title: CTC_CSF7_CSF_20CTC

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: We combined and precipitated 30 µL Cy3 labeled test DNA, 30 µL Cy5 labeled reference DNA and 100 µg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4°C. We the final hybridization mixture containing 7ul dH20, 14µL  20% SDS, and 49 µL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73°C for 15 min and then incubated the samples at 37°C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37°C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: Raw test/ref log2 ratios per spot have been observed in general to exhibit systematic variations of unknown origin across the array. To remove these, an in-house R package ('SpotCorrection'; publication in preparation) was employed. The observed log2 ratios are modeled as the sum of a genomic component (i.e. the desired signal) and a two-dimensional (2D) array component. The genomic and 2D components are iteratively estimated. The estimate of the 2D component after three iterations is then subtracted from the raw ratios. SpotCorrection also includes a relatively subtle correction based on clone GC content. No drastic changes in profiles are observed after correction. The resultant log2 ratios were analyzed by UCSF Sproc to yield the mean and standard deviation of the log2 ratios over replicate spots. The May 2004 freeze of the human genome sequence (hg17) was used to map the array CGH data.

source_name: Circulating Tumor Cells  isolated from Ceribral spinal fluid of metastatic breast cancer patient

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively.Briefly, DNA suspended in 11µL of water and 10µL of random prime mix was heated for 10mins at 100°C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8µL of 100mM dATP, 8µL of 100mM dGTP, 8µL of 100mM dTTP, 4µL of 100mM dCTP, 2µL 1M Tris, 0.4µL of 0.5M EDTA, and water), 1µL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6µL Exo-Klenow (40 U/µL) were added to the denatured DNA and incubated for 12 -20 hours at 37°C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from breast cancer patients. DNA from Tumor cells sorted in 10µL of TE was amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using breast tumor cell model systems, BT474 and MCF7, and CTCs metastatic breast cancer (MBC) patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: tumor type

value: Breast cancer

tag: tumor stage

value: Metastatic

value: Female

tag: source tissue

value: Ceribral spinal fluid

tag: source cell type

value: Circulating Tumor Cells

source_name: Promega reference Male genomic DNA

tag: reference

value: Promega Human Genomic DNA  cat#G147A


title: CTC_CSF6_CSF_20CTC

status: Public on Jan 09 2014

type: genomic

country: USA

molecule: genomic DNA

organism: Homo sapiens

tag: gender


title: Control_rep4

status: Public on Jan 10 2014

type: RNA

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Sample RNA (200 ng) was used together with a mouse universal reference RNA to synthesize, amplify and label cRNA using the Low Input Quick Amp Labeling Kit (Agilent Cat #: 5190-0444). Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP. Labeled cRNA was purified using the RNease Mini Kit (Qiagen). Amplification and labeling efficiency of cRNA were quantified using a NanoDrop spectrophotometer.

growth_protocol: 5-6 week old female specific pathogen free B6C3F1 mice were purchased from Charles River Breeding Laboratories (Portage, ME) and were allowed to acclimatize for at least 7 days prior to the start of the study. Feed (NIH-07; Zeigler Brothers, Inc., Gardners, PA) and tap water were available ad libitum. Mice were housed five per cage in polycarbonate cages in a specific pathogen free (SPF) and Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) accredited facility. All procedures were conducted in compliance with the Animal Welfare Act Regulations (9CFR1–4). Mice were handled and treated according to the guidelines provided in the National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals (ILAR, 1996; http://dels.nas.edu/ilar/).

extract_protocol: Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 1.83 and RINs > 8.9.

treatment_protocol: Mice were dosed via oral gavage for 21 days. Four different doses of furan dissolved in corn oil were used: 1, 2, 4 and 8 mg/kg bw.  Control animals were gavaged with cornoil oil only.   Tissues were collected 4 hours following the final dose.

tag: treatment

value: Control

tag: tissue

value: liver

tag: strain

value: female

source_name: Universal Mouse Reference RNA

tag: sample type

value: universal reference


title: K329_CVID-Y

city: Dallas

first: Indira

last: Munagala

state: TX

address: 3434 Live Oak street

department: BIIR

institute: Baylor healthcare

hyb_protocol: Hybridize 12-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label: biotin

source_name: Whole blood

label_protocol: biotin

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: dataset

value: Training set

tag: illness

value: CVID with complications

tag: donor id

value: M

tag: age

tag: complication

value: A


title: CTC_CSF6_PT

source_name: Tumor Tissue isolated from Primary Tumor of metastatic breast cancer patient

value: Primary Tumor

value: Tumor Tissue


title: CTC_4038_PT


title: RA7

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: Primary human synovial fluid macrophages

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1)

source_name: RA-SM

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: FLS were obtained from the synovial tissues of RA or OA patients, and incubated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with fetal calf serum (FCS; Gibco, Carlsbad, CA) or with insulin-transferrin-selenium A (ITSA; Life Technologies, Gaithersburg, MD). Monocytes/macrophages were obtained from mononuclear cells of healthy controls (n=2) or from the synovial fluid of RA patients (n=6) using anti-CD14 magnetic beads (Miltenyi Biotec, Auburn, CA), according to the manufacturer’s instructions. To induce differentiation into macrophages, peripheral blood monocytes of healthy controls were cultured for 24 hours in RPMI 1640 medium supplemented with 10% FCS in the presence of human M-CSF (20 ng/ml).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Primary fibroblast-like synoviocytes from patient with rheumatoid arthritis or osteoarthritis treated with IL1β for 24 hour.

tag: cell line

value: No treatment

value: RA synovial fluid


title: RA6

value: Primary human synovial fluid macrophages


title: M120_CVID-Y

value: AG


title: SV40TAg, R3

city: Cambridge

first: Usue

last: Laresgoiti

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description:
95926
ChIP-chip WT lymphocytes SV40TAg R3.
Biological replicate 3.

hyb_protocol: NimbleChip ChIP-chip User's Guide v1.0.

scan_protocol: NimbleChip ChIP-chip User's Guide v1.0.

data_processing:
NimbleChip ChIP-chip User's Guide v1.0.
Each feature on the array has a corresponding scaled log2 ratio, which is the ratio of the input signals for the experimental (IP) and control (input) samples co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Centering is performed by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value.

source_name: SV40TAg ChIP DNA from lymph node-derived primary lymphocytes

label_protocol: NimbleChip ChIP-chip User's Guide v1.0.

growth_protocol: Not cultured.

extract_protocol:
Lymph nodes were extracted from 4-week-old mice and mechanically dissociated between two pieces of ground glass.
T lymphocytes were crosslinked by addition of formaldehyde to 1.1% final concentration. Crosslinking was allowed to proceed at room temperature for 10 min and was stopped with glycine. Cells were washed with PBS, collected by centrifugation and lysed on ice for 10 min with a buffer containing 5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF and 1X of protease inhibitor cocktail (ROCHE). Nuclei were collected by centrifugation, resuspended in 50 mM Tris-Cl pH 8, 10 mM EDTA pH 8.0, 1% SDS, 1mM PMSF and 1X protease inhibitor cocktail and incubated 10 min on ice. Chromatin was sonicated to an average length of 300-400 bp. After microcentrifugation, the supernatant was diluted 10 fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl pH 8.0, 167 mM NaCl, 1 mM PMSF and protease inhibitor cocktail) and pre-cleared with protein A-sepharose (Amersham. 50% slurry, blocked with BSA) at 4ºC for 2 hours. 100-120 μg of precleared chromatin were incubated overnight at 4ºC with 4-5 μg of each antibody (E2F2, Santa Cruz Biotechnology, cat# sc-633; SV40Tag, Santa Cruz Biotechnology, cat# sc-147). Next, samples were incubated with protein A-sepharose at 4ºC for 2 hours. Immune complexes were recovered and washed once with Low Salt Wash Buffer (20 mM Tris-Cl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), High Salt Wash Buffer (20 mM Tris-Cl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8, 500 mM NaCl) and LiCl Wash Buffer (10 mM Tris-Cl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% Na-deoxycholate, 1 mM EDTA pH 8.0) and three times with TE buffer. The elution of the immune complexes was carried out with a buffer containing 0.1 M NaHCO3 and 1% SDS. Crosslinking was reversed by addition of NaCl to a final concentration of 200 mM followed by an overnight incubation at 65ºC, and RNA was removed with 10 μg of RNase A. Proteins were digested with 80 μg of proteinase K at 42ºC in 2 hours and the DNA extracted with phenol-chloroform and ethanol precipitation. DNA obtained by standard ChIP experiments together with 20 ng of total input DNA was amplified by Ligation Mediated Polymerase Chain Reaction (LMPCR), following manufacturer's recommendation (Roche NimbleGen).

tag: strain/background

tag: genotype/variation

value: wild type

value: 4 weeks

tag: cell type

value: lymph node-derived primary lymphocytes

tag: chip antibody

source_name: Input DNA from lymph node-derived primary lymphocytes


title: E2F2, R3

description:
95987
ChIP-chip WT lymphocytes E2F2 R3.
Biological replicate 3.

source_name: E2F2 ChIP DNA from lymph node-derived primary lymphocytes


title: T347_CVID-Y

value: SE


title: CTC_4037_PT

tag: tumor type

value: Breast cancer

tag: tumor stage

value: Metastatic

value: Female

tag: source tissue

tag: source cell type

value: Promega Human Genomic DNA  cat#G147A


title: D276_CVID-Y

value: Training set

value: CVID with complications

tag: gender

value: F

value: ASG


title: RA8

tag: treatment

tag: tissue


title: RA4


title: CTC_CSF5_CSF_20CTC

value: Ceribral spinal fluid

value: Circulating Tumor Cells

tag: reference


title: SV40TAg, R1

description:
96271
ChIP-chip WT lymphocytes SV40TAg R1.
Biological replicate 1.


title: RA3

value: No treatment

value: RA synovial fluid


title: CTC_4038_CSF_20CTC


title: CTC_4039_CSF_7CTC


title: CTC_4037_CSF_20CTC_1


title: Control2

description: Primary human peripheral blood mononuclear cells of healthy controls

source_name: Healthy monocytes

value: peripheral blood


title: RA1

value: Primary human synovial fluid macrophages


title: SV40TAg, R2

description:
99090
ChIP-chip WT lymphocytes SV40TAg R2.
Biological replicate 2.

value: wild type

value: 4 weeks


title: C355_CVID-Y

tag: dataset

tag: illness

value: M

value: AL


title: L255_CVID-Y

tag: donor id

tag: age

value: G


title: CTC_4039_PT

value: Breast cancer

value: Metastatic

value: Female

value: Primary Tumor

value: Tumor Tissue


title: C77_CVID-Y

value: Training set

value: CVID with complications

tag: complication


title: Control1

tag: cell line

value: Primary human peripheral blood mononuclear cells of healthy controls


title: G92_CVID-Y

value: A


title: CTC_4039_MET

source_name: Tumor Tissue isolated from Site of metastesis  of metastatic breast cancer patient

value: Site of metastesis

value: Promega Human Genomic DNA  cat#G147A


title: CTC_4015_LN_1

source_name: Tumor Tissue isolated from Lymph Node of metastatic breast cancer patient

value: Lymph Node


title: E2F2, R1

description:
96362
ChIP-chip WT lymphocytes E2F2 R1.
Biological replicate 1.

tag: strain/background

tag: genotype/variation

value: wild type

value: lymph node-derived primary lymphocytes


title: E2F2, R2

description:
95977
ChIP-chip WT lymphocytes E2F2 R2.
Biological replicate 2.

value: 4 weeks

tag: cell type

tag: chip antibody


title: CTC_108_CSF_50CTC

tag: tumor type

tag: tumor stage

value: Ceribral spinal fluid

value: Circulating Tumor Cells


title: CTC_4015_CSF_20CTC

value: Breast cancer

tag: source tissue

tag: source cell type


title: CTC_4011_PT

value: Metastatic

tag: gender


title: D232_CVID-Y

value: F

value: G


title: B344_CVID-Y

value: AS


title: CTC_4011_CSF_20CTC_T4

value: Female


title: F110_CVID-Y

value: Training set

value: CVID with complications

value: ASG


title: CTC_4011_CSF_20CTC_T5


title: K84_CVID-Y

value: M

value: E


title: D85_CVID-Y

value: GL


title: DRG RSS6

city: Paris

first: Karine

last: Thibault

address: 10 rue Vauquelin

country: France

institute: ESPCI

description: replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: All manipulations and statistical analyses were performed with the R freeware. For Illumina beadchip data, all spots with a detection p-value greater than 0.05% were excluded. A two-way ANOVA was performed, using vincristine treatment as the first factor and analgesic treatment as the second factor.

organism: Rattus norvegicus

source_name: saline saline

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted with Trizol reagent with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 10 days of vincristine/saline treatment to induce neuropathic pain followed by 5 days of morphine/oxycodone or saline treatment

tag: strain

value: sprague-dawley

value: 3 months

tag: tissue

value: dorsal root ganglion


title: C86_CVID-Y

tag: dataset

value: L


title: DRG RSS2

description: replicate 2


title: CTC_4011_CSF_15CTC_T3

value: Ceribral spinal fluid

value: Circulating Tumor Cells

tag: reference

value: Promega Human Genomic DNA  cat#G147A


title: CTC_4011_CSF_12CTC_T1

value: Breast cancer

value: Metastatic


title: DRG RSS1

description: replicate 1


title: G335_CVID-Y

tag: illness

tag: donor id

value: F


title: L19_CVID-Y

tag: age

tag: complication

value: ASGL


title: M124_CVID-Y

value: Training set

value: ASL


title: DRG RSOx4

description: replicate 4

source_name: saline oxycodone


title: DRG RSOx2

description: replicate 2


title: DRG RSOx1

description: replicate 1


title: DRG RSS3

description: replicate 3


title: H115_CVID-Y

value: CVID with complications

value: SL


title: CTC_112_CSF_36CTC

value: Female


title: P101_CVID-Y

value: M


title: F6_CVID-Y

value: AE


title: CTC_4014_CSF_1CTC_2


title: C14_CVID-Y


title: DRG RSOx3

description: replicate 3

value: sprague-dawley

value: 3 months


title: DRG RSM4

description: replicate 3

source_name: saline morphine

value: dorsal root ganglion


title: CTC_4015_PT

value: Primary Tumor

value: Tumor Tissue


title: DRG RSM5

description: replicate 4


title: CTC_4014_CSF_20CTC

value: Ceribral spinal fluid

value: Circulating Tumor Cells

value: Promega Human Genomic DNA  cat#G147A


title: DRG RSM1

description: replicate 1


title: DRG RSM2

description: replicate 2


title: DRG RVS7

description: replicate 4

source_name: vincristine saline


title: DRG RVS6

description: replicate 3


title: DRG RVS4

description: replicate 1


title: CTC_4014_CSF_1CTC_1

source_name: Circulating Tumor Cells  isolated from Ceribral spinal fluid of metastatic breast cancer patient

value: Breast cancer

value: Metastatic


title: CTC_4011_CSF_20CTC_T2

source_name: Promega reference Male genomic DNA


title: K2_CVID-Y

value: Training set


title: E61_CVID-Y

value: F

value: ASL


title: DRG RVOx7

description: replicate 4

source_name: vincristine oxycodone


title: G100_CVID-Y

value: CVID with complications

value: LE


title: DRG RVS5

description: replicate 2


title: DRG RVOx2

description: replicate 1


title: DRG RVOx5

description: replicate 3


title: CTC_4015_PB_20CTC

source_name: Circulating Tumor Cells  isolated from Peripheral Blood of metastatic breast cancer patient

value: Female

value: Peripheral Blood


title: DRG RVM7

description: replicate 4

source_name: vincristine morphine

value: sprague-dawley


title: S135_CVID-Y

source_name: Whole blood

value: SGL


title: DRG RVOx3

description: replicate 2

value: 3 months

value: dorsal root ganglion


title: CTC_CSF1_CSF_500CTC


title: DRG RVM3

description: replicate 3


title: K42_CVID-Y

value: M

value: ASG


title: CTC_CSF2_CSF_200CTC

value: Ceribral spinal fluid

value: Circulating Tumor Cells


title: CTC_108_PB_7CTC_PB

value: Breast cancer

value: Promega Human Genomic DNA  cat#G147A


title: DRG RVM1

description: replicate 1


title: NaF 2 mM for 6 h incubation

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: ROE2 cells incubated with NaF (2 mM) for 6 h

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: Rat oral epithelial cell line ROE2

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Rat oral epithelial ROE2 cells were cultured in DMEM/F12 medium supplemented with 2% FBS, 1% ITES (2.0 mg/l insulin, 2.0 mg/l transferrin, 0.122 mg/l ethanolamine and 9.14 μg/l sodium selenite), and 10 ng/ml epidermal growth factor (EGF) in a collagen type I-precoated culture dish at 33˚C.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: NaF was dissolved in sterilized water. Rat oral epithelial ROE2 cells were cultivated in DMEM/F12 medium supplemented with 2% FBS for 24 h at 37˚C, followed by incubation in DMEM/F12 medium supplemented with 2% FBS and NaF (0 or 2 mM) for 3, 6 and 12 h at 37˚C. The cells treated with vehicle (sterilized water; 1% v/v) only served as control.

value: A transgenic rat (Wistar strain) which has a tsSV40 large T-antigen gene [pSVtsA58ori(-)-2]

value: 18-day-old fetus

value: tongue

tag: cell line

value: oral epithelial cell line ROE2

tag: life span

value: infinite

tag: morphology

value: epithelial-like

tag: treatment

value: DMEM/F12 medium supplemented with NaF (2 mM)

tag: time

value: 6 h


title: DRG RVM2

description: replicate 2

value: sprague-dawley


title: D294_CVID-Y

value: Training set

value: CVID with complications

value: F

value: A


title: B244_CVID-Y

value: ASL


title: NaF 2 mM for 3 h incubation

description: ROE2 cells incubated with NaF (2 mM) for 3 h

value: 3 h


title: W105_CVID-N

value: CVID no complications

value: No comp


title: C45_CVID-Y

value: M


title: NaF 0 mM for 12 h incubation

description: ROE2 cells incubated with NaF (0 mM) for 12 h

value: A transgenic rat (Wistar strain) which has a tsSV40 large T-antigen gene [pSVtsA58ori(-)-2]

value: 18-day-old fetus

value: DMEM/F12 medium supplemented with NaF (0 mM)


title: NaF 2 mM for 12 h incubation

description: ROE2 cells incubated with NaF (2 mM) for 12 h

value: tongue

value: oral epithelial cell line ROE2

value: infinite


title: Control (vehicle only)

description: ROE2 cells incubated with vehicle

value: epithelial-like

value: vehicle (sterilized water)

value: control


title: NaF 0 mM for 3 h incubation

description: ROE2 cells incubated with NaF (0 mM) for 3 h


title: shJMJD2A_3

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: R/Bioconductor. 'affy' package. Raw data processed using the 'rma' function.

label_protocol: Samples were processed with the Whole Transcript Assay Kit as recommended by the manufacturer (Affymetrix)

growth_protocol: KYSE150 cells were cultured in D-MEM/F-12 1:1 (Invitrogen) supplemented with 10% FBS (Hyclone).

extract_protocol: RNeasy (Qiagen)

treatment_protocol: KYSE150 cells were transfected with the indicated pRetrosuper shRNA constructs using Fugene 6 (Roche Diagnostics) according to manufacturer's instructions and selected 24h after transfection with 2 μg/ml puromycin for 72 h prior to harvesting.

tag: shRNA


title: shJMJD2C_shJMJD2A_3


title: P197_CVID-N

value: Training set


title: C299_CVID-N


title: L102_CVID-N

value: F


title: B254_CVID-N


title: shJMJD2C_shJMJD2A_1


title: shJMJD2A_2


title: shJMJD2C_shJMJD2A_2


title: CTC_4015_LN_3

tag: tumor type

value: Breast cancer

tag: tumor stage

value: Metastatic

value: Female

tag: source tissue

value: Lymph Node

value: Tumor Tissue

value: Promega Human Genomic DNA  cat#G147A


title: shJMJD2C_3


title: M5_CVID-N

value: CVID no complications

tag: gender

value: M

value: No comp


title: shCtrl_3

value: Scrambled


title: shJMJD2C_2


title: shJMJD2A_1


title: shCtrl_2


title: shJMJD2C_1


title: K348_CVID-N


title: H89_CVID-N


title: C317_CVID-N


title: HC2 Blood Vdelta1_CD161nega_rep1

city: Tsukuba

first: Seiji

last: Segawa

address: 1-1-1, Tennoudai

department: Faculty of Medicine

institute: University of Tsukuba

description: Gene expression of CD161-nega Vdelta1 cells

hyb_protocol: 0.5 ug of Cy3-labelled cDNA hybridized to Agilent SurePrint G3 Human GE Microarray (8×60K) for 17 hours 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 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 using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (v.10.7.3.1, Agilent). We examined the gene variations among CD161-negative and CD161-positive samples. And, we analyzed the gene expression of CD161-positive Samples to CD161-negative Samples. We showed the normalized data using CD161-negative Samples as a baseline. In the Sample data tables (normalized data tables), $B!H(B0$B!I(B values mean $B!H(BLog2 0$B!I(B. So, the CD161-negative Samples have only $B!H(B0$B!I(B values.

source_name: Peripheral Blood Mononuclear cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Genomic Enzymatic Labeling 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 prepared using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the instructions supplied by the manufactuer.

tag: tissue

value: whole blood

value: female

tag: cell type


title: HC3 Blood Vdelta1_CD161posi_rep1

description: Gene expression of CD161-posi Vdelta1 cells


title: HC1 Blood Vdelta1_CD161nega_rep1

value: male


title: HC2 Blood Vdelta1_CD161posi_rep1


title: shCtrl_1


title: HC3 Blood Vdelta1_CD161nega_rep1


title: D38_CVID-N

tag: dataset


title: C78_CVID-N

tag: illness


title: C279_CVID-N

tag: donor id


title: HC1 Blood Vdelta1_CD161posi_rep1

tag: age


title: F212_CVID-N

tag: complication


title: NaF 0 mM for 6 h incubation

description: ROE2 cells incubated with NaF (0 mM) for 6 h

tag: strain

value: A transgenic rat (Wistar strain) which has a tsSV40 large T-antigen gene [pSVtsA58ori(-)-2]

value: 18-day-old fetus

value: tongue

tag: cell line

value: oral epithelial cell line ROE2

value: infinite

value: epithelial-like

value: DMEM/F12 medium supplemented with NaF (0 mM)

value: 6 h


title: B140_CVID-N

value: Training set

value: F


title: DNA methylation status of MDS-24

city: Smithville

first: Yue

last: Lu

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description: 19 of 19. human MDS patient

hyb_protocol: Followed standard Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US23502362 Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: The ratios of hybridization intensities were adjusted by using Lowess normalization.

source_name: bone marrow

label_protocol: Followed standard Agilent protocol

extract_protocol: Genomic DNA was extracted using a standard phenol–chloroform method

tag: disease state

value: MDS

value: bone marrow

value: 73 years old

tag: fab

value: RAEB

source_name: whole blood

value: 21 years old

value: control

value: blood


title: DNA methylation status of MDS-22

description: 18 of 19. human MDS patient

value: Unknown


title: Cyp1b1 null low fat diet mouse liver replicate 3

city: Madison

first: Justin

last: Bushkofsky

state: WI

address: 2500 Overlook Terrace

department: Medicine Endocrinology, Diabetes and Metabolism

institute: University of Wisconsin Madison

description: 3 samples pooled

hyb_protocol: A dye flop experimental design was used in the hybridization. When total RNA is greater than 20ug, Genisphere cDNA50 kit (Genisphere, Hatfield, PA) is used and when its less than 20ug, the Genisphere cDNA350 kit is used for labeling and hybridizing.

scan_protocol: Slides are scanned on an Agilent DNA Microarray Scanner, model G2565BA

data_processing: EDGE software (Mol. Pharm. Vol. 67, No. 4, 2005) was used to perform a limma analysis of the data.

source_name: Liver hepatocytes, low fat diet

growth_protocol: Mice were housed in a AAALAC accreditated facility with 12hr light cycles and temperature control.

extract_protocol: Total RNA was isolated using a Qiagen RNA easy isolation kit as described by the manufacturer.

treatment_protocol: Mice were weaned onto either 10% fat (low fat) or 60% fat (high fat) diet at 3 weeks of age and sacrificed at 14 weeks.

value: liver hepatocytes

tag: diet

value: low fat

tag: strain/genotype

value: Cyp1b1 null

value: Male

value: 14 weeks

source_name: Pooled wild-type low fat diet liver


title: Cyp1b1 null high fat diet mouse liver replicate 1

description: 3 samples pooled

source_name: Liver hepatocytes, high fat diet

label_protocol: When total RNA is greater than 20ug, Genisphere cDNA50 kit (Genisphere, Hatfield, PA) is used and when its less than 20ug, the Genisphere cDNA350 kit is used for labeling and hybridizing.

value: high fat


title: Cyp1b1 null high fat diet mouse liver replicate 2

description: 3 samples pooled


title: Cyp1b1 null high fat diet mouse liver replicate 3

description: 3 samples pooled


title: DNA methylation status of MDS-21

description: 17 of 19. human MDS patient

value: 80 years old

value: RAEB-T


title: V32_CVID-N

value: Training set

value: CVID no complications

value: M

value: No comp


title: S36_CVID-N

value: F


title: DNA methylation status of MDS-18

description: 14 of 19. human MDS patient

value: MDS

value: bone marrow

value: 61 years old

value: 21 years old


title: Cyp1b1 null low fat diet mouse liver replicate 2

description: 3 samples pooled

value: liver hepatocytes


title: DNA methylation status of MDS-17

description: 13 of 19. human MDS patient

value: 73 years old

value: RAEB

value: 42 years old

value: control

value: blood


title: DNA methylation status of MDS-19

description: 15 of 19. human MDS patient

value: 56 years old

value: 43 years old


title: Cyp1b1 null low fat diet mouse liver replicate 1

description: 3 samples pooled

value: low fat

value: Cyp1b1 null

value: Male

value: 14 weeks


title: M172_CVID-N

value: Training set

value: CVID no complications

value: M

value: No comp


title: DNA methylation status of MDS-20

description: 16 of 19. human MDS patient

value: MDS

value: bone marrow

value: 67 years old

value: RAEB-T

value: 21 years old


title: M293_CVID-N

value: F


title: DNA methylation status of MDS-14

description: 10 of 19. human MDS patient

value: 72 years old

value: RAEB

value: control

value: blood


title: Wild-type high fat diet mouse liver replicate 3

description: 3 samples pooled

value: liver hepatocytes

value: high fat

value: low fat


title: DNA methylation status of MDS-15

description: 11 of 19. human MDS patient

value: 61 years old

value: CMML

value: 40 years old


title: G68_CVID-N

value: Training set

value: CVID no complications

value: No comp


title: DNA methylation status of MDS-10

description: 6 of 19. human MDS patient

value: MDS

value: bone marrow

value: 71 years old


title: DNA methylation status of MDS-12

description: 8 of 19. human MDS patient

value: RAEB-T

value: Unknown


title: DNA methylation status of MDS-13

description: 9 of 19. human MDS patient

value: 72 years old

value: RAEB

value: 33 years old


title: M31_CVID-N

value: F


title: DNA methylation status of MDS-11

description: 7 of 19. human MDS patient

value: 80 years old

value: control

value: blood


title: Wild-type high fat diet mouse liver replicate 1

description: 3 samples pooled

value: liver hepatocytes

value: high fat

value: Male

value: 14 weeks

value: low fat


title: DNA methylation status of MDS-16

description: 12 of 19. human MDS patient

value: MDS

value: 70 years old

value: RA


title: DNA methylation status of MDS-06

description: 2 of 19. human MDS patient

value: bone marrow

value: 75 years old

value: 21 years old


title: L54_CVID-N

value: Training set

value: CVID no complications

value: No comp


title: W163_CVID-N

value: F


title: DNA methylation status of MDS-09

description: 5 of 19. human MDS patient

value: 81 years old

value: CMML

value: 43 years old

value: control


title: Wild-type low fat diet mouse liver replicate 2

description: 3 samples pooled

value: liver hepatocytes

value: Male


title: DNA methylation status of MDS-07

description: 3 of 19. human MDS patient

value: 40 years old

value: blood


title: W191_CVID-N

value: M


title: Wild-type low fat diet mouse liver replicate 1

description: 3 samples pooled

value: low fat

value: 14 weeks


title: B300_CVID-N


title: R1_CVID-N


title: Wild-type high fat diet mouse liver replicate 2

description: 3 samples pooled

value: high fat


title: Wild-type low fat diet mouse liver replicate 3

description: 3 samples pooled


title: DNA methylation status of MDS-08

description: 4 of 19. human MDS patient

value: MDS

value: bone marrow

value: 62 years old

value: RAEB

value: 42 years old


title: CSF.X4039CSF.50CD45

description: Control

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing:
Amplification curves were processed using SDS 2.4 and analyzed using RQ Manager 1.2.1 to obtain mean cycle threshold (Ct) of the triplicate measurements for each gene.
The mean Ct for ACTB and GAPDH was used to calculate for the ∆Cts

label: FAM

label_protocol:
Reverse transcription (RT) and preamplification were performed using Taqman® PreAmp Cells-to-CT™ kit (Ambion, Texas) following manufacturer’s instructions with some modification. These steps were performed in the same tube the cells were sorted into to avoid any loss of nucleic acids.  RT was performed on total RNA in the whole cell lysate (11µL) by adding 12.5µL of 2X RT buffer, 1.25µL of 20X RT enzyme and 0.25µL of nuclease free water and incubated in a thermal cycler for 60 min at 37°C and 5 min at 95°C to inactivate the RT enzyme. Specific transcript preamplification was performed by adding 50µL of Taqman® PreAmp Master and 25µL of the Custom PreAmp Pool to the RT reaction mix (25µL) and incubated in a thermal cycler for 10 min at 95°C followed by 14 cycles at 95°C for 15 sec and 60°C for 4 min. The Custom PreAmp Pool contained 63 Taqman® assays. The same set of Taqman® assays were also printed onto the TLDA card and used for subsequent RT-PCR. The primers for RPS18 were not included in the custom pool due to the already high expression level of this gene. Note that each assay contained specific primers for transcript specific preamplification.
Preamplified cDNA was diluted to 1/32 by adding 12.5µL of cDNA from the completed RT reaction to 187.5µL of nuclease free water and 200µL of Taqman® Universal PCR Master Mix (no UNG). Two samples were loaded in each TLDA card (100 µL per port; 4 ports per sample). RT-PCR was performed using the ABI PRISM 7900HT.

extract_protocol: Cells were sorted into reaction tubes containing 9.5µL of lysis buffer and 0.5 µL of DNAse. Lysis reaction was carried out for 5 min at room temperature and 1µL of Stop solution was added and incubated for 2 min and immediately placed on ice. Whole cell lysates were then stored in -80°C until further use.

treatment_protocol: Cell isolation via IE/FACS: If a patient had ≥1 CTC/mL the remaining volume of blood was subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) within 24-32 hr after blood draw. In the initial step, magnetic beads coated with EpCAM mAb are used to enrich for tumor cells. Enriched samples are then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+/CD45-) from leukocytes (CD45+/EpCAM-) during sorting. This procedure allows for the isolation of small pools cells, which can be subjected to downstream molecular analyses.

tag: cancer type

value: Breast cancer

value: Metastatic

value: Female

value: Ceribral spinal Fluid

tag: source cell type

tag: matched leukocyte sample


title: S213_CVID-N

value: Training set

value: CVID no complications

tag: gender

value: No comp


title: DNA methylation status of MDS-05

description: 1 of 19. human MDS patient

tag: tissue

value: 79 years old

value: 21 years old

value: control

value: blood


title: CSF.X4039CSF.20CTC.T2

description: Test

tag: tumor stage

tag: source tissue

value: CSF

value: no pair


title: CSF.X4039CSF.20CTC

description: Test


title: CSF.X4038CSF.40CD45.T3

description: Control


title: P4_CVID-N

tag: dataset

tag: illness

value: M


title: CSF.X4038CSF.25CD45

description: Control


city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description:
mAG-rep4
mAG(cy3) vs mKO2(cy5) biological replicate 2 dyeswap

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: 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 and LOWESS normalization.

source_name: FACS-sorted mKO2 positive cells

label_protocol: Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44K whole human genome arrays (Agilent Design # 014850) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

growth_protocol: The transfections of Fucci Green/Red (provided by Dr. Atsushi Miyawaki, RIKEN-BSI, Japan) were performed using a lentiviral transfection protocol. For generating subcutaneous tumor models, Fucci-expressing HCT116 cells were injected into subcutaneous tissue of immunocompromised NOD/SCID mice four before the isolation. Tumors were harvested from the subcutaneous tissue and were processed by using collagenase/dispase (Roche #10 269 638 001) and DNase (Roche #11 284 932 001). Fucci mAG and mKO2-expressing cells were sorted from the processed tumor by using FACSAria II (BD Bioscience, CA).

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

value: HCT 116

tag: genotype/variation

value: Fucci red (mKO2;G1) expressing cells

source_name: FACS-sorted mAG positive cells

value: Fucci green (mAG; S/G2/M) expressing cells


description:
mAG-rep1
mKO2(cy3) vs mAG(cy5) biological replicate 1


description:
mAG-rep3
mKO2(cy3) vs mAG(cy5) biological replicate 2


description:
mAG-rep2
mAG(cy3) vs mKO2(cy5) biological replicate 1 dyeswap


title: H41_CVID-N

tag: donor id

value: F

tag: age

tag: complication


title: XLA6_XLA

value: Test set

value: Healthy

value: XLA


title: XLA2_XLA


title: XLA3_XLA


title: HC113_HC

value: HC


title: M167_CVID-N

value: Training set

value: CVID no complications


title: HC115_HC


title: C14-ER_Control-HC


title: XLA1_XLA


title: B336_CVID-N

value: No comp


title: XLA4_XLA


title: HC110_HC


title: C18-MV_Control-HC


title: C13-JL_Control-HC


title: HC101_HC


title: HC111_HC


title: HC106_HC


title: CSF.X4038CSF.20CTC.1.T2

description: Test

value: Breast cancer

value: Metastatic

value: Female

value: Ceribral spinal Fluid


title: HC102_HC


title: HC105_HC


title: CSF.X4038CSF.20CTC.1

description: Test

value: CSF


title: CSF.X4038CSF.20CTC.1.T3

description: Test


title: C11-SL_Control-HC


title: CSF.X4037CSF.50CD45.T5

description: Control


title: HC114_HC

value: M


title: CSF.X4037CSF.50CD45.T2

description: Control


title: CSF.X4037CSF.20CTC.1.T5

description: Test


title: CSF.X4037CSF.20CTC.1.T4

description: Test

value: no pair


title: HC112_HC


title: HC100_HC


title: HC103_HC


title: HC108_HC


title: HC104_HC


title: CSF.X4037CSF.20CTC.1.T3

description: Test


title: HC109_HC


title: CSF.X4038CSF.20CTC.T4

description: Test


title: M374_CVID-Y

value: CVID with complications

value: SL


title: F116_CVID-Y

value: A


title: C313_CVID-Y

value: Test set

value: F

value: SGL


title: C4-AC_Control-HC

value: Healthy

value: HC


title: CSF.X4037CSF.20CTC.1.T2

description: Test


title: B415_CVID-Y

value: E


title: C20-MRW_Control-HC

value: Training set


title: C16-SP_Control-HC


title: C9-MP_Control-HC


title: C3-JF_Control-HC


title: G401_CVID-Y

value: GE


title: C5-KA_Control-HC


title: H94_CVID-Y


title: R328_CVID-Y

value: AG


title: CSF.CSF6.50CD45.T2

description: Control

value: Breast cancer

value: Metastatic

value: Female


title: CSF.X4037CSF.20CTC.1

description: Test

value: Ceribral spinal Fluid

value: CSF


title: CSF.CSF6.50CD45

description: Control


title: C12-JP_Control-HC

value: M


title: C333_CVID-Y

value: CVID with complications

value: LE


title: P376_CVID-Y

value: Test set

value: G


title: A91_CVID-Y


title: CSF.CSF6.20CTC.1.T8

description: Test


title: A366_CVID-Y

value: F

value: A


title: V332_CVID-Y


title: CSF.CSF6.50CD45.T8

description: Control


title: C2-LT_Control-HC

value: Healthy

value: HC


title: C8-JC_Control-HC

value: Training set


title: C1-MG_Control-HC


title: R121_CVID-Y

value: S


title: CSF.CSF6.20CTC.1.T6

description: Test

value: no pair


title: C15-AS_Control-HC


title: P81_CVID-Y

value: AS


title: C7-DR_Control-HC


title: JBB49_Control-HC


title: XLA7_XLA

value: XLA


title: D417_CVID-Y

value: SLE


title: M361_CVID-Y

value: ASGL


title: DR  72_Control-HC

value: DR  72


title: S175_CVID-Y

value: M

value: ASGE


title: CSF.CSF6.20CTC.1.T4

description: Test

value: Breast cancer

value: Metastatic

value: Female

value: Ceribral spinal Fluid

value: CSF


title: SM 68_Control-HC

value: Healthy

value: SM 68

value: F


title: CSF.CSF6.20CTC.1.T7

description: Test


title: CSF.CSF6.20CTC.1.T2

description: Test


title: CC 60_Control-HC

value: Training set

value: CC 60

value: HC


title: S108_CVID-N

value: Test set

value: CVID no complications

value: no complications


title: CSF.CSF5.20CTC.1

description: Test


title: CSF.CSF5.50CD45

description: Control


title: DNA methylation status of RUNX(D171N)-6

description: 3 of 3. RUNX1 mouse model

source_name: spleen

tag: model

value: spleen

value: 8.2 months old

tag: strain

value: 13 months old

value: control


title: C303_CVID-N


title: SV 60_Control-HC

value: SV 60

value: M


title: P126_CVID-N


title: DNA methylation status of RUNX(D171N)-13

description: 2 of 3. RUNX1 mouse model

value: 7.8 months old


title: CM 79_Control-HC

value: CM 79


title: B381_CVID-N


title: MR 73_Control-HC

value: Healthy

value: MR 73


title: D52_CVID-N


title: J372_CVID-N

value: F


title: R413_CVID-N


title: tooth germs at Embryonic day 12

city: Seoul

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

description: miRNA

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using Genowiz 4.0TM (Ocimum Biosolutions, India)

source_name: tooth germs at Embryonic day 12

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Emrbyos were collected from pregnant mice at E11, E12, E14, and E16.

extract_protocol: Total RNA extraction

treatment_protocol: no treatment

value: ICR

value: mandibular molar tooth germ

value: Embryonic day 12


title: tooth germs at Embryonic day 16

description: miRNA

source_name: tooth germs at Embryonic day 16

value: Embryonic day 16


title: tooth germs at Embryonic day 11

description: miRNA

source_name: tooth germs at Embryonic day 11

value: Embryonic day 11


title: TM  81_Control-HC

value: Training set

value: TM  81

value: HC


title: DNA methylation status of RUNX(S291fs)-58

description: 1 of 3. RUNX1 mouse model

value: spleen

value: 7.6 months old

value: 13 months old


city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Targets were combined and purified using Microcon YM-30 filter (Millipore, Billerica, USA). The microarray slides were pretreated with blocking solution (1% BSA fraction V, 20x SSC and 5% SDS) at 50°C for 30 min, then washed with 2x SSC (3 min) and 0.2xSSC (3 min). For hybridization, Lifter Slips (Erie Scientific, Portsmouth, USA) were placed on the slides. Labels were adjusted to 80 µl volumes and contained 1.3x Denhardt’s, 3x SSC, 0.3% SDS, 0.67 μg/μl polyadenylate and 1.4 μg/μl yeast tRNA. Hybridization was carried out overnight at 60°C in a water bath; the ArrayIt® Hybridization Chamber was used. Next, slides were washed in 0.5x SSC/0.1% SDS (15 min), 0.5x SSC/0.01% SDS (15 min) and twice in 0.06x SSC (3 min each) at room temperature in dim lighting with gentle agitation. Slides were dried using ArrayIt® Microarray High-Speed Centrifuge.

scan_protocol: Arrays were scanned with GenePix 4100A DNA microarray scanner  (Molecular Devices, California, USA) at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Heart tissue of Atlantic salmon reared under elevated temperature, time 1, pool of nine fish

label_protocol: Samples with 10 μg RNA in each were labeled with Cy3-dUTP and Cy5-dUTP (Amersham Biosciences, UK) during cDNA synthesis using the SuperScript III reverse transcriptase kit (Invitrogen).

growth_protocol: Atlantic salmon (initial average weight 2 kg) were kept in closed-containment tanks with saltwater under controlled conditions for 56 days with temperature treatment

extract_protocol: RNA was isolated using TRIzol® (Invitrogen), and purified with PureLink RNA mini kits

treatment_protocol: After 50 days acclimation period all fish were weighed (average body weight 2.0 ± 0.4 kg), and the temperature in three of the tanks was increased to 19°C at a rate of 1°C per day, while the three remaining tanks were kept at 14°C

value: Heart

source_name: Heart tissue of Atlantic salmon reared under control temperature, time 1, pool of nine fish


source_name: Heart tissue of Atlantic salmon reared under control temperature, time 2, pool of nine fish

source_name: Heart tissue of Atlantic salmon reared under elevated temperature, time 2, pool of nine fish


title: D35_CVID-N

source_name: Whole blood

value: Test set

value: CVID no complications

value: M

value: no complications


title: breast_SK-BR-3_AMO

city: shanghai

first: qian

last: jin

address: libing road

country: China

institute: MSP

description: SK-AMO

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)

data_processing:
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).

source_name: breast

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: MGC-803 and SK-BR-3 cells were grown in RPMI medium 1640 (Gibco, USA) with 10% FBS (Gibco, USA) and cultured at 37℃ in a humidified atmosphere with 5% CO2

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 micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were transfected with AMO-miR-100 and negative control with Lipofectamine RNAiMax transfection reagent (Life Technology, USA) according to the manufacturer’s manual. Six to eight hours later, the medium was replaced by fresh medium and cultured. cells were harvested until apoptosis occured. approximately 24h to 48h .

tag: cell line

tag: cell type

value: human breast cancer cells

tag: transfected with


title: CSF.CSF6.20CTC.1

description: Test

tag: cancer type

value: Breast cancer

value: Metastatic

value: Female

value: Ceribral spinal Fluid

tag: source cell type

value: CSF


title: tooth germs at Embryonic day 14

description: miRNA

source_name: tooth germs at Embryonic day 14

value: ICR

value: mandibular molar tooth germ

value: Embryonic day 14


title: lymphoid organs 0h

city: hangzhou

first: Tianzhi

last: Huang

address: HANGZHOU

institute: ZJU

description: lymphoid organs 0h post WSSV infection

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Penaeus japonicus

source_name: lymphoid organs of shrimp

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using TRK-1001 kit (LC Sciences) according to the manufacturer’s instructions.

tag: time point

tag: infection

value: WSSV

value: lymphoid organs


title: lymphoid organs 24h

description: lymphoid organs 24h post WSSV infection

tag: tissue


title: DNA methylation status of NHD13-8

description: 2 of 3. NHD13 mouse model

source_name: bone marrow

value: bone marrow

value: 12 months old

value: FVB

value: 11 months old

value: control


title: S296_CVID-N

value: Test set

value: CVID no complications

tag: gender

value: F

value: no complications


title: hemocytes 48h

description: hemocytes 48h post WSSV infection

source_name: hemocytes of shrimp

value: hemocytes


title: DNA methylation status of NHD13-7

description: 3 of 3. NHD13 mouse model


title: breast_SK-BR-3_control

description: SK-NC

value: human breast cancer cells

value: transfection reagent (negative control)


title: hemocytes 0h

description: hemocytes 0h post WSSV infection


title: DNA methylation status of NHD13-9

description: 1 of 3. NHD13 mouse model

value: 9 months old


title: O206_CVID-N

tag: dataset


title: gastric_MGC-803_AMO

description: MGC-AMO

source_name: gastric

value: human gastric cancer cells


title: gastric_MGC-803_control

description: MGC-NC


title: lymphoid organs 48h

description: lymphoid organs 48h post WSSV infection


title: gill 48h

description: gill 48h post WSSV infection

source_name: gill of shrimp

value: gill


title: S425_CVID-N

tag: illness


title: hemocytes 24h

description: hemocytes 24h post WSSV infection

value: WSSV


title: Human skeletal muscle myoblasts, in differentiation media (day 3)

city: San Diego

first: Dave

last: Robbins

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were normalized according to a log-scale robust multi-array analysis (RMA) method in Expression Console (Affymetrix)

label_protocol: Biotinylated cRNA were prepared using the Message Amp II kit two-round protocol from 100 ng total RNA

growth_protocol: MyoD-infected iPSCs were seeded on collagen-coated plates in iPSC culture media without basic FGF and supplemented with the ROCK inhibitor Thiazovivin. The next day media was changed to induction media (DMEM and 15% FBS) containing 1µg/ml Dox. Media was changed 4 days later to Dox-containing differentiation media (low-glucose DMEM and 5% horse serum).

extract_protocol: Total RNA was isolated post incubation with the PicoPure RNA Isolation kit

treatment_protocol: Cells were treated with or without 1µg/ml doxycycline to induce expression of MyoD.


title: gill 0h

description: gill 0h post WSSV infection


title: L242_CVID-N

value: M


title: C282_CVID-N


title: OA96+IL1B

description: Primary fibroblast-like synoviocytes from patient with osteoarthritis treated with IL1β for 24 hour.

source_name: OA-FLS

value: Primary human fibbroblast-like synoviocytes

tag: treatment

value: Treated with IL1B 10ng

value: Female

value: OA synovial tissue


title: MyoD-infected DMD-specific iPSCs (GM05112-M5.1), day 8 post-dox addition


title: iPSCs from healthy donor (feeder-free)

description: iPSCs from healthy donor (feeder-free)

source_name: iPSCs from healthy donor (feeder-free)

value: iPSCs from healthy donor (feeder-free)


title: MyoD-infected DMD-specific iPSCs (GM05112-M5.1), day 3 post-dox addition


title: OA116+IL1B


title: Human skeletal muscle myoblasts, in expansion media


title: MyoD-infected DMD-specific iPSCs (GM05112-M5.1), untreated (feeder-free)


title: OA116

description: Primary fibroblast-like synoviocytes from patient with osteoarthritis

value: No treatment


title: OA115+IL1B


title: lipid-blast vs. ctl-lipid-blast Slide 88 4

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

description: This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Auto-gain scanning with Tecan technology.

data_processing: Background correction, intra and between array normalisation, limma algorithm for statistical comparion. Data normalization was done with FlexArray 1.6.1. Reference: Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada, URL : http://genomequebec.mcgill.ca/FlexArray)

organism: Bos taurus

source_name: lipid-blast

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.

extract_protocol: This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

treatment_protocol: Early embryos were cultured to 8-16 cells stage under control IVC condition (day 3) then treated with lipid added to IVC until blastocyst stage (day 7).

tag: sample type

value: in vitro

tag: developmental stage

value: pooled blastocysts

tag: breed (cattle)

value: holstein

tag: time of embryo collection

value: 170 hpf (hours post-in-vitro fertilization)

tag: bsa source

value: sigma

value: serum-extracted lipids

tag: number per pool

tag: tissue or cell type

value: embryo

source_name: ctl-lipid-blast


title: OA115

tag: cell line


title: B220_CVID-N

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label_protocol: biotin

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

value: Test set

value: CVID no complications

tag: donor id

value: F

tag: age

tag: complication

value: no complications


title: lipid-blast vs. ctl-lipid-blast Slide 88 3


title: OA96

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1)

label_protocol: Refer to the Illumina Gene Expression System Manual

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Primary human fibbroblast-like synoviocytes


title: iPSCs from healthy donor (on feeders)

description: iPSCs from healthy donor (on feeders)

source_name: iPSCs from healthy donor (on feeders)

tag: cell type

value: iPSCs from healthy donor (on feeders)


title: ctl-lipid-blast vs. lipid-blast Slide 88 2


title: RA57+IL1B

description: Primary fibroblast-like synoviocytes from patient with rheumatoid arthritis treated with IL1β for 24 hour.

source_name: RA-FLS

value: Treated with IL1B 10ng

value: Female

tag: tissue

value: RA synovial tissue


title: RA55+IL1B

tag: gender


title: ctl-lipid-blast vs. lipid-blast Slide 88 1


title: RA42+IL1B


title: KO2

city: Cleveland

first: Mukesh

middle: K

last: Jain

state: OH

address: 2103 Cornell Road

department: Medicine

institute: Case Western Reserve University

description: Expression data from 18h-fasted WT versus KLF15-null mice: heart

hyb_protocol: Hybridization is carried out according to the Affymetrix GeneChip Manual.  Twnety ug of IVT material is the nominal amount used on the GeneChip arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45C overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate was protocols matched to the specific chip type on a Model 450 Fluidics station process.

scan_protocol: Scanning is carried out on an Affymetrix Model 7000 scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 7000 scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant

data_processing: The GCOS default analysis algorithms and parameters for normalization and transformation were used. There was no scaling done.

source_name: 18h fasted hearts

label_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.  Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed.  Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carreid according to standard Affymetrix protocls using the Affymetrix GeneChip Cleanup Module (Affymetrix Cataolg # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried our on a Bio-tek UV Plate Reader.

extract_protocol: Total RNA from flash frozen samples extracted using Trizol (Invitrogen) as per manufacturer's instructions.

value: male

tag: strain

value: heart

tag: genotype/variation


title: GSK3B shRNA replicate 2

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method (PMID: 15705192).

source_name: Xenograft of Panc-1 (Human pancreatic carcinoma) cell line, in mouse

label_protocol: 3-5 micrograms of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Five million Panc-1 control or GSK3B shRNA cells were implanted bilaterally and subcutaneously into the flanks of 3-5 week old, female, athymic nude mice. Animals were handled according to a protocol approved by the University of Michigan Committee for Use and Care of Animals. Xenografts were grown to at least 250mm3 followed by harvesting, snap freezing, and tumor tissue microdissection.

extract_protocol: Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: xenograft

value: Panc-1 human pancreatic carcinoma cell line, grown in mice

tag: treatment

value: GSK3B shRNA


title: KO1


title: GSK3B shRNA replicate 3


title: ctl-lipid-blast vs. lipid-blast Slide 87 4

tag: sample type

value: in vitro

tag: developmental stage

value: pooled blastocysts

value: holstein

value: 170 hpf (hours post-in-vitro fertilization)


title: control shRNA replicate 2

value: control shRNA


title: KO3


title: control shRNA replicate 4


title: GSK3B shRNA replicate 1


title: lipid-blast vs. ctl-lipid-blast Slide 87 2

tag: breed (cattle)

tag: time of embryo collection

value: sigma

value: serum-extracted lipids

value: embryo


title: gill 24h

description: gill 24h post WSSV infection

tag: time point

tag: infection

value: WSSV

value: gill


title: WT3

value: wild type


title: ctl-lipid-blast vs. lipid-blast Slide 87 3

tag: bsa source

tag: number per pool

tag: tissue or cell type


title: RA55

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

institute: Cedars-Sinai Medical Center

description: Primary fibroblast-like synoviocytes from patient with rheumatoid arthritis

tag: cell line

value: Primary human fibbroblast-like synoviocytes

value: No treatment

value: Female


title: control shRNA replicate 3


title: WT4

value: male

value: heart


title: P72_CVID-Y

city: Dallas

first: Indira

last: Munagala

address: 3434 Live Oak street

institute: Baylor healthcare

hyb_protocol: Hybridize 12-Sample Beadchip

tag: dataset

value: Test set

tag: illness

value: CVID with complications

tag: donor id

value: F

tag: age

tag: complication

value: A


title: WT2

tag: gender

tag: strain

tag: tissue

tag: genotype/variation


title: lipid-blast vs. ctl-lipid-blast Slide 87 1

tag: sample type

value: in vitro

tag: developmental stage

value: pooled blastocysts

tag: breed (cattle)

value: holstein

value: 170 hpf (hours post-in-vitro fertilization)

tag: treatment


title: control shRNA replicate 1

tag: xenograft

value: Panc-1 human pancreatic carcinoma cell line, grown in mice

value: control shRNA


title: RA42

hyb_protocol: Standard Illumina hybridization protocol

value: RA synovial tissue


title: PP4_FAIMOS_97_204A_U133p2_100ng.CEL

status: Public on Jan 08 2014

city: Hørsholm

first: Thomas

last: Jensen

address: Venlighedsvej 1

department: lab

institute: MPI

hyb_protocol: affymetrix standard protocol for U133p2 arrays

data_processing: R software. RMA normalising.

source_name: blood

label_protocol: affymetrix Hyb Wash Stain

extract_protocol: Rneasy

tag: Sex

value: female


title: PP4_FAIMOS_98_205A_U133p2_100ng.CEL

scan_protocol: affymetrix standard protocol for U133p2 arrays


title: PP4_FAIMOS_96_203A_U133p2_100ng.CEL


title: PP4_FAIMOS_95_202A_U133p2_100ng.CEL


title: WT1

value: wild type


title: PP4_FAIMOS_88_187A_U133p2_100ng.CEL


title: PP4_FAIMOS_9_018A_U133p2_100ng.CEL

tag: core

value: IRSS 018A

tag: arm

value: c


title: PP4_FAIMOS_94_201A_U133p2_100ng.CEL


title: PP4_FAIMOS_90_190A_U133p2_100ng.CEL


title: PP4_FAIMOS_87_185A_U133p2_100ng.CEL


title: PP4_FAIMOS_89_189A_U133p2_100ng.CEL


title: RA57

tag: cell line

value: Primary human fibbroblast-like synoviocytes

value: No treatment

value: Female


title: PP4_FAIMOS_83_173A_U133p2_100ng.CEL


title: PP4_FAIMOS_81_169A_U133p2_100ng.CEL


title: PP4_FAIMOS_85_176A_U133p2_100ng.CEL


title: PP4_FAIMOS_84_174A_U133p2_100ng.CEL


title: PP4_FAIMOS_80_165A_U133p2_100ng.CEL


title: PP4_FAIMOS_86_177A_U133p2_100ng.CEL


title: PP4_FAIMOS_78_157A_U133p2_100ng.CEL


title: PP4_FAIMOS_93_195A_U133p2_100ng.CEL


title: PP4_FAIMOS_8_015A_U133p2_100ng.CEL

value: IRSS 015A

value: b


title: PP4_FAIMOS_76_154A_U133p2_100ng.CEL


title: PP4_FAIMOS_75_153A_U133p2_100ng.CEL


title: PP4_FAIMOS_77_156A_U133p2_100ng.CEL


title: PP4_FAIMOS_82_170A_U133p2_100ng.CEL


title: PP4_FAIMOS_79_160A_U133p2_100ng.CEL


title: PP4_FAIMOS_7_014A_U133p2_100ng.CEL

value: IRSS 014A


title: PP4_FAIMOS_72_138A_U133p2_100ng.CEL


title: PP4_FAIMOS_73_142A_U133p2_100ng.CEL


title: PP4_FAIMOS_69_132A_U133p2_100ng.CEL


title: PP4_FAIMOS_66_126A_U133p2_100ng.CEL


title: PP4_FAIMOS_68_128A_U133p2_100ng.CEL


title: PP4_FAIMOS_62_119A_U133p2_100ng.CEL


title: PP4_FAIMOS_65_125A_U133p2_100ng.CEL


title: PP4_FAIMOS_99_206A_U133p2_100ng.CEL


title: PP4_FAIMOS_74_149A_U133p2_100ng.CEL


title: PP4_FAIMOS_71_137A_U133p2_100ng.CEL


title: PP4_FAIMOS_70_136A_U133p2_100ng.CEL


title: PP4_FAIMOS_64_123A_U133p2_100ng.CEL


title: PP4_FAIMOS_61_116A_U133p2_100ng.CEL


title: PP4_FAIMOS_56_107A_U133p2_100ng.CEL


title: PP4_FAIMOS_67_127A_U133p2_100ng.CEL


title: PP4_FAIMOS_6_012A_U133p2_100ng.CEL

value: IRSS 012A


title: PP4_FAIMOS_58_112A_U133p2_100ng.CEL


title: PP4_FAIMOS_60_115A_U133p2_100ng.CEL


title: PP4_FAIMOS_54_103A_U133p2_100ng.CEL


title: PP4_FAIMOS_55_106A_U133p2_100ng.CEL


title: PP4_FAIMOS_57_109A_U133p2_100ng.CEL


title: PP4_FAIMOS_52_101A_U133p2_100ng.CEL


title: PP4_FAIMOS_59_114A_U133p2_100ng.CEL


title: PP4_FAIMOS_50_099A_U133p2_100ng.CEL


title: PP4_FAIMOS_53_102A_U133p2_100ng.CEL


title: PP4_FAIMOS_51_100A_U133p2_100ng.CEL


title: PP4_FAIMOS_48_095A_U133p2_100ng.CEL


title: PP4_FAIMOS_5_010A_U133p2_100ng.CEL

value: IRSS 010A


title: PP4_FAIMOS_47_094A_U133p2_100ng.CEL


title: PP4_FAIMOS_44_090A_U133p2_100ng.CEL


title: PP4_FAIMOS_49_097A_U133p2_100ng.CEL


title: PP4_FAIMOS_92_194A_U133p2_100ng.CEL


title: PP4_FAIMOS_45_091A_U133p2_100ng.CEL


title: PP4_FAIMOS_42_087A_U133p2_100ng.CEL

value: IRSS 087A

value: nd


title: PP4_FAIMOS_91_191A_U133p2_100ng.CEL


title: PP4_FAIMOS_46_093A_U133p2_100ng.CEL


title: PP4_FAIMOS_37_080A_U133p2_100ng.CEL

value: IRSS 080A


title: PP4_FAIMOS_40_084A_U133p2_100ng.CEL

value: IRSS 084A


title: PP4_FAIMOS_39_083A_U133p2_100ng.CEL

value: IRSS 083A


title: PP4_FAIMOS_38_082A_U133p2_100ng.CEL

value: female

value: IRSS 082A


title: PP4_FAIMOS_36_079A_U133p2_100ng.CEL

value: IRSS 079A


title: PP4_FAIMOS_41_085A_U133p2_100ng.CEL

value: IRSS 085A


title: PP4_FAIMOS_34_074A_U133p2_100ng.CEL

value: IRSS 074A

value: c


title: PP4_FAIMOS_31_057A_U133p2_100ng.CEL

value: IRSS 057A


title: PP4_FAIMOS_25_044A_U133p2_100ng.CEL

value: IRSS 044A


title: PP4_FAIMOS_28_050A_U133p2_100ng.CEL

value: IRSS 050A

value: b


title: PP4_FAIMOS_23_038A_U133p2_100ng.CEL

value: IRSS 038A


title: PP4_FAIMOS_33_062A_U133p2_100ng.CEL

value: IRSS 062A


title: PP4_FAIMOS_21_036A_U133p2_100ng.CEL

value: IRSS 036A


title: PP4_FAIMOS_3_004A_U133p2_100ng.CEL

value: IRSS 004A


title: PP4_FAIMOS_35_076A_U133p2_100ng.CEL

value: IRSS 076A

value: nd


title: PP4_FAIMOS_30_053A_U133p2_100ng.CEL

value: IRSS 053A


title: PP4_FAIMOS_22_037A_U133p2_100ng.CEL

value: female

value: IRSS 037A


title: PP4_FAIMOS_2_002A_U133p2_100ng.CEL

value: IRSS 002A


title: PP4_FAIMOS_24_039A_U133p2_100ng.CEL

value: IRSS 039A


title: PP4_FAIMOS_29_051A_U133p2_100ng.CEL

value: IRSS 051A


title: PP4_FAIMOS_27_048A_U133p2_100ng.CEL

value: IRSS 048A


title: PP4_FAIMOS_18_032A_U133p2_100ng.CEL

value: IRSS 032A


title: PP4_FAIMOS_14_025A_U133p2_100ng.CEL

value: IRSS 025A


title: PP4_FAIMOS_20_034A_U133p2_100ng.CEL

value: IRSS 034A

value: c


title: PP4_FAIMOS_16_029A_U133p2_100ng.CEL

value: IRSS 029A


title: PP4_FAIMOS_19_033A_U133p2_100ng.CEL

value: IRSS 033A


title: PP4_FAIMOS_12_021A_U133p2_100ng.CEL

value: IRSS 021A

value: b


title: PP4_FAIMOS_11_020A_U133p2_100ng.CEL

value: IRSS 020A


title: PP4_5_008A_U133p2_100ng.CEL

hyb_protocol: affy hyb wash stain

scan_protocol: affy standard

data_processing: R

label_protocol: ambion messageamp

tag: rmh lab code

tag: trtlong

value: Faslodex 500mg

tag: histtype

value: Infiltrating Ductal Carcinoma

tag: tgrade

value: Moderately Differentiated(G2)

tag: responder status (us)at last visit

value: PR


title: PP4_FAIMOS_13_024A_U133p2_100ng.CEL

value: female

value: IRSS 024A

value: nd


title: PP4_FAIMOS_17_031A_U133p2_100ng.CEL

value: IRSS 031A


title: PP4_6_009A_U133p2_100ng.CEL

value: Faslodex 250mg

value: Poorly Differentiated(G3)

value: SD


title: PP4_FAIMOS_15_027A_U133p2_100ng.CEL

value: IRSS 027A

value: c


title: PP4_44_062A_U133p2_100ng.CEL

value: NE

tag: best response (if different)


title: PP4_FAIMOS_101_209A_U133p2_100ng.CEL


title: PP4_FAIMOS_10_019A_U133p2_100ng.CEL

value: IRSS 019A


title: PP4_FAIMOS_100_208A_U133p2_100ng.CEL


title: PP4_7_010A_U133p2_100ng.CEL

value: Not Done


title: PP4_9_013A_U133p2_100ng.CEL


title: PP4_FAIMOS_1_001A_U133p2_100ng.CEL

value: IRSS 001A


title: PP4_40_056A_U133p2_100ng.CEL


title: PP4_42_058A_U133p2_100ng.CEL

value: Faslodex 500mg


title: PP4_43_059A_U133p2_100ng.CEL

value: Infiltrating Lobular Carcinoma


title: PP4_41_057A_U133p2_100ng.CEL

value: Infiltrating Ductal Carcinoma


title: PP4_38_054A_U133p2_100ng.CEL

value: Moderately Differentiated(G2)


title: PP4_4_007A_U133p2_100ng.CEL

value: female


title: PP4_39_055A_U133p2_100ng.CEL


title: PP4_37_053A_U133p2_100ng.CEL

value: Unassessable(GX)


title: PP4_36_051A_U133p2_100ng.CEL


title: PP4_35_050A_U133p2_100ng.CEL


title: PP4_33_048A_U133p2_100ng.CEL


title: PP4_32_047A_U133p2_100ng.CEL

value: CARCINOMA MUCINOUS

value: Other


title: PP4_30_042A_U133p2_100ng.CEL

value: PR


title: PP4_3_006A_U133p2_100ng.CEL


title: PP4_31_044A_U133p2_100ng.CEL

value: Undifferentiated Carcinoma


title: PP4_29_041A_U133p2_100ng.CEL

value: Faslodex 250mg


title: PP4_28_040A_U133p2_100ng.CEL

value: PD


title: PP4_27_039A_U133p2_100ng.CEL

value: SD


title: PP4_22_031A_U133p2_100ng.CEL


title: PP4_20_029A_2_U133p2_100ng.CEL

value: Poorly Differentiated(G3)


title: PP4_34_049A_U133p2_100ng.CEL

value: NE


title: PP4_23_033A_U133p2_100ng.CEL

value: Well Differentiated(G1)


title: MouseCochleaBasal_03

city: Matsumoto

first: Shin-ya

last: Nishio

state: Nagano

address: 3-1-1 Asahi

department: Department of Otorhinolaryngology

institute: Shinshu University School of Medicine

description: Gene expression of mouse cochlea basal turn sample 3, replicate1

hyb_protocol: To analyze gene expression of each cochlea turn, 12 SurePrint G3 Mouse Exon Microarrays (4*180K format Agilent Technologies), which were spotted with 165,984 exon probes (24,547 genes), were hybridized to labeled cRNA (4 microarrays were used for each turn sample). Prior to the hybridization step, Cyanine 3-labeled cRNAs were fragmented using 25X fragmentation buffer at 60℃ in a water bath for 30 min and then hybridized to a microarray slide for 17 hours at 65℃ in a hybridization oven and washed using Gene Expression Wash Buffer (Agilent Technologies).

scan_protocol: Fluorescence intensities were measured with the Agilent Microarray Scanner (Agilent) using the scanning protocols specific for each microarray assay and raw microarray image files were created.

data_processing: The expression data were extracted from raw microarray image files using Agilent Feature Extraction Image Analysis Software (Version 10.7.3.1). The software also generated quality control reports using the protocol specific for the microarray assays as well as data files for analysis with GeneSpring GX (Version 11, Agilent Technologies). Signal intensities for each probe were normalized to the 75th percentile without baseline transformation.

source_name: Mouse cochlea basal turn sample 3, replicate 1

label_protocol: Total RNA (25ng each) was reverse transcribed with the Low Input Quick Amp Whole Transcriptome Labeling Kit (Agilent Technologies). After reverse transcription process, labeled cRNA was synthesized from cDNA by using T7 RNA polymerase mix and cyanine 3-CTP according to the manufacturer’s instructions. Labeled cRNA was purified using the Rneasy Mini kit® (QIAGEN).

extract_protocol: Four C57BL/6 mice aged 6 weeks cochlea samples including the lateral wall, stria vascularis, spiral ligament, spiral prominence, and the organ of corti were dissected and separated into the apical, middle and basal turns to compare gene expression profiles of each cochlea turn. All of these dissections were performed in RNAlater solution to prevent RNA degradation. Total RNA were extracted using the QIAGEN RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. The quality of the extracted total RNA was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: strain

tag: tissue

value: Cochlea basal turn

tag: gender

value: male

tag: age

value: 6 weeks old


title: MouseCochleaBasal_02

description: Gene expression of mouse cochlea basal turn sample 2, replicate1

source_name: Mouse cochlea basal turn sample 2, replicate 1


title: PP4_2_005A_U133p2_100ng.CEL

value: Faslodex 500mg

value: Infiltrating Ductal Carcinoma


title: PP4_25_036A_U133p2_100ng.CEL

value: female

value: Moderately Differentiated(G2)


title: PP4_14_020A_U133p2_100ng.CEL


title: PP4_26_037A_U133p2_100ng.CEL

value: Unassessable(GX)


title: PP4_17_025A_U133p2_100ng.CEL


title: MouseCochleaMiddle_02

description: Gene expression of mouse cochlea middle turn sample 2, replicate 1

source_name: Mouse cochlea middle turn sample 2, replicate 1

value: Cochlea middle turn


title: MouseCochleaMiddle_04

description: Gene expression of mouse cochlea middle turn sample 4, replicate 1

source_name: Mouse cochlea middle turn sample 4, replicate 1


title: PP4_19_028A_U133p2_100ng.CEL


title: PP4_18_027A_U133p2_100ng.CEL


title: MouseCochleaBasal_04

description: Gene expression of mouse cochlea basal turn sample 4, replicate1

source_name: Mouse cochlea basal turn sample 4, replicate 1


title: MouseCochleaBasal_01

description: Gene expression of mouse cochlea basal turn sample 1, replicate1

source_name: Mouse cochlea basal turn sample 1, replicate 1


title: PP4_21_030A_U133p2_100ng.CEL


title: MouseCochleaMiddle_03

description: Gene expression of mouse cochlea middle turn sample 3, replicate 1

source_name: Mouse cochlea middle turn sample 3, replicate 1


title: PP4_13_019A_U133p2_100ng.CEL

value: PR


title: PP4_10_014A_U133p2_100ng.CEL


title: PP4_15_021A-2_U133p2_100ng.CEL


title: PP4_16_024A_U133p2_100ng.CEL


title: MouseCochleaMiddle_01

description: Gene expression of mouse cochlea middle turn sample 1, replicate 1

source_name: Mouse cochlea middle turn sample 1, replicate 1


title: MouseCochleaApical_03

description: Gene expression of mouse cochlea apical turn sample 3, replicate 1

source_name: Mouse cochlea apical turn sample 3, replicate 1

value: Cochlea apical turn


title: PP4_12_018A_U133p2_100ng.CEL


title: MouseCochleaApical_01

description: Gene expression of mouse cochlea apical turn sample 1, replicate 1

source_name: Mouse cochlea apical turn sample 1, replicate 1


title: PP4_11_015A_U133p2_100ng.CEL

value: Faslodex 250mg


title: MouseCochleaApical_04

description: Gene expression of mouse cochlea apical turn sample 4, replicate 1

source_name: Mouse cochlea apical turn sample 4, replicate 1


title: CD34+2

city: Boston

first: Amy

middle: J

last: Wagers

state: MA

address: 1 Joslin Place

department: Islet Cell and Regenerative Biology

institute: Joslin Diabetes Center

description: Gene expression data from CD34+ non-myogenic human myofiber-associated cells

hyb_protocol: Biotinylated cRNA wqw hybridized to the Affymetrix Human Genome U133 Plus 2.0 array, washed and stained according to standard Affymetrix protocol (Affymetrix Hybridization, Wash and Stain kit).

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

data_processing: Data were analyzed using GenePattern.

source_name: Skeletal muscle

label_protocol: Biotinylated cRNA was prepared from total RNA using 3'IVT ExpressKit from Affymetrix.

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

treatment_protocol: Myofiber-associated cells were isolated from human muscle by two-step enzymatic digestion and mechanical dissociation. Individual cell subsets were isolated by combinatorial cell surface amrker staining and fluorescence-activated cell sorting.

tag: cell surface markers

tag: developmental stage

value: fetal


title: CD34+3


title: MouseCochleaApical_02

description: Gene expression of mouse cochlea apical turn sample 2, replicate 1

source_name: Mouse cochlea apical turn sample 2, replicate 1


title: CD34+1


title: hMFA2

description: Gene expression data from unfractionated human myofiber-associated cells

value: unfractionated


title: hMFA3


title: hSMP4

description: Gene expression data from human skeletal muscle precursor cells


title: WT

city: Beijing

first: Yan

last: Zhang

address: College of Lfe Sciences, Peking University

department: College of Life Sciences

institute: Peking Unversity

hyb_protocol: Following labeling, 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48C on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

data_processing: Data files were analyzed with Affymetrix miRNAQCtool using RMA background correction and quantile normalization (Default settings).Since the miRNA 2.0 array covers 131 organisms, we sorted out Mouse only.

source_name: wild type mice

label_protocol: A total of 1000ng of total RNA was labelled using the Genisphere HSR labelling Kit.

extract_protocol: none provided

value: hippocampus

tag: genotype

value: wild type

tag: genetic background


title: Huh7-IFIT1-Luc-rep2

type: other

city: Los Angeles

first: Meng

last: Li

address: 2003 Zonal Avenue

institute: University of Southern California

scan_protocol: Plates were read in an EnVision (Perkin Elmer) plate reader.

data_processing: Relativeluciferase activity was calculated as a fold change to the empty vectors. The empty vector used for normalization are pTCN and pTCP from TansOmic technologies and an AvaI cut and religated pCMVSport6 empty vector.

molecule: other

source_name: Huh7-IFIT1-Luc cells

growth_protocol: Huh7-IFIT1-Luc cells were cultured in DMEM with 10%FBS at 37C 5% CO2 incubator

extract_protocol: After 24hours of reverse transfection, the luciferase activity present in the cells was assayed by the direct addition of 40 ul of BriteLite reagent (Perkin Elmer) per well followed by a 1 minute incubation at room temperature to insure cell lysis had occurred.

treatment_protocol: Huh7-IFIT1-Luc cells were mixed with Fugene 6 transfection reagent (Roche) and plated directly onto pre-spotted cDNA clones present in each well of the plate (reverse transfection). 5,000 cells were used for each well in a total volume of 40 ul of complete cell culture media.  The plate was incubated for 24 hour incubation at 37C and 5% CO2.


title: AD

source_name: APP/PS1 mice

value: APP/PS1 mutant


title: hMFA1


title: Huh7-IFIT1-Luc-rep1


title: hSMP2


title: hSMP3


title: hSMP1


title: C_1

city: Curitiba

first: Danielle

last: Malheiros

state: Paraná

address: Centro Politecnico

department: Genetics

country: Brazil

institute: Federal University of Paraná

description: CodeLink™ Human Whole Genome Bioarrays comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes

hyb_protocol: Set the shaker speed to 300 rpm and incubate slides for 18–24 h at 37 ºC, maintaining a consistent hybridization time for comparative experiments. Post-hybridization wash.Remove the Flex Chamber using the hybridization removal tool to hold the bioarray in place while peeling the Flex Chamber off at a 60º angle. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75×TNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75×TNT, and incubate at 46 °C for exactly 1 h. Do not exceed 1 h incubation.

scan_protocol: The scanned output files (GenePix™4000B) of the CodeLink data set were analyzed using CodeLink Expression Analysis software (Amersham Biosciences, Piscataway, USA).

data_processing: Average difference values were normalised to median over the array. The data were filtered so that only those genes that were adequately measured on 75% of the arrays were included.

source_name: CD4+ T lymphocytes from peripheral blood

label_protocol: Biotin-labelled cRNA target is prepared by a linear amplification method. The poly(A)+ RNA subpopulation (within the total RNA population) is primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5′ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for anin vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA. This method produces approximately 1000-fold to 5000-fold linear amplification of the input poly(A) + RNA. Fragment cRNA. In 25 µl total volume, add 10 µg of cRNA to 5 µl of 5×fragmentation buffer and incubate at 94 ºC for 20 minutes. Prepare hybridization reaction mixture.Bring 10 µg of fragmented cRNA, 78 µl of hybridization buffer component A, and 130 µl of hybridization buffer component B to a final volume of 260 µl with water. Incubate at 90 ºC for 5 minutes and immediately chill on ice for 5–30 minutes.

extract_protocol: Total RNA from CD4+ T cells was isolated using the column purification system of the RNeasy Protect Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

tag: cell type

value: CD4+ T

tag: disease state

value: Controls

tag: Sex

value: Male


title: C_3


title: C_4


title: C_2


title: Loc_5

value: Pemphigus foliaceus

tag: clinical form

value: Localized

tag: treatment

value: Female


title: PV_1

value: Pemphigus vulgaris

value: Mucocutaneous


title: PV_4

value: Mucosal

value: prednisone


title: PV_2


title: C_5


title: GenUT_5

value: Generalized


title: PV_3


title: TS-2, 25 mg/kg, 2 wks, biological rep 3

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

institute: Pfizer

description: Gene expression data of liver collected from mouse on day 14 after repeated administration (once on Day 1, 4, 8, and 11) of toxic LNA gapmer sequence (TS-2) at 25 mg/kg by s.c. (dose volume of 10 mL/kg)

hyb_protocol: Purified cRNA was fragmented using a 5x fragmentation buffer, then a hybridization cocktail was prepared and added to the fragmentation product using the Hybridization, Wash and Stain kit (Affymetrix), applied to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) at the appropriate volume and concentration, and incubated at 45°C for 16 hours.

scan_protocol: Arrays were scanned by the Affymetrix GeneChip Scanner.

data_processing: Robust microarray analysis (RMA) background correction and quantile normalization were performed by utilizing an internal Microarray Data Analysis System (MiDAS) at Pfizer. All RNA samples utilized for transcriptomic data generation had RIN values >7.0 and passed quality control thresholds. Prior to analysis of differentially expressed genes, cRNA integrity was assessed by calculating specific 3’ to 5’ signal intensity ratios for beta-actin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) probe-sets and visualized to identify outlier samples by Principal Component Analysis (PCA). Three samples (one each in the NTS-1 group at 8 h, the TS-2 group at 16 h, and the HTS-3 at 8 h) in the early time course study and one sample in the NTS-1 group in the 2-week study, which had a 3’ to 5’ signal intensity ratio for GAPDH > 1.7 and showed a large separation from their cohorts on PCA plots, were removed due to poor cRNA and gene chip quality.

source_name: Liver collected from mice administered TS-2 (toxic LNA gapmer sequence) at 25 mg/kg for 2 wks (repeated administration)

label_protocol: RNA samples were converted into cRNA using the Single-Round RNA Amplification and Biotin Labeling System (Enzo) according to the manufacturer’s instructions.

growth_protocol: Male CD-1 mice, 6 to 8-week-old at the study initiation, were obtained from Charles River Laboratories. Animals were acclimated to the laboratory environment for a minimum of 3 days prior to initiation of dosing. All mice were housed under standard conditions with a 12-hour light/dark cycle and free access to Purina 5002 Certified Rodent Diet (PMI Nutrition International) and water.

extract_protocol: RNA was isolated from liver using the Qiagen RNeasy Mini Plus Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: All the LNA gapmers were dissolved in Dulbecco’s phosphate buffered saline (DPBS, Lonza). Animals were allocated to study groups using a computer-assisted randomization procedure based on body weights. Mice (10 mice/group at each time point) were administered vehicle (DPBS), NTS-1, TS-2, or HTS-3 at 25 mg/kg (dose volume of 10 mL/kg) by subcutaneous injection once on Day 1. Eight, 16, and 72 h after a single injection, mice were euthanized for the necropsy. Liver samples from the HTS-3 group were only collected at 8 and 16 h; the 72 h time point was not available since all mice at the 72 h time point in the HTS-3 group were found dead or sacrificed due to the moribund conditions on dDay 3 (at least 48 h post administration). 3 or 4 samples with the highest-ranking severity of minor hepatic hypertrophy score were selected for RNA isolation and subsequent gene expression analysis.

value: Liver

value: 6-8 wk-old at Dose Initiation


title: GenT_4


title: GenUT_3


title: TS-2, 25 mg/kg, 2 wks, biological rep 4


title: TS-2, 25 mg/kg, 2 wks, biological rep 5


title: GenT_5


title: TS-2, 25 mg/kg, 2 wks, biological rep 2


title: GenUT_4


title: GenT_3


title: TS-2, 25 mg/kg, 2 wks, biological rep 1


title: Vehicle DPBS, 2wks, biological rep 10

description: Gene expression data of liver collected from mouse on day 14 after repeated administration (once on Day 1, 4, 8, and 11) of vehicle (DPBS) by s.c. (dose volume of 10 mL/kg)

source_name: Liver collected from mice administered DPBS (vehicle) for 2 wks (repeated administration)


title: GenT_2


title: GenUT_2


title: Vehicle DPBS, 2wks, biological rep 9


title: Loc_3


title: Vehicle DPBS, 2wks, biological rep 8


title: Vehicle DPBS, 2wks, biological rep 7


title: Loc_4


title: CGE011

city: Quebec

first: Chantal

last: Guillemette

state: Qc

address: 2705 boul laurier

department: Pharmacy

institute: Laval University

description:
7976997082_D
HT115 shRNA UGT1A_i2 SN-38 0.5uM rep1

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Flexarray

source_name: HT115 shRNA UGT1A_i2 SN-38 0.5uM

label_protocol: biotin-labeled cRNA using Illumina® TotalPrep RNA Amplification Kit

growth_protocol: HT115 were grown in DMEM with 2 mM L-glutamine, 15% fetal bovine serum, 100 I.U./ml penicillin and 100µg/ml streptomycin. Cells were incubated at 37°C in a humidified incubator supplemented with 5% CO2.

extract_protocol: Total RNA from cells was isolated using the Tri-Reagent protocol as specified by the supplier. Total RNA was then purified with the RNeasy MinElute Cleanup kit.

treatment_protocol: HT115-shRNA cells were seeded in 150 mm dishes for 24 hours. The cells were treated with 0.5µM SN-38 or with the vehicle 0.1% DMSO for 48h

tag: cell line

value: colorectal cancer


title: Vehicle DPBS, 2wks, biological rep 6


title: CGE023

description:
7976997093_D
HT115 shRNA non-target SN-38 0.5uM rep2

source_name: HT115 shRNA non-target SN-38 0.5uM


title: Loc_1


title: Loc_2


title: NTS-1, 25 mg/kg, 2 wks, biological rep 4

description: Gene expression data of liver collected from mouse on day 14 after repeated administration (once on Day 1, 4, 8, and 11) of non-toxic LNA gapmer sequence at 25 mg/kg by s.c. (dose volume of 10 mL/kg)

source_name: Liver collected from mice administered NTS-1 (non-toxic LNA gapmer sequence) at 25 mg/kg for 2 wks (repeated administration)


title: CGE022

description:
7976997093_L
HT115 shRNA non-target vehicle rep2

source_name: HT115 shRNA non-target vehicle


title: CGE014

description:
7976997093_A
HT115 shRNA non-target SN-38 0.5uM rep1


title: CGE010

description:
7976997082_L
HT115 shRNA UGT1A_i2 vehicle rep1

source_name: HT115 shRNA UGT1A_i2 vehicle


title: NTS-1, 25 mg/kg, 2 wks, biological rep 3


title: CGE020

description:
7976997093_K
HT115 shRNA UGT1A_i2 SN-38 0.5uM rep2


title: CGE013

description:
7976997093_I
HT115 shRNA non-target vehicle rep1


title: GenT_1


title: NTS-1, 25 mg/kg, 2 wks, biological rep 2


title: plasma 9 postpartum [II]

city: Medford

first: Donna

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

description:
PL9P
gene expression from maternal blood 24-36 hours following scheduled term Cesarean section delivery

hyb_protocol: Approximately 15 μg of amplified and labeled cRNA from whole blood and 5 μg of amplified and labeled cDNA from plasma samples were fragmented and hybridized onto GeneChip Human Genome U133A microarrays (Affymetrix).  Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner (Affymetrix), using the GeneChip Microarray Suite 5.0 (Affymetrix).

data_processing: Samples in each data set (whole blood only, or whole blood vs. plasma) were quantile normalized in R 2.3.0 using the Affy package in Bioconductor 1.8.

source_name: postpartum maternal plasma

label_protocol: Samples were labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN, San Carlos, CA)

extract_protocol: Whole blood samples (7.5 cc) were obtained in 3 PaxGene (PreAnalytiX) tubes immediately prior to cesarean delivery and 24 to 36 hours postpartum and from the corresponding umbilical cord(s).  Samples were stored at room temperature for 6 to 36 hours prior to RNA extraction in accordance with the PaxGene blood RNA kit (PreAnalytiX) manufacturer’s protocol. During extraction, on-column DNase digestion (RNase-Free DNase Set; Qiagen) was performed to eliminate DNA contamination.  For plasma samples, whole blood was collected in 10-cc EDTA Vacutainer blood tubes (BD) and underwent an initial spin at 1,600 g for 10 minutes at 4°C. Harvested plasma was then transferred into microcentrifuge tubes and underwent an additional spin at 15,350 g for 10 minutes at 4°C to eliminate any residual cells. Plasma extraction was performed following the protocol in Ng E.K.O., et al. Clin. Chem. 2002;48:1212–1217.

value: plasma

tag: tissue source

value: postpartum


title: CGE006

description:
7976997093_F
HT115 shRNA non-target untreated rep2

source_name: HT115 shRNA non-target untreated


title: NTS-1, 25 mg/kg, 2 wks, biological rep 1


title: CGE002

description:
7976997093_E
HT115 shRNA UGT1A_i2 untreated rep1

source_name: HT115 shRNA UGT1A_i2 untreated


title: CGE003

description:
7976997082_I
HT115 shRNA non-target untreated rep1


title: CGE005

description:
7976997082_C
HT115 shRNA UGT1A_i2 untreated rep2


title: CGE019

description:
7976997093_C
HT115 shRNA UGT1A_i2 vehicle rep2