title: Baked Egg Reactive Patinent_28_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER28_EW


title: Baked Egg Tolerant Patinent_5_(Egg Whites Incubation)

status: Public on Oct 18 2016

type: RNA

city: New York

first: Roman

last: Kosoy

state: New York

address: 1468 Madison Avenue, 18-88

department: Genetics and Genomic Sciences

country: USA

institute: Mount Sinai School of Medicine

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET5_EW

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw microarray data were processed by Lumi package in R, with background adjustment, variance-stabilizing transformation, and quantile normalization within each batch.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: PBMCs were isolated from whole blood by Ficoll-Paque PLUS, washed, and cultured in AimV with 2.5% autologous plasma. 4 x 106 cells were plated in 1 ml in 24-well culture plates, in the presence or absence of 300 ug of egg white (EW) protein cleaned of endotoxin using Detoxi-Gel columns. Media was removed and cells harvested for RNA isolation using the Qiagen RNeasy mini kit according to manufacturer’s instructions.

tag: patient

tag: batch

tag: gender

value: Male

tag: incubation conditions

value: Purified Egg Whites Protein

tag: food allergy status

value: Baked EggTolerant

tag: cytokine measurements availability

value: No


title: Baked Egg Tolerant Patinent_4_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET4_M

value: Media


title: Baked Egg Reactive Patinent_20_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER20_EW

value: Female

value: Baked Egg Responsive


title: Baked Egg Reactive Patinent_17_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER17_M

value: Yes


title: Baked Egg Reactive Patinent_20_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER20_M


title: Baked Egg Reactive Patinent_18_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER18_EW


title: Baked Egg Reactive Patinent_19_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER19_M


title: Baked Egg Reactive Patinent_19_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER19_EW


title: Baked Egg Reactive Patinent_24_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER24_EW


title: Baked Egg Tolerant Patinent_5_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET5_M


title: Baked Egg Reactive Patinent_28_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER28_M


title: Baked Egg Reactive Patinent_23_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER23_M


title: Non Egg Allergic Patinent_2_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC2_M

value: Non Egg Allergic


title: Baked Egg Reactive Patinent_25_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER25_EW


title: Baked Egg Reactive Patinent_24_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER24_M


title: Baked Egg Reactive Patinent_21_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER21_EW


title: Baked Egg Reactive Patinent_26_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER26_M


title: Baked Egg Reactive Patinent_18_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER18_M


title: Non Egg Allergic Patinent_4_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC4_EW


title: Non Egg Allergic Patinent_1_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC1_M


title: Non Egg Allergic Patinent_3_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC3_M


title: Non Egg Allergic Patinent_5_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC5_M


title: Baked Egg Tolerant Patinent_2_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET2_M


title: Baked Egg Tolerant Patinent_4_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET4_EW


title: Non Egg Allergic Patinent_2_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC2_EW


title: Baked Egg Reactive Patinent_15_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER15_M


title: Baked Egg Tolerant Patinent_2_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET2_EW


title: Baked Egg Reactive Patinent_16_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER16_M


title: Non Egg Allergic Patinent_5_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
AC5_EW


title: Baked Egg Reactive Patinent_13_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER13_M


title: Baked Egg Tolerant Patinent_1_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET1_M


title: Baked Egg Tolerant Patinent_3_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET3_EW


title: Baked Egg Tolerant Patinent_3_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET3_M


title: Baked Egg Reactive Patinent_10_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER10_EW


title: Baked Egg Reactive Patinent_16_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER16_EW


title: Baked Egg Reactive Patinent_13_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER13_EW


title: Baked Egg Reactive Patinent_15_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER15_EW


title: Baked Egg Reactive Patinent_12_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER12_M


title: Baked Egg Reactive Patinent_11_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER11_EW


title: Baked Egg Reactive Patinent_11_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER11_M


title: Baked Egg Reactive Patinent_14_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER14_EW


title: Baked Egg Reactive Patinent_12_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER12_EW


title: Baked Egg Tolerant Patinent_1_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET1_EW


title: Baked Egg Reactive Patinent_10_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER10_M


title: Baked Egg Reactive Patinent_4_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER4_EW


title: Baked Egg Reactive Patinent_8_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER8_EW


title: Baked Egg Reactive Patinent_2_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER2_EW


title: Baked Egg Reactive Patinent_7_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER7_EW


title: Baked Egg Reactive Patinent_1_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER1_M


title: Baked Egg Reactive Patinent_3_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER3_EW


title: Baked Egg Reactive Patinent_5_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER5_EW


title: Baked Egg Reactive Patinent_7_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER7_M


title: Baked Egg Reactive Patinent_5_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER5_M


title: Baked Egg Reactive Patinent_9_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER9_EW


title: Baked Egg Reactive Patinent_3_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER3_M


title: Baked Egg Reactive Patinent_6_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER6_EW


title: Baked Egg Reactive Patinent_4_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER4_M


title: Baked Egg Tolerant Patinent_6_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BET6_M


title: Baked Egg Reactive Patinent_1_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER1_EW


title: Baked Egg Reactive Patinent_6_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER6_M


title: E14.5 WT placenta-1

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: wild type

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

label: biotin

organism: Mus musculus

source_name: WT placenta-1

label_protocol: Standard Affymetrix protocol

growth_protocol: Placentas were obtained from E14.5 wild-type and Syde1-knockout mice.

extract_protocol: Placentas were washed twice with ice-cold PBS. Total RNA was extracted with TRIzol reagent (Invitrogen) and purified with Qiagen Rneasy mini kit by following manufacturer's instructions.

treatment_protocol: For each conceptus, the uterine wall, fetus and yolk-sac were removed to isolate individual placenta by use of forceps and scissors.

tag: developmental stage

tag: tissue

value: placenta

tag: genotype

value: wild type


title: Dectin-2 KO Kupffer + SL4_co-cultured

city: Meguro-ku

first: Yoshitaka

last: Kimura

state: Tokyo

address: T block (56th Bldg.), Komaba 4-6-1

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

description: Gene expression data from Dectin-2-deficient Kupffer cells and SL4 cells cultured together

hyb_protocol: Using GeneChip Hybridization, Wash and Stain Kit (Affymetrix), 5 ug of cDNAs were hybridized for 18 hours at 45 °C and 60 r.p.m. on GeneChip Mouse Genome Array in GeneChip Hybridization Oven 645 (Affymetrix). GeneChips were washed and stained in GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software 4.0, followed by the normalization process using Affymetrix Expression Console Software 1.4 with MAS5 algorithm.

label_protocol: cDNAs were prepared from 20 ng of total RNA with Ovation Pico WTA System V2 Kit (NuGEN) and biotinylated with fragmentation using Encore Biotin Module Kit (NuGEN).

growth_protocol: Mice were maintained in conventional condition. SL4 cells were cultured in DMEM / F12 (Ham) containing 10% fetal bovine serum at 37 °C in 5% CO2

extract_protocol: Total RNA was extracted with NucleoSpin RNA II (MACHREY NAGEL) according to manufacturer's instructions.

treatment_protocol: CD45+ CD11b+ F4/80+ Kupffer cells were isolated by cell sorting. 1x105 of Kupffer cells were co-cultured with or cultured separately from 1x105 of SL4 cells in RPMI 1640 containing 10% fetal bivine serum with penicillin / streptomycin. Eight hours later, cells were lysed with a reagent of NucleoSpin RNA II (MACHREY NAGEL) according to manufacturer's instructions.

value: female (Kupffer cells)

tag: strain

value: C57BL/6 (both Kupffer cells and SL4 cells)

tag: cell

value: Kupffer cells and SL4 cells

value: Clec4n-/- (Kupffer cells)

tag: age

value: 12 week-old (Kupffer cells)


title: Dectin-2 KO Kupffer + SL4_separately cultured

description: Gene expression data from Dectin-2-deficient Kupffer cells and SL4 cells cultured separately


title: VND3207 treated sample 3

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

country: China

institute: Soochow University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression（8*60K）for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Gene expression in jejunum of VND3207-treated mice 6hr post 9Gy radiation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561 ) following the manufacturer's instructions.

treatment_protocol: Mice were divided into two groups (3 mice per group) and administered intragastrically with 100mg/kg VND3207 or equivalent volume of vehicle respectively. Vehicle treated mice were served as controls. Half hours later, all mice were given 9 Gy radiation. 6 hours post radiation, mice jejunum tissues were isolated and extracted total RNA.

value: Jejunum

value: male


title: Baked Egg Reactive Patinent_2_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER2_M

value: Male


title: E14.5 WT placenta-2

description: wild type

source_name: WT placenta-2


title: E14.5 Syde1-KO placenta-1

description: Syde1 knockout

source_name: KO placenta-1

value: Syde1 knockout


title: WT Kupffer + SL4_co-cultured

description: Gene expression data from wild-type Kupffer cells and SL4 cells cultured together

source_name: Wild-type Kupffer cells and SL4 cells cultured together

value: wild-type (Kupffer cells)


title: VND3207 treated sample 1

source_name: Gene expression in jejunum of VND3207-treated mice 6hr post 9Gy radiation, replicate 1


title: VND3207 treated sample 2

source_name: Gene expression in jejunum of VND3207-treated mice 6hr post 9Gy radiation, replicate 2


title: WT Kupffer + SL4_separately cultured

description: Gene expression data from wild-type Kupffer cells and SL4 cells cultured separately

source_name: Wild-type Kupffer cells and SL4 cells cultured separately


title: Vehicle treated control sample 2

source_name: Gene expression in jejunum of vehicle-treated mice 6hr post 9Gy radiation, replicate 2


title: Complicated malaria 8

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

description:
PVC-30
Gene expression of parasite isolates

hyb_protocol: The labeled cRNA samples were hybridized on to a custom P. vivax 8x15K array (AMADID: 022126) designed by Genotypic Technology Pvt. Ltd., Bangalore, India. 600ng of Cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization Kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanning was done using Agilent Microarray Scanner G Model G2565BA at 5 µm resolution.

data_processing: Obtained images after scanning were processed with Agilent’s Feature Extraction software to get raw data files. Raw data from each sample were imported into GeneSpring GX v12.5 (Agilent Technologies) and then quantile normalized.

organism: Plasmodium vivax

source_name: P. vivax parasites from patient's blood_complicated malaria

label_protocol: RNA sample preparation and labeling for microarray experimentation were performed following Agilent’s One-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp labeling kit). Total RNA (500ng) from each sample was reverse transcribed using Molony murine leukemia virus reverse transcriptase primed by oligodT with a T7 promoter primer. The cDNA generated was used as a template for in vitro transcription reaction which has T7 RNA Polymerase and Cy3-CTP mix. The dye Cy3-CTP was incorporated during this step. Labeled cRNA was processed and quality assessed for yields and specific activity. Cy3-labeled cRNA (600ng) was fragmented and hybridized onto custom designed genome-wide P. vivax 15K microarray (AMADID: 022126) at 65°C for 16hrs using Agilent’s Gene Expression Hybridization Kit (Part Number 5188-5242). The hybridized slides were subsequently washed with Agilent Gene Expression wash buffers (Part No: 5188-5327).

growth_protocol: P. vivax isolates were collected directly from infected patients with differing clinical symptoms.

extract_protocol: Total RNA extracted using TriReagent (Sigma Aldrich, USA) following manufacturer's instructions.

treatment_protocol: Blood was immediately (within 15min of collection) subjected to density gradient based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the Peripheral Blood Mononuclear Cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with Phosphate buffered saline (PBS) twice, lysed using 4 volumes of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

tag: patient age (yrs)

tag: patient gender

tag: clinical presentation

value: complicated malaria


title: Complicated malaria 3

description:
PVC-19
Gene expression of parasite isolates


title: Complicated malaria 9

description:
PVC-31
Gene expression of parasite isolates

value: female


title: Exosome profiles TISE_miRNA

city: Philadelphia

first: Prashanth

last: Vallabhajosyula

state: PA

address: 3400 Spruce Street

department: Surgery

institute: University of Pennsylvania

description:
Experssion data of transplant islet exosomes
miRNA

hyb_protocol: abeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 4.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: log2-transformed normalized signal intensities were calclulated from cel files using RMA as implemented in Partek Genomics Suite (v6.6, Partek, Inc. St. Louis, MO)

source_name: Human islets into mouse xenotransplantation

label_protocol: RNA samples were submitted to a tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

extract_protocol: RNA was extracted from cells and exosomes using Trizol, followed by RNeasy mini kit, according to manufacturer’s protocol (Qiagen, Germany).  For total protein isolation, exosomes were lysed in 1X RIPA buffer with 1X concentration of protease inhibitor cocktail (Sigma-Aldrich Co.).

value: pancreas

tag: cell type

value: islets

tag: cell compartment

value: exosome


title: Complicated malaria 5

description:
PVC-21
Gene expression of parasite isolates


title: 9_231_12hr_5

city: Boston

first: Shawn

last: Johnson

state: MA

address: 450 Brookline Avenue, Mayer Rm 434

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from dinaciclib treated MDA-MB-231 cells

hyb_protocol: Done according to Affymatrix protocol

scan_protocol: Done according to Affymatrix protocol

data_processing: Changes in transcription were measured using the Affymetrix HG-U133A2 array platform. Differences in genes were assessed using Ingenuity Pathway Analysis (IPA)

source_name: MDA-MB-231, dinaciclib treatment for 12 hours

growth_protocol: MDA-MB-231 cells were cultured at 37 degrees celsius in standard RPMI media (10%FBS + 1x Pen/Strep)

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

treatment_protocol: Dinaciclib was dissolved in DMSO and added directly to growth media

tag: cell line

value: breast cancer


title: Vehicle treated control sample 1

source_name: Gene expression in jejunum of vehicle-treated mice 6hr post 9Gy radiation, replicate 1


title: Vehicle treated control sample 3

source_name: Gene expression in jejunum of vehicle-treated mice 6hr post 9Gy radiation, replicate 3


title: Islet graft tissue_miRNA

description:
Experssion data of islet graft tissue
miRNA

value: whole cell


title: Complicated malaria 7

description:
PVC-28
Gene expression of parasite isolates


title: Complicated malaria 6

description:
PVC-27
Gene expression of parasite isolates


title: 7_231_12hr_4


title: Complicated malaria 4

description:
PVC-20
Gene expression of parasite isolates


title: Exosome profiles TISE_mRNA

description:
Expression data of transplant islet exosomes
long RNA

hyb_protocol: Labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99oC for 5 min and hybridized for 16 hours at 45oC to human transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara, CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal

data_processing:
log2-transformed normalized signal intensities were calclulated from cel files using RMA as implemented in Partek Genomics Suite (v6.6, Partek, Inc. St. Louis, MO)
The file Normalized_data_all_probesets.txt contains data for all analyzed probe sets and is available on the series record. 11 probe sets had no gene annotation information and were thus excluded from the sample data tables. These probes sets are:
TC01001343.hg.1
TC09000974.hg.1
TC0X000181.hg.1
TC11001890.hg.1
TC15000184.hg.1
TC15000193.hg.1
TC15001102.hg.1
TC16000429.hg.1
TC16000764.hg.1
TC17001285.hg.1
TC22000803.hg.1

label_protocol: Total RNA was converted to first- strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region. Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting ssDNA was  fragmented and biotinylated by terminal transferase end labeling.


title: Exosome profiles R-xeno_miRNA

description:
Experssion data of transplant islet exosomes under conditions of rejection
miRNA

source_name: Human islets into mouse xenotransplantation-rejected


title: 8_231_0hr_5

description: Gene expression data from baseline mRNA levels in MDA-MB-231 cells

source_name: MDA-MB-231, baseline


title: Uncomplicated malaria 2

description:
PVU-7
Gene expression of parasite isolates

source_name: P. vivax parasites from patient's blood_uncomplicated malaria

value: uncomplicated malaria


title: Baked Egg Reactive Patinent_8_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER8_M

source_name: PBMC

tag: patient

tag: batch

value: Media

value: Baked Egg Responsive

value: Yes


title: Uncomplicated malaria 4

description:
PVU-9
Gene expression of parasite isolates


title: Baked Egg Reactive Patinent_14_(Media Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER14_M

tag: gender

value: Female

tag: incubation conditions


title: Baked Egg Reactive Patinent_17_(Egg Whites Incubation)

description:
HumanHT-12_V4_0_R2_15002873_B.bgx
BER17_EW

value: Purified Egg Whites Protein

tag: food allergy status

tag: cytokine measurements availability


title: 5_231_12hr_F

tag: tissue


title: Complicated malaria 1

description:
PVC-1
Gene expression of parasite isolates

value: male


title: Complicated malaria 2

description:
PVC-2
Gene expression of parasite isolates


title: IL-17RA KO2-B

city: Pittsburgh

first: Partha

middle: Sarathi

last: Biswas

address: 203 Lothrop Street

department: Medicine

institute: University of Pittsburgh

description: Replicate 2

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: Mouse kidney

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

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

tag: genotype/variation

tag: infection

value: Candida albicans

value: 8 weeks

value: Kidney


title: IL-17RA WT2-B

description: Replicate 2

tag: strain

value: wildtype


title: Uncomplicated malaria 5

description:
PVU-10
Gene expression of parasite isolates

value: female


title: Uncomplicated malaria 3

description:
PVU-8
Gene expression of parasite isolates


title: 6_231_0hr_4


title: UBC-KD-hBM-MSC1-P3

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: UBC gene KD was performed by siRNA transfection into hBM-MSCs of donor-1 at P3.

hyb_protocol: Complementary RNA was hybridized using the Agilent`s Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted with the Agilent Feature Extraction software package.
All data normalization and selection of up- and down-regulated genes was performed using Agilent GeneSpring GX 7.3

source_name: hBM-MSCs of donor-1

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.

growth_protocol: This study was approved by the Institutional Review Board, Seoul St. Mary’s Hospital (IRB approval number KC12CNSI0078). Three preparations of hBM-MSCs were purchased from Texas A&M Health Science Center, College of Medicine, Institute for Regenerative Medicine (Temple, TX, USA). To recover viable cells, a frozen vial of the hBM-MSCs was rapidly thawed, plated in a 150×25 mm culture dish and cultured using alpha-modified minimum essential medium (α-MEM; Gibco, Grand Island, NY, USA) containing 12.5% fetal bovine serum (FBS; Gibco), 1% glutamax™-I (Gibco) and 1% penicillin-streptomycin (Gibco) at 37oC and 5% CO2. Medium was changed every 3-4 days. Cultured hBM-MSCs were harvested at 70-80% confluency by treatment with 0.25% trypsin-EDTA. The number of harvested cells was counted using a C-Chip hemocytometer (SystemBükerTürk; Incyto, Cheonan, Korea) and cells were re-plated at a density of 300 cells/cm2. These processes continued until hBM-MSCs ceased proliferating. The proliferative activity of hBM-MSCs was expressed as PDT.

extract_protocol: RNA was prepared using theTrizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: UBC gene KD was performed by siRNA transfection into hBM-MSCs at P3. The specific sequence for human UBC gene siRNA (5′-GUGACACUAUCGAGAACGUTT-3′) was designed and synthesized by GenePharma (GenePharma Co., Ltd., Shanghai, China). hBM-MSCs at third passage were transfected with 100 nM UBC-siRNA using Lipofectamine RNAiMAX (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions.

tag: donor id

value: human bone marrow-mesenchymal stromal cells (hBM-MSCs)

value: UBC knockdown

tag: passage

value: passage 3

tag: sample group

value: early-passage


title: Islet graft tissue_mRNA

description:
Expression data of islet graft tissue
long RNA

value: pancreas

value: islets

value: whole cell


title: hBM-MSC3-7P

description: hBM-MSCs at passage 7 of donor-3

source_name: hBM-MSCs of donor-3

value: passage 7

value: late-passage


title: UBC-KD-hBM-MSC2-P3

description: UBC gene KD was performed by siRNA transfection into hBM-MSCs of donor-2 at P3.

source_name: hBM-MSCs of donor-2


title: Uncomplicated malaria 1

description:
PVU-4
Gene expression of parasite isolates

tag: patient age (yrs)

tag: patient gender

tag: clinical presentation

value: uncomplicated malaria


title: 4_231_0hr_E

tag: cell line

value: breast cancer


title: IL-17RA KO2-C

description: Replicate 2

tag: age


title: IL-17RA KO

description: Replicate 1


title: IL-17RA KO-B

description: Replicate 2


title: IL-17RA KO2

description: Replicate 1


title: hBM-MSC1-7P

description: hBM-MSCs at passage 7 of donor-1

tag: cell type


title: IL-17RA WT2-C

description: Replicate 2


title: timepoint 2_placebo_ participant 33

city: Auckland

first: Anna

last: Boss

address: 85 Park Rd

country: New Zealand

institute: University of Auckland

description: gene expression data in humans after supplementation with either olive leaf extract or placebo

hyb_protocol: samples were sent to the Ramciotti Centre for array analysis https://www.ramaciotti.unsw.edu.au/array/rna-analysis

data_processing: R statistic 3.3.1, package = Bioconductor - RMA normalisation (https://www.bioconductor.org/)

source_name: peripheral blood mononuclear cells

growth_protocol: participants took 20ml of either olive leaf extract or placebo per day for 8 weeks

extract_protocol: RNease Plus Mini Kit (QIAGEN, Victoria, Australia).

treatment_protocol: olive leaf extract and placebo were both in a vegetable glycerol matrix.

tag: cells analysed

value: PBMC

tag: timepoint at which blood was taken

value: timepoint 2

tag: supplement

value: placebo


title: IL-17RA WT-C

description: Replicate 1

value: Candida albicans

value: 8 weeks

value: Kidney


title: IL-17RA WT

description: Replicate 1

value: wildtype


title: IL-17RA KO-C

description: Replicate 1


title: hBM-MSC3-3P

description: hBM-MSCs at passage 3 of donor-3

value: human bone marrow-mesenchymal stromal cells (hBM-MSCs)


title: UBC-KD-hBM-MSC3-P3

description: UBC gene KD was performed by siRNA transfection into hBM-MSCs of donor-3 at P3.

value: UBC knockdown

value: passage 3


title: IL-17RA WT2

description: Replicate 2


title: hBM-MSC1-3P

description: hBM-MSCs at passage 3 of donor-1

value: early-passage


title: timepoint 2_placebo_ participant 25

scan_protocol: samples were sent to the Ramciotti Centre for array analysis https://www.ramaciotti.unsw.edu.au/array/rna-analysis


title: hBM-MSC2-7P

description: hBM-MSCs at passage 7 of donor-2


title: IL-17RA WT-B

description: Replicate 1


title: timepoint 2_placebo_ participant 32

label_protocol: samples were sent to the Ramciotti Centre for array analysis https://www.ramaciotti.unsw.edu.au/array/rna-analysis


title: timepoint 2_placebo_ participant 28


title: hBM-MSC2-3P

description: hBM-MSCs at passage 3 of donor-2


title: timepoint 2_placebo_ participant 17


title: timepoint 2_placebo_ participant 30


title: timepoint 2_placebo_ participant 22


title: timepoint 2_placebo_ participant 15


title: E14.5 Syde1-KO placenta-2

source_name: KO placenta-2

tag: developmental stage

value: placenta

tag: genotype

value: Syde1 knockout


title: timepoint 2_olive leaf extract_ participant 27

value: olive leaf extract


title: Reference_RNA

source_name: Reference RNAs

tag: sample type

value: Universal human reference RNAs (Agilent technologies)

value: Reference RNAs


title: timepoint 2_olive leaf extract_ participant 23


title: timepoint 2_olive leaf extract_ participant 31


title: timepoint 2_placebo_ participant 26


title: timepoint 2_olive leaf extract_ participant 21


title: timepoint 2_placebo_ participant 29


title: timepoint 2_olive leaf extract_ participant 20


title: timepoint 2_olive leaf extract_ participant 18


title: timepoint 2_placebo_ participant 3


title: timepoint 2_placebo_ participant 6


title: timepoint 2_olive leaf extract_ participant 12


title: timepoint 2_placebo_ participant 24


title: timepoint 2_placebo_ participant 16


title: timepoint 2_olive leaf extract_ participant 10


title: timepoint 2_olive leaf extract_ participant 14


title: timepoint 2_olive leaf extract_ participant 9


title: timepoint 2_olive leaf extract_ participant 7


title: timepoint 2_olive leaf extract_ participant 5

value: timepoint 1


title: DAAD-2 sensitive HEP3B cells treated with 2uM DAAD-2 for 72h_rep1

city: Karachi

first: Muhammad

middle: Ayaz

last: Mustufa

state: Sindh

address: Rafeequee Shaheed road

department: SRCCH

country: Pakistan

institute: PHRC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using BRB Array Tools V 4.2.0

source_name: Human HCC Cell line HEP3B

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA(Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: HEP3B and SNU449 Cells were plated in 10 cm2 Petri plates at 3-4 x 10 5 per plate  and incubated for 24 hours before treatment

extract_protocol: The total RNAs of treated and non-treated DAAD2-sensitive HEP3B and DAAD2-resistant SNU449 cells were isolated using Nucleospin RNA II kit (MN) according to manufacturer’s instructions

treatment_protocol: After 24 hours of growing, all control samples were treated with vehicle control 0.1% dimethyl sulfoxide (DMSO), DAAD-2-sensitive HEP3B cells were treatred with 2uM DAAD-2 and DAAD-2-resistant SNU-449 cells were treated with 20 uM DAAD-2 in triplicate for each sample and plates were further incubated for next 72 hours.

tag: treatment

value: 2uM DAAD-2 for 72h


title: DAAD-2 sensitive HEP3B cells treated with 2uM DAAD-2 for 72h_rep3


title: timepoint 2_olive leaf extract_ participant 4

value: PBMC


title: DAAD-2 sensitive HEP3B control samples treated with 0.1% DMSO for 72h_rep2

value: 0.1% DMSO for 72h


title: timepoint 1_placebo_ participant 32

value: placebo


title: DAAD-2 sensitive HEP3B cells treated with 2uM DAAD-2 for 72h_rep2


title: DAAD-2 sensitive HEP3B control samples treated with 0.1% DMSO for 72h_rep3


title: timepoint 1_placebo_ participant 30


title: DAAD-2 resistant SNU-449 cells treated with 20uM DAAD-2 for 72h_rep3

source_name: Human HCC Cell line SNU-449

value: 20uM DAAD-2 for 72h


title: timepoint 1_placebo_ participant 33


title: DAAD-2 resistant SNU-449 cells treated with 20uM DAAD-2 for 72h_rep2


title: DAAD-2 resistant SNU-449 cells treated with 20uM DAAD-2 for 72h_rep1


title: timepoint 2_olive leaf extract_ participant 1


title: timepoint 2_olive leaf extract_ participant 11

value: timepoint 2


title: DAAD-2 sensitive HEP3B control samples treated with 0.1% DMSO for 72h_rep1


title: timepoint 1_placebo_ participant 28


title: DAAD-2 resistant SNU-449 control samples treated with 0.1% DMSO for 72h_rep3


title: DAAD-2 resistant SNU-449 control samples treated with 0.1% DMSO for 72h_rep1


title: DAAD-2 resistant SNU-449 control samples treated with 0.1% DMSO for 72h_rep2


title: timepoint 1_placebo_ participant 26


title: timepoint 1_placebo_ participant 17


title: timepoint 1_placebo_ participant 25


title: timepoint 1_placebo_ participant 29


title: U1-FBS-R

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description: Total RNA was reverse-transcribed, pre-amplified with feature-specific primers, and loaded onto custom OpenArrays by liquid handling robot in the Johns Hopkins University DNA Analysis Facility. Quantitative real-time PCR was performed for 220 features.

data_processing:
SDS software (Thermo Fisher) was used to collect Cq data.
Cq data were processed using ExpressionSuite (Applied Biosystems/Thermo Fisher), Microsoft Excel, and R/Bioconductor. Cqs with amplification score > 1.15 were retained for further analysis. U6 data were not used. Normalization was performed to the geometric mean of ten abundant miRNAs (miRs-24, 17, 30b, 106a, 142-3p, 92a, 146a, 342-3p, 21, and 16). Missing values indicate wells that did not amplify or did not satisfy the amplification score criterion (raw data).

label: none (TaqMan probe label: FAM)

extract_protocol:
Total RNA was obtained from cultured cells using the mirVana total RNA isolation procedure; purity and concentration were assessed by NanoDrop.
RT and pre-amp: 100 ng total RNA per sample was reverse-transcribed using Megaplex primers, set A (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, set A (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.
qRT-PCR protocol: Pre-amplified cDNA was loaded onto custom TLDA cards. qRT-PCR was performed on an ABI 7800 instrument (Thermo Fisher) per manufacturer's recommendations.

tag: serum

value: EVR


title: timepoint 1_placebo_ participant 6


title: timepoint 1_placebo_ participant 3


title: timepoint 1_placebo_ participant 22


title: timepoint 1_placebo_ participant 24


title: ACH-2-FBS-R


title: ACH-2-TF-EVD

value: TF-EVD


title: timepoint 1_placebo_ participant 16


title: timepoint 1_olive leaf extract_ participant 31


title: timepoint 1_olive leaf extract_ participant 21


title: timepoint 1_placebo_ participant 15


title: MDM-TF-EVD

source_name: Monocyte-derived macrophages

value: Monocyte-derived macrophages


title: timepoint 1_olive leaf extract_ participant 10


title: timepoint 1_olive leaf extract_ participant 27


title: timepoint 1_olive leaf extract_ participant 23


title: timepoint 1_olive leaf extract_ participant 18


title: timepoint 1_olive leaf extract_ participant 14


title: SW48 DDX3+YAPsi

city: Taipei

first: Huei

address: Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Room 5, 12F, F building, No. 3, Park Street, Nangang District

institute: Taipei Medical University/ Graduate Institute of Cancer Biology and Drug Discovery

description:
DDX3+YAPsi
This sample contains raw data for two technical replicates.

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by G2505C scanner (635nm power 100 PMT 0 ; 532nm power N/A, PMT N/A) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: SW48 cells expressing DDX3 overexpression plasmid and YAP1 knockdown plasmid

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Cell were selected with G418 for four weeks. Stably transduced cells were use for this experiment.

tag: expression construct

value: SW48 cells expressing DDX3+YAPsi


title: timepoint 1_olive leaf extract_ participant 9


title: timepoint 1_olive leaf extract_ participant 7


title: timepoint 1_olive leaf extract_ participant 11


title: timepoint 1_olive leaf extract_ participant 12


title: timepoint 1_olive leaf extract_ participant 20


title: SW48 DDX3

description:
DDX3
This sample contains raw data for two technical replicates.

source_name: SW48 cells expressing DDX3 overexpression plasmid

value: SW48 cells expressing DDX3


title: U1-TF-EVD


title: MDM-UC-EVD

value: UC-EVD


title: kalibrator

status: Public on Oct 17 2016

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

country: Norway

institute: OUS- The Norwegian Radium Hospital

description: kalibrator

data_processing:
Data was global normalized using ExpressionSuit software (v.1.0.3)(life technologies)
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: FAM

source_name: serum

label_protocol: 30ng totRNA was used for reverse transcription. Preamplification was performed following manufactors protocol PN4399721

extract_protocol: totRNA was exctracted from 500µl serum using miRCURY RNA isolation kit for biofluids

tag: disease state

value: kalibrator


title: MDM-FBS-R


title: SW48 V

description:
pcDNA3.1 control
This sample contains raw data for two technical replicates.

source_name: SW48 cells expressing pcDNA3.1a

value: SW48 cells expressing pcDNA3.1


title: normal 13

description: test

value: normal


title: normal 14

description: test


title: normal 12

description: test


title: normal 15

description: test


title: normal 16

description: test


title: normal 11

description: test


title: normal 10

description: test


title: normal 9

description: test


title: normal 6

description: test


title: normal 7

description: test


title: normal 5

description: test


title: normal 1

description: test


title: timepoint 1_olive leaf extract_ participant 4

value: olive leaf extract


title: timepoint 1_olive leaf extract_ participant 5

value: timepoint 1


title: normal 3

description: test


title: normal 2

description: test


title: U1-UC-EVD


title: lung 37

description: test

value: lung


title: lung 36

description: test


title: lung 35

description: test


title: lung 34

description: test


title: normal 4

description: test


title: timepoint 1_olive leaf extract_ participant 1

value: PBMC


title: lung 32

description: test


title: lung 33

description: test


title: lung 31

description: test


title: normal 8

description: test


title: lung 27

description: test


title: lung 28

description: test


title: lung 29

description: test


title: lung 23

description: test


title: lung 38

description: test


title: lung 24

description: test


title: lung 25

description: test


title: lung 22

description: test


title: lung 20

description: test


title: lung 18

description: test


title: lung 17

description: test


title: lung 16

description: test


title: lung 14

description: test


title: lung 12

description: test


title: lung 15

description: test


title: lung 11

description: test


title: lung 13

description: test


title: lung 10

description: test


title: lung 9

description: test


title: lung 8

description: test


title: lung 7

description: test


title: lung 6

description: test


title: lung 5

description: test


title: lung 30

description: test


title: lung 4

description: test


title: lung 3

description: test


title: lung 26

description: test


title: lung 21

description: test


title: lung 19

description: test


title: lung 2

description: test


title: lung 1

description: test


title: COPD 16

description: test

value: COPD


title: COPD 11

description: test


title: COPD 12

description: test


title: COPD 13

description: test


title: COPD 15

description: test


title: COPD 14

description: test


title: COPD 9

description: test


title: COPD 8

description: test


title: COPD 6

description: test


title: COPD 7

description: test


title: COPD 10

description: test


title: COPD 5

description: test


title: COPD 4

description: test


title: COPD 3

description: test


title: COPD 1

description: test


title: COPD 2

description: test


title: Tumor_pEGFR-Lo_3

city: San Francisco

first: Joanna

last: Phillips

state: California

address: 1450 3rd Street

department: Neurosurgery

institute: UCSF

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Gladstone Institute Genomics Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw expression data was RMA normalized and Log2 transformed using Affymetrix Expression Console Software; core-exon analysis

source_name: pEGFR-Lo tumor cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mouse tumor progenitor cells were expanded in vitro in defined media

extract_protocol: Tumor cells were extracted from tumor-bearing brains by enzymatic digestion and ZsGreen-based FACsorting into RLT buffer (Rneasy mini kit, Qiagen)

treatment_protocol: FVB syngeneic mice were injected with 2µl of 200 000 cells/µl suspension

tag: host strain

value: FVB

tag: protocol

value: injected intracranially with mouse tumor progenitor cells

value: tumor cells isolated from in vivo tumors

tag: egfrviii activity

value: pEGFR-Lo


title: Tumor_pEGFR-Lo_2


title: Tumor_pEGFR-Hi_6

source_name: pEGFR-Hi tumor cells

value: pEGFR-Hi


title: Tumor_pEGFR-Hi_2


title: Tumor_pEGFR-Hi_3


title: NIL-BPH9 leaf shealth with 3h BPH infestaion, biological rep3

city: Wuhan

first: Rongzhi

last: Chen

address: 16, Luojia Mountain

institute: Wuhan University

description: Gene expression data from NIL-BPH9 leaf shealth with 3h BPH infestaion.

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. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0  (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Plants were grown in a controlled growth chamber. The fourth leaf of 3-week-old young plants were used as the material in all experiments.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad,CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified  total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and  RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Treat plants with BPH in different time points (as indicated) then sampled in the same time points.

tag: variety

tag: tissue

value: leaf shealth

value: Resistant to BPH

value: four-leaf stage


title: Tumor_pEGFR-Hi_1


title: NIL-BPH9 leaf shealth with 6h BPH infestaion, biological rep3

description: Gene expression data from NIL-BPH9 leaf shealth with 6h BPH infestaion.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0

tag: age


title: Tumor_pEGFR-Lo_1

tag: cell type


title: Tumor_pEGFR-Lo_4


title: Tumor_pEGFR-Lo_5


title: Tumor_pEGFR-Hi_5


title: Tumor_pEGFR-Lo_6


title: NIL-BPH9 leaf shealth with 3h BPH infestaion, biological rep1


title: 9311 leaf shealth with 6h BPH infestaion, biological rep2

description: Gene expression data from 9311 leaf shealth with 6h BPH infestaion.

value: Susceptible to BPH


title: NIL-BPH9 leaf shealth with 6h BPH infestaion, biological rep2


title: NIL-BPH9 leaf shealth without BPH infestaion (at 0h), biological rep3

description: Gene expression data from NIL-BPH9 leaf shealth without BPH infestaion (at 0h).


title: NIL-BPH9 leaf shealth without BPH infestaion (at 0h), biological rep1


title: 9311 leaf shealth with 3h BPH infestaion, biological rep3

description: Gene expression data from 9311 leaf shealth with 3h BPH infestaion.


title: 9311 leaf shealth without BPH infestaion (at 0h), biological rep3

description: Gene expression data from 9311 leaf shealth without BPH infestaion (at 0h).


title: 9311 leaf shealth with 3h BPH infestaion, biological rep1


title: 9311 leaf shealth with 6h BPH infestaion, biological rep3


title: NIL-BPH9 leaf shealth without BPH infestaion (at 0h), biological rep2


title: NIL-BPH9 leaf shealth with 3h BPH infestaion, biological rep2


title: 9311 leaf shealth with 6h BPH infestaion, biological rep1


title: 9311 leaf shealth without BPH infestaion (at 0h), biological rep2


title: 9311 leaf shealth with 3h BPH infestaion, biological rep2


title: NIL-BPH9 leaf shealth with 6h BPH infestaion, biological rep1


title: HaCaT_control_harvested24h_rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: HaCat cells in plate 2, without treatment, harvested after 24h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HaCaT cells, no blue light irradiation, harvested 24h after irradiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HaCaT cells were cultured under standard conditions at 37°C with 5% CO2. They were cultured in Dulbecco´s modified Eagle´s medium (DMEM) high glucose containing 10% fetal bovine serum (FBS), 1mM sodium pyruvate and 100U/mL penicillin/streptomycin.

treatment_protocol: Lumileds LUXEON Rebel LXML-PR01-0275 were used (Koninklijke Philips N.V., Eindhoven/Netherlands) with an intensity of 23mW/cm2 at an irradiation distance of 55mm, beam divergence was ±15° and a peak wavelength of 453 nm (blue light).

tag: light exposure

value: control

tag: platenr

tag: harvest time


title: HaCaT_control_harvested3h_rep3

description: HaCat cells in plate 3 without treatment, harvested after 3h

source_name: HaCaT cells, no blue light irradiation, harvested 3h after irradiation


title: Tumor_pEGFR-Hi_4


title: HaCaT_30minblue_harvested3h_rep1

description: HaCat cells in plate 1, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 3h

source_name: HaCaT cells, 30min blue light irradiation, harvested 3h after irradiation

value: blue light 30min


title: HaCaT_30minblue_harvested24h_rep2

description: HaCat cells in plate 2, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 24h

source_name: HaCaT cells, 30min blue light irradiation, harvested 24h after irradiation


title: HaCaT_control_harvested24h_rep3

description: HaCat cells in plate 3 without treatment, harvested after 24h


title: HaCaT_control_harvested24h_rep1

description: HaCat cells in plate 1, without treatment, harvested after 24h


title: HaCaT_control_harvested3h_rep2

description: HaCat cells in plate 2, without treatment, harvested after 3h


title: HaCaT_30minblue_harvested24h_rep1

description: HaCat cells in plate 1, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 24h


title: HaCaT_30minblue_harvested1h_rep3

description: HaCat cells in plate 3, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 1h

source_name: HaCaT cells, 30min blue light irradiation, harvested 1h after irradiation


title: HaCaT_control_harvested3h_rep1

description: HaCat cells in plate 1, without treatment, harvested after 3h


title: HaCaT_30minblue_harvested1h_rep1

description: HaCat cells in plate 1, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 1h


title: HaCaT_30minblue_harvested3h_rep3

description: HaCat cells in plate 3, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 3h


title: HaCaT_30minblue_harvested24h_rep3

description: HaCat cells in plate 3, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 24h


title: HaCaT_control_harvested1h_rep2

description: HaCat cells in plate 2, without treatment, harvested after 1h

source_name: HaCaT cells, no blue light irradiation, harvested 1h after irradiation


title: HaCaT_control_harvested1h_rep1

description: HaCat cells in plate 1, without treatment, harvested after 1h


title: HaCaT_30minblue_harvested3h_rep2

description: HaCat cells in plate 2, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 3h


title: HaCaT_control_harvested1h_rep3

description: HaCat cells in plate 3 without treatment, harvested after 1h


title: HaCaT_30minblue_harvested1h_rep2

description: HaCat cells in plate 2, irradiated with 452nm blue light (41.4J/cm², 23mW/cm²) for 30 min. and harvested after 1h


title: Female 2 [mas]

status: Public on Oct 16 2016

city: Cambridge

first: Joshua

address: 43 Vassar

institute: MIT

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RNA data normalized via RMA or MAS5 and analyzed on Affymetric Transcriptome Analysis 2.0

source_name: Female 2 [rma]

label_protocol: RNA samples were submitted to BioMicroCenter and run on an Affymetrix Mouse 430 2.0 chip

extract_protocol: RNA was extracted using RNA immunoprecipitation against FLAG+ neurons in the BLA.

treatment_protocol:
PABPC1-FLAG was expressed using the fos promoter in the basolateral amygdala.
Mice was exposed to footshocks or female mouse

tag: group

value: female


title: Female 3 [mas]

source_name: Female 3 [rma]


title: Obese_2.7

type: genomic

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 2

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: The data was normalized by GenoSplice for adjustment of type-2 bias using the BMIQ method (Teschendor et al., 2013) from ChAMP R package.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from CD73+CD90+CD105+ WJ MSC

label_protocol: Standard Illumina Protocol

growth_protocol: WJ-MSCs were grown on plastic in 10% FBS/DMEM

extract_protocol: genomic DNA was extracted using Qiagen columns; each sample of 500 ng DNA was bisulfite treated (EZ Zymo DNA Kit) according to manufacturer’s recommendations optimized for 450k array.

tag: developmental stage

value: Multipotent, undifferentiated CD73+CD90+CD105+ WJ MSC


title: Obese_1.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 3


title: Obese_2.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 1


title: Obese_2.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 2


title: Obese_3.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 2


title: Obese_3.7

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 3


title: Obese_3.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 3


title: Obese_1.7

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 1


title: Obese_1.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 1


title: Obese_3.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 2


title: Female 1 [mas]

source_name: Female 1 [rma]


title: Obese_3.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 6 replicate 1


title: Obese_2.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 4 replicate 1


title: Obese_2.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 3 replicate 3


title: Shock 3 [mas]

source_name: Shock 3 [rma]

value: shock


title: Obese_2.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor  4 replicate 3


title: Obese_1.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 1


title: Obese_3.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 7 replicate 1


title: Obese_1.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 2 replicate 2


title: Obese_1.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 2


title: Non_obese_3.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 2


title: Obese_3.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 5 replicate 3


title: Obese_1.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 1 replicate 3


title: Non_obese_3.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 2


title: 252644010227_S01_GE1_107_Sep09_1_1

city: Beijing

first: Chuanli

last: Zhou

address: No.2 YuanmingyuanWest Road

department: Department of Animal Breeding and Genetics

institute: China Agricultural University

description: Gene expression in pregnant sow blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Agilent Porcine Oligo Microarray（4×44K）(design ID：026440）) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA, Santa Clara, CA, US) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent) using default parameters to obtain Raw data. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

organism: Sus scrofa

source_name: Peripheral Blood, pregnant, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05-0.2ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent technologies Santa Clara, US) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, GmBH, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS  spectrophotometer.

extract_protocol: Total RNA was isolated from peripheral blood samples using blood total RNA fast extraction kit (Bioteke, Cat No. RP4001) and column purified using an RNeasy® Kit (QIAGEN, Cat No. 74104) according to the protocols. RNA quality was further assessed by calculating RIN (RNA integrity number) with an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). RNA samples that passed the quality control metrics, i.e. 2100 RIN >= 7.0 and 28S/18S > 0.7, were used for microarray analysis.

treatment_protocol: Peripheral blood sample was collected at 14 days after insemination from the submandibular vein of each sow, thoroughly mixed with the cell lysate (Bioteke, Beijing, China) within 20 min, and stored at -70°C until further processing.

value: whole blood

tag: gender

tag: parity

value: fifth


title: Obese_2.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from obese donor 4 replicate 2


title: Non_obese_3.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 1


title: Non_obese_3.7

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 3


title: Shock 1 [mas]

source_name: Shock 1 [rma]


title: 9311 leaf shealth without BPH infestaion (at 0h), biological rep1

description: Gene expression data from 9311 leaf shealth without BPH infestaion (at 0h).

tag: genotype


title: Non_obese_3.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 6 replicate 3


title: 252644010227_S01_GE1_107_Sep09_1_2

description: Gene expression in non-pregnant sow blood

source_name: Peripheral Blood, non-pregnant, replicate 4


title: Female 2 [rma]


title: Female 3 [rma]


title: Shock 2 [mas]

source_name: Shock 2 [rma]


title: 252644010227_S01_GE1_107_Sep09_1_4

source_name: Peripheral Blood, non-pregnant, replicate 2


title: 252644010226_S01_GE1_107_Sep09_1_4

source_name: Peripheral Blood, non-pregnant, replicate 1


title: Non_obese_2.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 1


title: Shock 3 [rma]


title: Non_obese_3.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 3


title: Female 1 [rma]


title: Non_obese_3.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 7 replicate 1


title: 252644010226_S01_GE1_107_Sep09_1_2

description: Gene expression in pregnant sow blood

source_name: Peripheral Blood, pregnant, replicate 3


title: 252644010226_S01_GE1_107_Sep09_1_1

description: Gene expression in pregnant sow blood

source_name: Peripheral Blood, pregnant, replicate 1


title: 252644010227_S01_GE1_107_Sep09_1_3

description: Gene expression in pregnant sow blood

source_name: Peripheral Blood, pregnant, replicate 2


title: Shock 2 [rma]


title: Non_obese_2.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 3


title: Shock 1 [rma]


title: LATS2+/+vsLATS2-/-

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

source_name: Embryonic fibroblast cells derived from LAT2-/- C57BL/6J mice

label_protocol: 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and  at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from MEFs derived from LATS2+/+ and LATS2-/- mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

tag: strain

value: embryonic fibroblasts

tag: genotype/variation

source_name: Embryonic fibroblast cells derived from LAT2+/+ C57BL/6J mice


title: Non_obese_2.7

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 5 replicate 2


title: Non_obese_2.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 3 replicate 3


title: Non_obese_2.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor  3 replicate 2


title: PD13116

status: Public on Oct 15 2016

city: Brussel

first: Yacine

last: Bareche

address: Rue Héger-Bordetstraat 1

country: Belgium

institute: Jules Bordet Institute

description: Gene expression data from breast tumor sample.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133 Plus 2 Array, Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner GCS3000.

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as implemented in the R/Bioconductor package frma.

source_name: ILC, grade 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (HuGen U133 Plus 2 array, Affymetrix).

growth_protocol: Not applicable.

treatment_protocol: Not applicable.

tag: disease status

value: Invasive lobular carcinoma (ILC)

value: Female

value: Breast cancer tumor

tag: tumor type

value: ILC

tag: subtype

value: Classic

tag: er

value: Positive

tag: pgr

value: Negative

tag: grade

tag: cellularity

value: No

tag: death


title: PD13118

tag: tissue

value: Yes


title: LATS2-/-vsLATS2+/+

description: KO(cy3)vsWT(cy5) dyeswap

tag: cell type


title: Non_obese_2.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 1


title: Non_obese_2.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 4 replicate 2


title: PD13128


title: Non_obese_1.4

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 1


title: PD13103

value: Trabecular


title: PD13110


title: PD13114


title: Non_obese_1.6

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 3


title: Non_obese_1.2

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 2


title: Non_obese_1.3

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 3


title: Non_obese_1.7

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 3 replicate 1


title: PD13095

source_name: ILC, grade 3

value: Solid


title: Non_obese_1.1

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 1 replicate 1


title: PD13101


title: PD13090


title: 252644010226_S01_GE1_107_Sep09_1_3

description: Gene expression in non-pregnant sow blood

source_name: Peripheral Blood, non-pregnant, replicate 3

value: female


title: PD13107


title: PD13089


title: PD13086


title: PD13096


title: PD13084

source_name: ILC, grade 1


title: PD13079


title: PD13083


title: PD13077


title: PD13078


title: PD13072


title: PD13081


title: PD13076


title: Non_obese_1.5

description: undifferentiated  CD73+CD90+CD105+ WJ MSC from non-obese donor 2 replicate 2

source_name: genomic DNA from CD73+CD90+CD105+ WJ MSC

value: Multipotent, undifferentiated CD73+CD90+CD105+ WJ MSC


title: PD13073


title: PD13075


title: PD13063


title: PD13065


title: PD13067


title: PD13071


title: PD9886


title: PD13064


title: PD13080


title: PD9914


title: PD13088


title: PD13074


title: PD13061


title: PD13070


title: PD13069


title: PD9885


title: PD13062

value: Mixed, non classic


title: PD9913


title: PD13082


title: PD13060


title: PD9908


title: PD13068


title: PD9906


title: PD9907


title: PD9910


title: PD13059


title: PD13054


title: PD9912


title: PD13055


title: PD9862


title: PD13052


title: PD13053


title: PD9884


title: PD9857


title: PD9863

value: Alveolar


title: PD9895


title: PD9858


title: PD13051


title: PD13047


title: PD13049


title: PD9905


title: PD9909


title: PD13045


title: PD13113


title: PD9880


title: PD13048


title: PD13046


title: PD9860


title: PD13056


title: PD13158


title: PD13157


title: PD9879


title: PD13152


title: PD13156


title: PD9883


title: PD13153


title: PD13151


title: PD13150


title: PD13147


title: PD13133


title: PD9890


title: PD13145


title: PD13140


title: PD9876


title: PD13134


title: PD9875

source_name: ILC, grade not available


title: PD13132


title: PD9873


title: PD13142


title: PD9898


title: PD13135


title: PD9902


title: PD13138


title: PD9868


title: PD13146


title: PD13149


title: PD13141


title: PD13131


title: PD13106


title: PD9874


title: PD9865


title: PD9859


title: PD9869


title: HeLa 2h control biological replicate C

city: Chicago

first: Gayle

middle: E

last: Woloschak

state: IL

address: 300 E Superior St, Tarry 4-713

department: Radiation Oncology

institute: Northwestern University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Initial data quality checks were performed using Bioconductor Lumi package

source_name: HeLa ctrl

label_protocol: Standard protocol was done Genomics Core Facility Northwestern University

growth_protocol: Total RNA was isolated using the PureLink RNA Mini kit

treatment_protocol: Nanoparticle treatments (~20ug/ml) lasting 2 or 4 h and matching untreated controls

tag: nanoparticle treated

value: untreated


title: PD13092


title: HeLa 4h control biological replicate D

extract_protocol: Standard protocol was done Genomics Core Facility Northwestern University


title: HeLa 4h treatment biological replicate C

source_name: HeLa NP

value: treated


title: HeLa 4h treatment biological replicate D


title: PD9894

value: Invasive lobular carcinoma (ILC)


title: HeLa 2h control biological replicate D


title: PD9893

value: Female


title: PD9871

value: Breast cancer tumor


title: PD9896

value: ILC


title: HeLa 2h treatment biological replicate D


title: HeLa 2h control biological replicate A technical replicate 2


title: HeLa 4h control biological replicate C


title: PD13155


title: PD9872


title: HeLa 4h treatment biological replicate A technical replicate 2


title: PD13057

value: Classic


title: HeLa 2h treatment biological replicate A technical replicate 2


title: HeLa 4h control biological replicate B


title: HeLa 2h treatment biological replicate C


title: HeLa 4h control biological replicate A technical replicate 2


title: HeLa 2h control biological replicate B


title: HeLa 4h treatment biological replicate B


title: HeLa 2h treatment biological replicate B


title: HeLa 4h control biological replicate A technical replicate 1


title: HeLa 4h treatment biological replicate A technical replicate 1


title: HeLa 2h treatment biological replicate A technical replicate 1


title: HeLa 2h control biological replicate A technical replicate 1


title: KO FACS PRRUB cells pool2

city: new orleans

first: IHOR

last: YOSYPIV

state: Louisiana

address: 1430 tulane ave.

department: PEDIATRICS

institute: Tulane University

description: array 4 WT1 vs. WT1

hyb_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

scan_protocol: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

data_processing: LogRatio extracts from Agilent Feature Extraction exports.

label_protocol: Scan Protocol: GE2_107

growth_protocol: Total RNA was isolated from EGFP+ collecting duct and ureteric bud cells FACS-sorted from postnatal day 1 HoxB7CreEGFP+; PRR flox/flox  and CreEGFP+ PRR+/+ using Qiagen RNA purification kit. The quality was checked using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

extract_protocol: Manufacturer's protocol (Agilent)

treatment_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

value: development tissue

tag: age

value: Postnatal day 1


title: PD13139

tag: gender

value: Positive

value: Negative


title: PD9867

value: Yes


title: PD13148

value: No


title: wild type FACS PRRUB cells pool1

description: array 1 WT1 vs. KO

source_name: PRR KO


title: wildttype FACS PRRUB cells pool2

description: array 2 WT2 vs. KO


title: KO FACS PRRUB cells pool1

description: array 3 WT2 vs. WT2


title: CM-C treatment at 12 hours, biological rep2

city: Mexico City

first: Ivan

last: Salido-Guadarrama

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

description:
CM-C12h_2
Gene expression data from P388D1 cell line exposed to CM-C after 12 hours

hyb_protocol: Labeled DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array in a hybridization cocktail . Washing and staining steps were carried out using GeneChip Fluidics Station 450

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara CA)

data_processing: Raw intensity data were pre-processed and quantile normalized using the robust multi-array average (RMA) expression measure function implemented within the oligo package of bioconductor. Log2 transformed expression values, obtained after RMA, were used to analyze the differential expressions between different groups was analyzed using empirical Bayes method implemented in the LIMMA package and P values were computed.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Whole-Transcript Sense Target Labeling Protocol

growth_protocol: Cell culturer were maintained in RPMI 1640 cell-culture medium (GIBCO/BRL, Grand Island, NY, USA), supplemented with 5% fetal bovine serum, 1% penicillin-streptomycin and 1 μM 2-mercaptoethanol at 37 °C and 5% CO2

extract_protocol: Trizol extraction of total RNA was performed using the AxyPrep Multisource Total RNA Miniprep kit (Axygen Scientific, Union City, CA, USA), according to the manufacturer’s instructions.

treatment_protocol: Non-infected macrophages were treated with conditioned medium from macrophages persistently infected with RSV virus (CM-MΦP) or with control-conditioned medium from non-infected macrophages (CM-C) for 3 and 12 h at 37ºC, 5% CO2

tag: cell line

value: macrophage-like cell line

value: methylcholanthrene induced

tag: treated with

tag: treatment duration


title: PD13143

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

value: Trabecular


title: CM-MΦP treatment at 12 hours, biological rep1

description:
CM-MΦP 12h_1
Gene expression data from P388D1 cell line exposed to CM-MΦP after 12 hours

value: conditioned medium from macrophages persistently infected with RSV virus (CM-MΦP)


title: lncRNA-CD8+CD28-T-nonagenarian5

city: Harbin

first: Yuhong

last: Wang

state: Heilongjiang

address: NO 23 Youzheng Street

institute: First Hospital of Harbin Medical University

description: LncRNA profiing expression in CD8+CD28+ Tcells in a 94-age-old Chinese male CMV carrier

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number 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 with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: CD8+CD28-T lymphocytes from No.5 Chinese nonagenarian with CMV-seropositivity

label_protocol: each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: After whole blood were collected from 10 healthy nonagenarians charaterizied with CMV seropositivity, peripheral blood monocyte (PBMC)  was individully isolated, and the CD8+CD28- T cell subset and CD8+CD28- T cell subset were sorted from PBMC using flow cytometry.

value: Male

value: peripheral blood monocyte


title: CM-C  treatment at 3 hours, biological rep2

description:
CM-C3h_2
Gene expression data from P388D1 cell line exposed to CM-C after 3 hours

value: control-conditioned medium from non-infected macrophages (CM-C)


title: PD9888

value: Invasive lobular carcinoma (ILC)

value: Female


title: CM-C treatment at 3 hours, biological rep1

description:
CM-C3h_1
Gene expression data from P388D1 cell line exposed to CM-C after 3 hours


title: 607 2015 Lgr5 Ep+ MIXED

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

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

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: genotype/variation

tag: treatment

value: 10mg TAM

tag: isolation

value: FACS

tag: staining

value: Epcam+/Lin-/DAPI-


title: CM-MΦP treatment at 12 hours, biological rep2

description:
CM-MΦP 12h_2
Gene expression data from P388D1 cell line exposed to CM-MΦP after 12 hours


title: 608 2015 Lgr5 Ep- MIXED

value: Epcam-/Lin-/DAPI-


title: lncRNA-CD8+CD28-T-nonagenarian4

source_name: CD8+CD28-T lymphocytes from No.4 Chinese nonagenarian with CMV-seropositivity


title: CM-MΦP treatment at 3 hours, biological rep1

description:
CM-MΦP 3h_1
Gene expression data from P388D1 cell line exposed to CM-MΦP after 3 hours


title: lncRNA-CD8+CD28-T-nonagenarian3

description: LncRNA profiing expression in CD8+CD28+ Tcells in a 94-age-old Chinese female CMV carrier

source_name: CD8+CD28-T lymphocytes from No.3 Chinese nonagenarian with CMV-seropositivity


title: Slide 347212

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F550 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown CDM medium with and without added 10mM methionine and harvested at respective mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: strain

value: D39 wild-type

value: 0 mM methionine

source_name: F650 Mean

value: 10 mM methionine


title: Slide 345325

description: Sample 2


title: 1123 2014 Lgr5 Ep+ MIXED


title: 605 2015 Lgr5 Ep+ MIXED


title: mCNV4-father_Illu

status: Public on Oct 14 2016

city: Houston

first: Pengfei

last: Liu

state: TX

address: 2450 Holcombe Blvd, O270F

institute: Baylor College of Medicine

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

label: cy3 and cy5

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

value: M


title: mCNV4-mother_Illu

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

value: F


title: mCNV7_Illu

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


title: CM-MΦP treatment at 3 hours, biological rep2

description:
CM-MΦP 3h_2
Gene expression data from P388D1 cell line exposed to CM-MΦP after 3 hours

value: macrophage-like cell line

value: methylcholanthrene induced


title: CM-C treatment at 12 hours, biological rep1

description:
CM-C12h_1
Gene expression data from P388D1 cell line exposed to CM-C after 12 hours


title: lncRNA-CD8+CD28-T-nonagenarian1

description: LncRNA profiing expression in CD8+CD28+ Tcells in a 95-age-old Chinese male CMV carrier

source_name: CD8+CD28-T lymphocytes from No.1 Chinese nonagenarian with CMV-seropositivity


title: mCNV3_Illu

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


title: lncRNA-CD8+CD28+T-nonagenarian4

source_name: CD8+CD28+T lymphocytes from No.4 Chinese nonagenarian with CMV-seropositivity


title: mCNV4_Illu


title: 1122 2014 Lgr5 Ep- MIXED


title: mCNV7-father_Illu


title: EppP63_1782

value: 2,5mg TAM


title: mCNV7-mother_Illu


title: lncRNA-CD8+CD28-T-nonagenarian2

description: LncRNA profiing expression in CD8+CD28+ Tcells in a 93-age-old Chinese female CMV carrier

source_name: CD8+CD28-T lymphocytes from No.2 Chinese nonagenarian with CMV-seropositivity


title: lncRNA-CD8+CD28+T-nonagenarian2

source_name: CD8+CD28+T lymphocytes from No.2 Chinese nonagenarian with CMV-seropositivity


title: 606 2015 Lgr5 Ep- MIXED


title: EppP63_1780


title: EpnP63_1781


title: lncRNA-CD8+CD28+T-nonagenarian1

source_name: CD8+CD28+T lymphocytes from No.1 Chinese nonagenarian with CMV-seropositivity

value: Male


title: lncRNA-CD8+CD28+T-nonagenarian3

source_name: CD8+CD28+T lymphocytes from No.3 Chinese nonagenarian with CMV-seropositivity

value: peripheral blood monocyte


title: lncRNA-CD8+CD28+T-nonagenarian5

source_name: CD8+CD28+T lymphocytes from No.5 Chinese nonagenarian with CMV-seropositivity


title: ripk3wt 12hpi RIPK3i 2

city: Philadelphia

first: Sid

last: Balachandran

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 12 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 12 hours, kinase inhibitor treated, replicate 2

hyb_protocol: 1.65 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 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression v2 4x44K Microarray (G4846A) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) and Grid: 026655_D_F_20100123).  Median Signals (without background subtraction) were quantile normalized. The following probes were removed: (i) Control probes; (ii) Probes which were absent in at least one of all pairs of technical replicates (absent = gIsPosAndSignif, gIsWellAboveBG, and gIsFound not all TRUE); (iii) Probes lacking an Entrez identifier.

source_name: Ripk3+/+ MEFs, dNS1 infected for 12 hours, kinase inhibitor treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng 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.

growth_protocol: MEFs were grown in DMEM supplemented with 15% FBS and antibiotics

extract_protocol: RNA was extracted with Trizol reagent following the manufacturer's recommendations.

treatment_protocol: MEFs were infected with PR8-ΔNS1 virus for 1 hour in serum-free medium with occasional gentle rocking and replaced with growth medium with or without inhibitor for the duration of experiment

value: Ripk3 +/+

tag: inhibitor

tag: infection

value: PR8-ΔNS1 virus

tag: time

value: MEF


title: ripk3wt 18hpi RIPK3i 1

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 18 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 18 hours, kinase inhibitor treated, replicate 1

source_name: Ripk3+/+ MEFs, dNS1 infected for 18 hours, kinase inhibitor treated


title: ripk3ko 12hpi 2

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 12 hours
ripk3-/- MEFs, dNS1 infected for 12 hours, replicate 2

source_name: Ripk3-/- MEFs, dNS1 infected for 12 hours

value: Ripk3 -/-


title: ripk3wt 6hpi RIPK3i 2

description:
gene epression of ripk3+/+ MEFs infected with dNS1 virus for 6 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 6 hours, kinase inhibitor treated, replicate 2

source_name: Ripk3+/+ MEFs, dNS1 infected for 6 hours, kinase inhibitor treated


title: ripk3ko 12hpi 1

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 12 hours
ripk3-/- MEFs, dNS1 infected for 12 hours, replicate 1


title: ripk3ko 6hpi 1

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 6 horus
ripk3-/- MEFs, dNS1 infected for 6 hours, replicate 1

source_name: Ripk3-/- MEFs, dNS1 infected for 6 hours


title: ripk3ko 6hpi 2

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 6 horus
ripk3-/- MEFs, dNS1 infected for 6 hours, replicate 2


title: ripk3ko mock 2

description:
basal gene expression of ripk3-/- MEFs
ripk3-/- MEFs, mock infected, replicate 2

source_name: Ripk3-/- MEFs, mock infected

value: control


title: ripk3wt 18hpi 1

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 18 hours
ripk3+/+ MEFs, dNS1 infected for 18 hours, replicate 1

source_name: Ripk3+/+ MEFs, dNS1 infected for 18 hours


title: ripk3wt 18hpi 2

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 18 hours
ripk3+/+ MEFs, dNS1 infected for 18 hours, replicate 2


title: ripk3wt 12hpi 2

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 12 hours
ripk3+/+ MEFs, dNS1 infected for 12 hours, replicate 2

source_name: Ripk3+/+ MEFs, dNS1 infected for 12 hours


title: ripk3wt mock RIPK3i 2

description:
gene expression of ripk3+/+ MEFs treated with kinase inhibitor
ripk3+/+ MEFs, mock infected, kinase inhibitor treated, replicate 2

source_name: Ripk3+/+ MEFs, mock infected, kinase inhibitor treated


title: ripk3wt 18hpi RIPK3i 2

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 18 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 18 hours, kinase inhibitor treated, replicate 2


title: ripk3wt 6hpi RIPK3i 1

description:
gene epression of ripk3+/+ MEFs infected with dNS1 virus for 6 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 6 hours, kinase inhibitor treated, replicate 1


title: ripk3wt mock RIPK3i 1

description:
gene expression of ripk3+/+ MEFs treated with kinase inhibitor
ripk3+/+ MEFs, mock infected, kinase inhibitor treated, replicate 1


title: ripk3wt 12hpi RIPK3i 1

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 12 hours with a treatment of kinase inhibitor
ripk3+/+ MEFs, dNS1 infected for 12 hours, kinase inhibitor treated, replicate 1


title: ripk3wt 12hpi 1

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 12 hours
ripk3+/+ MEFs, dNS1 infected for 12 hours, replicate 1


title: ripk3ko 18hpi 1

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 18 hours
ripk3-/- MEFs, dNS1 infected for 18 hours, replicate 1

source_name: Ripk3-/- MEFs, dNS1 infected for 18 hours


title: ripk3wt 6hpi 2

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 6 hours
ripk3+/+ MEFs, dNS1 infected for 6 hours, replicate 2

source_name: Ripk3+/+ MEFs, dNS1 infected for 6 hours


title: ripk3ko 18hpi 2

description:
gene expression of ripk3-/- MEFs infected with dNS1 virus for 18 hours
ripk3-/- MEFs, dNS1 infected for 18 hours, replicate 2


title: Valproic acid treated_3h_rep2

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

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.

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: growth phase

value: exponential phase

value: 6mM of Valproic acid for 3h


title: Untreated_Control_rep2 [re-analysis]

value: none (untreated control)


title: Untreated_Control_rep1 [re-analysis]


title: BAB3596_Nim

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.

tag: patient relationship


title: mCNV4_Nim


title: mCNV7_Nim


title: BAB3597_Nim


title: ripk3wt 6hpi 1

description:
gene expression of ripk3+/+ MEFs infected with dNS1 virus for 6 hours
ripk3+/+ MEFs, dNS1 infected for 6 hours, replicate 1

tag: cell type


title: ripk3wt mock 1

description:
basal gene expression of ripk3+/+ MEFs
ripk3+/+ MEFs, mock infected, replicate 1

source_name: Ripk3+/+ MEFs, mock infected


title: BAB3097_Nim


title: BAB3098_Nim


title: ripk3wt mock 2

description:
basal gene expression of ripk3+/+ MEFs
ripk3+/+ MEFs, mock infected, replicate 2


title: ripk3ko mock 1

description:
basal gene expression of ripk3-/- MEFs
ripk3-/- MEFs, mock infected, replicate 1


title: BAB3099_Nim