title: microRNA counts from HepG2 (ENCLB877ZDQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR257DJT/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human HepG2
experiment encode accession: ENCSR257DJT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB877ZDQ
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

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

source_name: Homo sapiens HepG2 immortalized cell line

label_protocol: Nanostring protocol

value: immortalized cell line

tag: description

tag: biosample encode accession

tag: lab

value: Barbara Wold, Caltech

value: 15 year

tag: Sex

value: male

tag: dev stage

value: child

tag: health state

value: hepatocellular carcinoma

tag: line

tag: link

value: ENCBS644SVK at ENCODE; https://www.encodeproject.org/ENCBS644SVK/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2


title: mCNV3_Nim

status: Public on Oct 14 2016

type: genomic

city: Houston

first: Pengfei

last: Liu

state: TX

address: 2450 Holcombe Blvd, O270F

country: USA

institute: Baylor College of Medicine

hyb_protocol: The standard manufacture's recommended protocol was used.

data_processing:
The data were processed and normalized using DEVA version 1.1.
Analysis was performed with the default parameters in the "CGH workflow with segmentation and background correction and waviness correction" pipeline provided in the DEVA software.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol.

tag: gender

value: F

tag: patient relationship

tag: cell line

value: M


title: BAB3598_Nim

scan_protocol: The standard manufacture's recommended protocol was used.


title: microRNA counts from endothelial cell of umbilical vein (ENCLB534VHC)

type: RNA

description:
https://www.encodeproject.org/experiments/ENCSR223FVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human HUVEC
experiment encode accession: ENCSR223FVU
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB534VHC
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

molecule: total RNA

source_name: Homo sapiens endothelial of umbilical vein primary cell newborn

value: endothelial cell of umbilical vein

value: primary cell

tag: age

value: unknown

value: not collected

value: newborn

tag: cell type

value: ENCBS719AAA at ENCODE; https://www.encodeproject.org/ENCBS719AAA/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/

value: ENCODE dbxrefs HUVEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HUVEC


title: microRNA counts from MCF-7 (ENCLB924QTY)

description:
https://www.encodeproject.org/experiments/ENCSR201IBH/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human MCF-7
experiment encode accession: ENCSR201IBH
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB924QTY
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: Barbara Wold, Caltech

value: 69 year

value: female

value: adult

value: breast cancer (adenocarcinoma)

value: ENCBS155VQC at ENCODE; https://www.encodeproject.org/ENCBS155VQC/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7


title: microRNA counts from HepG2 (ENCLB152MAK)

description:
https://www.encodeproject.org/experiments/ENCSR257DJT/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human HepG2
experiment encode accession: ENCSR257DJT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB152MAK
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: Homo sapiens HepG2 immortalized cell line

value: 15 year

value: male

value: child

value: hepatocellular carcinoma

value: ENCBS429YJD at ENCODE; https://www.encodeproject.org/ENCBS429YJD/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2


title: microRNA counts from HCT116 (ENCLB709LDV)

description:
https://www.encodeproject.org/experiments/ENCSR165GUQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human HCT116
experiment encode accession: ENCSR165GUQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB709LDV
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 immortalized cell line

value: immortalized cell line

value: Barbara Wold, Caltech

value: unknown

value: colorectal carcinoma

value: ENCBS004UZY at ENCODE; https://www.encodeproject.org/ENCBS004UZY/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-247.aspx

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ENCODE dbxrefs HCT-116; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HCT-116


title: microRNA counts from MCF-7 (ENCLB054JNR)

description:
https://www.encodeproject.org/experiments/ENCSR201IBH/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human MCF-7
experiment encode accession: ENCSR201IBH
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB054JNR
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: Homo sapiens MCF-7 immortalized cell line

value: 69 year

value: female

value: adult

value: breast cancer (adenocarcinoma)

value: ENCBS254AYH at ENCODE; https://www.encodeproject.org/ENCBS254AYH/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7


title: microRNA counts from endothelial cell of umbilical vein (ENCLB515FHL)

description:
https://www.encodeproject.org/experiments/ENCSR223FVU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human HUVEC
experiment encode accession: ENCSR223FVU
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB515FHL
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: endothelial cell of umbilical vein

value: primary cell

value: Homo sapiens endothelial of umbilical vein primary cell newborn

value: Barbara Wold, Caltech

value: not collected

value: newborn

value: ENCBS743IPG at ENCODE; https://www.encodeproject.org/ENCBS743IPG/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/

value: ENCODE dbxrefs HUVEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HUVEC


title: microRNA counts from HCT116 (ENCLB843JRS)

description:
https://www.encodeproject.org/experiments/ENCSR165GUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human HCT116
experiment encode accession: ENCSR165GUQ
assay title: microRNA counts
assembly: GRCh38
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB843JRS
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Homo sapiens HCT116 immortalized cell line

value: unknown

value: male

value: colorectal carcinoma

value: ENCBS009DQE at ENCODE; https://www.encodeproject.org/ENCBS009DQE/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-247.aspx

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ENCODE dbxrefs HCT-116; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HCT-116


title: microRNA counts from fibroblast of arm (ENCLB590ZLN)

description:
https://www.encodeproject.org/experiments/ENCSR138ZXT/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human fibroblast of arm
experiment encode accession: ENCSR138ZXT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB590ZLN
size range: <30

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: Thomas Gingeras, CSHL

value: 53 year

value: adult

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183


title: microRNA counts from K562 (ENCLB362ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AJL/
***************
biological replicate number: 1
technical replicate number: 1
description: Irvine Nanostring K562
experiment encode accession: ENCSR000AJL
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB362ZZZ

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 1.

value: Brenton Graveley, UConn

value: female

tag: passage number

value: chronic myelogenous leukemia (CML)

value: ENCBS087RNA at ENCODE; https://www.encodeproject.org/ENCBS087RNA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: microRNA counts from fibroblast of arm (ENCLB998DXA)

description:
https://www.encodeproject.org/experiments/ENCSR138ZXT/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human fibroblast of arm
experiment encode accession: ENCSR138ZXT
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-01-19
lab: Ali Mortazavi, UCI
library encode accession: ENCLB998DXA
size range: <30

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: male

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/


title: microRNA counts from K562 (ENCLB363ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AJL/
***************
biological replicate number: 2
technical replicate number: 1
description: Irvine Nanostring K562
experiment encode accession: ENCSR000AJL
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB363ZZZ

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 2.

value: 53 year

value: adult

value: ENCBS088RNA at ENCODE; https://www.encodeproject.org/ENCBS088RNA/


title: microRNA counts from GM12878 (ENCLB361ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AJK/
***************
biological replicate number: 2
technical replicate number: 1
description: Irvine Nanostring GM12878
experiment encode accession: ENCSR000AJK
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB361ZZZ

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: Ali Mortazavi, UCI

value: unknown

value: ENCBS090RNA at ENCODE; https://www.encodeproject.org/ENCBS090RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: microRNA counts from GM12878 (ENCLB360ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AJK/
***************
biological replicate number: 1
technical replicate number: 1
description: Irvine Nanostring GM12878
experiment encode accession: ENCSR000AJK
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB360ZZZ

value: female

value: ENCBS089RNA at ENCODE; https://www.encodeproject.org/ENCBS089RNA/


title: Valproic acid treated_3h_rep1

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G.

data_processing: The data were analyzed with RMA using Affymetrix Expression Console default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Saccharomyces cerevisiae

source_name: Valproic acid treated_3h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Saccharomyces cerevisiae strain (W1588-4c) was grown in standard Synthetic Complete liquid media (contain 2% glucose) at 30oC with orbital shaking.

extract_protocol: Total RNA was extracted from yeast cells by using heat/freeze RNA isolation method as previously described in [Schmitt ME, Brown TA, Trumpower BL. A Rapid and Simple Method for Preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Research, 1990; 18 (10): 3091–92.]. The quality of RNA was high as assessed by absorbance (260 and 280 nm), by Formaldehyde Agarose-Gel electrophoresis, and by Agilent 2100 Bioanalyzer.

treatment_protocol: The yeast cells (W1588-4c) were grown to exponential phase (OD600: ~1) and left untreated (Control) or treated with a dose of 6mM Valproic acid (freshly prepared stock in water) for 3h at 30oC with shaking.

tag: strain

tag: genotype/variation

tag: growth phase

value: exponential phase

tag: treated with

value: 6mM of Valproic acid for 3h


title: liver, infection,biological rep3

city: harbin

first: su

last: han

address: xuefu road

department: parasite

country: China

institute: harbin medical university

description: liver gene expression of rats at 3 weeks post-infection with clornorchis sinensis

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Expression Console(version1.3.1, Affymetrix).

organism: Rattus norvegicus

source_name: liver tissue 3 weeks post infection

label_protocol: Total RNA were amplified, labeled and purified by using FlashTag Biotin HSR RNA Labeling Kit (Cat#901911, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Wistar rats (5–6 weeks old, male) were housed in an air-conditioned room at 24°C under a 12-h dark/light cycle with free access to standard laboratory food and water. The rats were individually infected orally with 50 metacercariae. Parasitic infection was assessed by detection of parasite eggs in stool samples and pathological findings. Mock-infected control rats were similarly administered with 50 μl of sterile normal solution. All animal care and experimental procedures were conducted in accordance with the guidelines for animal use in toxicology.

extract_protocol: RNA  was  extracted  by  mirVanaTM  RNA  Isolation  Kit  (Applied  Biosystem  p/n   AM1556 ) following the manufacturer's instructions.

treatment_protocol: The animals were sacrificed at 3 weeks post-infection and the livers were harvested and preserved in TRIzol reagent (Shanghai Invitrogen Biotechnology Co., Ltd., Shanghai, China) at -80°C, according to the manufacturer’s protocol, until RNA extraction.

value: Wistar

tag: tissue

value: liver

tag: infection status

value: infected with Clonorchis sinensis

value: male


title: liver, infection,biological rep2


title: EpnP63_1783

status: Public on Oct 15 2016

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430PM strip arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using  the GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method and batch effect removal with ComBat

label: Biotin

organism: Mus musculus

source_name: FACS sorted tumor cells

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA were subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: qiagen kit

tag: treatment

value: 10mg TAM

tag: isolation

value: FACS

tag: staining

value: Epcam-/Lin-/DAPI-


title: liver, infection,biological rep1


title: liver,control, biological rep3

description: Liver gene expression of uninfected rats

source_name: liver tissue control

value: not infected


title: BAB3598_Agilent1M

description: human-human array CGH

hyb_protocol: Labeled proband and control samples were combined in a mass ratio of 1:1 with addition of human Cot-1 DNA (Life Technologies), 10X Agilent Blocking Agent (Agilent Technologies) and 2X Hi-RPM Hybridisation Buffer (Agilent Technologies). The mixture was incubated at 95°C for 3 min and then at 37°C for 30 min for pre-hybridization. Afterwards, the mixture was hybridized onto the array placed in a hybridization chamber (Agilent Technologies) in a rotating over (Agilent Technologies) for at least 40 hours at 65°C.

scan_protocol: Washing step after hybridization were performed following the manufacturer’s protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis version 7.2, Agilent Technologies) with Agilent Oligo CGH Wash Buffer 1 and 2 (Agilent Technologies), Acetonitrile (Sigma-Aldrich), and Stabilization and Drying Solution (Agilent Technologies). The dried slides were scanned on Agilent Microarray Scanner (Agilent Technologies) for image acquisition.

data_processing: The images after scanning were subsequently processed by Feature Extraction Software (Agilent Technologies) to generate FE files, which were subsequently imported into Agilent Genomic Workbench version 7.0 (Agilent Technologies) for copy number variation (CNV) analysis.

label_protocol: Genomic DNA from proband (test sample) and control (NA10851 or NA15510 depending on the gender of the proband) were digested with AluI and RsaI (Promega) for 2 hours at 37°C. Digestion product was run on 1% agarose gel for verification. Labeling of the digestion product was performed using BioPrime Array CGH Genomic Labelling Module (Life Technologies) following the manufacturer’s protocol. Cy5-dCTP and Cy3-dCTP from Cyanine Smart Pack dCTP (PerkinElmer) were used for proband and control digestion product, respectively. Labeling reaction was performed for 2 hours at 37°C. Labeling product underwent purification process using Amicon Ultra 0.5 Centrifugal Filter (30 kDa, Millipore). Labeling efficiency was quantitated using a NanoDrop ND-1000 UV-VIS spectrophotometer.

extract_protocol: DNA was isolated from peripheral blood or cultured lymphoblastoid cell lines with a Puregene kit (Gentra Systems), following the manufacturer’s protocol.

value: M


title: BAB3597_Agilent1M

description: human-human array CGH

value: F


title: BAB3596_cell_Agilent1M

description: human-human array CGH


title: BAB3099_cell_Agilent1M

description: human-human array CGH


title: BAB3598_cell_Agilent1M

description: human-human array CGH


title: BAB3097_cell_Agilent1M

description: human-human array CGH


title: liver,control, biological rep1


title: BAB3099_Agilent1M

description: human-human array CGH


title: BAB3597_cell_Agilent1M

description: human-human array CGH


title: BAB3098_Agilent1M

description: human-human array CGH


title: liver,control, biological rep2


title: BAB3596_Agilent1M

description: human-human array CGH


title: BAB3098_cell_Agilent1M

description: human-human array CGH


title: Donor#4 LPC(16:0)

city: Tuebingen

first: Christian

last: Klingler

address: Otfried-Mueller Street 10

department: Medical Clinic IV

country: Germany

institute: IDM at the University Hospital Tuebingen

description: treated with 10 µM LPC(16:0) for 24h

hyb_protocol: standard protocol by the Microarray Genechip Facility Tübingen Service.

data_processing: The facility provided scaled, normalized, annotated and quality controlled data sets.

source_name: human primary myotubes from donor #4

growth_protocol: Primary skeletal muscle cells were obtained from percutaneous needle biopsies of the lateral portion of quadriceps femoris (vastus lateralis) muscle of non-diabetic subjects. The donors gave informed written consent to the study. The Ethical Committee of the Tübingen University Medical Department had approved the protocol. Cells were grown in a 1:1 mixture of α-MEM and Ham’s F-12 supplemented with 20 % FBS, 1 % chicken embryo extract (Seralab, Haywards Heath, UK), 100 U/mL penicillin, 100 g/mL streptomycin, 2 mM L-glutamine, and 0.5 g/mL amphotericin B (Sigma-Aldrich, St. Louis, USA) till 70–80 % confluency. Cells were fused for 5-8 days to myotubes in α-MEM containing 2 % FBS, 2 mM L-glutamine, 100 U/mL penicillin, 100 g/mL streptomycin, and 0.5 g/mL amphotericin B. Experiments were performed in EMEM containing 2 % FBS, 2 mL L-glutamine, 100 U/mL penicillin, 100 g/mL streptomycin, and 0.5 g/mL amphotericin B.

extract_protocol: Cells were homogenized by QIAshredder (Qiagen, Hilden, Germany). Total RNA was extracted by RNeasy Mini-Kit (Qiagen).

treatment_protocol: Fully differentiated primary myotubes were treated with LPC(16:0), LPC(18:1) or solvent for 24h in EMEM

tag: donor id

value: donor #4

tag: donor status

value: non-diabetic subject

tag: tissue source

value: human primary myotubes


title: BAB3097_Agilent1M

description: human-human array CGH

tag: gender

tag: patient relationship


title: Donor#3 con

description: treated with solvent for 24h

scan_protocol: standard protocol by the Microarray Genechip Facility Tübingen Service.

source_name: human primary myotubes from donor #3

value: donor #3

value: quadriceps femoris (vastus lateralis) muscle

value: solvent for 24h


city: Boston

first: Hernan

last: Kopcow

state: MA

address: 330 Brookline Ave Rn 359

department: Medicine

institute: BIDMC

description: Human CD56Bright CD16-  CD9+ KIR+ i-dNK Donnor 97

hyb_protocol: Probes were hybridized using Affymetrix GeneChip hybridization kit materials • Cocktails wree heated  at 99° for 5 minutes, then 45° for 5 minutes then centrifuged at max speed for 1 minute • 200μl of hyb solution  were transferred to each array,  holes were taped .  samples were  hybridized 16 hours at 45° at 60rpm. Fluidics washing and staining was done in  FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using R/Bioconductor
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix) included in the GeneChip WT Plus Reagent Kit

growth_protocol: Does not apply

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, according to manufacture’s instructions

treatment_protocol: Human pNK cells were enriched from leukopacks using a negative enrichment Ab cocktail (NK RosetteSep, StemCell Technologies) following the manufacturer’s instructions. For microarray analysis CD3- CD56Bright CD16- pNK and CD3- CD56Dim CD16+ pNK cells were further purified by FACS sorting. DNK cells were isaolated as described in Caballi et al 2016 , briefly decidual tissue was minced with scissors and digested with 0.1% collagenase type IV and 0.01% DNAse I  30 minutes at 37ºC. The digestion was stopped by the addition of RPMI 1640 media containing 10% Fetal Bovine Serum. The digested tissue was then passed sequentially through 100μm, 70μm and 40μm cell strainers and washed with complete RPMI 1640 media, to obtain a single cell suspension. Cells were plated and incubated at 37ºC for up to 2 hrs . Decidual lymphocyte were  prepared from the overlaying cell suspension by density gradient centrifugation (Ficoll-Hypaque; GE Healthcare Life Sciences). Cells were isolated by  FACS  as CD3- CD56Bright CD16- cells. i-dNK cells: NK RosetteSep enriched pNK cells were seeded at 1 million cells/ml in  media containing 10 ng/ml Il-15 with the addition of recombinant human TGF-β1  at 2 ng/ml and  1 μM 5-aza-2-deoxycytidine (Aza) and cultured for 7 days under a 1%O2  5%CO2 atmosphere. idNK cells were isolated by FACS as CD3- CD16- CD56Bright CD9+ KIR+ idNK or  CD3- CD16+ CD56Dim CD9+ KIR+ idNK.

value: donor gender unknown


title: CD56Bright CD16- pNK Donnor B

description: Human CD56Bright CD16- pNK Donnor B

source_name: Human CD56Bright CD16- pNK Donnor B


title: Donor#3 LPC(16:0)

description: treated with 10 µM LPC(16:0) for 24h

label_protocol: standard protocol by the Microarray Genechip Facility Tübingen Service.


title: CD56Dim CD16+ CD9+ KIR+ i-dNK Donnor 25

description: Human CD56Dim CD16+  CD9+ KIR+ i-dNK Donnor 25


title: Donor#3 LPC(18:1)

description: treated with 10 µM LPC(18:1) for 24h


title: Donor#4 LPC(18:1)

description: treated with 10 µM LPC(18:1) for 24h


title: Donor#2 LPC(16:0)

description: treated with 10 µM LPC(16:0) for 24h

source_name: human primary myotubes from donor #2

value: donor #2


description: Human CD56Bright CD16- CD9+ KIR+ i-dNK Donnor 86


title: dNK 5-6wks

description: Human dNK 5-6wks

source_name: Human dNK 5-6wks

value: female donor


title: Donor#2 con

description: treated with solvent for 24h


title: CD56Bright CD16- pNK Donnor C

description: Human CD56Bright CD16- pNK Donnor C

source_name: Human CD56Bright CD16- pNK Donnor C


title: Donor#1 LPC(16:0)

description: treated with 10 µM LPC(16:0) for 24h

source_name: human primary myotubes from donor #1

value: donor #1


title: CD56Dim CD16+ pNK Donnor B

description: Human CD56Dim CD16+ pNK Donnor B

source_name: Human CD56Dim CD16+ pNK Donnor B


title: Donor#4 con

description: treated with solvent for 24h


title: dNK 4-5wks

description: Human dNK 4-5wks

source_name: Human dNK 4-5wks


title: CD56Bright CD16- pNK Donnor D

description: Human CD56Bright CD16- pNK Donnor D

source_name: Human CD56Bright CD16- pNK Donnor D


description: Human CD56Bright CD16-  CD9+ KIR+ i-dNK Donnor 96


title: Donor#1 con

description: treated with solvent for 24h


title: CD56Dim CD16+ CD9+ KIR+ i-dNK Donnor 86

description: Human CD56Dim CD16+  CD9+ KIR+ i-dNK Donnor 86


title: dNK 10 wks

description: Human dNK 10 wks

source_name: Human dNK 10 wks


title: CD56Dim CD16+ pNK Donnor C

description: Human CD56Dim CD16+ pNK Donnor C

source_name: Human CD56Dim CD16+ pNK Donnor C


title: Donor#1 LPC(18:1)

description: treated with 10 µM LPC(18:1) for 24h


title: CD56Dim CD16+ pNK Donnor D

description: Human CD56Dim CD16+ pNK Donnor D

source_name: Human CD56Dim CD16+ pNK Donnor D


title: VCAM1 shRNA-knocked down oligodendrocyte precursor cells_3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

source_name: oligodendrocyte precursor cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Oligodendrocyte precursor cells were islated from rat brains of embryonic day 15 and cultured in modified Raff medium.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: Oligodendrocyte precursor cells were treated with VCAM1 or luciferase shRNA for 20 hours.

value: brain

value: oligodendrocyte precursor

tag: knockdown

tag: developmental stage

value: embryonic day 15


title: Luciferase shRNA-knocked down oligodendrocyte precursor cells_3

tag: cell type

value: Luciferase


title: BAB3597_Illu

description:
family2-mother
526415

data_processing: The standard manufacture's recommended protocol was used. SNP genotype calls.

label: cy3 and cy5


title: BAB3598_Illu

description:
family2-father
526416

label_protocol: The standard manufacture's recommended protocol was used.


title: BAB3596_Illu

description:
family2-proband
526414


title: CD56Dim CD16+ CD9+ KIR+ i-dNK Donnor 97

description: Human CD56Dim CD16+  CD9+ KIR+ i-dNK Donnor 97


title: VCAM1 shRNA-knocked down oligodendrocyte precursor cells_2


title: Luciferase shRNA-knocked down oligodendrocyte precursor cells_2


title: Luciferase shRNA-knocked down oligodendrocyte precursor cells_1


title: VCAM1 shRNA-knocked down oligodendrocyte precursor cells_1


title: BAB3099_Illu


title: BAB3098_Illu


title: Donor#2 LPC(18:1)

description: treated with 10 µM LPC(18:1) for 24h


title: BAB3097_Illu


title: shMBNL1_9hr_rep2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

hyb_protocol: According to manufacturer's protocol

scan_protocol: According to manufacturer's protocol

data_processing:
Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybrydization signal. Normalized values are quantile-normalized. Final processed values are logFC of average stability measurements in shMBNL1 relative to shControl. The stability measurements are calculated as the 9 hr to 0 hr processed signal ratio.

source_name: MDA-MB-231 cells, shMBNL1, 9 hour amanitin

label_protocol: Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

growth_protocol: MDA-MB-231 cells were maintained at 37 degrees C, 5% CO2 and grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 1mM sodium pyruvate, 100 units/mL penicillin, 100 ug/mL streptomycin and 1ug/mL amphotericin B.

extract_protocol: RNA was extracted with a spin-column based total RNA isolation kit (Norgen Biotek) including on-column DNase I treatment according to the manufacturer's protocol.

treatment_protocol: Alpha-amanitin was added to cells in complete growth media to a final concentration of 10ug/mL. RNA was isolated from cells 0 and 9 hours post-alpha-amanitin treatment.

tag: Sex

value: female

tag: cell line

value: breast cancer


title: mCNV7-father_AgilentHD

description: human-human array CGH

value: M


title: mCNV3_CytoScan

data_processing: The standard manufacture's recommended protocol was used.


title: C replicate 3

city: Amsterdam

first: Jessica

last: Legradi

address: De Boelelaan 1087

department: IVM

country: Netherlands

institute: VU Amsterdam

description: Biological replicate 3 of 3

hyb_protocol: Hybridization protocol The hybridistaion of labelled probes was performed following Agilent Microarray hybridization Kit.

scan_protocol: Samples were scanned on Axon 4000B scanner and the images analysed used GenePix Pro 6.1

data_processing: The data was analysed using Matlab R2009b, data is background substracted, log2-values calculated and LOWESS-and centering normalized was performed. Dye-swaps were combined. Samples were labelled with Cy5 exposed, Cy3 control. Reverse is true for _swap.gpr raw data files.

label: Cy3, Cy5

organism: Danio rerio

source_name: zebrafish embryo 48 hpf

label_protocol: 2 μg of total RNA from each sample (exposure and control embryos) was labelled with Cy3 and Cy5-CTP according to Agilent Low RNA Input Linear Amplifaction Kit

growth_protocol: Adult fish were maintained in fish water at 28.5 °C, subjected to a photoperiod of 10 hours light and 14 hours dark, and fed with dry flake food and brine shrimp. Embryos were kept in embryo medium.

extract_protocol: Total RNA extraction following Rneasy Mini-Kit (Qiagen)

treatment_protocol: 24 hpf embryos were exposed for 24 hours with 7mg/L Chlorpyrifos and embryos were maintained in fish medium at 28.5°C as control

value: whole embryos

value: treatment:fish medium (control)

value: treatment:fish Chlorpyrifos (exposure)


title: mCNV7-mother_AgilentHD

description: human-human array CGH

value: F


title: shCTRL_9hr_rep2

source_name: MDA-MB-231 cells, shCTRL, 9 hour amanitin


title: C replicate 2

description: Biological replicate 2 of 3


title: mCNV4_CytoScan


title: mCNV7_CytoScan


title: shMBNL1_9hr_rep1


title: shCTRL_9hr_rep1


title: mCNV4-father_AgilentHD

description: human-human array CGH


title: mCNV4_AgilentHD

description: human-human array CGH


title: mCNV7_AgilentHD

description: human-human array CGH


title: shMBNL1_0hr_rep2

source_name: MDA-MB-231 cells, shMBNL1, 0 hour amanitin


title: A replicate 3

description: Biological replicate 3 of 3

treatment_protocol: 24 hpf embryos were exposed for 24 hours with 71.9 mg/L Aroclor 1254 and embryos were meintained in fish medium at 28.5°C as control

value: treatment:fish Aroclor 1254 (exposure)


title: A replicate 2

description: Biological replicate 2 of 3


title: shMBNL1_0hr_rep1


title: shCTRL_0hr_rep2

source_name: MDA-MB-231 cells, shCTRL, 0 hour amanitin


title: A replicate 1

description: Biological replicate 1 of 3


title: KT2440_light

status: Public on Oct 13 2016

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 50°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to a modified version of the FleX450-0005 protocol of the GeneChip Fluidics station 450 (Affymetrix)

scan_protocol: Signals were detected using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas putida

source_name: cDNA prepared from light culture of KT2440 in stationary phase

label_protocol: Labelling of the cDNA or DNA was achieved using a GeneChip WT Double-Stranded DNATerminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: P. putida KT2440 strain was grown in LB at 28°C at 135 strokes/min for 24 hrs under dark and light conditions.

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany) and RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI). After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel). cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA).

tag: strain

tag: culture condition

value: light

tag: growth phase

value: stationary phase


title: KT2440_dark

source_name: cDNA prepared from dark culture of KT2440 in stationary phase

value: dark


title: mCNV3_AgilentHD

description: human-human array CGH


title: BAB3097_AgilentHD

description: human-human array CGH


title: BAB3097_CytoScan


title: BAB3099_AgilentHD

description: human-human array CGH


title: BAB3597_AgilentHD

description: human-human array CGH


title: BAB3598_AgilentHD

description: human-human array CGH


title: BAB3098_AgilentHD

description: human-human array CGH


title: C replicate 1

description: Biological replicate 1 of 3

tag: tissue


title: BAB3596_AgilentHD

description: human-human array CGH


title: C9_H051

city: Palo Alto

first: Wen-Jun

last: Shen

address: 3801 Miranda Avenue

institute: Stanford University

hyb_protocol: The pre-hybridization of Rat OneArray® v1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in dulication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4200AL scanner (635nm power 100; PMT340 ) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: NDGA (Liver)

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA samples for the whole genome microarray (Rat OneArray® v1) were isolated from the liver, white adipose tissue (epididymal) and skeletal muscle (gastrocnemius) using Qiagen RNeasy Plus Mini Kit (Valencia, CA). The RNA analysis, including integrity and quantitation of RNA, was carried out using an Agilent RNA 6000 Nano Kit and an Agilent Bioanalyzer System (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Male Sprague-Dawley (SD) rats, obtained from Harlan Sprague-Dawley (Indianapolis, IN), were used in these studies. For dietary treatment of rats with NDGA, groups of SD rats were fed a standard chow diet for 1 week to acclimatize them to a new environment as described above. Subsequently, one group of rats switched to HFrD supplemented with 2.5 g NDGA/g HFrD and was maintained on this diet for 16 weeks. The second group of SD rats was maintained on HFrD alone for 16 weeks, while a third group of rats  continued to be fed a chow diet for 16 weeks.

value: Sprague-Dawley

value: male

tag: diet

value: HF-NDGA

value: Liver


title: T8_H048

source_name: HF-INS (Liver)

value: HF-INS


title: T9_H052

source_name: NDGA-INS (Liver)

value: HF-NDGA-INS


title: T8_H047


title: ED78

city: Cincinnati

first: Shiyu

last: Luo

state: OH

address: 3333 Burnet Ave

institute: CCHMC

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on the Illumina Hyb chamber Rack system.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a HiScan system (Illumina).

data_processing: Genomic DNA extracted from ESC line was genotyped using the Infinium Assay with the Illumina CytoSNP-850Kv1.1 BeadChip platform.

label: C-Bio and A-DNP

source_name: ESC-derived line

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using Multi-Sample amplification 1 mix (MA1), Multi-Sample amplification master mix (MA2) and Random Primer Mix (MSM). After incubation the amplified DNA was fragmented with fragmentation solution (FMS), precipitated with Precipitation solution (PM1) and resuspended in Resuspension, hybridization, and wash solution (RA1).

growth_protocol: ST blastocysts were freed from their zonae pellucidae and plated on mEF feeder layers on 4-well culture dishes for 5-7 days at 37°C, 3% CO2, 5% O2, and 92% N2 in medium (DMEM/F12 with 10% FBS, 10% KSR, 0.1 mM nonessential amino acids, 1 mM l-glutamine, 0.1 mM β-mercaptoethanol, 5 ng/ml basic fibroblast growth factor, 10μM ROCK inhibitor) as previously described8. Attached blastocyst outgrowths were manually minced into small pieces, re-plated onto fresh plates and maintained in knockout DMEM medium (Invitrogen) supplemented with 20% KSR, 0.1 mM nonessential amino acids, 1 mM l-glutamine, 0.1 mM β-mercaptoethanol, penicillin-streptomycin and 4 ng/ml  bFGF for further propagation and analysis.

extract_protocol: Extraction of genomic DNA from ESC lines was performed using Qiagen Puregene DNA isolation kit.

value: Female


title: MCF7_ADR

city: Daegu

first: Sarala

last: Manandhar

address: 80 Daehakro, Bukgu

department: College of Pharmacy

country: South Korea

institute: Kyungpook National University

description: Gene expression data

hyb_protocol: Fragmented cRNAs (12.5 μg) were hybridized at 45 °C for 16 h to a Human Gene ST array (HuGene-1-0-ST-v1; Affymetrix, Santa Clara, CA, USA).

scan_protocol: The hybridized probe array is stained with streptavidin phycoerythrin conjugate and scanned by the GeneChip® Scanner 3000

data_processing: Data were generated with GenPlex version 3.0 software (ISTECH, Korea).

source_name: Breast cancer cell line (MCF7) exposure to  increasing concentration of doxorubicin

label_protocol: Double-stranded cDNA is synthesized from total RNA or purified poly-A messenger RNA isolated from cells. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA.

growth_protocol: MCF7 and MCF7_ADR  breast cancer cells were grown in DMEM media 10% FBS and 1% penicillin/streptomycin at 37 °C  degree temperature  incubator with 5% CO2

extract_protocol: Total RNAs were isolated from MCF7 and MCF7-ADR cells using the Totally RNA kit (Ambion, Austin, TX, USA). Isolated total RNAs were purified using the RNeasy Mini kit (Qiagen, Valencia, CA, USA). RNA was quantified using NanoDrop spectrophotometer and quality monitor Agilent’s 2100 Bioanalyzer System (Agilent technologies, Santa clara, CA)

treatment_protocol: MCF7_ADR cells were developed with continuous exposure to  increasing concentration of doxorubicin upto 1 mM from MCF7 cell

value: Breast cancer cell line

tag: phenotype

value: Doxorubicin resistant


title: C9_H050


title: T9_H053


title: BAB3596_CytoScan

value: M


title: C8_H045

source_name: HF (Liver)

value: HF


title: mCNV4-mother_AgilentHD

description: human-human array CGH


title: T8_H046


title: C8_H043


title: C7_H039

source_name: CHOW (Liver)

value: CHOW


title: C7_H038


title: T7_H041

source_name: CHOW-INS (Liver)

value: CHOW-INS


title: C7_H037


title: T9_H054


title: T7_H042


title: hESO-13


title: T6_H036

source_name: NDGA-INS (GC Muscle)

value: GC Muscle


title: C6_H033

source_name: NDGA (GC Muscle)


title: C6_H031


title: T6_H034


title: C9_H049


title: C6_H032


title: C8_H044


title: T5_H030

source_name: HF-INS (GC Muscle)


title: STP3

value: Male


title: shCTRL_0hr_rep1

value: female

value: breast cancer


title: ED101


title: hESO-ST8


title: MCF7

description: Gene expression data

source_name: Breast cancer cell line

value: Doxorubicin sensitive


title: Common sperm

description: Common sperm


title: hESO-ST15


title: hESO-ST13


title: T6_H035

value: Sprague-Dawley

value: male


title: C5_H027

source_name: HF (GC Muscle)


title: hESO-ST10


title: C5_H026


title: C5_H025


title: T4_H024

source_name: CHOW-INS (GC Muscle)


title: T5_H029


title: hESO-12


title: ED81


title: T5_H028


title: T4_H022


title: T4_H023


title: T7_H040

value: Liver


title: T3_H017

source_name: NDGA-INS (Adipose tissue)

value: Adipose Tissue


title: T3_H016

value: HF-NDGA-INS


title: T3_H018


title: LN1-1

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalization.

source_name: Human oral squamous cell carcinoma cell line

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

growth_protocol: Cells were cultured in RPMI medium with 10% FBS at 37°C in an incubator containing 5% CO2.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

tag: generation

value: Subline by in vivo selection

value: oral squamous cell carcinoma

tag: host

value: mouse


title: C3_H013

source_name: NDGA (Adipose tissue)

value: HF-NDGA


title: STP2

value: Female


title: C4_H019

source_name: CHOW (GC Muscle)

value: CHOW


title: C4_H021


title: C3_H015


title: T2_H012

source_name: HF-INS (Adipose tissue)

value: HF-INS


title: T2_H011


title: C3_H014


title: C2_H009

source_name: HF (Adipose tissue)

value: HF


title: T2_H010


title: LN1-2


title: OEC-M1

value: Parental cells


title: C2_H008


title: C2_H007


title: C1_H003

source_name: CHOW (Adipose tissue)


title: T1_H006

source_name: CHOW-INS (Adipose tissue)

value: CHOW-INS


title: T1_H004


title: T1_H005


title: C1_H001


title: C4_H020

value: GC Muscle


title: C1_H002


title: High WBC BP-ALL ETV6-RUNX1 B10320

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

hyb_protocol: Agilent Human Gene Expression V.2 8X60 microarrays were hybridized using 600ng of Alexa 555 labeled aRNA.  Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 h at 65 °C. After hybridization, the slides were washed with Agilent GE wash buffers following Agilent’s protocol

scan_protocol: Slides were scanned using an Agilent dual laser scanner with extended dynamic range (XDR) at 5 micron resolution.

data_processing: Tiff images were analyzed with Agilent's feature extraction software (v11.0.1.1) using protocol GE1_1100_Jul11. Data were analyzed in GeneSpring v12. Data on each microarray were normalized using a 75th percentile shift.

source_name: Diagnostic bone marrow from B10320_High WBC

label_protocol: Alexa555 labeled aRNA was prepared from 100ng of total RNA using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, Madison, WI) and Agilent Spike-in Controls

growth_protocol: Mononuclear cells were purified by standard Ficoll-Hypaque density centrifugation, suspended in 90% fetal bovine serum and 10% DMSO, then stored in liquid nitrogen (vapor phase) until further processing.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). The quality of the extracted total RNAs were determined on an Agilent Bioanalyzer.

value: bone marrow

value: mononuclear cells

tag: age

value: F

tag: wbc (/cumm)


title: High WBC BP-ALL ETV6-RUNX1 B10321

source_name: Diagnostic bone marrow from B10321_High WBC

value: M


title: Low WBC BP-ALL ETV6-RUNX1 B10310

source_name: Diagnostic bone marrow from B10310_Low WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10315

source_name: Diagnostic bone marrow from B10315_Low WBC


title: High WBC BP-ALL ETV6-RUNX1  B10319

source_name: Diagnostic bone marrow from B10319_High WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10313

source_name: Diagnostic bone marrow from B10313_Low WBC


title: testisRNA_MC-LR_30d_rep3

city: Nanjing

first: Ling

last: Zhang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

description: piRNA expression data from mouse testis

hyb_protocol: The labeled samples were hybridized onto Arraystar Mouse piRNA Array in Agilent’s SureHyb Hybridization Chambers according to the manufacturer’s standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). Normalized signal for control probes are not available in the sample table but are available in the file 'Normalized_data_with_controls.txt' on the series record.

source_name: testisRNA, MC-LR, 30d, replicate 3

label_protocol:
Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1.Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2.Add 350 μL of Buffer RLT and mix well by pipetting.  3.Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4.Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5.Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6.Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7.Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8.Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9. Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).  From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.  Blank the instrument with 1.5 μL of 1x labeling solution.  Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).  The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:

Specific Activity = (Concentration of Cy3)/(Concentration of cRNA)*1000 = pmol Cy3 per μg cRNA

* If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: Pregnant mice were randomly divided into 2 groups: control group and MC-LR group, with each mouse kept separately. From gestation day 12 to postnatal day 21, 2 groups of pregnant mice were exposed to 0 and 10 μg/L of MC-LR through drinking water. The male offspring were breastfed after natural birth. 30 days after birth, the organs were promptly frozen in liquid nitrogen until further analysis.empty-2T, empty-4T, empty-5T were the three samples from 3 offsprings of different pregnant mice in control group. 10-3T, 10-4T, 10-7T were the three samples from 3 offsprings of different pregnant mice in MC-LR group.

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

treatment_protocol: Testes were manually selected under the dissecting scope, and promptly frozen in liquid nitrogen.

value: testis

tag: gender

value: male

tag: age (days)


title: testisRNA_MC-LR_30d_rep2

description: piRNA expression data from mouse testis

source_name: testisRNA, MC-LR, 30d, replicate 2


title: Low WBC BP-ALL ETV6-RUNX1 B10316

source_name: Diagnostic bone marrow from B10316_Low WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10311

source_name: Diagnostic bone marrow from B10311_Low WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10308

source_name: Diagnostic bone marrow from B10308_Low WBC


title: testisRNA_control_30d_rep3

description: piRNA expression data from mouse testis

source_name: testisRNA, control, 30d, replicate 3


title: Low WBC BP-ALL ETV6-RUNX1 B10309

source_name: Diagnostic bone marrow from B10309_Low WBC


title: High WBC BP-ALL ETV6-RUNX1  B10318

source_name: Diagnostic bone marrow from B10318_High WBC


title: High WBC BP-ALL ETV6-RUNX1  B10317

source_name: Diagnostic bone marrow from B10317_High WBC


title: testisRNA_MC-LR_30d_rep1

description: piRNA expression data from mouse testis

source_name: testisRNA, MC-LR, 30d, replicate 1


title: testisRNA_control_30d_rep1

description: piRNA expression data from mouse testis

source_name: testisRNA, control, 30d, replicate 1


title: testisRNA_control_30d_rep2

description: piRNA expression data from mouse testis

source_name: testisRNA, control, 30d, replicate 2


title: Low WBC BP-ALL ETV6-RUNX1 B10312

source_name: Diagnostic bone marrow from B10312_Low WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10307

source_name: Diagnostic bone marrow from B10307_Low WBC


title: Low WBC BP-ALL ETV6-RUNX1 B10314

source_name: Diagnostic bone marrow from B10314_Low WBC


title: n-6 colitic group-Replicate2

status: Public on Oct 12 2016

city: Mysore

first: Vijay kumar Reddy

last: Kondreddy

state: None Selected

address: Lab-115, B&N department, CFTRI, Mysore, India

department: Biochemistry

institute: CSIR-Central Food Tehnological research institute

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
S_Br2
Colon tissue of healthy Wistar rat

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to Agilent Custom Rat GXP 8X60K Array designed by Genotypic Technology Private Limited. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G25600D).

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX : 75th percentile shift method and gene based analysis was performed

source_name: n-6 colitic group

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Adult Wistar rats (n=36) were divided into four groups namely control (n=6), α-linolenic acid group (ALA) (n=10), fish oil group (n=10) and n-6 polyunsaturated group (n=10). The rats of the above groups were fed diet enriched with sunflower oil, ALA, fish oil or sunflower oil respectively, for 8 weeks

extract_protocol: RNA was extracted using the Trizol method following the manufacturer's recommendations.

treatment_protocol: Colitis was induced in rats with 5%dextran sulfate sodium (DSS) for 7 days.The rats were dissected and RNA was isolated from the colon tissues of rats, the samples from 6 rats were pooled and used for the microarray experiments. Global gene expression analysis was done in duplicates in each group and the results were compared to n-6 fatty acid group. α-linolenic acid (ALA) and fish oil rich in eicosapentaenoic acid and docosahexaenoic acid significantly attenuated the symptoms of colitis, compared to n-6 fatty acid group. Gene expression analysis has revealed that there is no common gene signature in the two groups.

value: Wistar

value: Colon

value: 14 weeks

tag: stress

value: Colitis induced using 5% dextran sulfate sodium for 7 days


title: fish oil colitic group-Replicate1

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
F_Br1
Colon tissue of healthy Wistar rat

source_name: fish oil colitic group

value: Female

value: fish oil


title: Control (healthy group)-Replicate2

description:
Gene expression in a healthy rat without dextran sulfate sodium treatment
C_Br2
Colon tissue of healthy Wistar rat

source_name: Control (healthy group)

value: control


title: fish oil colitic group-Replicate2

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
F_Br2
Colon tissue of healthy Wistar rat


title: n-6 colitic group-Replicate1

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
S_Br1
Colon tissue of healthy Wistar rat


title: α-linolenic acid colitic group-Replicate2

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
G_Br2
Colon tissue of healthy Wistar rat

source_name: α-linolenic acid colitic group

value: α-linolenic acid


title: α-linolenic acid colitic group-Replicate1

description:
Gene expression in rats after 5% dextran sulfate sodium treatment for 7 days
G_Br1
Colon tissue of healthy Wistar rat


title: Control (healthy group)-Replicate1

description:
Gene expression in a healthy rat without dextran sulfate sodium treatment
C_Br1
Colon tissue of healthy Wistar rat


title: brain stem  control/experimental replicate 4

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

address: 9500 S Euclid Ave

department: Genomics Core

institute: Cleveland Clinic Foundation

hyb_protocol: Samples representing individual brain parts were labeled using either Cy3 or Cy5 dyes and competitively hybridized to the arrays. We used a balanced design in the microarray experiment and controlled for dye effect by performing dye swaps. For hybridization, 900 ng cRNA of samples from control and experimental groups labeled with different dyes were mixed, fragmented and hybridized onto an Agilent 4×44K oligonucleotide microarray

scan_protocol: The microarray slides were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) and expression feature were extracted using GenePix Pro 6.0 software (Molecular Devices)

data_processing:
As preprocessing methods of gene expression intensities, we used within array loess normalization without background correction. For the between array normalization, we used the Aquantile method.
To identify the genes differentially expressed in the four brain regions of fish that had been exposed to an intruder and those that did not, we used the Rank Product [PMID: 15327980] analysis as implemented in R BioConductor.

organism: Gasterosteus aculeatus

source_name: control_brain stem_cy5

label_protocol: The samples were labeled using the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) following the manufacturer’s instructions.

growth_protocol: The fish were maintained in our laboratory in 104L tanks under 8:16h light/dark photoperiod during the winter period. An average of 10% of the water in the tanks was recycled each day. The adult fish were fed ad libitum with a mixture of bloodworms, serpula and mysis

extract_protocol: Each fish brain parts were individually dissected and placed immediately on ice in 500ml of TRIzol® Reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated immediately from individual brains using TRIzol® Reagent according to the manufacturer’s recommendation followed by on column purification with RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: Fish in the control and experimental groups were paired and matched by size and presented a gravid female confined in a flask in their tank.  The interaction between the residentmale and the female was video-recorded for 15 minutes and the videos were later scored for courtship behavior.

tag: origin

value: Navarro river, CA, USA

value: adult

tag: sample group

value: brain stem

source_name: experimental_brain stem_cy3

value: presented a female on their territory


title: brain stem  control/experimental replicate 5

tag: Sex


title: brain stem  control/experimental replicate 2

source_name: control_brain stem_cy3

source_name: experimental_brain stem_cy5


title: cerebellum control/experimental replicate 3

value: cerebellum


title: cerebellum control/experimental replicate 6


title: cerebellum control/experimental replicate 2


title: brain stem  control/experimental replicate 1


title: cerebellum control/experimental replicate 1


title: cerebellum control/experimental replicate 4


title: brain stem  control/experimental replicate 6


title: diencephalon control/experimental replicate 5

value: diencephalon


title: diencephalon control/experimental replicate 2


title: cerebellum control/experimental replicate 5


title: brain stem  control/experimental replicate 3


title: diencephalon control/experimental replicate 6


title: telencephalon control/experiemntal replicate 6

value: telencephalon


title: diencephalon control/experimental replicate 1


title: telencephalon control/experiemntal replicate 5


title: diencephalon control/experimental replicate 4


title: telencephalon control/experiemntal replicate 4


title: telencephalon control/experiemntal replicate 3


title: diencephalon control/experimental replicate 3


title: telencephalon control/experiemntal replicate 1


title: telencephalon control/experiemntal replicate 2


title: E2 treated T47D cells, biological rep1

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Gene expression data after E2 stimulation

hyb_protocol: Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.  The sample data tables do not contain data for the Affymetrix and ERCC controls. The supplementary file Normalized_data_with_controls.txt contains all normalized data including the controls and is available on the series record.

source_name: T47D breast cancer cell line_E2-treated

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

growth_protocol: Cells were maintained in 10% FBS containing media.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were cultured in steroid depleted media for 48 h and treated with ethnaol or 10 nM 17β-estradiol for 6 h.

tag: cell line

tag: cell type

value: breast cancer


title: vehicle treated T47D cells, biological rep1

description: Gene expression data using ethanol as vehicle control

source_name: T47D breast cancer cell line_vehicle-treated


title: vehicle treated T47D cells, biological rep3


title: E2 treated T47D cells, biological rep3


title: TB_UEXP_ScarNo_week6_3145

first: Ali

last: Filali

address: 10900  Euclid Avenue

department: Pathology

institute: CWRU

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to IlluminaHumanHT-12_V4  BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and various software packages from Bioconductor.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: Whole blood

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Gene expression microarrays were undertaken using unstimulated whole blood samples obtained from 42 and 51 infants at one and six weeks, respectively

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

tag: samplename

value: Whole blood

tag: sampletype

value: Latent tuberculosis (TB) Unexposed

tag: scar

value: No

value: M

tag: worm infection

tag: donor

tag: timepoint

tag: timepointunit

value: week


title: vehicle treated T47D cells, biological rep2


title: TB_UEXP_ScarYes_week6_3144

treatment_protocol: Gene expression microarrays were undertaken using unstimulated whole blood samples obtained from 42 and 51 infants at one and six weeks, respectively

tag: tissue

value: Yes


title: TB_UEXP_ScarNo_week6_3133

value: F


title: TB_UEXP_ScarNo_week6_3122


title: TB_UEXP_ScarYes_week6_3114


title: TB_EXP_ScarYes_week6_3130

value: Latent tuberculosis (TB) Exposed


title: TB_UEXP_ScarYes_week6_3107


title: TB_UEXP_ScarNo_week6_3118


title: TB_UEXP_ScarYes_week6_3124

value: Hookworm


title: TB_UEXP_ScarYes_week6_3105


title: TB_UEXP_ScarMissing_week6_3132


title: TB_EXP_ScarYes_week6_3134


title: TB_UEXP_ScarYes_week6_3110


title: TB_UEXP_ScarYes_week6_3143

value: Trichuris


title: TB_EXP_ScarYes_week6_3088


title: TB_UEXP_ScarYes_week6_3106


title: TB_UEXP_ScarNo_week6_3142


title: TB_UEXP_ScarYes_week6_3103


title: TB_EXP_ScarYes_week6_3113


title: TB_UEXP_ScarYes_week6_3094


title: TB_UEXP_ScarYes_week6_3121


title: TB_EXP_ScarYes_week6_3064


title: TB_EXP_ScarNo_week6_3104


title: TB_EXP_ScarMissing_week6_3086


title: TB_EXP_ScarNo_week6_3063


title: NB-12hr, Ductus, 4.txt

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: One µg of purified cRNA was fragmented to uniform size and applied to Agilent Sheep Gene Expression Microarray, 8 x 15K (Design ID 019921, Agilent Technologies) in hybridization buffer. The arrays were hybridized at 65° C for 17 hours in a shaking incubator and washed at 37° C for 1 min. Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies).  Annotations are based on the Agilent eArray annotation file dated January 2010 and manual annotation by blasting the probe sequence against NCBI database.

organism: Ovis aries

source_name: New born lamb Ductus - 12 hours after birth

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

extract_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, <1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  Following second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the labeled cRNA was assayed by spectrophotometry and Agilent Bioanalyzer.

treatment_protocol: In previous studies, we have described this technique in detail 2-4. Microarray analysis was conducted by utilizing the commercial services of GenUs Biosystems (Northbrook, Illinois). Briefly, DA and aorta segments (adjacent to DA) were homogenized and lysed in Trizol (Ambion, Austin, TX) and total RNA was isolated using phenol/chloroform extraction followed by purification over spin columns (Ambion). Total RNA concentration and purity of total RNA were measured by spectrophotometry at OD260/280 and the quality of the total RNA sample was assessed using an Agilent Bioanalyzer with RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

value: Ductus Arteriosus

tag: age

value: New Born - 12 hours old


title: TB_UEXP_ScarNo_week6_3072

tag: gender


title: TB_UEXP_ScarMissing_week6_3073


title: NB-12hr, Ductus, 3.txt


title: TB_UEXP_ScarYes_week6_3095


title: TB_EXP_ScarMissing_week6_3092


title: NB-12hr, Ductus, 2.txt


title: TB_UEXP_ScarNo_week6_3045


title: TB_UEXP_ScarNo_week6_3047


title: TB_UEXP_ScarYes_week6_3057


title: TB_UEXP_ScarYes_week6_3089


title: TB_UEXP_ScarYes_week6_3077


title: TB_UEXP_ScarYes_week6_3051


title: TB_UEXP_ScarNo_week6_3065


title: TB_EXP_ScarNo_week6_3035


title: NB-12hr, Aorta, 3.txt

source_name: New born lamb aorta - 12 hours after birth

value: Ascending Aorta


title: TB_UEXP_ScarYes_week6_3081


title: TB_UEXP_ScarYes_week6_3087


title: TB_UEXP_ScarYes_week6_3082


title: TB_EXP_ScarYes_week6_3052


title: TB_EXP_ScarNo_week6_3040


title: TB_UEXP_ScarNo_week6_3062


title: NB-12hr, Ductus, 1.txt


title: TB_EXP_ScarYes_week6_3074


title: Fetal Ductus, 140d, 4.txt

source_name: Fetal Sheep Ductus - 136 days gestational age

value: Fetus - 136 days old


title: NB-12hr, Aorta, 2.txt


title: Fetal Ductus, 140d, 1.txt


title: TB_UEXP_ScarYes_week6_3033


title: Fetal Ductus, 140d, 3.txt


title: Fetal Ductus, 140d, 2.txt


title: Fetal Ductus, 100d, 1.txt

source_name: Fetal Sheep Ductus - 97 days gestational age

value: Fetus - 97 days old


title: Fetal Ductus, 100d, 4.txt


title: Fetal Aorta, 140d, 4.txt

source_name: Fetal Sheep Aorta - 136 days gestational age


title: Fetal Ductus, 100d, 3.txt


title: NB-12hr, Aorta, 1.txt


title: TB_UEXP_ScarNo_week6_3021


title: Fetal Ductus, 100d, 2.txt


title: TB_UEXP_ScarYes_week6_3030


title: TB_UEXP_ScarMissing_week6_3028


title: Fetal Aorta, 140d, 2.txt


title: TB_EXP_ScarYes_week6_3017


title: Fetal Aorta, 140d, 3.txt


title: TB_UEXP_ScarYes_week6_3018


title: TB_UEXP_ScarNo_week6_3032


title: TB_UEXP_ScarNo_week6_3012


title: TB_UEXP_ScarYes_week6_3009


title: Daughter of Patient 1

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description: germline alterations

hyb_protocol: Performed following CytoScan Assay User Manual (P/N 703038 Ver.4)

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

data_processing:
The data were analyzed with the standard parameters of Chromosome Analysis Suite (ChAS) v3.1 software (Affymetrix)
ChAS v3.1 software results

source_name: Blood

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from peripheral blood of patients, mother of Patient 2 and four children and from breast tumor tissue (Patient 2) using the standard protocol of Gentra Puregene Blood Kit (Qiagen, Valencia, Ca, USA)

treatment_protocol: Not applicable

value: female


title: Fetal Aorta, 140d, 1.txt


title: TB_UEXP_ScarYes_week6_3010


title: TB_UEXP_ScarMissing_week6_3031


title: TB_EXP_ScarYes_week6_3003


title: NB-12hr, Aorta, 4.txt


title: TB_EXP_ScarNo_week6_3007


title: Fetal Aorta, 100d, 4.txt

source_name: Fetal Sheep Aorta - 97 days gestational age


title: Fetal Aorta, 100d, 1.txt


title: Fetal Aorta, 100d, 3.txt


title: TB_UEXP_ScarYes_week1_3107


title: Fetal Aorta, 100d, 2.txt


title: TB_UEXP_ScarMissing_week1_3132


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep3

city: yufu city

first: yoko

last: aoyagi

address: 1-1 Idaigaoka hamasamachi

institute: oita university

description: mRNA expression after 12d_dibutyryl-cAMP and dienogest

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

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

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

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate3

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: NESCs were obtained from premenopausal patients who had undergone hysterectomies for leiomyoma and had no evidence of endometriosis. NESCs were isolated from the corresponding tissues by enzymatic digestion. NESCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.

value: proliferative phase normal endometrium

value: Female

tag: treatment

value: 12d dibutyryl-cAMP and dienogest


title: TB_UEXP_ScarYes_week1_3143

value: Whole blood

value: Latent tuberculosis (TB) Unexposed


title: TB_UEXP_ScarNo_week1_3145

value: No

value: M

value: week


title: TB_EXP_ScarNo_week1_3117

value: Latent tuberculosis (TB) Exposed


title: TB_EXP_ScarYes_week1_3130

value: Yes

value: F


title: TB_UEXP_ScarYes_week1_3128


title: TB_EXP_ScarNo_week1_3104


title: TB_UEXP_ScarNo_week1_3142


title: TB_UEXP_ScarNo_week1_3133


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep2

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate2


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep1

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate1


title: TB_EXP_ScarNo_week1_3112


title: ABS-116

city: Winston Salem

first: Stephen

last: Walker

address: Medical Center Blvd

institute: Wake Forest University Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Genome Studio

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted from biopsy tissues by sonicating in the presence of TriReagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy MinelutePlus mini kit in accordance with the prescribed protocol provided with the kit. RNA quality was assessed with Agilent Bioanalyzer. For RNA isolation from blood, we used a QIAcube robotic workstation with RNeasyPlus kits following the manufacturer's protocols. As before, RNA quality was assessed with Agilent Bioanalyzer.

tag: sample type

value: typically developing

tag: disease state

value: non-inflamed

value: male


title: ABS-117


title: NESCs_12d_rep1

description: mRNA expression after 12d_10% charcoal-stripped heat-inactivated FBS

source_name: Proliferative phase normal endometrium, 12 days, replicate1

value: 12d 10% charcoal-stripped heat-inactivated FBS


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep4

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate4


title: TB_EXP_ScarYes_week1_3113


title: TB_UEXP_ScarYes_week1_3110


title: TB_EXP_ScarYes_week1_3134


title: NESCs_12d_rep2

source_name: Proliferative phase normal endometrium, 12 days, replicate2


title: NESCs_12d_rep3

source_name: Proliferative phase normal endometrium, 12 days, replicate3


title: TB_EXP_ScarMissing_week1_3092


title: ABS-114


title: ABS-115


title: ABS-112


title: TB_EXP_ScarYes_week1_3088


title: TB_EXP_ScarYes_week1_3079


title: ABS-113


title: ABS-111


title: TB_EXP_ScarMissing_week1_3086


title: TB_UEXP_ScarYes_week1_3055


title: ABS-102

source_name: colon


title: TB_EXP_ScarNo_week1_3063

source_name: Whole blood


title: ABS-109


title: TB_UEXP_ScarYes_week1_3038


title: TB_UEXP_ScarNo_week1_3044


title: ABS-108


title: ABS-105


title: TB_UEXP_ScarNo_week1_3045


title: ABS-106


title: E2 treated T47D cells, biological rep2

source_name: T47D breast cancer cell line_E2-treated

value: breast cancer


title: ABS-110


title: ABS-103


title: TB_EXP_ScarNo_week1_3069


title: ABS-104


title: TB_EXP_ScarYes_week1_3052


title: TB_UEXP_ScarNo_week1_3043


title: TB_EXP_ScarYes_week1_3064


title: TB_UEXP_ScarNo_week1_3047


title: TB_UEXP_ScarYes_week1_3029


title: ABS-107

value: female


title: ABS-101


title: TB_UEXP_ScarYes_week1_3030


title: ABS-98


title: TB_EXP_ScarNo_week1_3040


title: ABS-100


title: NLC from CLL patient 19

city: Toulouse

first: Mary

last: Poupot

address: avenue Hubert Curien

country: France

institute: Inserm U1037

description: Gene expression data from human nurse like cells from blood sample of CLL patients

hyb_protocol: cRNA was fragmented and hybridized to Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: he chips were then washed and scanned, according to the manufacturer’s instructions.

data_processing: RMA normalized and log2 transformed data for 19 NLC samples were done using the Affymetrix genechip array software.

label: biotine

source_name: Nurse Like Cells from patient 19

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Whole PBMC from untreated CLL patients (at IUCT-O) were collected by Ficoll gradient, cultured in-vitro during 14 days in complete medium RPMI 1640 supplemented with 10% fetal calf serum. Adherent NLC were collected by scraping culture wells at day 14. Cells were washed twice by PBS and their phenotype was assessed by immunostaining and flow cytometry (CD163+CD68+ NLC >98% purity) prior to RNA extraction.

extract_protocol: Total RNA was extracted of about 1 million NLC using TRIzolTM reagent (Invitrogen), according to the manufacturer’s instructions.

value: blood sample

tag: race

value: caucasian

value: between 60 and 90 years


title: ABS-97

tag: Sex


title: TB_UEXP_ScarYes_week1_3039

value: Whole blood


title: ABS-96


title: ABS-99


title: ABS-95


title: NLC from CLL patient 18

source_name: Nurse Like Cells from patient 18


title: TB_UEXP_ScarMissing_week1_3028

value: Latent tuberculosis (TB) Unexposed


title: ABS-93


title: NLC from CLL patient 11

source_name: Nurse Like Cells from patient 11


title: ABS-94


title: NLC from CLL patient 14

source_name: Nurse Like Cells from patient 14


title: TB_EXP_ScarNo_week1_3035

value: No


title: ABS-91


title: ABS-92


title: NLC from CLL patient 17

source_name: Nurse Like Cells from patient 17


title: TB_UEXP_ScarNo_week1_3021


title: TB_UEXP_ScarNo_week1_3027


title: ABS-89


title: TB_UEXP_ScarYes_week1_3033

value: M


title: TB_UEXP_ScarNo_week1_3032

value: week


title: NLC from CLL patient 12

source_name: Nurse Like Cells from patient 12


title: NLC from CLL patient 13

source_name: Nurse Like Cells from patient 13


title: NLC from CLL patient 15

source_name: Nurse Like Cells from patient 15


title: NESCs_12d_rep4

source_name: Proliferative phase normal endometrium, 12 days, replicate4

value: proliferative phase normal endometrium

value: Female


title: NLC from CLL patient 10

source_name: Nurse Like Cells from patient 10


title: NLC from CLL patient 16

source_name: Nurse Like Cells from patient 16


title: TB_UEXP_ScarMissing_week1_3031

value: F


title: NLC from CLL patient 8

source_name: Nurse Like Cells from patient 8


title: air control 3

city: Boston

first: Elizabeth

last: Moses

state: Massachusetts

address: 72 E Concord St Rm E635

department: Computational Biomedicine

institute: Boston University

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven at 640 at 45 deg. C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: RMA normalization was conducted using custom CDF: hugene10st_Hs_ENTREZG.cdf [Brainarray Version 17]

source_name: RNA from ALI-differentiated HBECs

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Primary human bronchial epithelial cells were grown at Air Liquid Interface for 21 days.

extract_protocol: Total RNA from cell cultures was isolated using miRNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Cells were exposed to tobacco smoke, e-cig aerosol or air in a smoking machine from VitroCell (Waldkirch, Germany) and rested for 24 hours before RNA isolation.

value: bronchial epithelial cells

tag: puff rate

value: 1 puff/min.

tag: total puffs

value: 48 puffs

tag: flavor

tag: nicotine concentration


title: ABS-88

source_name: whole blood

value: typically developing

value: non-inflamed

value: male


title: ABS-90


title: air control 1

tag: cell type


title: NLC from CLL patient 9

source_name: Nurse Like Cells from patient 9

value: blood sample


title: TB_UEXP_ScarNo_week1_3026

source_name: Whole blood

tag: samplename

tag: sampletype

tag: scar

tag: worm infection


title: air control 2


title: NLC from CLL patient 7

source_name: Nurse Like Cells from patient 7

tag: tissue

value: caucasian


title: NLC from CLL patient 6

source_name: Nurse Like Cells from patient 6

tag: age

value: between 60 and 90 years


title: ABS-87


title: Blu e-cig, menthol flavor, with nicotine 3

value: 2 puff/min.

value: 400 puffs

value: menthol


title: TB_EXP_ScarYes_week1_3017

value: Whole blood

value: Latent tuberculosis (TB) Exposed

value: Yes

tag: gender

tag: donor

tag: timepoint

tag: timepointunit


title: TB_UEXP_ScarNo_week1_3012

value: Latent tuberculosis (TB) Unexposed

value: No

value: week


title: TB_EXP_ScarYes_week1_3003

value: F


title: Blu e-cig, menthol flavor, with nicotine 2

value: bronchial epithelial cells


title: ABS-85

tag: sample type

value: typically developing

tag: disease state

value: female


title: TB_EXP_ScarNo_week1_3007

value: M


title: ABS-86

value: non-inflamed

tag: Sex

value: male


title: NLC from CLL patient 4

source_name: Nurse Like Cells from patient 4

value: blood sample

tag: race

value: caucasian

value: between 60 and 90 years


title: TB_UEXP_ScarYes_week1_3010


title: Blu e-cig, menthol flavor, with nicotine 1

tag: puff rate

value: 2 puff/min.

tag: total puffs

value: 400 puffs

tag: flavor

value: menthol


title: Blu e-cig, menthol flavor, no nicotine 3

tag: cell type

tag: nicotine concentration


title: ABS-84


title: NLC from CLL patient 3

source_name: Nurse Like Cells from patient 3


title: NLC from CLL patient 5

source_name: Nurse Like Cells from patient 5


title: ABS-83


title: Blu e-cig, menthol flavor, no nicotine 2


title: NLC from CLL patient 2

source_name: Nurse Like Cells from patient 2


title: TB_UEXP_ScarYes_week1_3009

tag: samplename

value: Whole blood

tag: sampletype

tag: scar

value: Yes


title: ABS-82


title: Blu e-cig, tobacco flavor, with nicotine 3

value: tobacco


title: Blu e-cig, tobacco flavor, with nicotine 2


title: NAc, heroin H-20

city: New York

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from human nucleus accumbens

hyb_protocol: Array hybridization was carried out using the 3'IVT PLUS reagent kit according the Affymetrix instructions.

scan_protocol: Scanning was performed using GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Raw data were normalized using the Robust Multichip Average from the Affymetrix Expression Console.

source_name: human nucleus accumbens, heroin user

label_protocol: Labeled cRNA was prepared according the the standard Affymetrix protocol using the 3'IVT PLUS reagent kit

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using TRI-Reagent from Sigma-Aldrich according to the manufacturer's instructions

treatment_protocol: not applicable

tag: age


title: ABS-81

source_name: terminal ileum


title: Blu e-cig, menthol flavor, no nicotine 1


title: ABS-80


title: NAc, heroin H-22

tag: gender


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep4

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate4

treatment_protocol: ECSCs were obtained from premenopausal patients who had undergone salpingo-oophorectomy or cystectomy for ovarian endometriotic cysts. ECSCs were isolated from the corresponding tissues by enzymatic digestion. ECSCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.

value: endometriotic cyst stromal cells

value: Female

tag: treatment

value: 12d dibutyryl-cAMP and dienogest


title: NAc, heroin H-21


title: ABS-79

value: typically developing


title: ABS-78


title: NAc, heroin H-18


title: Blu e-cig, tobacco flavor, with nicotine 1

value: bronchial epithelial cells


title: NAc, heroin H-19


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep2

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate2


title: NAc, heroin H-17

value: female


title: Blu e-cig, tobacco flavor, no nicotine 3


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep3

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate3


title: NAc, heroin H-16


title: Blu e-cig, tobacco flavor, no nicotine 2


title: Blu e-cig, tobacco flavor, no nicotine 1


title: ABS-76

value: non-inflamed


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep1

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate1


title: ECSCs_12d_rep4

source_name: endometriotic cyst stromal cells, 12 days, replicate4

value: 12d 10% charcoal-stripped heat-inactivated FBS


title: ECSCs_12d_rep3

source_name: endometriotic cyst stromal cells, 12 days, replicate3


title: NAc, heroin H-15


title: combustible tobacco, traditional cigarette 3

source_name: RNA from ALI-differentiated HBECs

value: 1 puff/min.

value: 48 puffs


title: combustible tobacco, traditional cigarette 2


title: ABS-74

value: male


title: NAc, heroin H-14


title: ABS-77


title: ECSCs_12d_rep1

source_name: endometriotic cyst stromal cells, 12 days, replicate1


title: ECSCs_12d_rep2

source_name: endometriotic cyst stromal cells, 12 days, replicate2


title: combustible tobacco, traditional cigarette 1


title: NAc, heroin H-11


title: ABS-73


title: ABS-72


title: ABS-71


title: NAc, heroin H-12


title: NLC from CLL patient 1

source_name: Nurse Like Cells from patient 1

tag: tissue

value: blood sample

value: caucasian

value: between 60 and 90 years


title: NAc, heroin H-13


title: NAc, heroin H-10


title: A5893_osteo5

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: TRAP+ multinuclear osteoclasts (OCs)

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: RAW 264.7 cells were routinely maintained in phenol red–free Alpha Minimum Essential Medium (Invitrogen, Carlsbad, CA) containing 10% FBS (HyClone), 100 U/ml penicillin, 100  g/ml streptomycin, and 25 ng/ml amphotericin B (Invitrogen) and cultured on 0.1% gelatin-coated (Sigma) dishes.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: To distinguish between proteomes of OPs, IOs, and OCs, we performed 3-plex SILAC and used mass spectrometry to quantify the proteome of each cell type. RAW 264.7 cells were subcultured in phenol red–free custom-made Alpha Minimum Essential Medium, as phenol red has an estrogen activity (20) that is reported to suppress RANKL-induced osteoclast formation, and arginine (Arg) and lysine (Lys) were replaced by 12C6-Arg and 14N2 12C6-Lys (light, Sigma), 13C6-Arg and 2H4-Lys (medium, Cambridge Isotope Laboratories, Tewksbury, MA), or 13C6 15N4-Arg and 13C6 15N2-Lys (heavy, Cambridge Isotope Laboratories). After these isotopes were fully incorporated into the cellular proteins (roughly four passages; each sample of medium- and heavy-labeled cells was checked to measure the label incorporation percentage), 412,300 cells of light-, medium-, and heavy-labeled cells were seeded onto 0.1% gelatin coated10-cm dishes (density: 7,500 cells/cm2) on day 0. Both medium- and heavy-labeled cells were treated with 40 ng/ml RANKL (R&D Systems, Minneapolis, MN) on day 1, and the medium was replaced with fresh medium with RANKL on day 3.The cells were harvested on day 5 post-treatment.

tag: cell line

value: mouse monocyte-macrophage cell line

tag: ligand

value: RANKL

tag: ligand conc.

value: 40 ng/mL

tag: incubation time

value: 5 days

tag: experimental replicate

tag: cell subtype

value: TRAP+ multinuclear osteoclasts (OCs).


title: A5897_trap4

source_name: intermediate osteoclasts

value: intermediate osteoclasts


title: ABS-75

tag: sample type

value: typically developing

tag: disease state

tag: Sex


title: ABS-70


title: NAc, heroin H-9


title: NAc, heroin H-8


title: ABS-69

source_name: whole blood

value: Autism Spectrum Disorder

value: inflamed


title: ABS-68

value: female


title: A5891_osteo3

tag: cell type


title: NAc, heroin H-7


title: A5892_osteo4

source_name: osteoclast precursor (OP)

value: osteoclast precursor (OP)


title: A5896_trap3


title: ABS-67


title: A5888_nt3


title: NAc, heroin H-6


title: ABS-66


title: NAc, heroin H-2


title: ABS-65


title: NAc, heroin H-5


title: A5887_nt2


title: A5889_osteo1


title: A5894_trap1


title: ABS-64


title: A5895_trap2


title: A5890_osteo2


title: NAc, heroin H-3


title: ABS-63


title: ABS-62


title: NAc, heroin H-1


title: A5886_nt1


title: NAc, heroin H-4


title: NAc, control C-27

source_name: human nucleus accumbens, control


title: ABS-47


title: NAc, control C-25


title: ABS-61


title: ABS-48


title: ABS-46


title: NAc, control C-26


title: NAc, control C-24


title: TB_UEXP_ScarYes_week1_3018

source_name: Whole blood

tag: samplename

value: Whole blood

value: Latent tuberculosis (TB) Unexposed

value: Yes

value: F

tag: worm infection

tag: donor

tag: timepoint

tag: timepointunit

value: week