title: VX2012004_PBMC_Day9


title: Longissimus_Genmascq_Pig_242

status: Public on Dec 31 2020

type: RNA

city: SAINT GILLES

first: Frederic

last: Herault

address: 16 le Clos

department: Animal Genetic

country: France

institute: INRAE

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

molecule: total RNA

organism: Sus scrofa

source_name: Longissimus lumborum muscle

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit following the manufacturer’s instructions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: M

tag: pig number

tag: ChIP


title: Longissimus_Genmascq_Pig_170

value: F


title: VX2012004_PBMC_Day3

city: Beijing

first: Yiming

last: Shao

state: Beijing

address: No. 155 Changbai Road, Changping District

department: National Center for AIDS/STD Control and Prevention

country: China

institute: Chinese Center for Disease Control and Prevention

hyb_protocol: After hybridization on Human PrimeView Arrays for 16 h at 45C and 60 rpm in Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA), slides were washed and stained with a Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA). Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: Initially, data quality was assessed by background level, 3 labeling bias, RNA quality and pair-wise correlation among samples. For the PrimeView chip, the customized CDF (version 22, ENTREZG) downloaded from the BrainArray website was performed in probe set mapping. IQR was applied for raw data filtering using the genefilter package, and the threshold was set to remove probes/genes with IQR less than the 50th percentile of the IQR across all probes/genes. Normalization was performed with RMA algorithm that includes global background adjustment and quantile normalization. The resulting matrix showed genes as rows and samples as columns was log2 transformed and used as input for linear modeling using the limma package. The limma package was performed to identify differentially expressed genes (DEG) at any time point post immunization, compared with baseline (Day 0). Empirical Bayes moderation of the standard error and Benjamini and Hochberg false-discovery rate (FDR) correction for multiple testing were employed, and the criteria for differentially expressed genes (DEG) were threshold fold change more than 1.3 and BH adjusted FDR less than 0.05.

label: Biotin

organism: Homo sapiens

source_name: human Day3

label_protocol: Total RNA were amplified, labeled and purified by using the GeneChip 3IVT Express Kit (Affymetrix, Santa Clara, CA, USA) followed the manufacturer instructions to obtain biotin labeled cRNA.

extract_protocol: After PMBC isolation, 1 million PBMC cells were lysed in 1 ml of TRIzol (Life technologies, Carlsbad, CA, USA) immediately and stored at -80C. The samples were thawed and RNA extracted following the manufacturer instructions. The quality of the RNA was assessed by using Nanodrop 2000 Spectrometer (Thermo Scientific, MA, USA) as well as by visualization of the integrity of the 28S and 18S band on Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).  Qualified total RNA was further purified by RNeasy micro kit (QIAGEN, GmBH, Germany) and removed genomic contamination by RNase-Free DNase Set (QIAGEN, GmBH, Germany).  The purified RNA was stored at -80C.

tag: cell type

value: PBMC

tag: time point

tag: nab respond

value: HighResponder

tag: vaccination interval regimen

tag: subject id


title: VX2012004_PBMC_Day7

source_name: human Day7


title: Longissimus_Genmascq_Pig_173


title: VX2012004_PBMC_Day1

source_name: human Day1


title: Longissimus_Genmascq_Pig_169


title: Longissimus_Genmascq_Pig_168


title: Longissimus_Genmascq_Pig_167


title: Longissimus_Genmascq_Pig_166


title: Longissimus_Genmascq_Pig_163


title: VX2012003_PBMC_Day28

source_name: human Day28

value: LowResponder


title: VX2012004_PBMC_Day0

source_name: human Day0


title: VX2012003_PBMC_Day14

source_name: human Day14


title: Longissimus_Genmascq_Pig_305


title: VX2012012_PBMC_Day7


title: Longissimus_Genmascq_Pig_161


title: VX2012003_PBMC_Day9

source_name: human Day9


title: Longissimus_Genmascq_Pig_159


title: VX2012003_PBMC_Day3


title: VX2012004_PBMC_Hour4

source_name: human Hour4


title: Longissimus_Genmascq_Pig_155


title: Longissimus_Genmascq_Pig_154


title: Longissimus_Genmascq_Pig_158


title: VX2012003_PBMC_Hour4


title: VX2012003_PBMC_Day1


title: Longissimus_Genmascq_Pig_148


title: VX2012001_PBMC_Day14

value: NonResponder


title: Longissimus_Genmascq_Pig_165


title: Longissimus_Genmascq_Pig_145


title: Longissimus_Genmascq_Pig_153


title: Longissimus_Genmascq_Pig_146


title: VX2012003_PBMC_Day0


title: VX2012003_PBMC_Day7


title: VX2012001_PBMC_Day9


title: Longissimus_Genmascq_Pig_143


title: VX2012001_PBMC_Day3


title: Longissimus_Genmascq_Pig_142


title: Longissimus_Genmascq_Pig_132


title: Longissimus_Genmascq_Pig_133


title: Longissimus_Genmascq_Pig_134


title: VX2012001_PBMC_Hour4


title: Longissimus_Genmascq_Pig_138


title: VX2012001_PBMC_Day7


title: VX2012001_PBMC_Day1


title: VX2012001_PBMC_Day28


title: Longissimus_Genmascq_Pig_144


title: Fructose 3

type: SRA

city: Swansea

first: Nick

last: Jones

state: Swansea

address: ILS1 Floor 2, Swansea University, Singleton Park

country: United Kingdom

institute: Swansea University

description: Isolated CD14+ monocytes

library_source: transcriptomic

data_processing:
Raw sequencing files were trimmed to remove adapter sequences and poor quality reads using TrimGalore.
Trimmed reads were aligned with the STAR aligner (v2.5.1b) to the GRCh38 assembly of the human genome
Raw counts were then calculated using Subread featureCounts (v1.5.1)
differential expression analysis comparing glucose and fructose treated monocytes was performed using DESeq2 (Bioconductor)
Differentially regulated genes were defined as those with a log2FC > ±1 and an adjusted p-value < 0.05. Heatmaps were generated using Morpheus (Broad Institute).
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file includes absolute counts

source_name: Monocyte

extract_protocol:
Monocyte RNA was extracted using the Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells (1 x10^6) were treated with glucose or fructose (both 11.1 mM) for 24 hours stimulated with LPS (10 ng/mL).

value: Monocyte


title: 203135920105_R04C01

type: genomic

city: New Haven

first: Gita

middle: A

last: Pathak

state: CT

address: 333 cedar St

country: USA

institute: Yale University

hyb_protocol: Illumina Infinium HD Methylation Assay

scan_protocol: Illumina iScan system

data_processing: The CpG sites were filtered using the ChAMP pipeline and normalized using BMIQ method

label: Cy3, Cy5

molecule: genomic DNA

source_name: Whole-blood

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: EZ-96 DNA methylation kit

treatment_protocol: Illumina Infinium HD Methylation Assay

tag: tissue

value: Whole blood

tag: outpatient surgeries (1=no; 2=yes)

tag: heart disease (1=no; 2=yes)

tag: age

value: Female

tag: race

value: African American

tag: genotype

value: carrier of Val122Ile mutation


title: 203135920105_R06C01


title: 203127070083_R07C01


title: 203127070116_R04C01


title: 203135920105_R05C01


title: 203127070116_R02C01


title: 203127070116_R03C01


title: 203135920105_R02C01


title: 203127070116_R01C01


title: 203135920105_R08C01


title: 203135920105_R01C01


title: 203135920105_R03C01


title: 203127070083_R08C01


title: VX2012001_PBMC_Day0


title: 203135920105_R07C01


title: 203127070117_R06C01


title: 203127070117_R02C01


title: 203127070117_R07C01


title: 203127070117_R08C01


title: 203127070116_R08C01


title: 203127070083_R06C01


title: 203127070116_R06C01


title: 203127070116_R07C01


title: 203127070117_R01C01


title: 203127070117_R03C01


title: 203127070117_R05C01


title: Fructose 2

description: Isolated CD14+ monocytes


title: 203127070083_R05C01


title: 203127070083_R04C01


title: Glucose 1

description: Isolated CD14+ monocytes


title: Fructose 1

description: Isolated CD14+ monocytes


title: Glucose 3

description: Isolated CD14+ monocytes


title: 203127070083_R02C01


title: 203127070079_R07C01


title: 203127070083_R01C01


title: 203127070083_R03C01


title: 203135920055_R06C01


title: 203135920055_R07C01


title: 203135920055_R08C01


title: 203127070079_R05C01


title: 203127070079_R03C01


title: 203127070079_R02C01


title: 203127070079_R06C01


title: Glucose 2

description: Isolated CD14+ monocytes


title: Semimembranosus_Genmascq_Pig_M88

source_name: Semimembranosus muscle


title: Semimembranosus_Genmascq_Pig_M93


title: Semimembranosus_Genmascq_Pig_M98


title: 203127070079_R08C01


title: Semimembranosus_Genmascq_Pig_M83


title: Semimembranosus_Genmascq_Pig_M96


title: Semimembranosus_Genmascq_Pig_M82


title: Semimembranosus_Genmascq_Pig_M73


title: Semimembranosus_Genmascq_Pig_M54


title: Semimembranosus_Genmascq_Pig_M57


title: Semimembranosus_Genmascq_Pig_M56


title: Semimembranosus_Genmascq_Pig_M84


title: 203135920055_R03C01


title: Semimembranosus_Genmascq_Pig_M95


title: 203135920055_R05C01


title: 203135920055_R04C01


title: 203135920055_R02C01


title: 203127070053_R08C01


title: 203127070053_R07C01


title: 203135920055_R01C01


title: 203127070053_R06C01


title: Semimembranosus_Genmascq_Pig_M53


title: Semimembranosus_Genmascq_Pig_M97


title: Semimembranosus_Genmascq_Pig_M52


title: Semimembranosus_Genmascq_Pig_M44


title: Semimembranosus_Genmascq_Pig_M43


title: Semimembranosus_Genmascq_Pig_M34


title: 203127070053_R05C01


title: 203127070053_R04C01


title: 203127070053_R03C01


title: 203127070053_R02C01


title: HA800: Adult single cell RNA sequencing material

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 University, Montreal Neurological Institut

country: Canada

institute: Montreal Neurological Institute

data_processing:
All preprocessing steps were performed using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Integration, clustering and differential expression analysis was done using R package Seurat (v3.1)
Genome_build: GRCh38

source_name: Human brain tissue

growth_protocol: For single-cell RNA sequencing, cells were sent for sequencing immediately ex-vivo

extract_protocol:
Single cells were obtained following mechanical and enzymatic (trypsin) dissociation as previously described (Cui et al. 2017). A isotonic Percoll gradient was used to remove myelin. The whole dissociated cell population was collected from the gradient (which sits between the myelin layer and the red blood cell layer), washed 3 times in PBS, and re-suspended at a concentration of 10^6 cells per ml. Fetal cell isolation does not require the percoll gradient step.
Made using the GemCode Single-Cell Instrument (10x Genomics) and Single Cell 3' Library & Gel Bead Kit v2 and Chip Kit (10x Genomics)

value: 51 years old

value: brain


title: 203127070052_R08C01

value: Male


title: Semimembranosus_Genmascq_Pig_M24


title: Semimembranosus_Genmascq_Pig_M22


title: HA738: Adult single cell RNA sequencing material

value: 62 years old


title: 203127070053_R01C01


title: 203127070052_R06C01


title: HA801: Adult single cell RNA sequencing material

value: 41 years old


title: Semimembranosus_Genmascq_Pig_M14


title: Semimembranosus_Genmascq_Pig_M19


title: Semimembranosus_Genmascq_Pig_M18


title: HA799: Pediatric single cell RNA sequencing material

value: 14 years old


title: 203127070052_R05C01


title: HA737: Adult single cell RNA sequencing material

value: 34 years old


title: Semimembranosus_Genmascq_Pig_922

value: F


title: Semimembranosus_Genmascq_Pig_M31


title: Semimembranosus_Genmascq_Pig_M15


title: Semimembranosus_Genmascq_Pig_920


title: Semimembranosus_Genmascq_Pig_M32


title: HA772: Pediatric single cell RNA sequencing material

value: 13 years old


title: Semimembranosus_Genmascq_Pig_M21


title: 203127070052_R03C01


title: HA796: Pediatric single cell RNA sequencing material

value: 17 months


title: 203127070052_R02C01


title: 203135920038_R08C01


title: HA785D: Pediatric single cell RNA sequencing material

value: 4 years old


title: HA776: Pediatric single cell RNA sequencing material

value: 2 years old


title: 203135920038_R07C01


title: Semimembranosus_Genmascq_Pig_919


title: 203135920038_R06C01


title: 203135920038_R02C01


title: Semimembranosus_Genmascq_Pig_916


title: Semimembranosus_Genmascq_Pig_906


title: Semimembranosus_Genmascq_Pig_913


title: Semimembranosus_Genmascq_Pig_914


title: Semimembranosus_Genmascq_Pig_898

value: M


title: 203127070030_R08C01

value: Whole blood


title: 203135920038_R03C01


title: Semimembranosus_Genmascq_Pig_892


title: HA780B: Pediatric single cell RNA sequencing material

value: 10 years old


title: 203127070030_R06C01

value: African American


title: 203127070030_R04C01

value: carrier of Val122Ile mutation


title: 203127070030_R07C01


title: Semimembranosus_Genmascq_Pig_889


title: Semimembranosus_Genmascq_Pig_893


title: Semimembranosus_Genmascq_Pig_891


title: 203127070030_R02C01


title: Semimembranosus_Genmascq_Pig_882


title: 203127070052_R01C01


title: 203127070030_R01C01


title: Semimembranosus_Genmascq_Pig_886


title: 203127070029_R08C01


title: HA773: Pediatric single cell RNA sequencing material


title: Semimembranosus_Genmascq_Pig_881


title: 203127070029_R07C01


title: 203127070029_R06C01


title: 203127070029_R03C01


title: 203127070029_R05C01


title: 203127070029_R02C01


title: 203127070029_R04C01


title: 203127070028_R08C01


title: 203127070030_R03C01


title: 203127070028_R03C01


title: 203135920021_R08C01


title: 203135920021_R04C01


title: 203127070028_R05C01


title: 203135920021_R05C01


title: 203127070028_R04C01


title: 203135920021_R07C01


title: 203127070028_R02C01


title: 203127070028_R01C01


title: 203135920021_R03C01


title: Semimembranosus_Genmascq_Pig_878


title: Semimembranosus_Genmascq_Pig_646


title: Semimembranosus_Genmascq_Pig_728


title: Semimembranosus_Genmascq_Pig_663


title: Semimembranosus_Genmascq_Pig_660


title: Semimembranosus_Genmascq_Pig_640


title: Semimembranosus_Genmascq_Pig_747


title: Semimembranosus_Genmascq_Pig_642


title: Semimembranosus_Genmascq_Pig_715


title: Semimembranosus_Genmascq_Pig_657


title: Semimembranosus_Genmascq_Pig_620


title: Semimembranosus_Genmascq_Pig_719


title: Semimembranosus_Genmascq_Pig_739


title: 203135920013_R07C01


title: 203135920021_R02C01


title: Semimembranosus_Genmascq_Pig_639


title: 203135920013_R08C01


title: 203135920021_R01C01


title: 203135920013_R06C01


title: Semimembranosus_Genmascq_Pig_736


title: Semimembranosus_Genmascq_Pig_622


title: 203135920013_R01C01


title: Semimembranosus_Genmascq_Pig_625


title: Semimembranosus_Genmascq_Pig_619


title: Semimembranosus_Genmascq_Pig_709


title: Semimembranosus_Genmascq_Pig_713


title: Semimembranosus_Genmascq_Pig_615


title: Semimembranosus_Genmascq_Pig_607


title: Semimembranosus_Genmascq_Pig_604


title: 203135920013_R02C01


title: Semimembranosus_Genmascq_Pig_609


title: Semimembranosus_Genmascq_Pig_539


title: Semimembranosus_Genmascq_Pig_547


title: Semimembranosus_Genmascq_Pig_530


title: Semimembranosus_Genmascq_Pig_551


title: Semimembranosus_Genmascq_Pig_556


title: Semimembranosus_Genmascq_Pig_535


title: 203135920013_R05C01


title: Semimembranosus_Genmascq_Pig_490


title: Semimembranosus_Genmascq_Pig_590


title: Semimembranosus_Genmascq_Pig_498


title: Semimembranosus_Genmascq_Pig_315


title: Semimembranosus_Genmascq_Pig_493


title: Semimembranosus_Genmascq_Pig_492


title: Semimembranosus_Genmascq_Pig_313


title: Semimembranosus_Genmascq_Pig_314


title: Semimembranosus_Genmascq_Pig_299


title: Semimembranosus_Genmascq_Pig_300


title: Semimembranosus_Genmascq_Pig_298


title: Semimembranosus_Genmascq_Pig_310


title: Semimembranosus_Genmascq_Pig_302


title: Semimembranosus_Genmascq_Pig_296


title: Semimembranosus_Genmascq_Pig_291


title: Semimembranosus_Genmascq_Pig_293


title: Semimembranosus_Genmascq_Pig_294


title: Semimembranosus_Genmascq_Pig_289


title: Semimembranosus_Genmascq_Pig_285


title: Semimembranosus_Genmascq_Pig_287


title: Semimembranosus_Genmascq_Pig_284


title: Semimembranosus_Genmascq_Pig_282


title: Semimembranosus_Genmascq_Pig_278


title: Semimembranosus_Genmascq_Pig_274


title: Semimembranosus_Genmascq_Pig_267


title: Grade IV rep8

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description: Glioma

hyb_protocol: Bisulphite converted DNA was labelled and hybridized to Human Infinium MethylomeEPIC beadchips following standard Illumina protocols

scan_protocol: Standard Illumina protocol

data_processing: The “minfi” software was used for data extraction, quality assessment, background correction (with the normal-exponential using out-of-band probes or Noob method) and filtering of probe sets located in SNPs and sexual chromosomes

source_name: Resected glioma

growth_protocol: No growth protocol

extract_protocol: Phenol-chloroform-isoamyl alcohol extraction from RIPA buffer homogenates

treatment_protocol: No treatment protocol

tag: histological diagnosis

value: Glioblastoma (IV)

value: Female


title: Semimembranosus_Genmascq_Pig_248


title: Grade IV rep6

description: Glioma

label_protocol: Bisulphite converted DNA was labelled and hybridized to Human Infinium MethylomeEPIC beadchips following standard Illumina protocols


title: Semimembranosus_Genmascq_Pig_263


title: Grade IV rep4

description: Glioma

value: Male


title: Grade II rep3

description: Glioma

value: Diffuse astrocytoma (II)


title: Grade IV rep7

description: Glioma


title: Semimembranosus_Genmascq_Pig_197


title: Grade IV rep1

description: Glioma


title: Grade II rep4

description: Glioma

value: Oligodendroglioma (II)


title: Semimembranosus_Genmascq_Pig_247


title: Grade II rep5

description: Glioma


title: Grade IV rep5

description: Glioma


title: Grade IV rep2

description: Glioma


title: Grade II rep2

description: Glioma


title: Grade II rep1

description: Glioma


title: Grade III rep1

description: Glioma

value: Anaplastic astrocytoma (III)


title: Semimembranosus_Genmascq_Pig_169


title: Semimembranosus_Genmascq_Pig_166


title: Semimembranosus_Genmascq_Pig_165


title: blood_elderly_male_04

city: Wuhan

first: Daixin

last: Huang

state: Hubei province

address: No. 13, Hangkong Road

department: Department of Forensic Medicine

institute: Huazhong University of Science and Technology

description: normal whole blood sample

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

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

data_processing: R package ChAMP v2.8.9

label: Cy5 and Cy3

source_name: whole blood, elderly, male, 60 years old

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood samples using QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) according to standard instructions

value: Han Chinese

tag: disease state

value: normal


title: Grade II rep6

description: Glioma


title: blood_elderly_male_03

description: normal whole blood sample

source_name: whole blood, elderly, male, 59 years old


title: blood_elderly_male_06

description: normal whole blood sample

source_name: whole blood, elderly, male, 61 years old


title: Semimembranosus_Genmascq_Pig_155


title: blood_elderly_female_06

description: normal whole blood sample

source_name: whole blood, elderly, female, 61 years old


title: blood_elderly_male_02

description: normal whole blood sample


title: Semimembranosus_Genmascq_Pig_159

value: F


title: blood_elderly_male_01

description: normal whole blood sample

source_name: whole blood, elderly, male, 58 years old


title: blood_elderly_female_07

description: normal whole blood sample

source_name: whole blood, elderly, female, 62 years old


title: blood_elderly_male_05

description: normal whole blood sample


title: blood_elderly_female_04

description: normal whole blood sample

source_name: whole blood, elderly, female, 60 years old


title: Semimembranosus_Genmascq_Pig_133


title: Semimembranosus_Genmascq_Pig_146


title: Semimembranosus_Genmascq_Pig_132


title: Grade IV rep3

description: Glioma


title: Longissimus_Genmascq_Pig_N93

source_name: Longissimus lumborum muscle


title: Semimembranosus_Genmascq_Pig_168


title: Longissimus_Genmascq_Pig_N89


title: blood_elderly_female_05

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_N87


title: Longissimus_Genmascq_Pig_N75


title: Longissimus_Genmascq_Pig_N83


title: Longissimus_Genmascq_Pig_N88


title: blood_elderly_female_01

description: normal whole blood sample

source_name: whole blood, elderly, female, 58 years old


title: blood_middle_aged_male_06

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 42 years old


title: blood_elderly_female_03

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_N73


title: blood_middle_aged_male_04

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 39 years old


title: Longissimus_Genmascq_Pig_N66


title: blood_middle_aged_male_01

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 36 years old


title: Longissimus_Genmascq_Pig_N65


title: Longissimus_Genmascq_Pig_N64


title: Semimembranosus_Genmascq_Pig_184


title: blood_middle_aged_female_07

description: normal whole blood sample

source_name: whole blood, middle-aged, female, 43 years old


title: Longissimus_Genmascq_Pig_N62


title: blood_middle_aged_male_03

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 38 years old


title: blood_middle_aged_female_05

description: normal whole blood sample

source_name: whole blood, middle-aged, female, 41 years old


title: Longissimus_Genmascq_Pig_N55


title: blood_middle_aged_female_06

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_N59


title: blood_middle_aged_female_02

description: normal whole blood sample

source_name: whole blood, middle-aged, female, 39 years old


title: Longissimus_Genmascq_Pig_N54


title: Longissimus_Genmascq_Pig_N53


title: Semimembranosus_Genmascq_Pig_148

source_name: Semimembranosus muscle


title: blood_elderly_female_02

description: normal whole blood sample

source_name: whole blood, elderly, female, 59 years old


title: Longissimus_Genmascq_Pig_N45


title: Longissimus_Genmascq_Pig_N51


title: Longissimus_Genmascq_Pig_N37


title: blood_youth_male_05

description: normal whole blood sample

source_name: whole blood, youth, male, 22 years old


title: 8_TE14-2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: MCF7aro continuously treated with EXE

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: MCF7aro continuously treated with EXE

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf)

growth_protocol: MCF7aro cells were cultured in MEM medium with 10% CD FBS.

extract_protocol: Qiagen RNA extraction kit was used according to manufacturer's guide

treatment_protocol: MCF7aro cells were cultured in hormone-stripped medium and treated with 1μM exemestane continuously or intermittently (2 weeks on and 1 week off) in the presence of 1nM testosterone. At week 14, EXE-treated cells as well as MCF7aro cells were hormone-stripped for 48h were harvested and RNA was extracted.Gene expression profiles in each cell line were analyzed by the Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays.

tag: cell line

tag: treatment

value: MCF7aro cells was cultured in MEM medium with 10% CD FBS in the presence of 1nM testesterone, and treated with 1μM exemestane continuously for 14 weeks


title: blood_middle_aged_female_01

description: normal whole blood sample

source_name: whole blood, middle-aged, female, 38 years old

tag: gender


title: Longissimus_Genmascq_Pig_N36

tag: pig number

tag: ChIP


title: blood_youth_male_06

description: normal whole blood sample


title: Grade III rep2

description: Glioma

source_name: Resected glioma

value: Anaplastic oligodendroglioma (III)


title: 9_TE14-3

description: MCF7aro continuously treated with EXE


title: Longissimus_Genmascq_Pig_N35


title: blood_youth_male_03

description: normal whole blood sample

source_name: whole blood, youth, male, 19 years old


title: blood_middle_aged_female_04

description: normal whole blood sample


title: blood_middle_aged_male_05

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 40 years old


title: 6_TEC-3

description: MCF7aro intermittently treated with EXE

source_name: MCF7aro intermittently treated with EXE

value: MCF7aro cells was cultured in MEM medium with 10% CD FBS in the presence of 1nM testesterone, and treated with 1μM exemestane with 2 weeks ON, 1 week OFF for 14 weeks


title: Longissimus_Genmascq_Pig_N29

source_name: Longissimus lumborum muscle


title: Longissimus_Genmascq_Pig_N27


title: 5_TEC-2

description: MCF7aro intermittently treated with EXE


title: Longissimus_Genmascq_Pig_N24


title: 4_TEC-1

description: MCF7aro intermittently treated with EXE


title: 2_AS-2

description: MCF7aro without EXE treatment

source_name: MCF7aro without EXE treatment

value: MCF7aro cells were cultured in MEM medium with 10% CD FBS for 48h


title: Longissimus_Genmascq_Pig_N17


title: Longissimus_Genmascq_Pig_N15


title: Longissimus_Genmascq_Pig_N33

value: M


title: Longissimus_Genmascq_Pig_N12


title: Longissimus_Genmascq_Pig_N14


title: Longissimus_Genmascq_Pig_N09


title: Longissimus_Genmascq_Pig_N22


title: Longissimus_Genmascq_Pig_N07


title: Longissimus_Genmascq_Pig_N08


title: 3_AS-3

description: MCF7aro without EXE treatment


title: blood_youth_male_04

description: normal whole blood sample

source_name: whole blood, youth, male, 21 years old


title: Longissimus_Genmascq_Pig_N06


title: blood_youth_female_04

description: normal whole blood sample

source_name: whole blood, youth, female, 19 years old


title: blood_youth_female_07

description: normal whole blood sample

source_name: whole blood, youth, female, 20 years old


title: blood_youth_female_05

description: normal whole blood sample


title: blood_youth_female_06

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_N04


title: blood_youth_male_02

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_N05


title: Longissimus_Genmascq_Pig_M96


title: Longissimus_Genmascq_Pig_M98


title: Longissimus_Genmascq_Pig_M97


title: Longissimus_Genmascq_Pig_N01


title: blood_youth_female_03

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_M99


title: Longissimus_Genmascq_Pig_M95


title: Longissimus_Genmascq_Pig_M92


title: Longissimus_Genmascq_Pig_M91


title: Longissimus_Genmascq_Pig_M88


title: blood_youth_male_01

description: normal whole blood sample


title: blood_youth_female_02

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_M89


title: Longissimus_Genmascq_Pig_M87


title: Longissimus_Genmascq_Pig_M84


title: Longissimus_Genmascq_Pig_M83


title: Longissimus_Genmascq_Pig_M81


title: Longissimus_Genmascq_Pig_M82


title: Longissimus_Genmascq_Pig_M77


title: blood_youth_female_01

description: normal whole blood sample

source_name: whole blood, youth, female, 18 years old


title: Longissimus_Genmascq_Pig_N25


title: Longissimus_Genmascq_Pig_M70


title: Longissimus_Genmascq_Pig_M52


title: Longissimus_Genmascq_Pig_M67


title: Longissimus_Genmascq_Pig_M73


title: Longissimus_Genmascq_Pig_M54


title: Longissimus_Genmascq_Pig_M53


title: blood_elderly_male_07

description: normal whole blood sample

source_name: whole blood, elderly, male, 62 years old


title: Longissimus_Genmascq_Pig_M43


title: Longissimus_Genmascq_Pig_M39


title: Longissimus_Genmascq_Pig_M44


title: Longissimus_Genmascq_Pig_M37


title: Longissimus_Genmascq_Pig_M47


title: FOXA1-IFNα (+)_Rep.2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

library_source: genomic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg38) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: LNCaP cells was treated with vehicle (PBS) or 100ng/L IFNα for 24 hours.

value: LNCaP

tag: cell type

value: prostate cancer

tag: passages

tag: knockdown

tag: rescue

tag: chip antibody

value: anti-FOXA1 #ab23738, Abcam


title: Longissimus_Genmascq_Pig_M30


title: Longissimus_Genmascq_Pig_M38


title: Longissimus_Genmascq_Pig_M40


title: Longissimus_Genmascq_Pig_M28


title: Longissimus_Genmascq_Pig_M32


title: Longissimus_Genmascq_Pig_M34


title: Longissimus_Genmascq_Pig_M31


title: Longissimus_Genmascq_Pig_N23


title: FOXA1-IFNα (+)_Rep.1


title: FOXA1-IFNα (-)_Rep.2


title: 7_TE14-1

description: MCF7aro continuously treated with EXE


title: blood_middle_aged_male_07

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 42 years old


title: FOXA1-IFNα (-)_Rep.1


title: Longissimus_Genmascq_Pig_M26


title: 1_AS-1

description: MCF7aro without EXE treatment


title: STAT2-shFOXA1+ FOXA1△αH3-IFNα (+)_Rep.2

value: anti-STAT2 #72604S, Cell Signaling Technology


title: Longissimus_Genmascq_Pig_M18


title: blood_youth_male_07

description: normal whole blood sample


title: Longissimus_Genmascq_Pig_M19


title: Longissimus_Genmascq_Pig_M24


title: Longissimus_Genmascq_Pig_M22


title: STAT2-shFOXA1+ FOXA1△αH3-IFNα (+)_Rep.1


title: Longissimus_Genmascq_Pig_M15


title: STAT2-shFOXA1+ FOXA1-R261G-IFNα (+)_Rep.2


title: blood_middle_aged_male_02

description: normal whole blood sample

source_name: whole blood, middle-aged, male, 38 years old


title: STAT2-shFOXA1+ FOXA1-WT-IFNα (+)_Rep.2


title: Longissimus_Genmascq_Pig_M14


title: STAT2-shFOXA1+ FOXA1-R261G-IFNα (+)_Rep.1


title: blood_middle_aged_female_03

description: normal whole blood sample

source_name: whole blood, middle-aged, female, 39 years old

value: Female


title: STAT2-shFOXA1+ FOXA1-WT-IFNα (+)_Rep.1


title: STAT2-shFOXA1-IFNα (+)_Rep.2


title: Longissimus_Genmascq_Pig_M12


title: STAT2-shFOXA1-IFNα (+)_Rep.1


title: Longissimus_Genmascq_Pig_M11


title: STAT2-shFOXA1-IFNα (-)_Rep.2


title: STAT2-Vector-IFNα (+)_Rep.1

value: vector control


title: STAT2-Vector-IFNα (+)_Rep.2


title: Longissimus_Genmascq_Pig_M10


title: Longissimus_Genmascq_Pig_M04


title: Longissimus_Genmascq_Pig_M06


title: Longissimus_Genmascq_Pig_M09


title: STAT2-Vector-IFNα (-)_Rep.2


title: STAT2-shFOXA1-IFNα (-)_Rep.1


title: STAT2-Vector-IFNα (-)_Rep.1


title: Longissimus_Genmascq_Pig_M27


title: Longissimus_Genmascq_Pig_M02


title: Longissimus_Genmascq_Pig_M03


title: Longissimus_Genmascq_Pig_988


title: Longissimus_Genmascq_Pig_993


title: Longissimus_Genmascq_Pig_999


title: Longissimus_Genmascq_Pig_986


title: Longissimus_Genmascq_Pig_984


title: Keratocytes_stretch_0 hr_rep1

city: Taiyuan

first: Jie

last: Song

state: Shanxi

address: NO. 79, Yingze West Road

institute: Taiyuan University of Technology

description: Gene expression after 0 hr in mechanical stretching human keratocytes

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) at 65℃ in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat. # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat. # 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat. #G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Keratocytes

label_protocol: Total RNA from each sample was amplified and labeled by Agilent's Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

growth_protocol: The primary human keratocytes were purchased from ScienCell Research Laboratories (USA). The cells were cultured in Fibroblast Medium (FM) (ScienCell, USA) supplemented with 2 % fetal bovine serum (FBS) (ScienCell, USA) and 1 % fibroblast growth supplement (FGS) (ScienCell, USA) at 37 °C in 5% CO2. Cells of the third passage were employed for further study.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RNA integrity number (RIN) to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US) and denaturing agarose gel electrophoresis.

treatment_protocol: Human keratocytes were plated at a density of 2 × 105/cm2 on 6-well elastomere Bioflex® plates (Flexcell Int. Corp., Hillsborough, NC, USA) with collagen I-coated silicon membrane bottom. When cells reached subconfluency, the medium was removed and replaced with complete serum and FGS free FM overnight. Thereafter, stretch was introduced onto the cells by applying a cyclic vacuum suction under the fexible bottomed plates by computer-controlled Flexcell® Tension Plus™ FX-4000™ system (Flexcell International Corporation, Hillsborough, NC, USA) (0-15% elongation, 0.5 Hz, sine waveform) for 0 h, 1 h and 6 h, respectively.

tag: cell

value: Keratocytes

tag: time point

tag: passage

value: the third passage


title: Keratocytes_stretch_0 hr_rep3


title: Longissimus_Genmascq_Pig_963


title: Longissimus_Genmascq_Pig_962


title: Longissimus_Genmascq_Pig_958


title: Longissimus_Genmascq_Pig_961


title: Longissimus_Genmascq_Pig_980


title: Keratocytes_stretch_1 hr_rep2

description: Gene expression after 1hr in mechanical stretching human keratocytes


title: Keratocytes_stretch_6 hr_rep3

description: Gene expression after 6hr in mechanical stretching human keratocytes


title: Keratocytes_stretch_6 hr_rep1


title: Keratocytes_stretch_6 hr_rep2


title: Keratocytes_stretch_1 hr_rep3


title: Keratocytes_stretch_0 hr_rep2


title: Keratocytes_stretch_1 hr_rep1


title: Longissimus_Genmascq_Pig_923


title: Longissimus_Genmascq_Pig_952


title: Longissimus_Genmascq_Pig_945


title: Longissimus_Genmascq_Pig_920


title: Longissimus_Genmascq_Pig_M93


title: 3010_WT_29

city: San Diego

first: Jun

last: Yin

address: 10901 N Torrey Pines Rd

department: Bioinformatics Core

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
RNA-seq data were aligned and summarized using OmicSoft’s Array Studio software (www.omicsoft.com/array-studio.php; Oshell.exe v10.0). Genes with critical issues on gene models were removed from statistical analysis. These issues included duplicated regions, high GC content, and overlapping transcripts. The RNA-seq dataset from each time point was analyzed separately. For each time point, genes with FPKQ ≥1 in ≥5 samples in the pairwise group comparison were selected for further statistical testing. Differential expression analysis was performed using DESeq2 v1.10.1 for group comparison. For a given comparison, raw read counts for genes were compared between the 2 conditions using DESeq2 following a negative binomial distribution, and gene expression fold changes were calculated using normalized counts. Genes with a Benjamini-Hochberg corrected P value <0.05 and fold change between the 2 conditions ≥2 or ≤0.5 were selected as significantly differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: The gene- and transcript-level expression of each RNA-Seq sample was reported by Oshell as an FPKM (Fragments per Kilobase per Million sequenced) value. FPKM is an expression measurement based on the count of library fragments that map to a given feature (gene or transcript) normalized for feature length and the number of fragments sequenced. These values were adjusted on a per-sample basis using 70th percentile normalization, yielding a final expression metric which we refer to as “FPKQ”.

organism: Mus musculus

source_name: Aortic arch

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). Animals were group-housed in polycarbonate cages. Each animal was identified with a subcutaneous electronic identification chip implanted in the lumbar area.

extract_protocol:
RNA sequencing (RNA-seq) analyses were performed on mice tissues in  satellite animals. At scheduled necropsy, a region of the aortic arch matching the scan region for µCT was collected using polymerase chain reaction clean procedures. In addition, the innominate, left carotid, and left subclavian arteries were each sectioned at their junctions with the aortic arch. The lumen of the aorta was flushed with RNase-free saline and the adventitial fat gently scraped away using a sterile cotton swab. The aortic tissue was then washed briefly in RNase-free saline, placed in cryo-tubes, snap-frozen in liquid nitrogen, and stored at –80°C. Samples were subjected to dry pulverization before being homogenized in buffer (350 µL of Qiagen RLT buffer with 10% BME [Qiagen, Germantown, MD, USA]). The homogenate was transferred to an RNase-free 1.5 mL centrifuge tube, after which 95 µL RNase-free water and 5 µL of a 20 mg/mL Proteinase K solution were added. Samples were incubated at 55°C for 10 minutes, centrifuged, and the supernatant collected. RNA was then extracted using an RNeasy Micro Kit (Qiagen) with on-column DNase treatment (Qiagen) according to the manufacturer’s instructions. RNA concentration and integrity were assessed using a Bioanalyzer (Agilent, Santa Clara, CA, USA). Samples with ≥80 ng total RNA that had RNA integrity numbers ≥7 were used for sequencing.
Library preparation and RNA-seq was performed by Q2 Solutions (Morrisville, NC). Sequencing libraries were created using the IlluminaTruSeq Stranded mRNA method.

treatment_protocol: C57BL/6 female mice (ApoE KO and wild-type [WT]) were obtained from Jackson Laboratories (Bar Harbor, ME, USA). Mice were provided a high-fat diet (TD.88137 adjusted-calories diet, 42% from fat [Envigo RMS, Indianapolis, IN, USA]), starting at 5–6 weeks old. Mice were OVX at 7–8 weeks old.  At 9–10 weeks old, ApoE KO-OVX and WT-OVX mice were randomized into 2 treatment groups (n=144/group), and each received either Veh or Scl-Ab 10 mg/kg, SC QW for 3, 8, or 16 weeks.  The Scl-Ab dose of 10 mg/kg QW was predicted to provide a 4-fold multiple of clinical exposure to romosozumab 210 mg QM, based on AUC. Fourteen mice from each group at each timepoint were designated as main study animals; at termination, they were anesthetized under isoflurane before undergoing a whole-body cardiac perfusion at each timepoint. Ten mice from each group at each timepoint were designated as satellite animals.  Thirteen-week-old C57BL/6 male mice (n=76 ApoE KO; n=9 WT) were obtained from Jackson Laboratories (Bar Harbor, ME, USA). Mice were provided a PMI Nutrition International Certified Rodent Chow No. 5CR4 (PMI Nutrition International Richmond IN) ad libitum throughout the study. At approximately 14 weeks of age, alzet pumps (Durect Corporation Cupertino CA; Model 1004 with a target infusion rate of 0.11 μL/hr), each containing 100 μL of Angiotensin II (Sigma Aldrich St Louis MO) at 15.27 mg/mL (ApoE KO) or 100 μL of Veh (WT), were implanted sc in the interscapular area. Two days later, ApoE KO mice were randomized into 2 treatment groups and each received either Veh or Scl-Ab 10 mg/kg, [Amgen Inc., Thousand Oaks, CA, USA]), SC QW for 4 weeks. WT mice received Veh. Due to mortality early in the study, primarily a consequence of aortic rupture (n=6 Veh; n=5 Scl-Ab), final group size for ApoE KO Veh- and Scl-Ab-treated mice was 32 and 33 respectively. Ten mice in each group were designated satellite animals; the remainder designated main study animals. At termination, main study animals were anesthetized under isoflurane before undergoing a whole-body cardiac perfusion at each timepoint.

tag: strain

tag: Sex

value: Male

tag: age

value: 14 weeks

value: Vehicle


title: Longissimus_Genmascq_Pig_922

value: F


title: PB_CD34_D7_H3K4me3_R2 (ChIP-seq)

city: Memphis

first: Mitch

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: st jude children's research hospital

data_processing:
Basecalls performed using CASAVA
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).
We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files.  We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.
Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: PB_CD34_Bulk_Erytrhoid Day7

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

value: primary CD34+ HSPCs

value: H3K4me3(Cell Signaling Technology, CST#9751)


title: 3009_WT_28


title: 3008_WT_27


title: Longissimus_Genmascq_Pig_919


title: 3007_WT_26


title: 3006_WT_25


title: PB_CD34_D7_H3K27me3_R2 (ChIP-seq)

value: H3K27me3(Cell Signaling Technology, CST#9733)


title: PB_CD34_D7_H3K27me3_R1 (ChIP-seq)


title: PB_CD34_D7_H3K4me3_R1 (ChIP-seq)


title: WT_GATA1_R2 (ChIP-seq)

value: erythroblast cells

value: GATA1 (Abcam, Ab11852)


title: WT_GATA1_R1 (ChIP-seq)


title: CD160+ peritumoral NK cells from HCC patient 7

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

description: Whole Human Genome Microarray 4x44K

hyb_protocol: Gene ExpressionEach slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructionsHybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US),

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US)settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction

source_name: CD160+ hepatic NK cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,OneOne -Color(Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US)

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: tissue

value: liver


title: CD160- hepatic NK cells

description: Whole Human Genome Microarray 4x44K

source_name: CD160- hepatic NK cells


title: 3005_WT_24


title: 3004_WT_23


title: Longissimus_Genmascq_Pig_914


title: Longissimus_Genmascq_Pig_918


title: 3002_WT_21


title: 3003_WT_22


title: CD160+ hepatic NK cells

description: Whole Human Genome Microarray 4x44K


title: CD160+ peritumoral NK cells from HCC patient 48

description: Whole Human Genome Microarray 4x44K


title: 3001_WT_20


title: F11KO_GATA1_R2 (ChIP-seq)

tag: cell line


title: CD160+ intratumoral NK cells from HCC patient 7

description: Whole Human Genome Microarray 4x44K


title: 2131_Scl_Ab_17

tag: treatment

value: AngII+Scl Ab


title: F11KO_GATA1_R1 (ChIP-seq)


title: 2033_Scl_Ab_19


title: Longissimus_Genmascq_Pig_916

tag: gender


title: 2032_Scl_Ab_18


title: 2030_Scl_Ab_16


title: 2028_Scl_Ab_14


title: 2029_Scl_Ab_15


title: 2015_Scl_Ab_13


title: 1113_Vehicle_2

value: AngII+Vehicle


title: 1129_Vehicle_7


title: 1032_Vehicle_9


title: 1030_Vehicle_8


title: 2013_Scl_Ab_11


title: 1028_Vehicle_6


title: 1027_Vehicle_5


title: 1015_Vehicle_4


title: 1014_Vehicle_3


title: C24_2

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

institute: Imperial College London

data_processing:
Pseudoalignment was performed using Kallisto (Bray et al., Nat Biotechnol 2016) and the WS235 transcriptome from Wormbase
Analysis of counts was performed using Sleuth using the Wald test for two sample comparison (Pimentel et al., Nat Methods 2017)
Genome_build: WS235
Supplementary_files_format_and_content: abundance.h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.

organism: Caenorhabditis elegans

source_name: Control_24h post L4

growth_protocol: The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). Gravid adults were bleached to obtain synchronized L4 stage animals which were then treated with M. humicola extract or infected with the pathogen.

extract_protocol:
The animals were collected by washing with M9 at respective time points and RNA was extracted using TRIzol ® reagent. The quality and quantity of RNA was determined respectively using agarose gel electrophoresis and Qubit fluorometer.
The library preparation was done using PE100 strand-specific library preparation protocol as previously described (Zhu et al., Plant Methods 2018)

treatment_protocol: Extract treatment was carried out at 20 °C on nematode growth medium seeded with 200 ml of OP50 E. coli culture. 300 ml of M. humicola extract was added on bacterial lawn prior to additon of animals. Same amount of water was added to control plates. The experiment was performed in triplicates and consisted of 200 animals on each plate. For infection set up, 50 L4 stage animals were added onto a plate with and without (control) 3 previously infected animals with M. humicola on a small bacterial lawn (100 ml) (Osman et al., Curr Biol 2018)

tag: genotype/variation

value: WT

tag: developmental stage

value: L4 stage animal

value: Control

tag: timepoint

value: 24h post L4


title: 1012_Vehicle_1


title: C24_3


title: X24_1

source_name: Extract Treated_24h post L4

value: Extract Treated


title: X24_3


title: 2112_Scl_Ab_10

value: Male


title: C12_3

source_name: Control_12h post L4

value: 12h post L4


title: X12_1

source_name: Extract Treated_12h post L4


title: C24_1


title: X24_2


title: X12_3


title: C12_2


title: X12_2


title: 2014_Scl_Ab_12

value: 14 weeks


title: C12_1


title: FIP+3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Relis Catus, Ensembl, 6.2
Supplementary_files_format_and_content: tad-delimited, raw counts

organism: Felis catus

source_name: mesenteric lymph node

extract_protocol:
RNA extracted with Qiagen RNeasy Mini Kit, then remaining DNA removed with ezDNase (Thermo Fisher Scientific).
TruSeq RNA stranded
PolyA, TruSeq RNA Kit

treatment_protocol: NA - all natural infections and clinical cases

tag: breed

value: BSH

tag: fip status

value: Pos

value: mesenteric lymph node


title: FIP+4

value: 4 m

value: Abyssinian


title: FIP+1

value: 5 m

value: DSH


title: FIP-FCoV+3

value: Neg

tag: fcov infection

value: FCoV+

tag: disease in non-fip

value: Round cell neoplasia


title: FIP-FCoV+2

value: 4 y

value: Havana

value: Nasal lymphoma


title: hMSCs, Donor F, rep2

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: 8A Biomedical Grove

department: Glycotherapeutics Group

country: Singapore

institute: Institute of Medical Biology

description:
Sample 12
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization after background subtraction on GenomeStudio (Illumina)

label: biotin

source_name: human bone marrow-mesenchymal stem cells

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA amplification kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed on the Agilent Bioanalyzer.

tag: individual

value: Donor F

value: male

tag: ethnicty

value: Caucasian

tag: cell type

value: bone marrow-mesenchymal stem cells

tag: capacity

value: low-growth capacity


title: exosomes from melanoma cell line M28, biological rep2

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

description:
metastatic
RNA data from melanoma-derived exosome

hyb_protocol: 1 ug of each labeled cRNA was fragmented by adding 5ul 10 × Blocking Agent and 1ul of 25 × Fragmentation Buffer, then heated the mixture at 60C for 30 min, finally 25ul 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50ul of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: The microarrays were scanned with an Agilent DNA Microarray Scanner G2505C, using Agilent Feature Extraction Software 11.0.1.1.

data_processing: Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering between two groups.

source_name: exosomes from melanoma cell line M28 in culture supernatant

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

growth_protocol: melanoma cell lines were cultured during 24h in exoFree media

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Exoquick TC reagent was used to purified exosomes from supernatant


title: hMSCs, Donor C, rep1

description:
Sample 5
replicate 1

value: Donor C

value: Hispanic

value: high-growth capacity


title: exosomes from melanoma cell line M28, biological rep1


title: hMSCs, Donor C, rep2

description:
Sample 6
replicate 2


title: hMSCs, Donor E, rep2

description:
Sample 10
replicate 2

value: Donor E

value: Black


title: hMSCs, Donor A, rep1

description:
Sample 1
replicate 1

value: Donor A


title: exosomes from melanoma cell line M117, biological rep2

source_name: exosomes from melanoma cell line M117 in culture supernatant


title: hMSCs, Donor E, rep1

description:
Sample 9
replicate 1


title: HepG2_PATZ1 siRNA_rep2

first: Zhen Long

last: Ng

address: 8 Medical Drive

department: Biochemistry

institute: National University of Singapore

description:
HepG2 siPATZ1 #2
Gene expression data from HepG2 cells treated with PATZ1 siRNA for 48h

hyb_protocol: 750ng of biotin-labeled cRNA were hybridized on the Illumina HT-12 version 4 beadchip according to Manufacturer’s instruction (Illumina, Inc., San Diego, CA)

scan_protocol: Beadchips were washed and stained according to Manufacturer’s instruction and scanned using Illumina BeadArray Reader (Illumina, Inc., San Diego, CA)

data_processing: The data were normalized by average normalization with Illumina GenomeStudio’s gene expression module.

source_name: HepG2_PATZ1 siRNA

label_protocol: Biotin-labeled cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion Inc.) from 250ng-500ng of total RNA.

growth_protocol: HepG2 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) High Glucose (GE Healthcare) supplemented with 10% heat inactivated fetal bovine serum (FBS; GE Healthcare). The cells were cultured in a 10 cm dish with 10 mL of medium and maintained at 5% CO2 at 37°C in a humidified incubator.

extract_protocol: Total RNA was extracted from cells with the TRIzol® reagent (Invitrogen). RNA concentration was quantified with the NanoDrop Spectrophotometer (ThermoFisher Scientific). Purfication of the total RNA was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. Quality control was performed with the Agilent 2100 Bioanalyzer.

treatment_protocol: 0.2 million HepG2 cells were seeded in a 6 well-plate and reverse transfection with either 60 pmol of scrambled control siRNA or PATZ1 siRNA was performed for 48 h. Transfections with siRNA were performed with Lipofectamine RNAiMax (Invitrogen) according to the manufacturer’s instructions.

value: liver cancer cells

value: PATZ1 siRNA knockdown


title: hMSCs, Donor B, rep2

description:
Sample 4
replicate 2

value: Donor B


title: hMSCs, Donor F, rep1

description:
Sample 11
replicate 1


title: HepG2_control siRNA_rep1

description:
HepG2 siCTRL #1
Gene expression data from HepG2 cells treated with control siRNA for 48h

source_name: HepG2_control siRNA

value: control siRNA knockdown


title: hMSCs, Donor D, rep1

description:
Sample 7
replicate 1

value: Donor D


title: hMSCs, Donor D, rep2

description:
Sample 8
replicate 2


title: HepG2_control siRNA_rep2

description:
HepG2 siCTRL #2
Gene expression data from HepG2 cells treated with control siRNA for 48h


title: HepG2_PATZ1 siRNA_rep1

description:
HepG2 siPATZ1 #1
Gene expression data from HepG2 cells treated with PATZ1 siRNA for 48h


title: exosomes from melanoma cell line M113, biological rep2

source_name: exosomes from melanoma cell line M113 in culture supernatant


title: exosomes from melanoma cell line M117, biological rep1


title: exosomes from melanoma cell line M6, biological rep2

source_name: exosomes from melanoma cell line M6 in culture supernatant


title: hMSCs, Donor A, rep2

description:
Sample 2
replicate 2


title: hMSCs, Donor B, rep1

description:
Sample 3
replicate 1


title: exosomes from melanoma cell line M6, biological rep1


title: FIP-FCoV-1

value: Birman

value: Neg

value: FCoV-

value: Pyothorax and pneumonia

value: mesenteric lymph node


title: FIP-FCoV-2

value: Bengal

value: Colonic adenocarcinoma


title: FIP-FCoV-3

value: House cat

value: Haemorrhage in brain


title: FIP-FCoV+1

value: 1 y

value: Maine Coon

value: FCoV+

value: Connective tissue abnormality and pleural effusion (FCoV RT-qPCR negative) => in paper just effusion in Thesis also connective tissue problem


title: exosomes from melanoma cell line M113, biological rep1


title: eye disc of ey>vg, simj, biologic rep 2

city: Sendai

first: Keita

last: Masuko

address: Aoba 6-3, Aramaki, Aoba-ku,

department: Pharmaceutical Science

country: Japan

institute: Tohoku University

hyb_protocol: Following fragmentation, 12 ug of aRNA were hybridized for 16 hr at 45˚C on GeneChip Drosophila Genome 2.0 Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5.0) using Affymetrix default analysis settings and global scalling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 30.

organism: Drosophila melanogaster

source_name: eye disc of ey>vg, simj

label_protocol: Biotinylated aRNA were prepared by in vitro transcription of two-round synthesized cDNA, according to the standard protocol of GeneChip 3' IVT Express Kit, from 100 ng total RNA.

growth_protocol: Flies for each genotype were raised on a standard cornmeal medium at room temperature. Third instar wandering larvae were dissected.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacture's instructions.

treatment_protocol: One hundred pairs of eye-entennal imaginal discs were dissected in cold PBS, and put them into Trizol reagent (Thermo Fisher Scientific).

value: eye-antennal imaginal disc

tag: genotype

value: ey-GAL4 UAS-vg UAS-simj

value: wandering 3rd instar larvae


title: eye disc of ey>vg, lacZ, biologic rep 2

source_name: eye disc of ey>vg, lacZ

value: ey-GAL4 UAS-vg UAS-lacZ

tag: age


title: eye disc of ey>lacZ, simj, biologic rep 1

source_name: eye disc of ey>lacZ, simj

tag: tissue

value: ey-GAL4 UAS-lacZ UAS-simj


title: eye disc of ey>lacZ, lacZ, biologic rep 2

source_name: eye disc of ey>lacZ, lacZ

value: ey-GAL4 UAS-lacZ UAS-lacZ


title: eye disc of ey>vg, simj, biologic rep 1


title: MP+CSE_Bu, biological rep2

city: Lucknow

first: Naibedya

last: Chattopadhyay

state: Uttar Pradesh

address: Sector 10, Jankipuram extension, Sitapur road

department: Endocrinology

country: India

institute: CSIR-CDRI

description: Gene expression data from MP+CSE_Bu group

hyb_protocol: Following fragmentation,  5.5 ug of  fragmented biotin labeled ss cDNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 7G, Affymetrix.

data_processing: The CEL files were generated after scanning the array-chips through GeneChip Scanner-7G (Affymetrix, CA). Further, the generated CEL files were converted into .rma-gene-ful.chp and .rma-alt-splice-dabg.chp files through Affymetrix Expression Console™ Software (version 1.3). Further, the data was analyzed through Transcriptome Analysis Console v3.0. After running ANOVA, a multi-testing correction has been performed using the Benjamini-Hochberg Step-Up FDR-controlling procedure for all the expressed genes and expressed PSRs/Junctions (i.e. expressed in at least one condition). (By default, the Alpha level has been set as 0.05 in False Discovery Rate field) 15.

organism: Rattus norvegicus

source_name: Femur bone of Sprague Dawley rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug of  fragmented ss cDNA (Gene chip Whole Transcriptome (WT) Expression array;P.No. 703147, Affymetrix).

growth_protocol: All animals were subjected to 12h dark-light cycle under controlled temperature(23-25oC) and humidity(50-60%).

extract_protocol: Femur bones were collected and snap freezed in liq N2. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: MP is methylprednisolone (5mg/kg given by subcutaneous route daily for 30 days). CSE-Bu is Cassia occidentalis extract's butanolic fraction given orally daily at 100mg/kg dose for 30 days.

value: femur bone

tag: strain

value: Sprague Dawley

tag: weight


title: MP+CSE_Bu, biological rep3


title: MP, biological rep4

description: Gene expression data from MP group


title: MP, biological rep2

description: Gene expression data from MP group


title: MP, biological rep1

description: Gene expression data from MP group


title: MP, biological rep3

description: Gene expression data from MP group


title: MP+CSE_Bu, biological rep1


title: Sputum_391331

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

institute: GSK

hyb_protocol: Labelled cDNA was hybridized onto HG-U133 GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analysed in R/Bioconductor, normalised by RMA  Data were analysed in R/Bioconductor, normalised by RMA  dadasdaData were analysed in R/Bioconductor, normalised by RMA  asdasdasData were analysed in R/Bioconductor, normalised by RMA

source_name: Sputum from COPD subject

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: intranasal

tag: patient diagnosis

value: COPD

value: sputum

tag: treatment

tag: Sex

value: M

tag: subject


title: Sputum_391330

tag: timepoint


title: eye disc of ey>lacZ, simj, biologic rep 2


title: Sputum_391323

value: Placebo


title: Sputum_391325


title: Sputum_391327


title: Sputum_391333


title: eye disc of ey>vg, lacZ, biologic rep 1


title: Sputum_391321

value: F


title: Sputum_391332


title: Sputum_391326


title: Sputum_391328


title: Sputum_391319


title: Sputum_391329


title: Sputum_391322


title: Sputum_391320


title: eye disc of ey>lacZ, lacZ, biologic rep 1


title: Vehicle, biological rep3

description: Gene expression data from vehicle group


title: Sputum_391318


title: Vehicle, biological rep2

description: Gene expression data from vehicle group


title: Vehicle, biological rep1

description: Gene expression data from vehicle group


title: Sputum_391324


title: Sputum_391317


title: Sputum_391300


title: Sputum_391308


title: Sputum_391307


title: Sputum_391306


title: Sputum_391303


title: Sputum_391315


title: Sputum_391311


title: Sputum_391304


title: Sputum_391309


title: Sputum_391290


title: Sputum_391310


title: Sputum_391298


title: Sputum_391295


title: Sputum_391312


title: Sputum_391299


title: Sputum_391302


title: Sputum_391301


title: Sputum_391316


title: Sputum_391297


title: Sputum_391292


title: Sputum_391289


title: Sputum_391314


title: Sputum_391305


title: Sputum_391293


title: Sputum_391294


title: Sputum_391313


title: Sputum_391291


title: Sputum_391296


title: Sputum_391288


title: Sputum_391287


title: Sputum_391284


title: Sputum_391286


title: Sputum_391272


title: Sputum_391274


title: Sputum_391280


title: Sputum_391283


title: Sputum_391262


title: Sputum_391267


title: Sputum_391271


title: Sputum_391276


title: Sputum_391273


title: Sputum_391275


title: Sputum_391260


title: Sputum_391270


title: Sputum_391282


title: Sputum_391263


title: Sputum_391281


title: Sputum_391264


title: Sputum_391279


title: Sputum_391285


title: Sputum_391268


title: Sputum_391269


title: Sputum_391266


title: Sputum_391258


title: Sputum_391278


title: Sputum_391259


title: Sputum_391265


title: Sputum_391261


title: Sputum_391257


title: Sputum_391256


title: Sputum_391253


title: Sputum_391246


title: Sputum_391240


title: Sputum_391247


title: Sputum_391238


title: Sputum_391241


title: Sputum_391277


title: Sputum_391255


title: Sputum_391236


title: Sputum_391252


title: Sputum_391254


title: Sputum_391233


title: Sputum_391244


title: Sputum_391239


title: Sputum_391249


title: Sputum_391243


title: Sputum_391237


title: Sputum_391248


title: Sputum_391230


title: Sputum_391235


title: Sputum_391231


title: Sputum_391251


title: Sputum_391250


title: Sputum_391234


title: Sputum_391245


title: Sputum_391232


title: Sputum_391242


title: Sputum_391229


title: Sputum_391228


title: Sputum_391227


title: Blood_391226

source_name: Whole Blood from COPD subject

value: whole blood


title: Blood_391225


title: Blood_391219


title: Blood_391216


title: Blood_391223


title: Blood_391220


title: Blood_391221


title: Blood_391211


title: Blood_391210


title: Blood_391213


title: Blood_391205


title: Blood_391217


title: Blood_391202


title: Blood_391222


title: Blood_391214


title: Blood_391215


title: Blood_391208


title: Blood_391207


title: Blood_391203


title: Blood_391206


title: Blood_391209


title: Blood_391198


title: Blood_391218


title: Blood_391224


title: Blood_391204


title: GANAB knock down UMUC3-2

city: Shen Zhen

first: GuoYu

last: Peng

address: 47 Youyi Road, Luohu District

institute: Shenzhen Luohu Hospital Group

data_processing:
Raw fastq were quality control use fastp.
Expression of genes and transcripts were quantified using Salmon and Tximport.
DESeq2 used to perform differential expression genes analysis.
Gene set enrichment analysis were performed by clusterProfiler.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts of genes for all RNA-Seq samples in csv format.
Supplementary_files_format_and_content: TPM of genes for all RNA-Seq samples in csv format.

source_name: bladder carcinoma cell line

growth_protocol: Cells were orthotopically transplanted to the bladders of C57 nude mice and cultured for 14 days.

extract_protocol:
Total RNA was extracted with TRIzol reagent.
200 ng of RNA was utilized for library preparation with the VAHTSTM Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd., Cat# NR604-01).

treatment_protocol: The mice were kept in normal condition.

tag: cell line

value: GANAB knock down


title: HeLa RNA

city: Beijing

first: Xiaowo

last: Wang

address: Qinghuayuan, Haidian

institute: Tsinghua University

data_processing:
TopHat (2.1.1)
Cufflinks (2.2.1)
miRDeep2 (0.1.2)
Genome_build: RNA: hg38
Genome_build: miRNA: hg19
Supplementary_files_format_and_content: isoforms.fpkm_tracking, FPKMs of RNAs
Supplementary_files_format_and_content: miRNA.count, counts of miRNAs

source_name: HeLa cell line

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA was enriched by Oligo(dT), ligated with adapters, and then sequenced by NovaSeq 6000 (Illumina).
Small RNA was isolated by PEG8000, ligated with adapters, and then sequenced by Hiseq2500 (Illumina)

value: HeLa


title: Control UMUC3-2

value: control


title: Control UMUC3-3


title: Blood_391199


title: GANAB knock down UMUC3-3


title: Blood_391212


title: Blood_391201


title: Blood_391196


title: Control UMUC3-1


title: GANAB knockdown UMUC3

data_processing:
Raw data was mapped using pipeline Cell Ranger (v3.1.0) with default parameters to obtain the UMI counts of each cell.
Genome_build: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary_files_format_and_content: Sparse matrices are stored in the Market Exchange Format (MEX) as .mtx.gz files. Gene and barcode sequences corresponding to row and column are provided as .tsv files.

extract_protocol:
Single cells were processed with Chromium Single Cell 3’ Reagent Kits v3 (10×Genomics) according to the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA-DPBS solution, and 10,000 cells were added to each channel. The cells were then partitioned into gel beads in emulsion in the GemCode instrument, then lysed before barcoded reverse transcript of RNA, followed by amplification, shearing, and 5’ adaptor and sample index attachment.
single-cell RNA-Sequencing

value: GANAB knockdown


title: Blood_391195


title: Blood_391200


title: GANAB knock down UMUC3-1


title: Blood_391197


title: Control UMUC3


title: meCLIP_HEK293_rep2_IP

city: Mobile

first: Justin

last: Roberts

state: AL

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

data_processing:
The resulting reads are analyzed via a modified computational pipeline based on the original eCLIP strategy that has been converted into a Snakemake workflow.
Briefly, the reads are initially inspected for appropriate quality using FastQC (v. 0.11.7).
The in-line unique molecular identifier (UMI) located within the ssDNA adapter (rand3Tr3) at the beginning of read 2 is extracted using UMI-tools (v. 1.0.0) to prepare the reads for downstream de-duplication.
The remaining non-random ssDNA adapter and indexed RNA adapters are then removed using Cutadapt (v. 2.4), with any reads less than 18bp being discarded. The trimmed reads are then briefly analyzed visually once more with FastQC to ensure all adapters are successfully removed.
Two mapping steps are then performed using the splicing-aware RNA aligner STAR (v. 2.7.1a). First the reads are mapped to the species appropriate version of RepBase (v18.05) with any successfully mapped reads being removed from further analysis. The remaining reads are then mapped to the full species appropriate genome with only uniquely mapping reads being included in final alignment. Subsequent removal of PCR duplicates is performed with UMI-tools using the previously extracted UMIs.
The final alignment file is sorted and indexed using samtools (v. 1.9) and variations from the reference genome are identified using the 'mpileup' command of samtools. An internally developed Java package is then employed to identify C-to-T mutations occurring within the m6A consensus motif at a set frequency threshold of greater than or equal to 2.5% and less than or equal to 50% of the total reads at a given position (with a minimum of 3 C-to-T mutations at a single site). The resulting m6A sites are then automatically compared to those identified in the corresponding input sample and any sites occurring in both are removed from the final list of m6As.
Genome_build: hg19
Supplementary_files_format_and_content: XLS files consisting of a list of annoated m6As and corresponding BED files (categorized by confidence) were generate using custom Java package. Indexed BAM files consisting of reads (read2) that were successfully mapped to the genome are supplied for visualization of overall library quality and C-to-T conversion frequencies relative to identified m6A sites.

source_name: embryonic kidney cells

extract_protocol:
Cells were cultured in appropriate media and total RNA was isolated using the Trizol (15596018, Invitrogen). Poly(A) selection was performed using the Magnosphere® Ultrapure mRNA Purification Kit (9186, Takara). RNA was fragemented at 70C for ~3min using RNA Fragmentation Reagents (AM8740, Ambion). A small amount (~500ng) of fragmented RNA was saved for use as the input sample.
Library was prepared using eCLIP-seq protocol with minor modifications. Briefly, the fragmented poly(A) RNA was incubated with anti-m6A antibody (Abcam Ab151230) and then crosslinked twice at 150 mJ/cm2 (254nm wavelength) using a Stratalinker UV Crosslinker. The RNA:antibody sample was incubated with Protein A/G Magnetic Beads (88803, Pierce) overnight at 4C and then a RNA adapter is ligated on the 3' end of the sample. The RNA:antibody complex is then ran on an SDS-PAGE gel and transferred to a nitrocellulose membrane to remove any non-crosslinked RNA. Following treatment with Proteinase K to remove nearly all of the antibody except the crosslinked amino acid, the RNA is isolated, one adapter is ligated, and the RNA is converted into cDNA for full library amplification. Sequencing of the cDNA libraries was primarily performed using an Illumina NovaSEQ 6000 to generate 2x150bp paired-end runs consisting of 40 million raw reads per sample.

value: embryonic kidney cells

value: overexpressing lncRNA HOTAIR

tag: rip antibody

value: anti-m6A antibody (Abcam Ab151230)


title: meCLIP_HEK293_rep3_IP


title: meCLIP_MDAMB231_rep3_IP

source_name: breast cancer cell

value: breast cancer cell


title: meCLIP_HEK293_rep1_IP


title: Blood_391192


title: Blood_391189


title: Blood_391186


title: Blood_391188


title: Blood_391190


title: meCLIP_MDAMB231_rep2_IP


title: Blood_391183


title: meCLIP_MDAMB231_rep1_IP


title: Blood_391187


title: Blood_391185


title: Blood_391193


title: Blood_391184


title: Blood_391181


title: meCLIP_MCF7_rep3_IP


title: meCLIP_MCF7_rep2_IP


title: meCLIP_MCF7_rep1_IP


title: Blood_391191


title: Blood_391179


title: Blood_391178


title: Blood_391176


title: Blood_391173


title: Blood_391175


title: Blood_391180


title: Blood_391182


title: Blood_391177


title: Blood_391194


title: Blood_391174


title: Blood_391170


title: Blood_391168


title: Blood_391162


title: Blood_391165


title: Blood_391172


title: Blood_391169


title: Blood_391155


title: Blood_391159


title: Blood_391164


title: Blood_391160


title: Blood_391163


title: Blood_391150


title: Blood_391161


title: Blood_391171


title: Blood_391156


title: Blood_391166


title: Blood_391158


title: Blood_391157


title: Blood_391153


title: Blood_391152


title: Blood_391154


title: Blood_391144


title: Blood_391151


title: Blood_391148


title: Blood_391146


title: Blood_391145


title: Blood_391149


title: Blood_391147


title: Blood_391142


title: Blood_391141


title: Blood_391143


title: Blood_391133


title: Blood_391139


title: Blood_391136


title: Blood_391125


title: Blood_391122


title: Blood_391140


title: Blood_391135


title: Blood_391121


title: Blood_391130


title: Blood_391129


title: Blood_391132


title: Blood_391167


title: Blood_391126


title: Blood_391124


title: Blood_391119


title: Blood_391138


title: Blood_391131


title: Blood_391118


title: Blood_391134


title: Blood_391123


title: Blood_391128


title: Blood_391137


title: Blood_391127


title: Blood_391120


title: Sputum_822990

hyb_protocol: Labelled cDNA was hybridized onto HG-U133  GeneChip oligonucleotide arrays (Affymetrix).

value: All NEMI

tag: visit

value: V6 DAY 84

tag: rin

tag: investigatorcountry

value: DENMARK


title: Blood_391116

value: COPD


title: Sputum_822987

value: sputum

value: SCREENING


title: Sputum_822989

value: V4 DAY 28

value: M


title: Sputum_822988

value: V3 DAY 12


title: Sputum_822985


title: Blood_391115

value: whole blood


title: Sputum_822984


title: Sputum_822986


title: Blood_391117


title: Sputum_822971

value: All Placebo

value: F


title: Sputum_822979


title: Sputum_822968


title: Sputum_822981


title: Sputum_822976


title: Sputum_822973


title: Sputum_822969


title: Sputum_822978


title: Sputum_822972


title: Sputum_822962


title: Sputum_822983


title: Sputum_822980


title: Sputum_822961


title: Sputum_822975


title: Sputum_822965


title: Sputum_822967


title: Sputum_822982


title: Sputum_822970


title: Sputum_822964


title: Sputum_822966


title: Sputum_822977


title: Sputum_822974


title: Sputum_822960


title: Sputum_822963


title: Sputum_822955


title: Sputum_822958


title: Sputum_822959


title: Sputum_822957


title: Sputum_822956


title: Sputum_822732

value: CANADA


title: Sputum_822722


title: Sputum_822729


title: Sputum_822727


title: Sputum_822731


title: Sputum_822728


title: Sputum_822730


title: Sputum_822720


title: Sputum_822721


title: Sputum_822724


title: Sputum_822717


title: CD34+_anti-HA-1 [Cut&Run]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University

description: processed data file: CD34_HA_merged_noNeg_nomodel_extsize300_q0.001_peaks.txt

data_processing:
Library strategy: Cut&Run
For Cut&Run:
Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+scer genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 (narrowPeak, q=0.001).
For HA Cut&Run +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using yeast spike-in for normalization.
bigWig files were generated using deepTools and bedGraph files were generated using Homer.
For ChIP-seq:
Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+dm3 genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Normalized bigWig files were generated with deepTools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig, bedGraph files
Supplementary_files_format_and_content: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv: Diffbind peak info
Supplementary_files_format_and_content: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv: Differential peak DESeq2
Supplementary_files_format_and_content: New_ZnF_q0.001_peaks.txt: MACS2 peaks
Supplementary_files_format_and_content: CD34_HA_merged_noNeg_nomodel_extsize300_q0.001_peaks.txt: MACS2 peaks

growth_protocol: Kasumi-1 cells were grown in RPMI +15% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6.

extract_protocol:
For Cut&Run, released DNA fragments were extracted using phenol:chloroform:IAA and ethanol precipitation. For ChIP-seq, after cross-link reversal, immunoprecipitated DNA was purified by Ampure beads.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: For H3K27ac, cells were treated with dTAG for 24 hours. For HA, cells were treated with dTAG for 18 hours.

tag: cell type

value: CD34+ cord blood cells

tag: genotype variation

tag: antibody

value: anti-HA


title: Sputum_822723


title: Sputum_822712


title: Sputum_822711


title: Sputum_822713


title: Sputum_822718


title: Sputum_822710


title: Sputum_822714


title: Kasumi-1_(-)dTAG_anti-H3K27ac [ChIP-seq]

data_processing:
For Cut&Run:
Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+scer genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 (narrowPeak, q=0.001).
For HA Cut&Run +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using yeast spike-in for normalization.
bigWig files were generated using deepTools and bedGraph files were generated using Homer.
For ChIP-seq:
Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+dm3 genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Normalized bigWig files were generated with deepTools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig, bedGraph files
Supplementary_files_format_and_content: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv: Diffbind peak info
Supplementary_files_format_and_content: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv: Differential peak DESeq2
Supplementary_files_format_and_content: New_ZnF_q0.001_peaks.txt: MACS2 peaks
Supplementary_files_format_and_content: CD34_HA_merged_noNeg_nomodel_extsize300_q0.001_peaks.txt: MACS2 peaks

value: No dTAG


title: Kasumi-1_(+)dTAG_anti-H3K27ac [ChIP-seq]

value: dTAG


title: Sputum_822725


title: Sputum_822715

value: All NEMI


title: CD34+_anti-HA-2 [Cut&Run]


title: Kasumi-1_parental_anti-ETO [Cut&Run]

description: processed data file: New_ZnF_q0.001_peaks.txt

source_name: Kasumi-1_parental cells

value: Parental

value: anti-ETO


title: Sputum_822719

value: COPD

value: V6 DAY 84


title: Sputum_822716

value: sputum

value: SCREENING


title: Kasumi-1_(+)dTAG_anti-HA-2 [Cut&Run]

description:
MB-4
processed data file: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv
processed data file: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv


title: Kasumi-1_(+)dTAG_anti-HA-1 [Cut&Run]

description:
MB-3
processed data file: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv
processed data file: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv


title: Kasumi-1_(-)dTAG_anti-HA-2 [Cut&Run]

description:
MB-2
processed data file: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv
processed data file: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv


title: Sputum_822709

value: M


title: Kasumi-1_(-)dTAG_anti-HA-1 [Cut&Run]

description:
MB-1
processed data file: 042420_HA_AE_Diffbind-peakinfo_q0.001.csv
processed data file: 042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv


title: Sputum_822708


title: MUT4_22_Cytoplasmic_1

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to hg38 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg38 whole genome using STAR.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth. Kallisto was used to 1) build a transcript index from the GenCode hg38 release Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100  -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg38
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: Immature MNs

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15].Details of the lines used in thus study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM).All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Biochemical subcellular fractionation was achieved for all cell stages using the Ambion PARIS kit (ThermoFisher Scientific) cell fractionation buffer, following the manufacturer's general protocol, and an 8M Urea Nuclear Lysis Buffer prepared in house. Initially, cells were washed once using ice-cold PBS. Cytosolic fraction was then obtained by lysing cells directly in ice-cold cell fractionation buffer (ThermoFisher Scientific) for 3-15 minutes, thus disrupting plasma membranes, whilst leaving nuclear membranes intact. Lysates were then centrifuged for 3 minutes at 500 x g at 4C. The supernatant was then collected, further centrifuged at maximum speed in a bench centrifuge at 4C for 1 minute, and the resulting supernatant was then processed as cytosolic fraction. Nuclear pellets from the first centrifugation step were gently washed once with cell fractionation buffer and then lysed on ice for 30 minutes in 8M Urea Nuclear Lysis Buffer, containing 50mM Tris-HCL (pH 8), 100mM NaCl, 0.1% SDS, and 1mM DTT. The resulting nuclear fraction was then homogenised using a QIAshredder (QIAGEN) to shred chromatin and reduce viscosity, before being further processed for RNA extraction.  Both lysis buffers were supplemented with 0.1 U/µl RiboLock RNase Inhibitor (ThermoFisher Scientific) and HALT Protease Inhibitor Complex (ThermoFisher Scientific).
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
500ng total RNA input was used with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®, with NEBNext® Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: Motor neuron (MN) differentiation was carried out using an adapted version of a previously published protocol (Hall et al., 2017). Briefly, iPSCs were first differentiated to neuroepithelium by plating on Geltrex-coated plates to 100% confluency in chemically defined medium consisting of DMEM/F12 Glutamax, Neurobasal, L-Glutamine, N2 supplement, non essential amino acids, B27 supplement, β-mercaptoethanol (all from Life Technologies) and insulin (Sigma). Treatment with small molecules from day 0-7 was as follows: 1µM Dorsomorphin (Millipore), 2µM SB431542 (Tocris Bioscience), and 3.3µM CHIR99021 (Miltenyi Biotec). Starting from day 8, the neuroepithelial layer was patterned for 7 days with 0.5µM retinoic acid and 1µM Purmorphamine. At day 14 pMN precursors were treated with 0.1µM Purmorphamine for a further 4 days before being terminally differentiated in 0.1 µM Compound E (Enzo Life Sciences) to promote cell cycle exit.

tag: cell line id

tag: genotype

value: VCP R191Q

tag: fraction

value: Cytoplasmic

tag: days of differentiation

tag: round of sequencing

value: round 1


title: MUT4_14_Nuclear_2

value: Nuclear


title: MUT4_22_Cytoplasmic_2


title: MUT4_14_Cytoplasmic_2


title: MUT4_14_Nuclear_1


title: MUT4_14_Cytoplasmic_1


title: Sputum_822726

tag: patient diagnosis

tag: tissue

tag: treatment

value: All Placebo

value: V4 DAY 28

value: CANADA


title: Sputum_822700

tag: Sex

value: F

tag: subject


title: Sputum_822707


title: Sputum_822703


title: Sputum_822706


title: Sputum_822705


title: Sputum_822702


title: Sputum_822704


title: Sputum_822701

value: V3 DAY 12


title: Sputum_822690

value: All NEMI


title: Sputum_822694


title: Sputum_822697


title: Sputum_822693


title: Sputum_822691


title: Sputum_822698


title: Sputum_822699


title: Sputum_822695


title: Sputum_822696


title: Sputum_822692


title: MUT4_7_Nuclear_1


title: MUT4_7_Nuclear_2


title: Sputum_553507


title: MUT4_7_Cytoplasmic_1


title: MUT4_3_Nuclear_2


title: MUT4_3_Cytoplasmic_2


title: MUT4_7_Cytoplasmic_2


title: MUT4_3_Nuclear_1


title: MUT4_0_Nuclear_2

source_name: iPSC


title: MUT4_3_Cytoplasmic_1


title: MUT4_0_Cytoplasmic_1


title: MUT4_0_Cytoplasmic_2


title: MUT4_35_Nuclear_2

source_name: Electrically active MNs


title: MUT4_0_Nuclear_1


title: Sputum_553508


title: MUT4_35_Nuclear_1


title: MUT4_35_Cytoplasmic_2


title: Sputum_553504


title: Sputum_553501


title: Sputum_553499


title: Sputum_553505


title: Sputum_553502


title: Sputum_553498


title: Sputum_553497


title: Sputum_553506


title: Sputum_553503


title: MUT4_22_Nuclear_2


title: Sputum_553495


title: MUT3_22_Cytoplasmic_2


title: MUT3_22_Cytoplasmic_1


title: MUT4_22_Nuclear_1


title: Sputum_553500


title: Sputum_553496


title: Sputum_553494


title: MUT3_14_Nuclear_1


title: MUT3_14_Nuclear_2


title: MUT4_35_Cytoplasmic_1


title: MUT3_14_Cytoplasmic_2


title: Sputum_553493


title: MUT3_14_Cytoplasmic_1


title: MUT3_7_Nuclear_2


title: Sputum_553491


title: Sputum_553492


title: Sputum_553490


title: Sputum_553487


title: MUT3_7_Nuclear_1


title: Sputum_553489


title: MUT3_7_Cytoplasmic_1


title: MUT3_3_Nuclear_2


title: MUT3_3_Nuclear_1


title: Sputum_553488


title: MUT3_3_Cytoplasmic_2


title: MUT3_7_Cytoplasmic_2


title: MUT3_0_Nuclear_1


title: MUT3_0_Nuclear_2


title: MUT3_0_Cytoplasmic_2


title: Sputum_553485


title: MUT3_0_Cytoplasmic_1


title: MUT3_35_Nuclear_2


title: Sputum_553482


title: MUT3_35_Nuclear_1


title: Sputum_553484


title: MUT3_35_Cytoplasmic_2


title: Sputum_553481


title: Sputum_515656


title: Sputum_553486


title: Sputum_515551


title: MUT3_22_Nuclear_2


title: MUT3_35_Cytoplasmic_1


title: MUT2_22_Cytoplasmic_2

value: VCP R155C


title: Sputum_553483


title: Sputum_515549


title: Sputum_515655


title: MUT2_14_Nuclear_2


title: Sputum_515546


title: Sputum_515545


title: Sputum_515553


title: Sputum_515657


title: Sputum_515547


title: Sputum_515542


title: Sputum_515543


title: Sputum_515550


title: Sputum_515548


title: Sputum_515541


title: MUT3_22_Nuclear_1


title: Sputum_515539


title: MUT2_14_Cytoplasmic_2


title: MUT2_14_Cytoplasmic_1


title: MUT2_7_Nuclear_2


title: MUT2_22_Cytoplasmic_1


title: MUT2_7_Cytoplasmic_2


title: MUT2_7_Nuclear_1


title: MUT2_7_Cytoplasmic_1


title: MUT2_14_Nuclear_1


title: MUT2_3_Nuclear_2


title: Sputum_515544


title: Sputum_515537

value: No Treatment


title: MUT2_3_Nuclear_1


title: Sputum_515527

value: COPD


title: Sputum_515536


title: Sputum_515540


title: MUT2_0_Nuclear_2


title: MUT2_3_Cytoplasmic_1


title: MUT2_0_Cytoplasmic_2


title: MUT2_0_Nuclear_1


title: MUT2_0_Cytoplasmic_1


title: MUT2_35_Nuclear_2


title: MUT2_35_Nuclear_1


title: HIGM2_ncsMBC_2

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

data_processing:
reads were trimmed using Trimmomatic
pre-processed and aligned using MethylCTools, with default parameters (V. Hovestadt, S. Picelli, B. Radlwimmer, M.Z. and P.L., unpublished data), which uses the Burrows-Wheeler alignment algorithm
methylation calling using methylCtools
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylaton callings  for each Sample

source_name: non-class-switched memory b cells

extract_protocol:
QIAamp DNA micro kit (Qiagen) according to the manufacturer’s protocol
30 ng of genomic DNA was used to produce four independent barcoded sequencing libraries per DNA sample using the tagmentation method (Wang, Q. et al. Tagmentation-based whole-genome bisulfite sequencing. Nat. Protoc. (2013). doi:10.1038/nprot.2013.118)

tag: source

value: fresh blood

value: non-class-switched memory b cells

tag: diagnosis

value: hyper-IgM syndrome type 2

tag: molecule subtype

value: Bisulfite-treated genomic DNA


title: HIGM2_ncsMBC_1


title: Sputum_515521

value: sputum

tag: visit

tag: rin

tag: investigatorcountry


title: Sputum_515520


title: Blood_822951

value: whole blood

value: M

value: DENMARK


title: Blood_822952


title: MUT2_3_Cytoplasmic_2

value: Cytoplasmic

value: round 1


title: MUT2_35_Cytoplasmic_1


title: MUT2_35_Cytoplasmic_2


title: HIGM2_NBC_1

source_name: naïve b cell

tag: cell type

value: naive b cell


title: Sputum_515524

value: All Placebo

value: CANADA


title: MUT2_22_Nuclear_2

tag: cell line id

value: Nuclear


title: Sputum_515522

value: All NEMI

value: SCREENING

value: F


title: Blood_822954

value: COPD

value: No Treatment


title: Sputum_515525

value: V4 DAY 28


title: Sputum_515526


title: Control_ncsMBC_1

value: fresh blood

value: non-class-switched memory b cells

value: healthy

value: Bisulfite-treated genomic DNA


title: MUT2_22_Nuclear_1

tag: genotype

value: VCP R155C


title: Blood_822953

value: whole blood

value: V6 DAY 84

value: M

value: DENMARK


title: Sputum_515523

value: sputum

value: CANADA


title: MUT1_22_Cytoplasmic_2

tag: fraction

value: Cytoplasmic

value: round 1


title: HIGM2_NBC_2

value: naive b cell

value: hyper-IgM syndrome type 2


title: Blood_822950

value: COPD

value: All NEMI

value: SCREENING


title: Blood_822949


title: Blood_822946


title: Control_ncsMBC_2

value: fresh blood

value: non-class-switched memory b cells


title: Control_NBC_1

value: healthy

value: Bisulfite-treated genomic DNA


title: MUT1_14_Nuclear_1

value: VCP R155C

value: Nuclear

tag: days of differentiation


title: MUT1_22_Cytoplasmic_1

tag: round of sequencing


title: MUT1_14_Nuclear_2


title: Blood_822948

tag: patient diagnosis

value: whole blood

value: V4 DAY 28

value: M


title: MUT1_14_Cytoplasmic_2


title: Blood_822947

tag: tissue

value: V3 DAY 12

value: DENMARK


title: MUT1_14_Cytoplasmic_1

value: Cytoplasmic

value: round 1


title: MUT1_7_Nuclear_2


title: MUT1_7_Nuclear_1


title: Control_NBC_2

value: naive b cell


title: MUT1_7_Cytoplasmic_2


title: MUT1_3_Nuclear_2


title: Blood_822944

value: COPD

tag: treatment

value: F


title: Blood_822941

value: All Placebo

value: V6 DAY 84

tag: Sex


title: Blood_822939

tag: subject


title: MUT1_0_Nuclear_2


title: Blood_822945

value: All NEMI


title: MUT1_3_Cytoplasmic_1


title: MUT1_3_Nuclear_1


title: Blood_822938

value: SCREENING


title: Blood_822940


title: Blood_822942


title: Blood_822943


title: MUT1_3_Cytoplasmic_2


title: MUT1_0_Nuclear_1


title: MUT1_0_Cytoplasmic_1


title: Blood_822937


title: MUT1_7_Cytoplasmic_1


title: MUT3_3_Cytoplasmic_1

value: VCP R191Q


title: Blood_822936


title: MUT1_35_Nuclear_2

value: VCP R155C


title: Blood_822933


title: Blood_822934


title: Sputum_515552

value: sputum

value: CANADA


title: Blood_822935

value: whole blood


title: Blood_822928


title: Blood_822932


title: Blood_822929

value: V4 DAY 28


title: MUT1_35_Nuclear_1

value: Nuclear


title: Blood_822931

value: DENMARK


title: Blood_822930


title: MUT1_35_Cytoplasmic_1

value: Cytoplasmic


title: MUT1_22_Nuclear_1

value: round 1


title: MUT1_35_Cytoplasmic_2


title: CTRL5_14_Nuclear_1

value: Wildtype


title: MUT1_22_Nuclear_2


title: CTRL5_14_Nuclear_2


title: CTRL5_22_Cytoplasmic_2


title: CTRL5_22_Cytoplasmic_1


title: CTRL5_14_Cytoplasmic_2


title: Blood_822924

value: COPD

value: V3 DAY 12


title: Blood_822926

value: All Placebo

value: F


title: Blood_822921

value: All NEMI


title: Blood_822918

value: No Treatment

value: SCREENING

value: M


title: Blood_822922

value: V6 DAY 84


title: Blood_822925


title: Blood_822919


title: Blood_822927


title: CTRL5_7_Nuclear_2


title: CTRL5_7_Nuclear_1


title: CTRL5_7_Cytoplasmic_2


title: CTRL5_14_Cytoplasmic_1


title: Blood_822923


title: Blood_822920


title: Blood_822917


title: CTRL5_3_Nuclear_1


title: Blood_822914


title: CTRL5_7_Cytoplasmic_1


title: CTRL5_3_Nuclear_2


title: CTRL5_3_Cytoplasmic_2


title: Blood_822915


title: CTRL5_0_Nuclear_2


title: Sputum_515538

value: sputum

value: CANADA