title: CTRL_3

description: matrix.txt

value: control


title: CTRL_1

status: Public on May 31 2020

type: SRA

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: matrix.txt

library_source: transcriptomic

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38.27) using STAR 2.6.1d with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

molecule: total RNA

organism: Mus musculus

source_name: PASMCs

growth_protocol: Anaeestetise and heparinise the animal interperitoneally and place one incision into the right heart ventricle and insert the catheter into the pulmonary artery and another incision into the left ventricle for drainage. Perfuse the lung with 3 ml PBS and instill the lung with 3 ml Iron-Agarose (0.5% Iron III Oxide and 0.5% Agarose in Medium 199). And then instill agarose (1% Agarose in Medium 199) into the trachea until the lung is completely filled. Wait shortly, then pull out the catheter and close the ligature and remove the lung out of the thorax and incubate the lung in the cold PBS for 10 minutes. Under a sterile hood, remove heart, aorta, oesophagus and any connective tissue from the lung and add 1-2ml of PBS to the lung lobes and mince the lobes into small pieces with scalpels. Pipette the minced lung slurry into sterile 50 ml conical tube. Add 10-30ml PBS and place tube into the magnetic holder (Invitrogen, MPC-1 Magnet,12001D), wait shortly, then aspirate and discard the liquid. Repeat 3 times. After washing, resuspend the lung pellet into 3 ml Collagenase type 2 (80U/ml in Medium 199 + 1% Pen/Strep) and place on a petri dish and incubate it for 1hour at 37°C. After incubation homogenize the tissue-Collagenase solution by aspirating and releasing it several times through a 15G needle and then an 18G needle. Wash via magnetic holder 3 times with PromoCell medium containing supplements and pour the pellets into a culture dish. Four days later, pour the supernatant into a new conical tube and wash the pellet via magnetic holder 3 times with PBS and culture the iron-containing pellet with PromoCell medium containing supplements. Once there are cells grown around the particles, the iron can be washed off and either seeded again or thrown away. Once the particles are taken off, media should be changed every 2 days.

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set; Qiagen) to avoid contamination by genomic DNA according to manufacturer's instructions.
Whole transcriptome libraries were constructed with SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian.

treatment_protocol: The cells were stimulated in Promocell medium without supplements with BMP9 (R&D 5566-BP-010) and BMP10 (R&D 6038-BP) at 1 ng/mL and 5 ng/mL respectively for 6 hours.

tag: strain

tag: cell type

value: smooth muscle cells

tag: treatment


title: monocyte_NOD_CpG_2

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

country: USA

institute: NIH/NIDDK

description:
516
mouse supplemental table.csv

data_processing:
remove adapter sequences: Paired-end RNA sequencing reads were trimmed to remove Illumina’s adapter sequences.
remove poor quality reads and/or reads mapping to mouse rRNA and tRNA sequences using ArrayStudio package. Trim reads with base quality score (Sanger Quality Score) < 10. Filter out reads if trim length is < 25 bp. Filter out reads if maximal base quality score is < 15. Filter out reads if average quality score is < 10. Filter out reads if poly AGCT rate is >=80%. Filter out the pair of reads if either read fails the filtering criteria.
align reads to mouse reference genome (Build38) using OSA version 4 (Hu et al., 2012).
Obtain transcript counts data using RSEM package (Li and Dewey, 2011) and NCBI mouse RefSeq gene model (released July 2015).
criteria-based filtering: transcripts with zero counts in more than two third of the smaples were discarded from downstream analysis to reduce noise in the expression data.
quantile normalization and CPM conversion with limma voom
ComBat to remove batch effects from sort date (only for nonRag KO samples). Used with defaults, no co-variates, and for each subset separately. Performed after conversion to CPM within the voom function, but before calculation of precision weights within Voom function.
Differential gene expression: Calculation of precision weights using limma voom. Limma eBayes and topTable functions, utilizing the precision weights calculated from Voom normalization.
Genome_build: Build38
Supplementary_files_format_and_content: supplementary file is an excel file that includes CPM values for each Sample (before and after post processing steps) and Differential Expression results on separate tabs

molecule: polyA RNA

source_name: spleen

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA isolation kit per the manufacturer’s protocol
Low-input RNA sequencing libraries were generated from about 300 pg of total RNA using SMART-seq v4 Ultra Low Input RNA kit (Clontech, CA). All samples were subjected to 14 PCR amplification cycles to minimize PCR biases (Bhargava et al., 2014). Amplified cDNA libraries were later fragmented through sonication to obtain 200 – 500 bp fragments. Standard Illumina sequencing libraries were prepared using Rubicon ThruPLEX DNA-seq kit (Rubicon Genomics, MI) according to manufacturer’s protocol. Sample barcoded libraries were sequenced on Illumina’s NextSeq 500 instrumentation using NextSeq 300 Cycle Kit, High Output, V1 reagents (Illumina, CA) and data analysis workflow, bcl2fastq -v2.17.1.14, to obtain 150 bp paired-end reads.

treatment_protocol: sacrificed mice and collected tissues 5 hours after IP injection

value: monocyte

tag: tissue

value: spleen

tag: in-vivo treatment

value: CpG

value: NOD

tag: sort date

value: RNAseq run 2

tag: number of cells

tag: volume (ul)

tag: post extraction volume (ul)

tag: post extraction concentration from bioanalyzer (pg/ul)

tag: post extraction total quantity (pg)

tag: post extraction rin

tag: input to cdna contruction (pg)


title: HC08_LPS

type: RNA

data_processing:
Normalization of Nanostring nCounter data was performed as described previously (Urrutia A et al.), using nSolver (v. 2.5) for quality and negative and positive control analysis. Differences in RNA input were normalized using six housekeeping genes (EEF1G, RPL19, PPIA, TBP, G6PD, POLR2A), selected with the geNorm method. We estimated a lower limit of detection (LoD) of 4 counts using genes with consistent, low, non-zero expression across multiple samples, and retained 520 genes with expression above this LoD in greater than or equal to 1/3 of samples from any stimulation in either subject group. Multi-dimensional scaling (MDS) of gene counts revealed batch differences associated with the sample quantification method; ComBat in the sva R package was used to remove this batch effect prior to downstream analyses. Data were log2 transformed, and differential gene expression was determined using limma-voom, accounting for non-independence of samples from the same subject using limma’s duplicateCorrelation. Comparisons of the stimulation effect between groups used the interaction term between disease status and stimulus to capture the difference between groups in the change from the unstimulated sample. Multiple comparisons were adjusted using the Benjamini-Hochberg false discovery rate (FDR).
value definition: nonlog2 geNorm normalized values

organism: Homo sapiens

source_name: whole blood

extract_protocol: After blood draw and incubation, supernatant and cells were separated for downstream assays of secreted proteins and mRNA, respectively.  Gene expression was quantified from stimulated whole blood samples using the Nanostring nCounter Human Immunology kit v2, which profiles 579 immunology-related genes and 15 reference genes. Total mRNA was extracted from TruCulture cell pellets stabilized in Trizol LS (Sigma) using a modified protocol of the NucleoSpin 96 RNA tissue kit protocol (Macherey-Nagel) as previously described (Urrutia A et al. Standardized whole-blood transcriptional profiling enables the deconvolution of complex induced immune responses. Cell Rep. 2016). 100 ng of total RNA were analyzed per sample.

treatment_protocol: Peripheral blood was drawn directly into TruCulture tubes (Myriad RBM, Austin, Texas, USA) for stimulation following manufacturer’s instructions and as previously described. Tubes were pre-loaded with cell culture media and one of the following immune stimuli: SEB (0.4 ug/ml), IL-1B (25 ng/ml or 1760 IU/ml), LPS (1 ng/ml), IFN-B (1000 IU/ml), polyIC (20 ug/ml), or a no-stimulus null control, with stimulus concentrations previously determined  (Duffy D et al. Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli. Immunity 2014).

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

value: whole blood


title: HC08_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: tissue


title: HC08_IFNb

value: IFNb

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes


title: HC08_PolyIC

value: PolyIC

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC08_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: tissue


title: T1D11_IFNb

value: type 1 diabetes

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes


title: BMP_stim_2

description: matrix.txt

tag: strain

tag: cell type

value: smooth muscle cells

tag: treatment

value: BMP9 (R&D 5566-BP-010) and BMP10 (R&D 6038-BP) at 1 ng/mL and 5 ng/mL


title: CTRL_2

description: matrix.txt

value: control


title: monocyte_NOD_CpG_3

description:
517
mouse supplemental table.csv

value: monocyte

value: spleen

tag: in-vivo treatment

value: CpG

tag: sort date

tag: number of cells

tag: volume (ul)

tag: post extraction volume (ul)

tag: post extraction concentration from bioanalyzer (pg/ul)

tag: post extraction total quantity (pg)

tag: post extraction rin

tag: input to cdna contruction (pg)


title: T1D11_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D11_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes


title: control cells

city: Minato-ku

first: Satomi

last: Yogosawa

state: Tokyo

address: 3-25-8, Nishi-shinbasi

department: Department of Biochemistry

country: Japan

institute: Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using Rneasy mini kit (QIAGEN) according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: breast cancer

tag: culture method

value: in vitro culture


title: T1D11_PolyIC

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)


title: monocyte_NOD_CpG_1

description:
515
mouse supplemental table.csv

tag: tissue

tag: in-vivo treatment

tag: strain

value: NOD

tag: sort date

value: RNAseq run 2

tag: number of cells

tag: volume (ul)

tag: post extraction volume (ul)

tag: post extraction concentration from bioanalyzer (pg/ul)

tag: post extraction total quantity (pg)

tag: post extraction rin

tag: input to cdna contruction (pg)


title: BMP_stim_3

description: matrix.txt

tag: cell type

tag: treatment


title: monocyte_B6g7_CpG_2

description:
519
mouse supplemental table.csv


title: bone metastasized cells

source_name: bone metastasis

tag: cell line

tag: culture method

value: in vivo bone metastasis xenograft


title: monocyte_B6g7_CpG_1

description:
518
mouse supplemental table.csv


title: monocyte_B6g7_CpG_3

description:
520
mouse supplemental table.csv


title: T1D11_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

value: whole blood


title: Nerve Macrophage, Aged, Rep 2

city: Montreal

first: Jo Anne

last: Stratton

state: Quebec

address: 3801 University Road

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

description: Sample 4

data_processing:
After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Alignment was performed using bwa 0.7.12 in “mem” alignment mode against mm10 reference genome with default parameters.
R programming language for GenomicAlignments, Pheatmap, and DESeq2 packages. Expression was summarized at the gene level using the “union” mode of summarize overlaps. A false discovery rate corrected p-value of 0.05 for the Wald test was used for linear model of factors.
Genome_build: mm10
Supplementary_files_format_and_content: Text file including FPKM values for each sample

source_name: Sciatic nerve-derived at Day 3 post-nerve injury

extract_protocol:
All cells were sorted directly into lysis buffer (Ambion), then triturated and vortexed before storage at -80 °C. For RNA extractions, all samples were processed together following manufacturers recommendations (AM1561, Ambion). Total RNA extracts were quantitated using a Qubit Fluorimeter and the Qubit HS assay kit (Invitrogen). All samples were subjected to reverse transcription and Multiple Displacement Amplification (MDA) with REPLI-g SensiPhi DNA Polymerase and oligo-dT primers as per the Qiagen REPLI-g Single Cell RNA Library preparation kit (150073) and the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Cx3cr1-GFP+/- :Ccr2-RFP+/-

tag: tissue

value: Nerve

tag: genotype

value: CCR2+ Cx3cr1+

tag: cell type

value: Macrophages

tag: time point

value: Day 3 post

tag: protocol

value: nerve injury

tag: age

value: 15 months

value: Female


title: Nerve Macrophage, Aged, Rep 1

description: Sample 3

tag: Sex


title: T1D11_IL1

tag: patientid

tag: disease

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: absolute lymphocytes (cells/µl)


title: HC10_IL1

value: Healthy control

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: Nerve Macrophage, Young, Rep 2

description: Sample 2

tag: strain

tag: genotype

tag: cell type

tag: time point

tag: protocol

tag: age

value: 3 months

tag: Sex


title: T1D08_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: absolute lymphocytes (cells/µl)


title: T1D08_IFNb

value: IFNb

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D08_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

value: whole blood


title: T1D08_Null

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)


title: Nerve Macrophage, Young, Rep 1

description: Sample 1

tag: strain

value: Cx3cr1-GFP+/- :Ccr2-RFP+/-

tag: tissue

value: Nerve

tag: genotype

tag: cell type

tag: time point

tag: protocol

tag: age


title: T1D08_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC09_PolyIC

value: tecan

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: HC09_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent neutrophils


title: T1D08_IL1

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: T1D05_IL1

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: HC09_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent neutrophils


title: HC09_LPS

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: T1D05_PolyIC

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: T1D05_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent neutrophils


title: T1D05_LPS

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: T1D05_SEB

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: T1D05_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent neutrophils


title: HC02_IFNb

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC02_LPS

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: Thorne-RNA-seq

city: Aiken

first: Nathan

last: Hancock

state: SC

address: 471 University Parkway

department: Department of Biology and Geology

institute: University of South Carolina Aiken

description: control rep2

data_processing:
Illumina CASAVA v1.8 software was used for basecalling
Reads were filtered by removing reads containing adapter, reads containing ploy-N and low quality reads using custom perl scripts
Filtered reads were mapped to the reference genome using HISAT2 version 2.1.0-beta with the mismatch parameter set to 2
FPKM values were determined using Htseq version 0.6.1 with the addition of the "-m union" parameter
Differential expression was calculated using DESeq2
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: PRJNA605018_read_counts.txt is a tab-delimited text file with FPKM values for each gene in each  library
Supplementary_files_format_and_content: PRJNA605018_DESeq2_output.csv is a comma-delimited file containing normalized readcounts using DESeq2

organism: Glycine max

source_name: meristem tips

growth_protocol: The plants were grown in a greenhouse for one month.

extract_protocol:
The tissue was ground in liquid nitrogen before using Trizol Reagent to purify the RNA according to the manufacturer’s recommendations.
Standard illumina based RNA-seq methods by Novogene

treatment_protocol: 5cm meristem tips including immature trifoliates were flash frozen in liquid nitrogen.

tag: cultivar

value: Thorne

tag: mmping20f insertion @ chr08

tag: transgenic

value: no


title: HC02_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: percent neutrophils

tag: percent eosinophils


title: HC02_Null

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC02_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: T162845-RNA-seq

description: control rep1

tag: cultivar

tag: mmping20f insertion @ chr08

tag: transgenic

value: yes


title: T162822-RNA-seq

description: mutant rep2


title: HC02_SEB

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils


title: HC03_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC03_LPS

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: HC09_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils


title: HC09_Null

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: NEXTflex HC 3

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

description:
total RNA
BioO-21

data_processing:
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using cutadapt v1.15 with parameter -m 10
Remaining reads were mapped to the synthetic miRNA reference or customized miRNA reference based on miRBase v21 using Bowtie v1.1.2 with parameter -a and --norc, no mismatches allowed
Reads were counted a custom python script
Genome_build: synthetic miRNA reference and customized miRNA reference based on miRBase v21

source_name: Lymphocytes

extract_protocol:
Synthetic miRNA samples: no RNA extraction needed, human samples: RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
NEBNext, NEXTflex

tag: library prep kit

value: NEXTflex

tag: mix type/state

tag: replicate


title: NEXTflex HC 2

description:
total RNA
BioO-20


title: HC03_Null

tag: patientid

tag: disease

tag: stimulusid

value: qubit

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: HC03_IL1

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma


title: HC03_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: il-1 beta

tag: tnf-alpha


title: T1D09_PolyIC

value: type 1 diabetes

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

value: male

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: NEXTflex HC 1

description:
total RNA
BioO-19

tag: library prep kit

tag: mix type/state

value: Healthy control

tag: replicate


title: NEXTflex RA 2

description:
total RNA
BioO-17

value: Disease state:rheumatoid arthritis


title: NEXTflex RA 1

description:
total RNA
BioO-16


title: T1D09_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma


title: T1D09_IL1

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: il-1 beta

tag: tnf-alpha


title: T1D09_IFNb

tag: patientid

tag: disease

tag: stimulusid

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tissue


title: THP-1_Control

city: Kyoto

first: Ken

last: Morita

address: 53 Kawahara-cho, Syogoin, Sakyo-ku

department: Human Health Sciences

institute: Kyoto University

description: Gene expression data from control THP-1 cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450 using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Control THP-1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using GeneChip 3'IVT PLUS Reagent Kit from 250 ng total RNA.

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with heat-inactivated 10% FBS at 37 ℃, 5 % CO2.

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions (Qiagen RNeasy Mini Kit).

treatment_protocol: Cells were treated with doxycycline (Wako Pure Chemical Industries, Ltd) at 3 μM for 48 hours to induce gene expressions.

value: Leukemic cell line

tag: cell line


title: THP-1_DPYSL2A

description: Gene expression data from THP-1 cells transduced with DPYSL2A.

source_name: THP-1 cells transduced with DPYSL2A


title: NEBNext HC 3

description:
total RNA
NEB-21

tag: library prep kit

value: NEBNext

tag: mix type/state

tag: replicate


title: NEBNext HC 1

description:
total RNA
NEB-19


title: THP-1_KLF4

description: Gene expression data from THP-1 cells transduced with KLF4.

source_name: THP-1 cells transduced with KLF4


title: T162821-RNA-seq

description: mutant rep1

tag: cultivar

tag: mmping20f insertion @ chr08

tag: transgenic


title: HC03_IFNb

value: IFNb

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta


title: T1D16_IL1

tag: patientid

tag: disease

tag: stimulusid

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tnf-alpha

tag: tissue

value: whole blood


title: infected coral larvae, 72h_S3

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Sequenced reads were mapped to Cladocopium transcriptome (Levin et al 2016, MBE) using bowtie2 with DEFAULT parameters
transcript abundances were estimated from libraries mapped to the refrenece transcriptome using RSEM
Raw counts were analyzed to infer differential expression in edgeR package in the R environment. Symbiotic samples at 3, 12, 48 and 72 h were comapred to triplicate culture condition from Levin et al 2016
To comapre samples across time points, expression values in Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated followed by log2normalization and centring by substacting mean value form all counts per gene (row).
control data: cultured treatment was used as aproxy for free-living lifestyle obtained from (Levin et al., 2016) (GEO database GSE72763)
Genome_build: Cladocopium transcriptome (Levin et al 2016, MBE)
Supplementary_files_format_and_content: tab-delimited text files include expression values in FPKM for each Sample
control_FPKM_matrix.txt represents third-party reanalysis of control samples from GSE72763.
The transcriptome assembly used for mapping (GSE72763_MI_min250_nr.fasta.gz) can be found at the foot of the GSE72763 record.

organism: Cladocopium goreaui

source_name: infected coral larvae

growth_protocol: Larvae were raised in FSW

extract_protocol:
Larvae were removed from FSW, flash frozen in liquid Nitrogen and lysed twice for 20s at 4.0 m s−1 in Lysing Matrix D tubes (MP Biomedicals, Australia) containing 960 µL of lysis/binding solution plus 80 µL of the Plant RNA Isolation Aid (Ambion, USA) on a FastPrep®-24 Instrument (MP Biomedicals, Australia). RNA was bound to the columns, washed multiple times, eluted in 40 μL of RNase-free water and stored at -80°C . Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exposure of symbiont-free larvae to native algal symbionts (normally found in the adult) and sampling larvae at 3, 12, 48 and 72 hours post colonization

tag: strain

value: Cladocopium goreaui; ITS2 type C1

tag: developmental stage

value: larva

tag: treatment

value: Exposure to native algal symbionts

tag: time

value: 72hr post infection


title: NEBNext RA 3

description:
total RNA
NEB-18

tag: library prep kit

tag: mix type/state

tag: replicate


title: T1D16_Null

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta


title: infected coral larvae, 72h_S2

tag: strain

tag: developmental stage

tag: treatment

tag: time


title: NEBNext RA 2

description:
total RNA
NEB-17

tag: library prep kit

tag: mix type/state

tag: replicate


title: T1D09_SEB

tag: patientid

tag: disease

tag: stimulusid

value: SEB

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tnf-alpha

tag: tissue


title: NEXTflex RA 3

description:
total RNA
BioO-18

tag: library prep kit

value: NEXTflex

tag: mix type/state


title: NEBNext RA 1

description:
total RNA
NEB-16

tag: replicate


title: T1D16_IFNb

tag: patientid

tag: disease

value: qubit

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta


title: infected coral larvae, 48h_S2

tag: strain

tag: developmental stage

tag: treatment

tag: time

value: 48hr post infection


title: infected coral larvae, 48h_S3


title: T1D09_Null

value: type 1 diabetes

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

value: male

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tnf-alpha

tag: tissue


title: T1D16_LPS

tag: patientid

tag: disease

value: LPS

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta


title: NEBNext HC 2

description:
total RNA
NEB-20

tag: library prep kit

tag: mix type/state

value: Healthy control

tag: replicate


title: infected coral larvae, 48h_S1

tag: strain

tag: developmental stage

tag: treatment

tag: time


title: infected coral larvae, 12h_S3

value: 12hr post infection


title: CTRL cGAMP 12 B2

city: Strasbourg

first: Nelson

middle: Eduardo

last: Martins

address: 2 Allee Konrad Roentgen

country: France

institute: CNRS UPR9022/IBMC

data_processing:
Base-calling was done by HiSeq X Ten
Reads trimmed with Trimmomatic (-leading 3, -trailing 3, -slidingwindow 4:20 -maxinfo 100:0.2 -minlength 80) and mapped with STAR (v2.5.3.) using default parameters except maximum intron size <30kbp
Counts were aggregated at the gene level using featureCounts, assigning reads overlapping multiple genes to all of them (-O) and counting multimapping reads (-M)
Normalized read counts were obtained with DESeq2, based on a factorial design of Genotype and Treatment, with experimental batch as an additional variable
Genome_build: BDGP6.22
Supplementary_files_format_and_content: counts

organism: Drosophila melanogaster

source_name: Whole Organism

growth_protocol: Drosophila were kept in standard cornmeal agar medium at 25ºC, 12h:12h light/dark cycle

extract_protocol:
Total RNA extraction using Trizol
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

treatment_protocol: Intrathoraric injection of 69 nl of Tris, 2'3' cGAMP or cyclic-di-GMP

tag: genotype

tag: life stage

value: Adults (3-5 days old)


title: infected coral larvae, 12h_S1


title: CTRL cGAMP 12 B1


title: infected coral larvae, 72h_S1


title: CTRL cGAMP 24 B1


title: HC07_IFNb

tag: patientid

tag: disease

tag: stimulusid

value: IFNb

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

value: female

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)

tag: tnf-alpha

tag: tissue


title: HC07_LPS

tag: patientid

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

value: whole blood


title: CTRL cGAMP 24 B3

tag: genotype

tag: treatment

tag: life stage


title: infected coral larvae, 3h_S2

tag: strain

value: Cladocopium goreaui; ITS2 type C1

tag: developmental stage

value: larva

tag: time

value: 3hr post infection


title: HC07_Null

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: absolute lymphocytes (cells/µl)


title: CTRL cGAMP 6 B2

tag: genotype

tag: treatment

tag: life stage


title: CTRL cGAMP 6 B3


title: CTRL cGAMP 6 B1


title: HC12_IFNb

tag: patientid

tag: disease

tag: percent lymphocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HC07_PolyIC

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils


title: infected coral larvae, 3h_S1

tag: strain

tag: developmental stage

tag: treatment

value: Exposure to native algal symbionts

tag: time


title: HC07_SEB

tag: patientid

tag: disease

value: SEB

tag: percent lymphocytes

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: CTRL cGAMP 24 B2

tag: genotype

tag: life stage


title: CTRL cGMP 24 B3

value: c-di-GMP


title: T1D16_SEB

tag: stimulusid

tag: extractionbatch

tag: quantmachine

value: qubit

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: tissue


title: CTRL cGMP 24 B2

tag: treatment


title: infected coral larvae, 12h_S2

tag: strain

tag: developmental stage

tag: time


title: HC12_SEB

tag: patientid

tag: disease

value: tecan

tag: percent lymphocytes

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: HC07_IL1

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: tissue


title: infected coral larvae, 3h_S3

tag: strain

tag: developmental stage

tag: treatment

tag: time


title: CTRL cGAMP 12 B3

tag: genotype

tag: life stage


title: HeLa Cells GABATKO_RNAseq

city: ALBUQUERQUE

first: Suresh

last: Kumar

state: NM

address: 3901 Indian School Rd NE, Apt D407

department: MGM

institute: University of new Mexico l

data_processing:
Sequencing reads were aligned to the reference genome using HISAT2 package
The mapped reads of each sample were assembled using StringTie. All transcriptomes from samples were merged to reconstruct a comprehensive transcriptome using perl scripts (LC Sciences, USA).
After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (Fragments Per Kilobase Million)
The differentially expressed mRNAs and genes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: GRCh38

source_name: Human epethelial adenocarcinoma from cervix

growth_protocol: Cells were grown in DMEM media supllemented with 10% BSA.

extract_protocol:
RNA was isolated using TRIzol method
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001, RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp)

treatment_protocol: Cells were incubated in EBSS for 2h to induce autophagy.

tag: passages

tag: cell line

value: HeLa

tag: genotype/variation

value: GABATKO


title: HeLa Cells WT_RNAseq 3

value: wild type


title: HeLa Cells WT_RNAseq 2


title: HeLa Cells ATG3KO_RNAseq


title: HC12_PolyIC

tag: patientid

tag: disease

value: Healthy control

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: ageatdraw

tag: Sex

tag: percent lymphocytes

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma

tag: il-1 beta

tag: tnf-alpha


title: CTRL cGMP 24 B1

tag: genotype

tag: treatment

tag: life stage

value: Adults (3-5 days old)


title: HC12_LPS

tag: patientid

tag: disease

tag: stimulusid

value: LPS

tag: extractionbatch

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: tissue


title: CTRL cGMP 12 B2


title: T1D10_IFNb

value: type 1 diabetes

value: IFNb

tag: quantmachine

tag: ageatdraw

tag: Sex

value: female

tag: percent lymphocytes

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: HeLa Cells WT_RNAseq 1

tag: passages

tag: cell line

tag: genotype/variation


title: CTRL cGMP 12 B3

tag: genotype

tag: treatment

tag: life stage


title: T1D10_LPS

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: absolute neutrophils

tag: absolute eosinophils

tag: il-1 beta

tag: tnf-alpha

tag: tissue

value: whole blood


title: T1D10_IL1

tag: ageatdraw

tag: Sex

tag: percent lymphocytes

tag: percent monocytes

tag: percent neutrophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: HC12_Null

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: diabetes duration at draw (yrs)

tag: hba1c at draw (%)

tag: closest hba1c to draw


title: CTRL cGMP 6 B2

tag: genotype

tag: treatment

tag: life stage


title: CTRL cGMP 6 B1


title: T1D10_Null

tag: ageatdraw

tag: Sex

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent monocytes

tag: percent neutrophils

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: T1D10_PolyIC

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: diabetes duration at draw (yrs)

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: HC12_IL1

tag: ageatdraw

tag: Sex

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils


title: CTRL Tris 24 B3

tag: genotype

tag: treatment

value: Tris

tag: life stage


title: CTRL cGMP 12 B1


title: CTRL Tris 24 B2


title: T1D10_SEB

tag: patientid

tag: disease

tag: stimulusid

tag: extractionbatch

tag: quantmachine

tag: diabetes duration at draw (yrs)

tag: percent monocytes

tag: percent neutrophils

tag: il-1 beta

tag: tnf-alpha

tag: tissue


title: HeLa Cells HexaKO_RNAseq

tag: passages

tag: cell line

tag: genotype/variation

value: HexaKO


title: CTRL Tris 24 B1

tag: genotype


title: CTRL Tris 12 B2

tag: treatment


title: CTRL Tris 6 B3

tag: life stage


title: psAP2 vector control replicate 2

city: Tokyo

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

institute: National Institute of Infectious Diseases

data_processing:
Real-time analysis (RTA) software was used for base calling.
Sequenced reads were trimmed for TruSeq adaptor sequence, and masked for low-complexity and low-quality sequence by using cutadapt software ver. 1.13, then further analyzed for the quality by using FastQC software ver. 0.11.5.
Quality controlled reads were mapped to E. histolytica genome release version 1.3 in AmoebaDB using TopHat software ver. 2.1.1 (Bowtie software ver. 2.3.3.1).
Mapped reads were assembled using Cufflinks software ver. 2.2.1. Assembled data were merged and transcripts were predicted using cuffmerge tool in the Cufflinks software.
The differential gene expression analysis was performed using cuffdiff tool to analyse the difference between mock vector and CPBF2 gene silencing plasmid transfected cells.
Supplementary_files_format_and_content: genes.read_group_tracking: Excel file, raw fragment counts of transcripts in 6 samples (at the 4th column).
Supplementary_files_format_and_content: genes.fpkm_tracking: Excel file, normalized and averaged FPKM value of the mock vector transfected and CPBF2 gene silenced strain.
Supplementary_files_format_and_content: gene_exp.diff: Excel file, analyzed data for differentially expressed genes in mock vector transfected and CPBF2 gene sileced strain.

organism: Entamoeba histolytica

source_name: Trophozoite

growth_protocol: Standard protocl for E. histolytica axenic cuture with BIS medium.

extract_protocol:
Logarithmic growth phase of E. histolytica trophozoites were harvested then total RNA was extracted using Trizol reagent.
RNA-seq libraries were generated by using TruSeq stranded mRNA kit. The protocol included polyA plus RNA purification, RNA fragmentation, random hexamer primed cDNA synthesis, linker ligation, PCR amplification, and gel purification. The libraries were then subjected to 100 nt paired-end sequencing using an Illumina HiSeq2500.

tag: strain

tag: transfected plasmid

value: psAP2 (empty vector)

tag: expression of cpbf2

value: normal


title: CTRL Tris 12 B1


title: CPBF2 gene-silenced strain replicate 3

value: psAP2-cpbf2 (vector for silencing cpbf2)

value: silenced


title: CPBF2 gene-silenced strain replicate 1


title: CTRL Tris 12 B3


title: CPBF2 gene-silenced strain replicate 2


title: CTRL Tris 6 B2


title: psAP2 vector control replicate 3


title: CTRL Tris 6 B1


title: CTRL cGMP 6 B3

value: c-di-GMP


title: psAP2 vector control replicate 1


title: WT_seedling_WGBS

status: Public on May 30 2020

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
Raw reads were trimmed using trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Trimmed reads were aligned to the TAIR10 reference genome including mitochondira and chloroplast contigs using Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/). Multimapped reads were kept and randomly allocated.
CG/CHG/CHH Methylation was extracted from the bismark BAM file using the bismark_methylation_extractor command using the following parameters; --comprehensive --cytosine_report --bedGraph --CX
Single_C: We used a Perl script to convert the extracted methylation from bismark_methylation_extrator into single-c files for each sequence context (CG, CHG, CHH)
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data for individual cytosines (single-c).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seedlings were grown on MS/agar plates without glucose supplementation. Sterilised seeds were sown directly onto plates and stratified for three days at 4°C before being grown in 16h light: 8h dark at 23°C in a walk-in growth room (long day conditions) or 8h light:16h dark at 22°C in a Sanyo growth cabinet (short day conditions) until 14 days old.

extract_protocol:
DNA was extracted using a modified CTAB method (Dean et al., 1992).
Single-end bisulfite-sequencing libraries for Illumina sequencing were constructed with Ovation Ultralow Methyl-Seq Library Systems (Nugen, 0336) and EpiTect Fast Bisulfite Conversion (Qiagen, 59802) kits according to the kit protocols, except for the incorporation of two rounds of bisulfite conversion. Sequencing was performed on site at the John Innes Centre using a Nextseq 500.

value: Seedling

tag: age

value: 14 days old

value: wild-type


title: icu11-3_seedlings_WGBS


title: T1D16_PolyIC

tag: patientid

tag: disease

tag: stimulusid

value: PolyIC

tag: extractionbatch

tag: quantmachine

value: tecan

tag: ageatdraw

tag: Sex

value: male

tag: hba1c at draw (%)

tag: closest hba1c to draw

tag: glucose (mg/dl) at draw

tag: percent lymphocytes

tag: absolute neutrophils

tag: absolute eosinophils

tag: percent eosinophils

tag: absolute monocytes

tag: absolute lymphocytes (cells/µl)

tag: gm-csf

tag: ifn-gamma


title: 149_sam2

type: genomic

city: Memphis

first: Jose Vladimir

last: Sandoval Sierra

state: TN

address: 66 North Pauline street

department: Preventive Medicine

institute: UTHSC

description: CpG methylation

hyb_protocol: Bisulphite converted DNA hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina scaner

data_processing: Raw intensity data files (idat files) for both mouse and human samples were processed using the R package Minfi.

label: Cy3, Cy5

source_name: Saliva

label_protocol: Illumina

extract_protocol: DNA Genotek PrepIT L2P kit

tag: person id

tag: sample collection (visit)

tag: age

tag: self reported race

value: Hispanic

tag: self reported sex

value: Female

tag: prescribed opioid drugs

value: Oxycodone 5mg

tag: number of days on opioids

tag: cumulative opioid dose (morphine milligram equivalents)


title: 153_sam3

description: CpG methylation

value: African-American

value: Male


title: 148_sam2

description: CpG methylation


title: 143_sam3

description: CpG methylation

value: Caucasian

value: Hydrocodone 5mg


title: 152_sam1

description: CpG methylation

value: Oxycodone 5mg and Codeine 30mg


title: 144_sam2

description: CpG methylation


title: 145_sam2

description: CpG methylation


title: 153_sam2

description: CpG methylation


title: 146_sam3

description: CpG methylation

value: Oxycodone 10mg


title: 157_sam1

description: CpG methylation


title: 156_sam1

description: CpG methylation


title: 146_sam2

description: CpG methylation


title: 143_sam1

description: CpG methylation


title: 145_sam1

description: CpG methylation


title: 164_sam1

description: CpG methylation

value: Native-American


title: 146_sam1

description: CpG methylation


title: 148_sam3

description: CpG methylation


title: 152_sam3

description: CpG methylation


title: 145_sam3

description: CpG methylation


title: 142_sam3

description: CpG methylation

value: Asian


title: 164_sam2

description: CpG methylation


title: 142_sam2

description: CpG methylation


title: 144_sam1

description: CpG methylation


title: 149_sam1

description: CpG methylation


title: 142_sam1

description: CpG methylation


title: 143_sam2

description: CpG methylation


title: 159_sam1

description: CpG methylation


title: 152_sam2

description: CpG methylation


title: 157_sam2

description: CpG methylation


title: 148_sam1

description: CpG methylation


title: 140_sam1

description: CpG methylation


title: 137_sam3

description: CpG methylation


title: 134_sam3

description: CpG methylation


title: 139_sam3

description: CpG methylation


title: 139_sam2b

description: CpG methylation


title: 137_sam1

description: CpG methylation


title: 137_sam2

description: CpG methylation


title: 130_sam2

description: CpG methylation


title: 122_sam1

description: CpG methylation


title: 130_sam3

description: CpG methylation


title: 129_sam1

description: CpG methylation


title: 132_sam3

description: CpG methylation


title: 132_sam1

description: CpG methylation


title: 128_sam1

description: CpG methylation


title: 130_sam1

description: CpG methylation


title: 139_sam1

description: CpG methylation


title: 132_sam2

description: CpG methylation


title: 124_sam3

description: CpG methylation


title: 124_sam1

description: CpG methylation


title: 126_sam1

description: CpG methylation


title: 128_sam3

description: CpG methylation


title: 124_sam2

description: CpG methylation


title: 134_sam2

description: CpG methylation


title: 129_sam2

description: CpG methylation


title: 129_sam3

description: CpG methylation


title: 127_sam1

description: CpG methylation


title: 121_sam2

description: CpG methylation


title: 134_sam1

description: CpG methylation


title: 121_sam1

description: CpG methylation


title: 119_sam1

description: CpG methylation


title: 121_sam3

description: CpG methylation


title: 120_sam3

description: CpG methylation


title: 118_sam2

description: CpG methylation


title: 118_sam1

description: CpG methylation


title: 120_sam1a

description: CpG methylation


title: 116_sam3

description: CpG methylation


title: 118_sam3

description: CpG methylation


title: 115_sam2

description: CpG methylation


title: 114_sam2

description: CpG methylation

value: Middle-eastern


title: 116_sam1

description: CpG methylation


title: 115_sam1

description: CpG methylation


title: 116_sam2

description: CpG methylation


title: 115_sam3

description: CpG methylation


title: 113_sam2

description: CpG methylation


title: 113_sam1

description: CpG methylation


title: 112_sam2

description: CpG methylation


title: 113_sam3

description: CpG methylation


title: WT-mDF 22

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

description:
14 days in culture
raw_count_table.tsv

data_processing:
Quality assessment with FastQC Version 0.11.2
Read trimming with trimmomatic version 0.33
Reads were aligned to genome and gene level counts were generated with STAR version 2.4.2a using annotations version 86 (GRCm38.86) from Ensembl
Genome_build: GRCm38 (primary assembly) release 86
Supplementary_files_format_and_content: tab delimited text containing gene-level counts. Counts in the matrix are not normalized

source_name: Skin fibroblast

growth_protocol: Fibroblasts were derived from the skin and lungs of wild type and Rel-/- mice.  Skin: After euthanasia, and 70% ethanol sterilization, skin samples (3cm x 1cm) were collected from the dorsal area. Skin samples were washed again in 70% ethanol and then washed in PBS. They were cut into small into small pieces (1mm3) and explants were allowed to adhere for 5 minutes, after which fibroblast growth media (Dulbecco’s Modified Eagle Medium; Biosera) supplemented with 10% foetal bovine serum, Pen-Strep, sodium, pyruvate and L‑glutamine (Invitrogen Corp) was added. Explants were left undisturbed for 7 days after setup and then analysed for fibroblast outgrowth, skin tissue was then removed from the dish. Media was changed every 3 days and dermal fibroblasts were harvested for RNA extraction by scraping the dish at day 14. Lungs:  tissue was chopped into roughly 5mm pieces in sterile phosphate-buffered saline and tissue pieces placed in 100-mm tissue culture dishes containing  complete DMEM. The medium was replenished approximately every 3 days. After 14 days, the fibroblasts growing out of the explants were harvested for RNA extraction y scraping the dish.

extract_protocol:
Total RNA was isolated using an RNeasy Plus micro-kit  (Qiagen, D:74034) according to manufacturer's instructions.   Samples were stored in aliquot at – 80 °C prior to use. All reagents, plastic ware, and supplies used were sterile, nuclease free, and of molecular biology grade. RNA purity (A260/A280>1.80) and concentration were determined using nanodrop spectrophotometer (Thermo Fisher scientific, Delaware USA). RNA integrity was studied using the 2100 Bioanalyzer System (Agilent) and RNA 6000 Pico Kit. A RNA Integrity Number (RIN) of 8 was considered the lowest cut-off for RNA Sequencing.
RNA libraries were prepared using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB) in accordance with the manufacturer's recommendations.

treatment_protocol: WT and Rel -/- Fibroblasts were cultured under basal conditions (unstimulated) in 2 dimesions  on tissue culture grade plastic

tag: strain

tag: genotype

value: Wild Type

tag: treatment

value: unstimulated explant cultured skin fibroblast


title: KO-mDF 20

description:
14 days in culture
raw_count_table.tsv

value: Rel -/-


title: KO-mDF 19

description:
14 days in culture
raw_count_table.tsv


title: KO-mDF 18

description:
14 days in culture
raw_count_table.tsv


title: 114_sam3

description: CpG methylation


title: 108_sam1

description: CpG methylation


title: WT-mDF 11

description:
14 days in culture
raw_count_table.tsv


title: KO-mLF 8

description:
14 days in culture
raw_count_table.tsv

source_name: Lung fibroblast

value: unstimulated explant cultured lung fibroblast


title: KO-mLF 10

description:
14 days in culture
raw_count_table.tsv


title: 114_sam1

description: CpG methylation


title: 107_sam2

description: CpG methylation


title: 107_sam3

description: CpG methylation


title: WT-mLF 3

description:
14 days in culture
raw_count_table.tsv


title: 105_sam3

description: CpG methylation


title: WT-mLF 23

description:
14 days in culture
raw_count_table.tsv


title: 106_sam1

description: CpG methylation


title: 105_sam2

description: CpG methylation


title: WT-mLF 1

description:
14 days in culture
raw_count_table.tsv


title: 108_sam2

description: CpG methylation


title: 128_sam2

description: CpG methylation


title: WT-mLF 4

description:
14 days in culture
raw_count_table.tsv


title: 123_sam1

description: CpG methylation


title: 107_sam1

description: CpG methylation


title: S13_19 ECII _6months_APPPS1_neg

city: Boston

first: Jean-Pierre

last: Roussarie

state: MA

address: 72 E Concord Street

department: Anatomy & Neurobiology

institute: Boston University School of Medicine

description: ECII _6months_APPPS1_neg

data_processing:
RNAseq reads were mapped to the mouse genome Ensembl 75 using STAR (version 2.3.0e, default parameters)
gene level counts were quantified using htseq-count (version 0.9.1)
Genes were subjected to an expression detection threshold of 1 count per million reads per gene in more than 3 samples
Genome_build: Ensembl 75

source_name: Brain

extract_protocol:
see bacTRAP protocol in Roussarie et al., Neuron, 2020
5 ng of immunoprecipitated RNA was reverse transcribed and amplified using the Ovation RNAseq v2 kit. cDNA were then ultrasonicated and used to generate sequencing library using the Truseq RNA sample prep kit

treatment_protocol: no treatment

tag: cell type

value: ECII

tag: mouse age

value: 6 months

tag: Sex

value: M

tag: appps1 positive/negative

value: neg


title: S13_18 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos

value: pos


title: S13_17 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos

value: F


title: S13_16 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: S13_20 ECII _6months_APPPS1_neg

description: ECII _6months_APPPS1_neg


title: S13_14 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: S13_15 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: S13_11 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: S13_21 ECII _6months_APPPS1_neg

description: ECII _6months_APPPS1_neg


title: S13_10 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: JP215 ECII_5months_344N1-Rasgrp2

value: 4-5 months


title: 104_sam2

description: CpG methylation

value: Caucasian

value: Female

value: Oxycodone 5mg


title: 101_sam1

description: CpG methylation

value: Hydrocodone 5mg


title: KO-mLF 9

description:
14 days in culture
raw_count_table.tsv


title: JP214 ECII_5months_344N1-Rasgrp2


title: 101_sam3

description: CpG methylation


title: JP213 ECII_5months_344N1-Rasgrp2


title: JP212 V1_5months_181A2-Calca


title: 105_sam1

description: CpG methylation

value: Hispanic


title: 104_sam1

description: CpG methylation


title: JP203 CA1_5months_Cck


title: JP210 V1_5months_181A2-Calca


title: S13_12 ECII _6months_APPPS1_pos

description: ECII _6months_APPPS1_pos


title: JP198 ECII_5months_307B16-Sh3bgrl2-#33


title: JP201 CA1_5months_Cck


title: JP200 ECII_5months_307B16-Sh3bgrl2-#33


title: JP211 V1_5months_181A2-Calca


title: JP172 S1_24months_68J22-Cartpt

value: 24 months


title: JP199 ECII_5months_307B16-Sh3bgrl2-#33


title: JP171 S1_24months_68J22-Cartpt


title: 120_sam2

description: CpG methylation


title: 101_sam2

description: CpG methylation


title: JP169 V1_24months_181A2-Calca


title: JP167 V1_24months_181A2-Calca


title: JP168 V1_24months_181A2-Calca


title: 102_sam1

description: CpG methylation

value: African-American


title: 112_sam1

description: CpG methylation

value: Male


title: JP166 CA3_24months_Gprin3


title: JP165 CA3_24months_Gprin3


title: JP163 CA2_5months_329L1-Cacng5


title: JP161 CA2_5months_329L1-Cacng5


title: JP162 CA2_5months_329L1-Cacng5


title: JP159 DG_24months_126C5-Sstr4-#19

value: DG


title: 112_sam3

description: CpG methylation


title: JP160 DG_24months_126C5-Sstr4-#19


title: 104_sam3

description: CpG methylation


title: JP157 CA1_24months_126C5-Sstr4-#7


title: JP170 S1_24months_68J22-Cartpt


title: JP164 CA3_24months_Gprin3


title: JP156 CA1_24months_126C5-Sstr4-#7


title: JP155 CA1_24months_126C5-Sstr4-#7


title: JP154 CA1_24months_Cck


title: WT-mLF 5

description:
14 days in culture
raw_count_table.tsv

value: Wild Type

value: unstimulated explant cultured lung fibroblast


title: JP153 CA1_24months_Cck


title: F152-C-L004

city: Newcatle Upon Tyne

first: Helen

middle: R

last: Griffin

address: William Leech Building, Floor 3, Medical School

data_processing:
Raw sequence reads were trimmed to 50bp with FastX-toolkit v.0.0.14.
Reads were aligned to complete reference genomes, using the STAR aligner v.2.5.3a.
Transcript counts were obtained with HTSeq v.0.9.1.
Differential expression analysis was performed with DESeq2 v.1.12.4.
Genome_build: hg38 (iNPCs) or danRer11 (zebrafish embryos)
Supplementary_files_format_and_content: text file with per gene read counts generated by HTSeq

source_name: Induced Neuronal Progenitor Cells

extract_protocol:
RNA was extracted using mirVana miRNA isolation kit (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fibroblast derived iNPCs

value: Wild type

tag: replicate

tag: sequence lane


title: F152-C-L002


title: F152-B-L004


title: F152-C-L001


title: JP158 DG_24months_126C5-Sstr4-#19

value: M

value: neg


title: JP152 CA1_24months_Cck


title: JP150 ECII_24months_307B16-Sh3bgrl2-#33

value: ECII


title: F153-NPC-3-L004


title: F152-A-L002


title: JP149 ECII_24months_307B16-Sh3bgrl2-#33


title: F152-B-L001


title: F152-A-L004


title: JP148 ECII_24months_307B16-Sh3bgrl2-#26


title: F152-B-L002


title: F152-A-L001


title: JP147 ECII_24months_307B16-Sh3bgrl2-#26


title: F152-A-L003


title: F153-NPC-3-L002


title: JP146 ECII_24months_307B16-Sh3bgrl2-#26


title: JP143 ECII_24months_344N1-Rasgrp2


title: JP140 ECII_24months_199D5-Rasgrp2


title: JP151 ECII_24months_307B16-Sh3bgrl2-#33


title: F153-NPC-2-L003


title: F152-C-L003


title: F153-NPC-2-L004


title: JP142 ECII_24months_199D5-Rasgrp2


title: F152-B-L003


title: JP141 ECII_24months_199D5-Rasgrp2


title: F153-NPC-2-L002


title: F153-NPC-3-L001


title: JP144 ECII_24months_344N1-Rasgrp2


title: F153-NPC-3-L003


title: JP145 ECII_24months_344N1-Rasgrp2


title: F153-NPC-1-L004


title: F153-NPC-2-L001


title: F153-NPC-1-L003


title: JP120 S1_4months_68J22-Cartpt

value: 4-5 months


title: JP118 S1_12months_68J22-Cartpt

value: 12 month


title: KO-mLF 7

description:
14 days in culture
raw_count_table.tsv

value: Rel -/-


title: JP119 S1_12months_68J22-Cartpt


title: F153-NPC-1-L002


title: JP117 S1_12months_68J22-Cartpt


title: F008-NPC-3-L003


title: JP202 CA1_5months_Cck


title: JP113 V1_12months_181A2-Calca


title: F008-NPC-3-L002


title: F008-NPC-2-L003


title: F153-NPC-1-L001


title: F008-NPC-2-L004


title: JP110 CA2_5months_329L1-Cacng5


title: F008-NPC-3-L004


title: JP111 V1_12months_181A2-Calca


title: F008-NPC-2-L002


title: JP112 V1_12months_181A2-Calca


title: JP108 CA2_5months_329L1-Cacng5


title: F008-NPC-3-L001


title: JP109 CA2_5months_329L1-Cacng5


title: JP101 CA1_12months_126C5-Sstr4-#7


title: F008-NPC-2-L001


title: F008-NPC-1-L004


title: JP121 S1_4months_68J22-Cartpt


title: JP122 S1_4months_68J22-Cartpt


title: JP100 CA1_12months_126C5-Sstr4-#7


title: F008-NPC-1-L003


title: JP099 CA1_12months_126C5-Sstr4-#7


title: F008-NPC-1-L002


title: F008-NPC-1-L001


title: JP098 DG_12months_126C5-Sstr4-#19


title: JP097 DG_12months_126C5-Sstr4-#19


title: EXOSC9-NPC-3-L004


title: EXOSC9-NPC-2-L004


title: EXOSC9-NPC-2-L002


title: JP095 ECII_12months_307B16-Sh3bgrl2-#33


title: EXOSC9-NPC-2-L003


title: JP091 ECII_5months_307B16-Sh3bgrl2-#26


title: JP094 ECII_12months_307B16-Sh3bgrl2-#33


title: JP096 DG_12months_126C5-Sstr4-#19


title: JP092 ECII_5months_307B16-Sh3bgrl2-#26


title: EXOSC9-NPC-3-L003


title: EXOSC9-NPC-3-L001


title: JP093 ECII_12months_307B16-Sh3bgrl2-#33


title: EXOSC9-NPC-1-L004


title: JP089 ECII_12months_307B16-Sh3bgrl2-#26


title: EXOSC9-NPC-2-L001


title: JP087 CA3_12months_Gprin3


title: EXOSC9-NPC-1-L003


title: JP086 CA3_12months_Gprin3


title: JP085 CA3_12months_Gprin3


title: EXOSC9-NPC-1-L002


title: JP084 CA1_5months_Cck


title: JP083 CA1_5months_Cck


title: EXOSC9-NPC-3-L002


title: EXOSC8-NPC3-L003


title: JP082 CA1_5months_Cck


title: EXOSC8-NPC3-L004


title: JP126 ECII_5months_307B16-Sh3bgrl2-#26


title: JP090 ECII_12months_307B16-Sh3bgrl2-#26


title: JP081 CA1_12months_Cck


title: EXOSC8-NPC3-L002


title: EXOSC8-NPC2-L004


title: JP079 CA1_12months_Cck


title: JP080 CA1_12months_Cck


title: EXOSC8-NPC2-L003


title: JP076 CA2_12months_329L1-Cacng5


title: EXOSC8-NPC2-L001


title: EXOSC8-NPC1-L004


title: JP078 CA2_12months_329L1-Cacng5


title: EXOSC8-NPC1-L003


title: EXOSC8-NPC1-L001


title: EXOSC8-NPC1-L002


title: EXOSC9-NPC-1-L001


title: JP075 ECII_12months_344N1-Rasgrp2


title: JP073 ECII_12months_344N1-Rasgrp2


title: JP072 ECII_12months_199D5-Rasgrp2


title: EXOSC3-NPC-3-L004


title: JP070 ECII_12months_199D5-Rasgrp2


title: JP049 S1_5months_68J22-Cartpt


title: EXOSC3-NPC-3-L003


title: EXOSC8-NPC3-L001


title: JP048 S1_5months_68J22-Cartpt


title: EXOSC3-NPC-3-L002


title: EXOSC8-NPC2-L002


title: EXOSC3-NPC-3-L001


title: JP050 S1_5months_68J22-Cartpt


title: JP077 CA2_12months_329L1-Cacng5


title: EXOSC3-NPC-2-L003


title: JP040 CA2_5months_329L1-Cacng5


title: EXOSC3-NPC-2-L001


title: JP074 ECII_12months_344N1-Rasgrp2


title: EXOSC3-NPC-2-L002


title: JP039 CA2_5months_329L1-Cacng5


title: EXOSC3-NPC-2-L004


title: EXOSC3-NPC-1-L004


title: JP035 CA3_5months_Gprin3


title: EXOSC3-NPC-1-L002


title: JP029 DG_5months_126C5-Sstr4-#19


title: EXOSC3-NPC-1-L003


title: EXOSC3-NPC-1-L001


title: JP027 DG_5months_126C5-Sstr4-#19


title: HP1155-Non-Tumor-Stroma-RNA

city: Buffalo

first: Yue

last: Wu

state: Ny

address: 665 Elm St

institute: Roswell Park Cancer Institute Dept or Urology

data_processing:
base pair quality control by fastqc (v0.10.1)
Splieced alignment Bowtie (v1.0.1) and TopHat(V2.0.13) allwoing 1 mismatch per read using joint genome reference strategy (hg19 and mm10 respecitive resSeq UCSC annotations)
Lane replicates mereged with Merge Same Files from Picard (v.1.97)
Second pass QC with RSeQC(v.2.6.3)
read counts proccessed with HTSeq (v0.6.0). Resulting read counts also normalized to TPM
Genome_build: hg19
Supplementary_files_format_and_content: Counts_TPM.csv: TPM counts in csv file with genes as rows and samples as columns,  Counts_Raw.csv: Raw counts in csv file with genes as rows and samples as columns

source_name: Prostate

growth_protocol: Fresh benign prostate tissue specimens were procured from the Pathology Network Shared Resources (PNSR) at Roswell Park Comprehensive Cancer Center (RPCCC).  The protocol (NHR005009) for the use of fresh prostate tissue specimens was approved by the Institutional Review Board (IRB). Male Hsd:Athymic Nude-Fox1nu nude mice (12 weeks of age) were purchased from Envigo (Indianapolis, IN)[24].  Mice were castrated surgically and implanted subcutaneously with silastic tubing (catalog number 508-008 from VWR, Radnor, PA) manually packed with dry testosterone (T) crystals 3-5 days before transplantation with fresh tissue. This procedure standardized the levels of circulating T between mice at levels comparable to circulating T in adult male humans, (i.e., “humanized” mouse hosts) [25].   All experimental procedures were approved by the RPCCC Institutional Animal Care and Use Committee (IACUC) and were performed by trained staff of the RPCCC Mouse Tumor Model Resource (MTMR) core facility under IACUC protocol 1044M.  Fresh prostate tissue specimens were received from the RPCCC PNSR in transport medium that contained Cellgro phenol red-free RPMI1640 medium from Corning life Sciences (Corning, NY) supplemented with 10% charcoal-stripped fetal bovine serum (CS-FBS);  CS-FBS was prepared as described [26].  Tissue was cut into cubes 2-3 mm per side, pieces of tissue to be transplanted were coated with Matrigel from Corning Life Sciences, and the pieces were inserted individually at the subcutaneous site.  A total of 5-8 pieces of tissue were transplanted to each “humanized” mouse.  The resulting xenografts were considered to be established stably after 30 days.

extract_protocol:
Fresh tissue and Primary xenograft tissue was enriched into specific cell types (Epithelial, Endothleial, Stromal) with magnetic bead enrichment from Thermo Fisher Scientific. RNA was isolated from each enriched cell population specimen using miRNease Micro kits from Qiagen (Germantown, MD) following the manufacturer’s instructions, with modification.  RNA was eluted 3 times, each time with 17 μL RNase-free H2O, and all the eluents were combined.  DNase treatment was performed using a Turbo DNA-free Kit from Thermo Fisher Scientific.  After the DNase treatment, RNA was concentrated using an RNA Clean & Concentrator kit from Zymo Research (Irvine, CA).  Quantitative assessment of the total RNA yield was performed using the Qubit Broad Range RNA kit from Thermo Fisher Scientific
Sequencing libraries for each specimen were prepared from 100 ng of total RNA using the TruSeq Stranded Total RNA kit from Illumina Inc.  Ribosomal RNA (rRNA) was depleted from the total RNA, and the remaining RNA was purified and fragmented.  The fragmented RNA was primed for cDNA synthesis and reverse transcribed into a first strand cDNA using random primers.  The RNA templates were removed, and replacement DNA strands were synthesized to generate double stranded DNA (dsDNA) with dTTP incorporated in place of UTP, resulting in blunt-ended dsDNA.  AMPure XP beads from Beckman Coulter (Brea, CA) were used to recover the dsDNA from the second strand reaction mix.  A single ‘A’ nucleotide was then added to the 3’-ends of the blunt fragments.  Multiple indexing adapters that contained a single ‘T’ nucleotide on the 3’- end of the adapters were ligated to the ends of the dsDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries were amplified by PCR, purified using Ampure XP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape From Agilent Technologies.   The DNA libraries were quantitated using KAPA Biosystems qPCR kits, and a sub-specimen from multiple libraries were pooled at equimolar concentrations, following experimental design criteria.

tag: individual

value: Stromal

tag: tissue source

value: Fresh Tissue


title: JP028 DG_5months_126C5-Sstr4-#19


title: JP033 CA3_5months_Gprin3


title: HP1155-Non-Tumor-Epi-RNA

value: Epithelial


title: HP1155-Non-Tumor-Endo-RNA

value: Endothelial


title: HP1147-NT-Stroma-Fresh


title: JP022 CA1_5months_126C5-Sstr4-#7


title: JP041 CA2_5months_329L1-Cacng5


title: JP021 CA1_5months_126C5-Sstr4-#7


title: HP1147-NT-Epi-Fresh


title: JP016 ECII_5months_307B16-Sh3bgrl2-#33


title: JP017 ECII_5months_307B16-Sh3bgrl2-#33


title: HP1146-NT-Stroma-Fresh


title: JP015 ECII_5months_307B16-Sh3bgrl2-#33


title: JP034 CA3_5months_Gprin3


title: JP010 ECII_5months_307B16-Sh3bgrl2-#26


title: JP003 ECII_5months_199D5-Rasgrp2


title: HP1145-NT-Stroma-Fresh


title: JP002 ECII_5months_199D5-Rasgrp2


title: JP011 ECII_5months_307B16-Sh3bgrl2-#26


title: HP1146-NT-Endo-Fresh


title: HP1140-NT-Stroma-Fresh


title: HP1140-NT-Epi-Fresh


title: HP1131-NT-Stroma-Xen-Pre

value: Primmary Tissue Xenograft


title: JP001 ECII_5months_199D5-Rasgrp2


title: HP1140-NT-Endo-Fresh


title: exosc8-ZF2_L004

organism: Danio rerio

source_name: Zebrafish embryos

value: 5dpf embryos

value: exosc8 -/-


title: JP023 CA1_5months_126C5-Sstr4-#7


title: HP1109-NT-Stroma-Xen-Pre


title: HP1147-NT-Endo-Fresh


title: HP1131-NT-Epi-Xen-Pre


title: HP1104-NT-Stroma-Xen-Pre


title: HP1146-NT-Epi-Fresh


title: exosc8-ZF2_L001


title: TS-12: ex vivo LMP1 expressing non-transformed B cells

city: Berlin

first: Thomas

last: Sommermann

address: Robert-Rossle-Str. 10

institute: Max Delbruck Center for Molecular Medicine

data_processing:
Adapters and low quality reads trimmed using trim-galore version 0.4.2
reads mapped to reference genome using STAR version 2.5.1b
used STAR with --quantMode GeneCounts to produce counts by genes
Genome_build: mm10 (GRCm38)

source_name: spleen

growth_protocol: ex vivo

extract_protocol:
FACS-sorted cells were pelleted and RNA was extracted using a Rneasy kit (Quiagen)
Illumina TruSeq RNA

tag: secondary host

tag: secondary host strain

value: primary LMP1-expressing mouse B cells

tag: facs-sort

value: CD19+,humanCD2+(marker LMP1-TG)

tag: tissue

value: spleen


title: TS-13: ex vivo LMP1 expressing non-transformed B cells


title: exosc8-ZF2_L003


title: HP1145-NT-Epi-Fresh


title: TS-11: secondary LMP1-Lymphoma 47

source_name: liver

value: secondary LMP1-expressing mouse B cell lymphoma

value: liver


title: HP1109-NT-Endo-Xen-Pre


title: HP1145-NT-Endo-Fresh


title: HP1104-PreCast-Endo


title: TS-14: ex vivo LMP1 expressing non-transformed B cells


title: TS-10: secondary LMP1-Lymphoma 46


title: HP1099-PreCast-Epi


title: exosc8-ZF1_L004


title: exosc8-ZF1_L003


title: HP1098-PreCast-Epi


title: HP1098-PreCast-Endo


title: TS-9: secondary LMP1-Lymphoma 45


title: exosc8-ZF1_L002


title: exosc8-ZF2_L002


title: HP1131-NT-Endo-Xen-Pre


title: TS-7: secondary LMP1-Lymphoma 40


title: exosc8-ZF1_L001


title: HP1097-PreCast-Epi


title: TS-8: secondary LMP1-Lymphoma 43


title: 1096-Epi


title: HP1097-PreCast-Endo


title: Control-ZF3_L004

value: Wild type


title: TS-6: secondary LMP1-Lymphoma 39


title: 1096-Endo


title: HP1104-PreCast-Epi


title: 1091-Endo


title: Control-ZF3_L002


title: HP1087-Endo


title: HP1099-PreCast-Endo


title: HP1087-Epi


title: TS-5: secondary LMP1-Lymphoma 37


title: TS-4: secondary LMP1-Lymphoma 35


title: HP1085-epi


title: Control-ZF3_L001


title: HP1085-endo


title: Control-ZF2_L004


title: 1084epi


title: Control-ZF2_L003


title: 1091-Epi


title: Control-ZF2_L002


title: TS-2: secondary LMP1-Lymphoma 33


title: TS-3: secondary LMP1-Lymphoma 34

source_name: lymphonode

value: lymphonode


title: Control-ZF2_L001


title: TS-1: secondary LMP1-Lymphoma 32


title: Control-ZF1_L004


title: Control-ZF3_L003


title: Control-ZF1_L003


title: Control-ZF1_L002


title: KR_TS_039: iLMP1 rv-Rel day 6

data_processing:
Adapters and low quality reads trimmed using trim-galore version 0.4.2
reads mapped to reference genome using STAR version 2.5.1b
used STAR with --quantMode GeneCounts to produce counts by genes
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: csv file containing read counts per gene

extract_protocol: FACS-sorted cells were pelleted and RNA was extracted using a Rneasy kit (Quiagen)

value: MACS sorted CD43- B cells

value: TAT-cre treated and cultured for 6 days

tag: transduction on day 1

value: MSCV-Rel-iGFP

tag: facs sorting

value: humanCD2+(reporter for LMP1) GFP+ (reporter for MSCV)


title: Control-ZF1_L001


title: KR_TS_038: iLMP1 rv-Rel day 6

tag: strain


title: KR_TS_033: iLMP1 rv-EBF1 day 6

tag: genotype


title: exosc9-ZF3_L004

value: exosc9 -/-


title: KR_TS_032: iLMP1 rv-EBF1 day 6

tag: treatment


title: KR_TS_015: secondary LMP1-Lymphoma 46

data_processing:
Library strategy: Exome-Seq
Paired-end reads from each lane were mapped to the reference genome using bwa mem
PCR duplicates were marked using picard-tools-1.141
Read groups were added using picard-tools-1.141
Reads were realigned locally around indels using GATK v3.4
Paired-end information was fixed using picard-tools-1.141
Quality scores were recalibrated using GATK v3.4
Reads from different lanes for the same samples were merged to single bam files using GATK v3.4
Mutations were called using MuTect 1.1.7 with dbSNPv137 input
Genome_build: mm10
Supplementary_files_format_and_content: VCF files of mutation calls

source_name: liver/spleen

extract_protocol: FACS-sorted cells were pelleted and gDNA was extracted using a Nucleopspin tissue kit (Macherey-Nagel)

tag: hspc donor

tag: cell type

value: liver/spleen


title: KR_TS_016: secondary LMP1-Lymphoma 47


title: exosc9-ZF3_L003


title: Z (8) 4

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

description: Gene expression in THP-1 cells after 4 h in presence of NPZnO exposure (8 µg/mL)

hyb_protocol: Six hundred ng of CTP-Cy3-labelled cRNA were fragmented at 60°C for 30 min in a reaction volume of 25 µL following the manufacturer’s instructions. 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v3 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent).

scan_protocol: Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.

source_name: THP-1, 4 h, 8 µg/mL of NPZnO, replicate 4

label_protocol: CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (specific activity > 10 pmol Cy3 / µg cRNA, BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyzer).

growth_protocol: THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in DMEM medium supplemented with 15 % of heat-inactivated fetal bovine serum, 2mM L-glutamine, as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma Aldrich). Cells were incubated at 37°C in an atmosphere composed of 95 % air, 5 % CO2 and medium are changed every 2-3 days.

extract_protocol: The quality of the RNA extracted by RNA-Solv Reagent (Omega Bio-tek, USA) was determined by spectrophotometry (A260nm/A280nm, A260nm/A230nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 7.5, Agilent 2100 Bioanalyzer, Santa Clara, CA, USA).

treatment_protocol: THP-1 was differentiated into macrophages by 24-h incubation with 10 ng/mL phorbol 12-myristate 13-acetate (PMA; Sigma, St. Louis, MO) in Petri dish at a density of 5 x 104 cells / mL. Cells were then incubated without (control) or with zinc oxide nanoparticles (2 or 8 µg/mL) for 4 h in absence of fetal bovine serum.

tag: cell line

value: peripheral blood

tag: gender

value: male

tag: age


title: exosc9-ZF3_L002

value: 5dpf embryos

tag: replicate

tag: sequence lane


title: KR_TS_014: secondary LMP1-Lymphoma 45


title: KR_TS_031: iLMP1 rv-EBF1 day 6


title: 1084endo

tag: individual

value: Endothelial

tag: tissue source

value: Fresh Tissue


title: Z (8) 1

source_name: THP-1, 4 h, 8 µg/mL of NPZnO, replicate 1


title: C4

description: Gene expression in THP-1 cells after 4 h in absence of NPZnO exposure (0 µg/mL)

source_name: THP-1, 4 h, 0 µg/mL of NPZnO, replicate 4


title: Z (2) 1

description: Gene expression in THP-1 cells after 4 h in presence of NPZnO exposure (2 µg/mL)

source_name: THP-1, 4 h, 2 µg/mL of NPZnO, replicate 1


title: C3

source_name: THP-1, 4 h, 0 µg/mL of NPZnO, replicate 3


title: Z (2) 4

source_name: THP-1, 4 h, 2 µg/mL of NPZnO, replicate 4


title: C1

source_name: THP-1, 4 h, 0 µg/mL of NPZnO, replicate 1


title: Z (8) 3

source_name: THP-1, 4 h, 8 µg/mL of NPZnO, replicate 3


title: Z (2) 3

source_name: THP-1, 4 h, 2 µg/mL of NPZnO, replicate 3


title: Z (2) 2

source_name: THP-1, 4 h, 2 µg/mL of NPZnO, replicate 2


title: Z (8) 2

source_name: THP-1, 4 h, 8 µg/mL of NPZnO, replicate 2


title: KR_TS_024: iLMP1 rv-GFP day 6

value: MSCV-iGFP


title: C2

source_name: THP-1, 4 h, 0 µg/mL of NPZnO, replicate 2


title: KR_TS_023: iLMP1 rv-GFP day 6

value: spleen


title: exosc9-ZF2_L004

source_name: Zebrafish embryos


title: KR_TS_013: secondary LMP1-Lymphoma 43

tag: secondary host

tag: secondary host strain

value: secondary LMP1-expressing mouse B cell lymphoma

value: CD19+,humanCD2+(marker LMP1-TG)


title: KR_TS_012: secondary LMP1-Lymphoma 40

tag: facs-sort

tag: tissue


title: exosc9-ZF2_L002


title: Cortex, KI-treated group, rep9

city: Fontenay-aux-Roses

first: Maâmar

last: Souidi

address: 31 Avenue de la Division Leclerc

institute: IRSN

description: Gene expression of treated group

hyb_protocol: One-color microarray protocol from Agilent

scan_protocol: The raw fluorescence signals were scanned with Agilent Technologies scanner G2505C

data_processing: FeatureExtractor spot analysis software 10.7.3.1

organism: Rattus norvegicus

source_name: cortex potasium iodide

treatment_protocol: Tissue was instantly deep-frozen in liquid nitrogen and then stored at -80°C until RNA isolation. Total RNA was extracted from both tissues, thyroid and cortex respectively, using mirVana™ Isolation Kit (ThermoFisher Scientific, France) according to the manufacturer’s protocol.  RNA quality control was performed using the kit RNA 6000 nano (Agilent Technologies, Waldbronn, Germany) on an Agilent 2100 Bioanalyzer System (Agilent Technologies, Waldbronn, Germany). Quality of RNA was defined by a 260/280 absorbance ratio> 1.8; a 260/230 ratio > 1.5 and a RIN value > 7.5 were desired.

value: Wistar

value: Cortex cerebellum

value: KI-treated group


title: KR_TS_021: iLMP1/EBNA3A day 6

source_name: spleen

value: MACS sorted CD43- B cells

value: TAT-cre treated and cultured for 6 days

tag: transduction on day 1

tag: facs sorting

value: humanCD2+(reporter for LMP1) BFP (reporter for EBNA3A)


title: KR_TS_022: iLMP1 rv-GFP day 6

tag: strain

tag: genotype

value: humanCD2+(reporter for LMP1) GFP+ (reporter for MSCV)


title: exosc9-ZF2_L003

value: exosc9 -/-


title: KR_TS_010: secondary LMP1-Lymphoma 37

tag: hspc donor

value: liver/spleen


title: KR_TS_011: secondary LMP1-Lymphoma 39

tag: cell type


title: exosc9-ZF2_L001


title: Cortex, KI-treated group, rep8

description: Gene expression of treated group

label_protocol: One-color microarray protocol from Agilent

extract_protocol: Total RNA was extracted from both tissues, thyroid and cortex respectively, using mirVana™ Isolation Kit (ThermoFisher Scientific, France)

value: male

tag: treatment


title: exosc9-ZF1_L003

value: 5dpf embryos


title: KR_TS_018: iLMP1 day 6

value: humanCD2+(reporter for LMP1)


title: KR_TS_020: iLMP1/EBNA3A day 6


title: exosc9-ZF1_L004


title: KR_TS_007: secondary LMP1-Lymphoma 32


title: KR_TS_006: secondary LMP1-Lymphoma 31


title: KR_TS_005: Tail-DNA #4

source_name: embryo

value: embryonic leg

value: no sort

value: embryo


title: KR_TS_019: iLMP1/EBNA3A day 6

value: spleen


title: Cortex, KI-treated group, rep6

description: Gene expression of treated group

tag: gender


title: exosc9-ZF3_L001


title: exosc9-ZF1_L002


title: KR_TS_017: iLMP1 day 6


title: Cortex, KI-treated group, rep2

description: Gene expression of treated group


title: Cortex, KI-treated group, rep4

description: Gene expression of treated group


title: Cortex, KI-treated group, rep5

description: Gene expression of treated group


title: exosc9-ZF1_L001


title: KR_TS_004: Tail-DNA #2


title: Cortex, KI-treated group, rep1

description: Gene expression of treated group


title: exosc8-ZF3_L004

value: exosc8 -/-


title: KR_TS_016: iLMP1 day 6


title: KR_TS_009: B cells

value: wt

value: non (ex vivo analysis)


title: KR_TS_002: B cells


title: KR_TS_001: B cells


title: exosc8-ZF3_L002


title: exosc8-ZF3_L003


title: Cortex, KI-treated group, rep7

description: Gene expression of treated group

value: Wistar

value: Cortex cerebellum

value: KI-treated group


title: Double KO Exp#2

city: Cincinnati

first: Mark

middle: Jordan

last: Althoff

state: OH

address: 3333 Burnett Avenue

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: Yap1 and Taz null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#2

data_processing:
Reads were aligned with TopHat software, using  mm10 as the reference genome and Reads Per Kilobase of transcript per Million mapped reads (RPKM) as output.
RPKM were log2-transformed and baselined to the median expression of the average of each class of samples.
Analysis of differential gene expression and gene ontology (GO) pathway analyses using Altanalyze software v2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted from sorted hematopoietic stem cells derived from Mx1Cre;Wt or ScribbleΔ/Δ, TazΔ/Δ;Yap1Δ/Δ and ScribbleΔ/Δ;Taz Δ/Δ;Yap1Δ/Δ mice one week following polyinositide/cytidine (polyI:C) administration and gene deletion using RNeasy Mini Kit (QIAGEN).
The initial amplification step was performed with the Ovation RNA-Seq System v2 (Tecan Genomics) and the cDNA concentration and size were measured using the Qubit dsDNA BR assay and a DNA 1000 Chip, respectively. The subsequent libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). Briefly, 1ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.

treatment_protocol: Induction of Cre recombinase expression in inducible transgenic animals was achieved by 6 injections of polyinositide/cytidine (polyI:C) at an intraperitoneal dose of 10 mg/kg every other day in Mx1-CreTg/- animal.

value: hematopoietic stem cells


title: Cortex, control group, rep7

description: Gene expression of control group

source_name: cortex control

value: control group


title: Double KO Exp#1

description: Yap1 and Taz null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#1


title: Triple KO Exp#1

description: Scribble, Yap1 and Taz null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#1


title: Triple KO Exp#2

description: Scribble, Yap1 and Taz null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#2


title: Cortex, control group, rep8

description: Gene expression of control group


title: MCF7 SIX1 overexpressing cells treated by 10 µM 8430 replicate 3

city: Aurora

first: Heide

last: Ford

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

description:
MCF7_SIX1_8430_HTSeq_counts.txt
MCF7_SIX1_8430_HTSeq_RPKM.txt

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
fastq files from 2 separate lanes were merged for each sample to obtain sufficient read depth.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

growth_protocol: MCF7 cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, and 2mM L-glutamine

extract_protocol:
Total RNA was isolated from MCF7 using Direct-zol RNA Miniprep Kit (Zymo Research R2052)
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: MCF7 cells were treated by either DMSO or compound 8430 at 1 or 10 µM

tag: disease state

value: Mammary gland adenocarcinoma

tag: genotype/variation

value: SIX1 overexpressing


title: exosc8-ZF3_L001

tag: replicate

tag: sequence lane


title: MCF7 SIX1 overexpressing cells treated by 10 µM 8430 replicate 1


title: Cortex, control group, rep6

description: Gene expression of control group

value: male


title: Scribble KO Exp#1

description: Scribble null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#1

value: Scribble-/-


title: Scribble KO Exp#2

description: Scribble null hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#2


title: HP1109-NT-Epi-Xen-Pre

source_name: Prostate

tag: individual

value: Epithelial

tag: tissue source

value: Primmary Tissue Xenograft


title: Wt Exp#2

description: Wt hematopoietic stem cells isolated from mice at 1 week post Cre induction, Exp#2

value: Wild type


title: D4_KO_input [ChIP-seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

data_processing:
Paired-end reads for ChIP-seq were aligned to the mouse mm10 genome using Bowtie2 with the ‘‘-X 2000’’ options.
The Picard was used to remove PCR duplicates and Samtools was used to remove low quality reads (MAPQ < 30).
The MACS2 software calls the ChIP-seq peak with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using deepTools.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were routinely cultivated on mitotically inactivated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20% Knockout Serum Replacement, 1× Glutamine Max, 1× NEAA, 1× Pen/Strep, 0.1 mM 2-mercaptoethanol, 1000 U ml-1 LIF, 1 μM PD0325901 and 3 μM CHIR99021. MEFs were grown in DMEM high glucose supplemented with 15% FBS and 1× Pen/Strep.

extract_protocol: ChIP was performed as described previously (Liu et al., 2015).

treatment_protocol: The EpiLCs induction were performed by seeding 1.0×10e5 ESCs into a well of a 12-well plate coated with 16.7 mg/ml human plasma fibronectin in N2B27 medium containing 20 ng/ml Activin A, 12 ng/ml bFGF, and 20% KSR. The culture medium was changed every day.

tag: cell line

value: Atg7 KO

value: ESC to EpiLC transition

tag: time point

tag: chip antibody


title: MCF7 SIX1 overexpressing cells treated by 10 µM 8430 replicate 2


title: D4_KO_H3K4me3 [ChIP-seq]


title: D4_KO_H3K4me1 [ChIP-seq]


title: D4_KO_Nanog [ChIP-seq]

value: Nanog


title: MCF7 SIX1 overexpressing cells treated by 1 µM 8430 replicate 2


title: MCF7 SIX1 overexpressing cells treated by 1 µM 8430 replicate 1


title: Cortex, control group, rep5

description: Gene expression of control group

tag: tissue


title: D4_Ctr_Nanog [ChIP-seq]

value: Control


title: D4_KO_H3K27ac [ChIP-seq]


title: Cortex, control group, rep3

description: Gene expression of control group