran


title: PMA 1_CTCF _ChIP-seq

description: ChIP-seq


title: PMA 1.2_HiC_R1

description: In situ HiC


title: PMA 2_HiC_R1

description: In situ HiC


title: genomic DNA from sample 343

description: whole blood case sample


title: genomic DNA from sample 11

description: whole blood case sample


title: PMA 1.1_HiC_R1

description: In situ HiC


title: US 2_RNAseq

description: RNAseq


title: genomic DNA from sample 484

description: whole blood case sample


title: PMA 1_H3K4me1 _ChIP-seq

description: ChIP-seq


title: Ecoli 1_HiC_R1

description: In situ HiC


title: genomic DNA from sample 375

description: whole blood case sample


title: genomic DNA from sample 178

description: whole blood control sample


title: genomic DNA from sample 145

description: whole blood control sample


title: genomic DNA from sample 287

description: whole blood case sample


title: genomic DNA from sample 116

description: whole blood case sample


title: US 1_H3K4me1 _ChIP-seq

description: ChIP-seq


title: Blood Bmem 3

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Melbourne Bioinformatics.
Reads were mapped to the Mus musculus reference genome (mm10) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: mm10
Supplementary_files_format_and_content: CSV/tab-delimited text files include raw counts or CPM values
Supplementary_files_format_and_content: iBALT subsets_degust_Voom_Limma.csv: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw counts all subsets.txt: Raw counts -- HTseq

source_name: influenza PR8-infected mice

extract_protocol:
RNA was isolated from sorted cells using a QIAGEN RNeasy Plus Micro Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: cell type

value: Live/Dead negative, F4/80-, Streptavidin-, CD3-, CD45+, B220+ and intravenous CD45.2-, CD38hi, GL7-


title: US 2_HiC_R1

description: In situ HiC


title: Blood Bmem 2


title: genomic DNA from sample 265

description: whole blood control sample

tag: diagnosis

value: whole blood


title: Spleen GC 3

value: Spleen

value: Live/Dead negative, F4/80-, Streptavidin-, CD3-, CD45+, B220+ and intravenous CD45.2-, CD38lo, GL7+


title: US 1.2_HiC_R1

description: In situ HiC


title: MLN GC 2

value: Mediastinal lymph node


title: genomic DNA from sample 41

description: whole blood case sample

tag: education level

value: F


title: genomic DNA from sample 402

description: whole blood case sample

tag: history of myocardial infarction


title: US 1.1_HiC_R1

description: In situ HiC


title: US 1_RAD21 _ChIP-seq

description: ChIP-seq


title: MLN Bmem 3


title: PMA 6_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 472

description: whole blood control sample

value: control

tag: Sex


title: genomic DNA from sample 158

description: whole blood control sample


title: MLN Bmem 2


title: PMA 5_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 24

description: whole blood case sample


title: genomic DNA from sample 66

description: whole blood case sample


title: PMA 4_Input_ChIP-seq

description: ChIP-seq


title: Lung GC 2

value: Lung


title: Spleen GC 2


title: genomic DNA from sample 12

description: whole blood case sample


title: genomic DNA from sample 271

description: whole blood case sample


title: genomic DNA from sample 237

description: whole blood control sample


title: genomic DNA from sample 500

description: whole blood control sample


title: Ecoli 5_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 446

description: whole blood control sample


title: genomic DNA from sample 376

description: whole blood case sample


title: genomic DNA from sample 272

description: whole blood control sample


title: Spleen Bmem 3


title: genomic DNA from sample 55

description: whole blood case sample


title: Ecoli 3_Input_ChIP-seq

description: ChIP-seq


title: T cell 2

value: Live/Dead negative, B220- CD3+


title: genomic DNA from sample 77

description: whole blood case sample


title: Ecoli 2_Input_ChIP-seq

description: ChIP-seq


title: T cell 1


title: Ecoli 1_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 303

description: whole blood case sample


title: genomic DNA from sample 277

description: whole blood case sample


title: genomic DNA from sample 291

description: whole blood case sample


title: Blood Bmem 1


title: US 9_Input_ChIP-seq

description: ChIP-seq


title: MLN GC 1


title: US 8_Input_ChIP-seq

description: ChIP-seq


title: Spleen Bmem 2


title: Ecoli 4_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 210

description: whole blood control sample


title: genomic DNA from sample 231

description: whole blood case sample


title: MLN Bmem 1


title: genomic DNA from sample 39

description: whole blood case sample


title: genomic DNA from sample 300

description: whole blood control sample


title: genomic DNA from sample 220

description: whole blood control sample


title: US 7_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 363

description: whole blood case sample


title: genomic DNA from sample 144

description: whole blood control sample


title: genomic DNA from sample 436

description: whole blood case sample


title: Lung GC 1


title: Spleen GC 1


title: US 4_Input_ChIP-seq

description: ChIP-seq


title: US 6_Input_ChIP-seq

description: ChIP-seq


title: Spleen Bmem 1


title: genomic DNA from sample 186

description: whole blood control sample


title: genomic DNA from sample 411

description: whole blood control sample


title: genomic DNA from sample 106

description: whole blood case sample


title: genomic DNA from sample 217

description: whole blood control sample


title: genomic DNA from sample 264

description: whole blood control sample


title: US 2_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 214

description: whole blood control sample


title: US 1_Input_ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 69

description: whole blood case sample


title: genomic DNA from sample 239

description: whole blood control sample


title: genomic DNA from sample 468

description: whole blood control sample


title: PMA 2_H3K4me3 _ChIP-seq

description: ChIP-seq


title: US 2_H3K4me3 _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 83

description: whole blood case sample


title: genomic DNA from sample 312

description: whole blood case sample


title: genomic DNA from sample 242

description: whole blood control sample


title: genomic DNA from sample 384

description: whole blood case sample


title: genomic DNA from sample 290

description: whole blood control sample


title: US 2_H3K4me1 _ChIP-seq

description: ChIP-seq


title: Ecoli_H3K27ac _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 103

description: whole blood case sample


title: genomic DNA from sample 522

description: whole blood case sample


title: genomic DNA from sample 45

description: whole blood case sample


title: US_H3K27ac _ChIP-seq

description: ChIP-seq


title: Ecoli_CTCF _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 342

description: whole blood case sample


title: genomic DNA from sample 169

description: whole blood control sample


title: genomic DNA from sample 502

description: whole blood control sample


title: genomic DNA from sample 511

description: whole blood control sample


title: US 3_CTCF _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 476

description: whole blood case sample


title: genomic DNA from sample 114

description: whole blood case sample


title: PMA 2_CTCF _ChIP-seq

description: ChIP-seq


title: US 2_CTCF _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 245

description: whole blood control sample


title: genomic DNA from sample 112

description: whole blood case sample


title: genomic DNA from sample 62

description: whole blood case sample


title: genomic DNA from sample 394

description: whole blood control sample


title: US 1_CTCF _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 82

description: whole blood case sample


title: PMA 2_RAD21 _ChIP-seq

description: ChIP-seq


title: genomic DNA from sample 310

description: whole blood control sample


title: genomic DNA from sample 528

description: whole blood case sample


title: input DNA

city: St Louis

first: nidhi

last: rohatgi

state: MO

address: 660 S Euclid Ave

department: pathology and immunology

institute: washington university in st. louis

data_processing:
ChIP-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad (H3K4me3) or HOMER2 annotatePeaks.pl (H3K27me3).
Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Osteoclast cells

growth_protocol: Bone Marrow Derived Macrophages were plates in 150 MM TC plates at a density of 6X10e6 cells in presence of RANK ligand (50ng/ml) and CMG (2%). The preosteoclast were harvested on Day2

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

value: Osteoclast

tag: genotype

value: ASXL1 WT

tag: strain


title: H3K27me3_ChIPSeq KO

value: ASXL1 KO


title: genomic DNA from sample 151

description: whole blood case sample

value: case

tag: age

tag: snp based principle component 1


title: US 2_RAD21 _ChIP-seq

description: ChIP-seq


title: H3K27me3_ChIPSeq WT


title: genomic DNA from sample 308

description: whole blood case sample

value: M

tag: snp based principle component 2

tag: cellcount-nk


title: genomic DNA from sample 117

description: whole blood case sample

tag: cellcount-bcell

tag: tissue


title: genomic DNA from sample 238

description: whole blood case sample


title: genomic DNA from sample 338

description: whole blood case sample


title: genomic DNA from sample 337

description: whole blood control sample


title: genomic DNA from sample 87

description: whole blood case sample


title: Ecoli 2_SMC3 _ChIP-seq

description: ChIP-seq

tag: chip antibody


title: genomic DNA from sample 382

description: whole blood control sample


title: Ecoli 1_SMC3 _ChIP-seq

description: ChIP-seq


title: H3K4me3_ChIPSeq KO


title: US 1_SMC3 _ChIP-seq

description: ChIP-seq


title: H3K4me3_ChIPSeq WT


title: genomic DNA from sample 317

description: whole blood control sample


title: genomic DNA from sample 19

description: whole blood case sample


title: genomic DNA from sample 415

description: whole blood case sample


title: Input_ChIP-Seq

city: Marseille

first: Yasmina

last: Kermezli

address: Luminy

institute: AIX Marseille university

data_processing:
Sequenced reads were trimmed using sickle tool V.1.33
trimmed fastq files were aligned to mm9 genome assembly using bowtie2
bigwig files were generated by bam2wig.py & wigToBigWig tools
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated by bam2wig.py & wigToBigWig tools

source_name: Input

growth_protocol: The P5424 line was grown in RPMI-1640 GlutaMAX ™ medium (Thermo Fisher Scientific, 61870-010), supplemented with 10% fetal calf serum (Thermo Fisher Scientific, 10270-106) at 37°C, 5% CO2.

extract_protocol:
The extraction of total RNA was performed using the RNeasy Plus Mini kit (Qiagen) according to the protocol recommended by the supplier.
libraries preparation using the TruSeq RNA Library Prep Kit v2 (Illumina).

tag: cell line

value: pro-T-cell line

tag: genotype/variation

value: Rag2 and P53 knockout


title: genomic DNA from sample 480

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 224

description: whole blood control sample

tag: diagnosis


title: P5424_non-stimulated_ChIP-Seq_H3K4me3

tag: cell type

tag: treatment

value: before PMA-Ionomycin stimulation


title: P5424_stimulated_ChIP-Seq_H3K4me3

value: after PMA-Ionomycin stimulation


title: genomic DNA from sample 63

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: Sex

value: whole blood


title: genomic DNA from sample 141

description: whole blood control sample

tag: age


title: P5424_stimulated_ChIP-Seq_H3K27Ac


title: genomic DNA from sample 531

description: whole blood case sample

tag: snp based principle component 1


title: SA97

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

description:
SAMPLE 129
Cystectomy
Bladder

data_processing:
Applied Biosystem's Sequence Detection System (SDS 2.2) software was used to compute Ct values using the default threshold and baseline parameters.
Delta Ct values were generated by subtracting experimental genes from endogenous control gene (RNU48-001006).
Fold-change values were created by subtracting the Target sample delta Ct from the control Sample delta Ct (Sample1 was used as control), then evaluated in the expression 2^-(delta-deltaCt).

label: TaqMan

source_name: Sarcomatoid carcinoma

label_protocol: Human Pool A v2.1.

extract_protocol: MasterPure Complete from Epicenter Biotechnologies.

value: Sarcomatoid carcinoma


title: SA103

description:
SAMPLE 131
Cystectomy
Bladder


title: genomic DNA from sample 407

description: whole blood case sample

tag: snp based principle component 2


title: SA100

description:
SAMPLE 130
Cystectomy
Bladder


title: genomic DNA from sample 254

description: whole blood control sample

tag: cellcount-nk


title: SA96

description:
SAMPLE 128
Cystectomy
Bladder


title: P5424_non-stimulated_ChIP-Seq_H3K27Ac


title: SA94

description:
SAMPLE 127
Cystectomy
Bladder


title: genomic DNA from sample 532

description: whole blood case sample

tag: cellcount-bcell


title: PMA-IONO_RNA-Seq_Replicate3


title: genomic DNA from sample 320

description: whole blood control sample

tag: tissue


title: genomic DNA from sample 512

description: whole blood control sample


title: PMA 1_RAD21 _ChIP-seq

description: ChIP-seq

tag: chip antibody


title: genomic DNA from sample 523

description: whole blood case sample


title: SA104

description:
SAMPLE 132
Cystectomy
Bladder


title: SA91

description:
SAMPLE 126
Cystectomy
Bladder


title: genomic DNA from sample 345

description: whole blood control sample


title: PMA-IONO_RNA-Seq_Replicate1

tag: cell line


title: SA90

description:
SAMPLE 125
Cystectomy
Bladder


title: genomic DNA from sample 268

description: whole blood case sample


title: genomic DNA from sample 213

description: whole blood case sample


title: genomic DNA from sample 385

description: whole blood case sample


title: P5424_DMSO_RNA-Seq_Replicate3

tag: genotype/variation


title: genomic DNA from sample 181

description: whole blood control sample

tag: cellcount-mono


title: SA87

description:
SAMPLE 123
Cystectomy
Bladder


title: P5424_DMSO_RNA-Seq_Replicate1


title: genomic DNA from sample 327

description: whole blood control sample

tag: cellcount-gran


title: genomic DNA from sample 171

description: whole blood control sample

tag: diagnosis


title: P5424_DMSO_RNA-Seq_Replicate2

tag: cell type


title: SA85

description:
SAMPLE 122
Cystectomy
Bladder


title: PMA-IONO_RNA-Seq_Replicate2

tag: treatment


title: SA82

description:
SAMPLE 121
Cystectomy
Bladder


title: genomic DNA from sample 202

description: whole blood case sample

tag: education level


title: SA80

description:
SAMPLE 120
Cystectomy
Bladder


title: genomic DNA from sample 333

description: whole blood control sample

tag: history of myocardial infarction


title: RNAi screening and timecourse Replicate 2

city: Nijmegen

first: Georgina

last: Peñalosa Ruiz

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

description:
tet-OSKM lentiviral cassette was induced with doxycycline
INV_1_JPGIII003_26

data_processing:
Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were matched samples using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to Mus musculus genome version mm10, and hereafter matched to the gencode.vM13.annotation transcriptome
Count table was generated using the standard settings of the CELseq2 pipeline
Sample quality controls, filtering genes and samples, and normalization were all performed with "scater" R package version 1.3.49
Batch effect was corrected by regression with "scran" R package version 1.6.9
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .txt file (tab delimited) containing all counts from all samples
Supplementary_files_format_and_content: .txt file (tab delimited) containing all normalized and batch effect corrected values from all samples

source_name: primary Mouse Embryonic Fibroblasts transduced with tet-STEMCCA lentiviruses containing Oct4, Sox2, Klf4 and c-Myc transgenes.

growth_protocol: Passage 1 MEFs were plated on gelatin-coated plates at a density of 10 000 cells per cm2. Next day they were incubated for 24 hours with inducible tet-OSKM (STEMCCA) and rtTA  lentiviruses at an MOI of 1. Reprogramming medium was composed of DMEM, 10 % FBS, 2ug/mL doxycycline, 3uM chiron, 0.25 uM Alk5i (TGFb-inhibitor), 50 ug/mL ascorbic acid and LIF.

extract_protocol:
RNA was isolated with the kit Quick-RNA microprep from Zymo Research (Cat# R1051), according to the manufacturer's instructions
CELseq2 library construction (T. Hashimshony et al.)

treatment_protocol: After OSKM-rtTA transduction, cells were reverse transfected with 40 nM pooled siRNAs and RNAiMAX lipofectamine. 24 hours post-transfection, cells were re-plated on gelatin-coated wells, and induced for reprogramming with doxycycline and reprogramming medium. For the timecourse the cells were not treated, only re-plated on gelatin coated wells to start reprogramming.

tag: passages

value: Reprogrammed at passage 2

tag: strain

tag: genotype

value: Wild-type

tag: file description

value: This sequencing file includes all the barcoded samples corresponding to the RNAi screen and the timecourse, Replicate 2


title: RNAi screening and timecourse Replicate 3

description:
tet-OSKM lentiviral cassette was induced with doxycycline
INV_1_JPGIII003_27

value: This sequencing file includes all the barcoded samples corresponding to the RNAi screen and the timecourse, Replicate 3


title: genomic DNA from sample 120

description: whole blood case sample

tag: age

tag: Sex

value: F

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk


title: genomic DNA from sample 164

description: whole blood control sample

value: control

tag: cellcount-bcell

tag: tissue


title: genomic DNA from sample 330

description: whole blood control sample

tag: cellcount-mono

tag: cellcount-gran


title: RNAi screening and timecourse Replicate 1

description:
tet-OSKM lentiviral cassette was induced with doxycycline
INV_1_JPGIII003_25

value: This sequencing file includes all the barcoded samples corresponding to the RNAi screen and the timecourse, Replicate 1


title: genomic DNA from sample 91

description: whole blood case sample

tag: diagnosis


title: Wdr5-Day6-R2

description: tet-OSKM lentiviral cassette was induced with doxycycline

data_processing:
RNA-seq reads from mouse cells were mapped to genome mm10 using STAR version 2.5.2b with --quantMode geneCounts
Low-count gene filtering and normalization by log-cpm (log2-counts per million reads) were done with R package edgeR  version 3.20.9
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab delimited text files (.txt) containing normalized values in log counts per million reads

extract_protocol:
RNA was isolated with the kit Quick-RNA microprep from Zymo Research (Cat# R1051), according to the manufacturer's instructions
200 ng total RNA were used to start the double-strand cDNA sysnthesis and library preparation with the Kapa RNA Hyper Prep Kit with Ribo Erase (Roche, #KK8561)  following standard Illumina protocols

treatment_protocol: After OSKM-rtTA transduction, cells were reverse transfected with 40 nM pooled siRNAs and RNAiMAX lipofectamine. 24 hours post-transfection, cells were re-plated on gelatin-coated wells, and induced for reprogramming with doxycycline and reprogramming medium.

tag: time when rna was collected

value: Day 6 of reprogramming

tag: sirna

value: transfected with Wdr5 siRNA


title: SA89

description:
SAMPLE 124
Cystectomy
Bladder


title: SA77

description:
SAMPLE 118
Cystectomy
Bladder


title: SA78

description:
SAMPLE 119
Cystectomy
Bladder


title: genomic DNA from sample 67

description: whole blood case sample

value: case

tag: education level

tag: history of myocardial infarction


title: Wdr5-Day6-R1

tag: strain

tag: passages


title: genomic DNA from sample 313

description: whole blood case sample


title: genomic DNA from sample 126

description: whole blood case sample

value: M


title: genomic DNA from sample 111

description: whole blood case sample


title: SA76

description:
SAMPLE 117
Cystectomy
Bladder


title: genomic DNA from sample 32

description: whole blood case sample


title: genomic DNA from sample 498

description: whole blood control sample


title: SA75

description:
SAMPLE 116
Cystectomy
Bladder


title: genomic DNA from sample 336

description: whole blood NA sample


title: genomic DNA from sample 142

description: whole blood control sample